From a944faa2b1c9ac4cec8fa47aa9e38de52f1824fb Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 20 Jul 2022 11:32:55 -0500 Subject: [PATCH 1/8] rename our local type stubs dir As per https://github.com/python/mypy/pull/13155#issuecomment-1190220245 --- .gitignore | 6 ++---- MANIFEST.in | 2 +- Makefile | 10 +++++----- cwltool.Dockerfile | 4 ++-- {typeshed => mypy-stubs}/arcp/__init__.pyi | 0 {typeshed => mypy-stubs}/arcp/generate.pyi | 0 {typeshed => mypy-stubs}/arcp/parse.pyi | 0 {typeshed => mypy-stubs}/argcomplete/__init__.pyi | 0 {typeshed => mypy-stubs}/bagit.pyi | 0 {typeshed => mypy-stubs}/black/__init__.pyi | 0 {typeshed => mypy-stubs}/cachecontrol/__init__.pyi | 0 {typeshed => mypy-stubs}/cachecontrol/adapter.pyi | 0 {typeshed => mypy-stubs}/cachecontrol/cache.pyi | 0 .../cachecontrol/caches/__init__.pyi | 0 .../cachecontrol/caches/file_cache.pyi | 0 {typeshed => mypy-stubs}/cachecontrol/compat.pyi | 0 {typeshed => mypy-stubs}/cachecontrol/controller.pyi | 0 {typeshed => mypy-stubs}/cachecontrol/filewrapper.pyi | 0 {typeshed => 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mypy-stubs}/shellescape/__init__.pyi (100%) rename {typeshed => mypy-stubs}/shellescape/main.pyi (100%) rename {typeshed => mypy-stubs}/subprocess.pyi (100%) rename {typeshed => mypy-stubs}/urllib/__init__.py (100%) rename {typeshed => mypy-stubs}/urllib/parse.pyi (100%) diff --git a/.gitignore b/.gitignore index afe30e282..90b180709 100644 --- a/.gitignore +++ b/.gitignore @@ -28,10 +28,8 @@ venv3/ # pycharm .idea/ -# typshed repo -typeshed/2and3/schema_salad -typeshed/2and3/ruamel/yaml - +# local stubs +mypy-stubs/ruamel/yaml #mypy .mypy_cache/ diff --git a/MANIFEST.in b/MANIFEST.in index ad1647692..8e2a853da 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -3,7 +3,7 @@ include MANIFEST.in include LICENSE.txt include *requirements.txt mypy.ini tox.ini include gittaggers.py Makefile cwltool.py -recursive-include typeshed *.pyi +recursive-include mypy-stubs *.pyi include tests/* include tests/tmp1/tmp2/tmp3/.gitkeep include tests/tmp4/alpha/* diff --git a/Makefile b/Makefile index 9f717cf11..6a3c54022 100644 --- a/Makefile +++ b/Makefile @@ -110,7 +110,7 @@ diff_pydocstyle_report: pydocstyle_report.txt ## codespell : check for common mispellings codespell: - codespell -w $(shell git ls-files | grep -v cwltool/schemas | grep -v cwltool/jshint/ | grep -v typeshed) + codespell -w $(shell git ls-files | grep -v cwltool/schemas | grep -v cwltool/jshint/ | grep -v mypy-stubs) ## format : check/fix all code indentation and formatting (runs black) format: @@ -177,14 +177,14 @@ mypy3: mypy mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES)) if ! test -f $(shell python -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \ then \ - rm -Rf typeshed/ruamel/yaml ; \ + rm -Rf mypy-stubs/ruamel/yaml ; \ ln -s $(shell python -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \ - typeshed/ruamel/ ; \ + mypy-stubs/ruamel/ ; \ fi # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed - MYPYPATH=$$MYPYPATH:typeshed mypy $^ + MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^ mypyc: $(PYSOURCES) - MYPYPATH=typeshed CWLTOOL_USE_MYPYC=1 pip install --verbose -e . \ + MYPYPATH=mypy-stubs CWLTOOL_USE_MYPYC=1 pip install --verbose -e . \ && pytest -rs -vv ${PYTEST_EXTRA} shellcheck: FORCE diff --git a/cwltool.Dockerfile b/cwltool.Dockerfile index bc1a4b348..b20243c9a 100644 --- a/cwltool.Dockerfile +++ b/cwltool.Dockerfile @@ -9,10 +9,10 @@ RUN pip install toml -rmypy-requirements.txt "$(grep ruamel requirements.txt)" \ "$(grep schema.salad requirements.txt)" # schema-salad is needed to be installed (this time as pure Python) for # cwltool + mypyc -RUN CWLTOOL_USE_MYPYC=1 MYPYPATH=typeshed pip wheel --no-binary schema-salad --wheel-dir=/wheels .[deps] +RUN CWLTOOL_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad --wheel-dir=/wheels .[deps] RUN rm /wheels/schema_salad* RUN pip install black -RUN SCHEMA_SALAD_USE_MYPYC=1 MYPYPATH=typeshed pip wheel --no-binary schema-salad \ +RUN SCHEMA_SALAD_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad \ $(grep schema.salad requirements.txt) black --wheel-dir=/wheels RUN pip install --force-reinstall --no-index --no-warn-script-location --root=/pythonroot/ /wheels/*.whl # --force-reinstall to install our new mypyc compiled schema-salad package diff --git a/typeshed/arcp/__init__.pyi b/mypy-stubs/arcp/__init__.pyi similarity index 100% rename from typeshed/arcp/__init__.pyi rename to mypy-stubs/arcp/__init__.pyi diff --git a/typeshed/arcp/generate.pyi b/mypy-stubs/arcp/generate.pyi similarity index 100% rename from typeshed/arcp/generate.pyi rename to mypy-stubs/arcp/generate.pyi diff --git a/typeshed/arcp/parse.pyi b/mypy-stubs/arcp/parse.pyi similarity index 100% rename from typeshed/arcp/parse.pyi rename to mypy-stubs/arcp/parse.pyi diff --git a/typeshed/argcomplete/__init__.pyi b/mypy-stubs/argcomplete/__init__.pyi similarity index 100% rename from typeshed/argcomplete/__init__.pyi rename to mypy-stubs/argcomplete/__init__.pyi diff --git a/typeshed/bagit.pyi b/mypy-stubs/bagit.pyi similarity index 100% rename from typeshed/bagit.pyi rename to mypy-stubs/bagit.pyi diff --git a/typeshed/black/__init__.pyi b/mypy-stubs/black/__init__.pyi similarity index 100% rename from typeshed/black/__init__.pyi rename to mypy-stubs/black/__init__.pyi diff --git a/typeshed/cachecontrol/__init__.pyi b/mypy-stubs/cachecontrol/__init__.pyi similarity index 100% rename from typeshed/cachecontrol/__init__.pyi rename to mypy-stubs/cachecontrol/__init__.pyi diff --git a/typeshed/cachecontrol/adapter.pyi b/mypy-stubs/cachecontrol/adapter.pyi similarity index 100% rename from typeshed/cachecontrol/adapter.pyi rename to mypy-stubs/cachecontrol/adapter.pyi diff --git a/typeshed/cachecontrol/cache.pyi b/mypy-stubs/cachecontrol/cache.pyi similarity index 100% rename from typeshed/cachecontrol/cache.pyi rename to mypy-stubs/cachecontrol/cache.pyi diff --git a/typeshed/cachecontrol/caches/__init__.pyi b/mypy-stubs/cachecontrol/caches/__init__.pyi similarity index 100% rename from typeshed/cachecontrol/caches/__init__.pyi rename to mypy-stubs/cachecontrol/caches/__init__.pyi diff --git a/typeshed/cachecontrol/caches/file_cache.pyi b/mypy-stubs/cachecontrol/caches/file_cache.pyi similarity index 100% rename from typeshed/cachecontrol/caches/file_cache.pyi rename to mypy-stubs/cachecontrol/caches/file_cache.pyi diff --git a/typeshed/cachecontrol/compat.pyi b/mypy-stubs/cachecontrol/compat.pyi similarity index 100% rename from typeshed/cachecontrol/compat.pyi rename to mypy-stubs/cachecontrol/compat.pyi diff --git a/typeshed/cachecontrol/controller.pyi b/mypy-stubs/cachecontrol/controller.pyi similarity index 100% rename from typeshed/cachecontrol/controller.pyi rename to mypy-stubs/cachecontrol/controller.pyi diff --git a/typeshed/cachecontrol/filewrapper.pyi b/mypy-stubs/cachecontrol/filewrapper.pyi similarity index 100% rename from typeshed/cachecontrol/filewrapper.pyi rename to mypy-stubs/cachecontrol/filewrapper.pyi diff --git a/typeshed/cachecontrol/serialize.pyi b/mypy-stubs/cachecontrol/serialize.pyi similarity index 100% rename from typeshed/cachecontrol/serialize.pyi rename to mypy-stubs/cachecontrol/serialize.pyi diff --git a/typeshed/cachecontrol/wrapper.pyi b/mypy-stubs/cachecontrol/wrapper.pyi similarity index 100% rename from typeshed/cachecontrol/wrapper.pyi rename to mypy-stubs/cachecontrol/wrapper.pyi diff --git a/typeshed/coloredlogs/__init__.pyi b/mypy-stubs/coloredlogs/__init__.pyi similarity index 100% rename from typeshed/coloredlogs/__init__.pyi rename to mypy-stubs/coloredlogs/__init__.pyi diff --git a/typeshed/galaxy/__init__.pyi b/mypy-stubs/galaxy/__init__.pyi similarity index 100% rename from typeshed/galaxy/__init__.pyi rename to mypy-stubs/galaxy/__init__.pyi diff --git a/typeshed/galaxy/exceptions/__init__.pyi b/mypy-stubs/galaxy/exceptions/__init__.pyi similarity index 100% rename from typeshed/galaxy/exceptions/__init__.pyi rename to mypy-stubs/galaxy/exceptions/__init__.pyi diff --git a/typeshed/galaxy/exceptions/error_codes.pyi b/mypy-stubs/galaxy/exceptions/error_codes.pyi similarity index 100% rename from typeshed/galaxy/exceptions/error_codes.pyi rename to mypy-stubs/galaxy/exceptions/error_codes.pyi diff --git a/typeshed/galaxy/jobs/__init__.pyi b/mypy-stubs/galaxy/jobs/__init__.pyi similarity index 100% rename from typeshed/galaxy/jobs/__init__.pyi rename to mypy-stubs/galaxy/jobs/__init__.pyi diff --git a/typeshed/galaxy/jobs/metrics/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/__init__.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/__init__.pyi rename to mypy-stubs/galaxy/jobs/metrics/__init__.pyi diff --git a/typeshed/galaxy/jobs/metrics/collectl/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/collectl/__init__.pyi rename to mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi diff --git a/typeshed/galaxy/jobs/metrics/collectl/cli.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/cli.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/collectl/cli.pyi rename to mypy-stubs/galaxy/jobs/metrics/collectl/cli.pyi diff --git a/typeshed/galaxy/jobs/metrics/collectl/processes.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/processes.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/collectl/processes.pyi rename to mypy-stubs/galaxy/jobs/metrics/collectl/processes.pyi diff --git a/typeshed/galaxy/jobs/metrics/collectl/stats.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/stats.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/collectl/stats.pyi rename to mypy-stubs/galaxy/jobs/metrics/collectl/stats.pyi diff --git a/typeshed/galaxy/jobs/metrics/collectl/subsystems.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/subsystems.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/collectl/subsystems.pyi rename to mypy-stubs/galaxy/jobs/metrics/collectl/subsystems.pyi diff --git a/typeshed/galaxy/jobs/metrics/formatting.pyi b/mypy-stubs/galaxy/jobs/metrics/formatting.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/formatting.pyi rename to mypy-stubs/galaxy/jobs/metrics/formatting.pyi diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/instrumenters/__init__.pyi rename to mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/collectl.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/instrumenters/collectl.pyi rename to mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/core.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/instrumenters/core.pyi rename to mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi rename to mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/env.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/instrumenters/env.pyi rename to mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/meminfo.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/instrumenters/meminfo.pyi rename to mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/uname.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi similarity index 100% rename from typeshed/galaxy/jobs/metrics/instrumenters/uname.pyi rename to mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi diff --git a/typeshed/galaxy/objectstore/__init__.pyi b/mypy-stubs/galaxy/objectstore/__init__.pyi similarity index 100% rename from typeshed/galaxy/objectstore/__init__.pyi rename to mypy-stubs/galaxy/objectstore/__init__.pyi diff --git a/typeshed/galaxy/objectstore/azure_blob.pyi b/mypy-stubs/galaxy/objectstore/azure_blob.pyi similarity index 100% rename from typeshed/galaxy/objectstore/azure_blob.pyi rename to mypy-stubs/galaxy/objectstore/azure_blob.pyi diff --git a/typeshed/galaxy/objectstore/pulsar.pyi b/mypy-stubs/galaxy/objectstore/pulsar.pyi similarity index 100% rename from typeshed/galaxy/objectstore/pulsar.pyi rename to mypy-stubs/galaxy/objectstore/pulsar.pyi diff --git a/typeshed/galaxy/objectstore/rods.pyi b/mypy-stubs/galaxy/objectstore/rods.pyi similarity index 100% rename from typeshed/galaxy/objectstore/rods.pyi rename to mypy-stubs/galaxy/objectstore/rods.pyi diff --git a/typeshed/galaxy/objectstore/s3.pyi b/mypy-stubs/galaxy/objectstore/s3.pyi similarity index 100% rename from typeshed/galaxy/objectstore/s3.pyi rename to mypy-stubs/galaxy/objectstore/s3.pyi diff --git a/typeshed/galaxy/objectstore/s3_multipart_upload.pyi b/mypy-stubs/galaxy/objectstore/s3_multipart_upload.pyi similarity index 100% rename from typeshed/galaxy/objectstore/s3_multipart_upload.pyi rename to mypy-stubs/galaxy/objectstore/s3_multipart_upload.pyi diff --git a/typeshed/galaxy/tool_util/__init__.pyi b/mypy-stubs/galaxy/tool_util/__init__.pyi similarity index 100% rename from typeshed/galaxy/tool_util/__init__.pyi rename to mypy-stubs/galaxy/tool_util/__init__.pyi diff --git a/typeshed/galaxy/tool_util/cwl/__init__.pyi b/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi similarity index 100% rename from typeshed/galaxy/tool_util/cwl/__init__.pyi rename to mypy-stubs/galaxy/tool_util/cwl/__init__.pyi diff --git a/typeshed/galaxy/tool_util/cwl/cwltool_deps.pyi b/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi similarity index 100% rename from typeshed/galaxy/tool_util/cwl/cwltool_deps.pyi rename to mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi diff --git a/typeshed/galaxy/tool_util/cwl/parser.pyi b/mypy-stubs/galaxy/tool_util/cwl/parser.pyi similarity index 100% rename from typeshed/galaxy/tool_util/cwl/parser.pyi rename to mypy-stubs/galaxy/tool_util/cwl/parser.pyi diff --git a/typeshed/galaxy/tool_util/cwl/representation.pyi b/mypy-stubs/galaxy/tool_util/cwl/representation.pyi similarity index 100% rename from typeshed/galaxy/tool_util/cwl/representation.pyi rename to mypy-stubs/galaxy/tool_util/cwl/representation.pyi diff --git a/typeshed/galaxy/tool_util/cwl/runtime_actions.pyi b/mypy-stubs/galaxy/tool_util/cwl/runtime_actions.pyi similarity index 100% rename from typeshed/galaxy/tool_util/cwl/runtime_actions.pyi rename to mypy-stubs/galaxy/tool_util/cwl/runtime_actions.pyi diff --git a/typeshed/galaxy/tool_util/cwl/schema.pyi b/mypy-stubs/galaxy/tool_util/cwl/schema.pyi similarity index 100% rename from typeshed/galaxy/tool_util/cwl/schema.pyi rename to mypy-stubs/galaxy/tool_util/cwl/schema.pyi diff --git a/typeshed/galaxy/tool_util/deps/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/__init__.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/__init__.pyi rename to mypy-stubs/galaxy/tool_util/deps/__init__.pyi diff --git a/typeshed/galaxy/tool_util/deps/brew_exts.pyi b/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/brew_exts.pyi rename to mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi diff --git a/typeshed/galaxy/tool_util/deps/brew_util.pyi b/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/brew_util.pyi rename to mypy-stubs/galaxy/tool_util/deps/brew_util.pyi diff --git a/typeshed/galaxy/tool_util/deps/commands.pyi b/mypy-stubs/galaxy/tool_util/deps/commands.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/commands.pyi rename to mypy-stubs/galaxy/tool_util/deps/commands.pyi diff --git a/typeshed/galaxy/tool_util/deps/conda_compat.pyi b/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/conda_compat.pyi rename to mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi diff --git a/typeshed/galaxy/tool_util/deps/conda_util.pyi b/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/conda_util.pyi rename to mypy-stubs/galaxy/tool_util/deps/conda_util.pyi diff --git a/typeshed/galaxy/tool_util/deps/container_resolvers/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/container_resolvers/__init__.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/container_resolvers/__init__.pyi rename to mypy-stubs/galaxy/tool_util/deps/container_resolvers/__init__.pyi diff --git a/typeshed/galaxy/tool_util/deps/container_resolvers/explicit.pyi b/mypy-stubs/galaxy/tool_util/deps/container_resolvers/explicit.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/container_resolvers/explicit.pyi rename to mypy-stubs/galaxy/tool_util/deps/container_resolvers/explicit.pyi diff --git a/typeshed/galaxy/tool_util/deps/container_resolvers/mulled.pyi b/mypy-stubs/galaxy/tool_util/deps/container_resolvers/mulled.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/container_resolvers/mulled.pyi rename to mypy-stubs/galaxy/tool_util/deps/container_resolvers/mulled.pyi diff --git a/typeshed/galaxy/tool_util/deps/containers.pyi b/mypy-stubs/galaxy/tool_util/deps/containers.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/containers.pyi rename to mypy-stubs/galaxy/tool_util/deps/containers.pyi diff --git a/typeshed/galaxy/tool_util/deps/dependencies.pyi b/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/dependencies.pyi rename to mypy-stubs/galaxy/tool_util/deps/dependencies.pyi diff --git a/typeshed/galaxy/tool_util/deps/docker_util.pyi b/mypy-stubs/galaxy/tool_util/deps/docker_util.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/docker_util.pyi rename to mypy-stubs/galaxy/tool_util/deps/docker_util.pyi diff --git a/typeshed/galaxy/tool_util/deps/dockerfiles.pyi b/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/dockerfiles.pyi rename to mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi diff --git a/typeshed/galaxy/tool_util/deps/installable.pyi b/mypy-stubs/galaxy/tool_util/deps/installable.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/installable.pyi rename to mypy-stubs/galaxy/tool_util/deps/installable.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/__init__.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/_cli.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/_cli.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/_cli.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/_cli.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/mulled_build.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/mulled_build.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/mulled_build_channel.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_channel.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/mulled_build_channel.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_channel.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/mulled_build_files.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/mulled_build_files.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/mulled_build_tool.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_tool.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/mulled_build_tool.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_tool.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/mulled_search.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_search.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/mulled_search.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/mulled_search.pyi diff --git a/typeshed/galaxy/tool_util/deps/mulled/util.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/mulled/util.pyi rename to mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi diff --git a/typeshed/galaxy/tool_util/deps/requirements.pyi b/mypy-stubs/galaxy/tool_util/deps/requirements.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/requirements.pyi rename to mypy-stubs/galaxy/tool_util/deps/requirements.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/__init__.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/resolvers/__init__.pyi rename to mypy-stubs/galaxy/tool_util/deps/resolvers/__init__.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.pyi rename to mypy-stubs/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/conda.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/conda.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/resolvers/conda.pyi rename to mypy-stubs/galaxy/tool_util/deps/resolvers/conda.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/galaxy_packages.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/galaxy_packages.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/resolvers/galaxy_packages.pyi rename to mypy-stubs/galaxy/tool_util/deps/resolvers/galaxy_packages.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/homebrew.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/homebrew.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/resolvers/homebrew.pyi rename to mypy-stubs/galaxy/tool_util/deps/resolvers/homebrew.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/modules.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/modules.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/resolvers/modules.pyi rename to mypy-stubs/galaxy/tool_util/deps/resolvers/modules.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/resolver_mixins.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/resolver_mixins.pyi similarity index 100% rename from typeshed/galaxy/tool_util/deps/resolvers/resolver_mixins.pyi rename to mypy-stubs/galaxy/tool_util/deps/resolvers/resolver_mixins.pyi diff --git a/typeshed/galaxy/tool_util/deps/resolvers/tool_shed_packages.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/tool_shed_packages.pyi 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rename from typeshed/shellescape/main.pyi rename to mypy-stubs/shellescape/main.pyi diff --git a/typeshed/subprocess.pyi b/mypy-stubs/subprocess.pyi similarity index 100% rename from typeshed/subprocess.pyi rename to mypy-stubs/subprocess.pyi diff --git a/typeshed/urllib/__init__.py b/mypy-stubs/urllib/__init__.py similarity index 100% rename from typeshed/urllib/__init__.py rename to mypy-stubs/urllib/__init__.py diff --git a/typeshed/urllib/parse.pyi b/mypy-stubs/urllib/parse.pyi similarity index 100% rename from typeshed/urllib/parse.pyi rename to mypy-stubs/urllib/parse.pyi From 633222772c2abe237082c708a88145e98fcf43f8 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 20 Jul 2022 11:43:26 -0500 Subject: [PATCH 2/8] upgrade minimum ruamel.yaml versions --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 7ec64a4d3..38e42d041 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,5 @@ requests>=2.4.3 +ruamel.yaml>=0.16.0,<0.17.22;python_version>='3.10' ruamel.yaml>=0.15,<0.17.22 rdflib>=4.2.2,<6.3 rdflib>= 4.2.2, < 6.0.0;python_version<='3.6' From 04a27077e68c5828522e8a89bbab4fb8c5d45553 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 20 Jul 2022 23:17:31 -0500 Subject: [PATCH 3/8] WIP: fix types --- mypy-stubs/arcp/__init__.pyi | 4 +- mypy-stubs/arcp/generate.pyi | 10 - mypy-stubs/arcp/parse.pyi | 24 +- mypy-stubs/argcomplete/__init__.pyi | 32 +- mypy-stubs/bagit.pyi | 79 +-- mypy-stubs/cachecontrol/__init__.pyi | 3 - mypy-stubs/cachecontrol/adapter.pyi | 30 -- mypy-stubs/cachecontrol/cache.pyi | 22 +- mypy-stubs/cachecontrol/caches/file_cache.pyi | 41 +- mypy-stubs/cachecontrol/controller.pyi | 37 +- mypy-stubs/cachecontrol/filewrapper.pyi | 8 - mypy-stubs/cachecontrol/serialize.pyi | 12 - mypy-stubs/cachecontrol/wrapper.pyi | 23 +- mypy-stubs/coloredlogs/__init__.pyi | 21 +- mypy-stubs/galaxy/exceptions/__init__.pyi | 32 +- mypy-stubs/galaxy/jobs/__init__.pyi | 1 - mypy-stubs/galaxy/jobs/metrics/__init__.pyi | 5 +- .../galaxy/jobs/metrics/collectl/__init__.pyi | 1 - .../jobs/metrics/instrumenters/__init__.pyi | 1 + .../jobs/metrics/instrumenters/collectl.pyi | 2 + 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mypy-stubs/galaxy/util/pastescript/loadwsgi.pyi create mode 100644 mypy-stubs/galaxy/util/pastescript/serve.pyi create mode 100644 mypy-stubs/galaxy/util/path/__init__.pyi create mode 100644 mypy-stubs/galaxy/util/path/ntpath.pyi create mode 100644 mypy-stubs/galaxy/util/path/posixpath.pyi create mode 100644 mypy-stubs/galaxy/util/permutations.pyi create mode 100644 mypy-stubs/galaxy/util/renamed_temporary_file.pyi create mode 100644 mypy-stubs/galaxy/util/rules_dsl.pyi create mode 100644 mypy-stubs/galaxy/util/sanitize_html.pyi create mode 100644 mypy-stubs/galaxy/util/script.pyi create mode 100644 mypy-stubs/galaxy/util/search.pyi create mode 100644 mypy-stubs/galaxy/util/template.pyi create mode 100644 mypy-stubs/galaxy/util/tool_shed/__init__.pyi create mode 100644 mypy-stubs/galaxy/util/tool_shed/common_util.pyi create mode 100644 mypy-stubs/galaxy/util/tool_shed/encoding_util.pyi create mode 100644 mypy-stubs/galaxy/util/tool_shed/xml_util.pyi create mode 100644 mypy-stubs/galaxy/util/tool_version.pyi create mode 100644 mypy-stubs/galaxy/util/ucsc.pyi create mode 100644 mypy-stubs/galaxy/util/validation.pyi create mode 100644 mypy-stubs/galaxy/util/watcher.pyi create mode 100644 mypy-stubs/galaxy/util/web_compat.pyi create mode 100644 mypy-stubs/galaxy/util/yaml_util.pyi create mode 100644 mypy-stubs/galaxy/util/zipstream.pyi create mode 100644 mypy-stubs/prov/dot.pyi delete mode 100644 mypy-stubs/prov/serializers/__init__.pyi create mode 100644 mypy-stubs/rdflib/collection.pyi delete mode 100644 mypy-stubs/rdflib/paths.pyi create mode 100644 mypy-stubs/rdflib/resource.pyi diff --git a/mypy-stubs/arcp/__init__.pyi b/mypy-stubs/arcp/__init__.pyi index 8eb5f17cf..794fdbf6c 100644 --- a/mypy-stubs/arcp/__init__.pyi +++ b/mypy-stubs/arcp/__init__.pyi @@ -1,5 +1,5 @@ -from .generate import arcp_hash as arcp_hash, arcp_location as arcp_location, arcp_name as arcp_name, arcp_random as arcp_random, arcp_uuid as arcp_uuid -from .parse import is_arcp_uri as is_arcp_uri, parse_arcp as parse_arcp +from .parse import is_arcp_uri as is_arcp_uri +from .parse import parse_arcp as parse_arcp ARCP: str NI: str diff --git a/mypy-stubs/arcp/generate.pyi b/mypy-stubs/arcp/generate.pyi deleted file mode 100644 index a4d59a758..000000000 --- a/mypy-stubs/arcp/generate.pyi +++ /dev/null @@ -1,10 +0,0 @@ -from base64 import urlsafe_b64decode as urlsafe_b64decode -from typing import Any, Optional - -SCHEME: str - -def arcp_uuid(uuid: Any, path: str = ..., query: Optional[Any] = ..., fragment: Optional[Any] = ...): ... -def arcp_random(path: str = ..., query: Optional[Any] = ..., fragment: Optional[Any] = ..., uuid: Optional[Any] = ...): ... -def arcp_location(location: Any, path: str = ..., query: Optional[Any] = ..., fragment: Optional[Any] = ..., namespace: Any = ...): ... -def arcp_name(name: Any, path: str = ..., query: Optional[Any] = ..., fragment: Optional[Any] = ...): ... -def arcp_hash(bytes: bytes = ..., path: str = ..., query: Optional[Any] = ..., fragment: Optional[Any] = ..., hash: Optional[Any] = ...): ... diff --git a/mypy-stubs/arcp/parse.pyi b/mypy-stubs/arcp/parse.pyi index 146d4f8f7..207328f7d 100644 --- a/mypy-stubs/arcp/parse.pyi +++ b/mypy-stubs/arcp/parse.pyi @@ -1,25 +1,25 @@ +from typing import Any, Tuple, Union from urllib.parse import ParseResult -from typing import Any from uuid import NAMESPACE_URL as NAMESPACE_URL SCHEME: str -def is_arcp_uri(uri: Any): ... -def parse_arcp(uri: Any): ... -def urlparse(uri: Any): ... +def is_arcp_uri(uri: str) -> bool: ... +def parse_arcp(uri: str) -> "ARCPParseResult": ... +def urlparse(uri: str) -> Union["ARCPParseResult", ParseResult]: ... class ARCPParseResult(ParseResult): def __init__(self, *args: Any) -> None: ... @property - def prefix(self): ... + def prefix(self) -> str: ... @property - def name(self): ... + def name(self) -> str: ... @property - def uuid(self): ... + def uuid(self) -> str: ... @property - def ni(self): ... - def ni_uri(self, authority: str = ...): ... - def nih_uri(self): ... - def ni_well_known(self, base: str = ...): ... + def ni(self) -> str | None: ... + def ni_uri(self, authority: str = ...) -> str | None: ... + def nih_uri(self) -> str | None: ... + def ni_well_known(self, base: str = ...) -> str | None: ... @property - def hash(self): ... + def hash(self) -> Tuple[str, str] | None: ... diff --git a/mypy-stubs/argcomplete/__init__.pyi b/mypy-stubs/argcomplete/__init__.pyi index 47f9165a8..f9204a07b 100644 --- a/mypy-stubs/argcomplete/__init__.pyi +++ b/mypy-stubs/argcomplete/__init__.pyi @@ -1,22 +1,18 @@ -from typing import Any, Optional import argparse -class CompletionFinder: - always_complete_options: Any = ... - exclude: Any = ... - validator: Any = ... - print_suppressed: Any = ... - completing: bool = ... - default_completer: Any = ... - append_space: Any = ... - def __init__(self, argument_parser: Optional[argparse.ArgumentParser] = ..., always_complete_options: bool = ..., exclude: Optional[Any] = ..., validator: Optional[Any] = ..., print_suppressed: bool = ..., default_completer: Any = ..., append_space: Optional[Any] = ...) -> None: ... - def __call__(self, argument_parser: argparse.ArgumentParser, always_complete_options: bool = ..., exit_method: Any = ..., output_stream: Optional[Any] = ..., exclude: Optional[Any] = ..., validator: Optional[Any] = ..., print_suppressed: bool = ..., append_space: Optional[Any] = ..., default_completer: Any = ...) -> None: ... - def collect_completions(self, active_parsers: Any, parsed_args: Any, cword_prefix: Any, debug: Any): ... - def filter_completions(self, completions: Any): ... - def quote_completions(self, completions: Any, cword_prequote: Any, last_wordbreak_pos: Any): ... - def rl_complete(self, text: Any, state: Any): ... - def get_display_completions(self): ... +from typing import Any, Optional -class ExclusiveCompletionFinder(CompletionFinder): ... +class CompletionFinder: + def __call__( + self, + argument_parser: argparse.ArgumentParser, + always_complete_options: bool = ..., + exit_method: Any = ..., + output_stream: Optional[Any] = ..., + exclude: Optional[Any] = ..., + validator: Optional[Any] = ..., + print_suppressed: bool = ..., + append_space: Optional[Any] = ..., + default_completer: Any = ..., + ) -> None: ... autocomplete: CompletionFinder - diff --git a/mypy-stubs/bagit.pyi b/mypy-stubs/bagit.pyi index 1f640a561..2b0f5b9f2 100644 --- a/mypy-stubs/bagit.pyi +++ b/mypy-stubs/bagit.pyi @@ -1,7 +1,7 @@ import argparse -from typing import Any, Optional, Tuple, List, Generator, Dict +from typing import Any, Dict, Iterator, List, Optional, Tuple -def find_locale_dir(): ... +from _typeshed import Incomplete TRANSLATION_CATALOG: Any MODULE_NAME: Any @@ -15,8 +15,6 @@ HASH_BLOCK_SIZE: Any open_text_file: Any UNICODE_BYTE_ORDER_MARK: str -def make_bag(bag_dir: Any, bag_info: Optional[Any] = ..., processes: int = ..., checksums: Optional[Any] = ..., checksum: Optional[Any] = ..., encoding: str = ...): ... - class Bag: valid_files: Any = ... valid_directories: Any = ... @@ -30,68 +28,23 @@ class Bag: path: Any = ... def __init__(self, path: Optional[Any] = ...) -> None: ... @property - def algs(self): ... + def algs(self) -> List[str]: ... @property - def version(self): ... - def manifest_files(self) -> None: ... + def version(self) -> str: ... + def manifest_files(self) -> Iterator[str]: ... def tagmanifest_files(self) -> None: ... def compare_manifests_with_fs(self) -> Tuple[List[str], List[str]]: ... - def compare_fetch_with_fs(self): ... - def payload_files(self) -> None: ... - def payload_entries(self): ... + def compare_fetch_with_fs(self) -> List[str]: ... + def payload_files(self) -> Iterator[str]: ... + def payload_entries(self) -> Dict[str, str]: ... def save(self, processes: int = ..., manifests: bool = ...) -> None: ... - def tagfile_entries(self): ... - def missing_optional_tagfiles(self) -> Generator[str, None, None]: ... - def fetch_entries(self) -> None: ... - def files_to_be_fetched(self) -> None: ... + def tagfile_entries(self) -> Dict[str, str]: ... + def missing_optional_tagfiles(self) -> Iterator[str]: ... + def fetch_entries(self) -> Iterator[Tuple[str, str, str]]: ... + def files_to_be_fetched(self) -> Iterator[str]: ... def has_oxum(self) -> bool: ... - def validate(self, processes: int = ..., fast: bool = ..., completeness_only: bool = ...): ... - def is_valid(self, fast: bool = ..., completeness_only: bool = ...): ... + def validate( + self, processes: int = ..., fast: bool = ..., completeness_only: bool = ... + ) -> bool: ... + def is_valid(self, fast: bool = ..., completeness_only: bool = ...) -> bool: ... def validate_fetch(self) -> None: ... - -class BagError(Exception): ... - -class BagValidationError(BagError): - message: Any = ... - details: Any = ... - def __init__(self, message: Any, details: Optional[Any] = ...) -> None: ... - -class ManifestErrorDetail(BagError): - path: Any = ... - def __init__(self, path: Any) -> None: ... - -class ChecksumMismatch(ManifestErrorDetail): - path: Any = ... - algorithm: Any = ... - expected: Any = ... - found: Any = ... - def __init__(self, path: Any, algorithm: Optional[Any] = ..., expected: Optional[Any] = ..., found: Optional[Any] = ...) -> None: ... - -class FileMissing(ManifestErrorDetail): ... -class UnexpectedFile(ManifestErrorDetail): ... - -class FileNormalizationConflict(BagError): - file_a: Any = ... - file_b: Any = ... - def __init__(self, file_a: Any, file_b: Any) -> None: ... - -def posix_multiprocessing_worker_initializer() -> None: ... -def normalize_unicode_py3(s: Any): ... -def normalize_unicode_py2(s: Any): ... -normalize_unicode = normalize_unicode_py3 - -def build_unicode_normalized_lookup_dict(filenames: Any): ... -def get_hashers(algorithms: Any): ... -def make_manifests(data_dir: Any, processes: Any, algorithms: Any = ..., encoding: str = ...): ... -def generate_manifest_lines(filename: Any, algorithms: Any = ...): ... -def force_unicode_py2(s: Any): ... -force_unicode = str - -class BagArgumentParser(argparse.ArgumentParser): - bag_info: Any = ... - def __init__(self, *args: Any, **kwargs: Any) -> None: ... - -class BagHeaderAction(argparse.Action): - def __call__(self, parser: Any, _: Any, values: Any, option_string: Optional[Any] = ...) -> None: ... - -def main() -> None: ... diff --git a/mypy-stubs/cachecontrol/__init__.pyi b/mypy-stubs/cachecontrol/__init__.pyi index 3a894cc06..d8c9745da 100644 --- a/mypy-stubs/cachecontrol/__init__.pyi +++ b/mypy-stubs/cachecontrol/__init__.pyi @@ -6,7 +6,4 @@ from typing import Any from .wrapper import CacheControl as CacheControl -# from .adapter import CacheControlAdapter as CacheControlAdapter -# from .controller import CacheController as CacheController - __email__ = ... # type: Any diff --git a/mypy-stubs/cachecontrol/adapter.pyi b/mypy-stubs/cachecontrol/adapter.pyi deleted file mode 100644 index d24c2af18..000000000 --- a/mypy-stubs/cachecontrol/adapter.pyi +++ /dev/null @@ -1,30 +0,0 @@ -# Stubs for cachecontrol.adapter (Python 2) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -from requests.adapters import HTTPAdapter - -from .cache import DictCache as DictCache -from .controller import CacheController as CacheController -from .filewrapper import CallbackFileWrapper as CallbackFileWrapper - -class CacheControlAdapter(HTTPAdapter): - invalidating_methods = ... # type: Any - cache = ... # type: Any - heuristic = ... # type: Any - controller = ... # type: Any - def __init__( - self, - cache=None, - cache_etags=True, - controller_class=None, - serializer=None, - heuristic=None, - *args, - **kw - ): ... - def send(self, request, **kw): ... - def build_response(self, request, response, from_cache=False): ... - def close(self): ... diff --git a/mypy-stubs/cachecontrol/cache.pyi b/mypy-stubs/cachecontrol/cache.pyi index c4f507b41..04b98f2ea 100644 --- a/mypy-stubs/cachecontrol/cache.pyi +++ b/mypy-stubs/cachecontrol/cache.pyi @@ -1,19 +1,5 @@ -# Stubs for cachecontrol.cache (Python 2) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - class BaseCache: - def get(self, key): ... - def set(self, key, value): ... - def delete(self, key): ... - def close(self): ... - -class DictCache(BaseCache): - lock = ... # type: Any - data = ... # type: Any - def __init__(self, init_dict=None): ... - def get(self, key): ... - def set(self, key, value): ... - def delete(self, key): ... + def get(self, key: str) -> str | None: ... + def set(self, key: str, value: str) -> None: ... + def delete(self, key: str) -> None: ... + def close(self) -> None: ... diff --git a/mypy-stubs/cachecontrol/caches/file_cache.pyi b/mypy-stubs/cachecontrol/caches/file_cache.pyi index 2410374d7..229c143ba 100644 --- a/mypy-stubs/cachecontrol/caches/file_cache.pyi +++ b/mypy-stubs/cachecontrol/caches/file_cache.pyi @@ -1,30 +1,31 @@ -# NOTE: This dynamically typed stub was automatically generated by stubgen. - from os import PathLike -from typing import Any, Callable, Union +from typing import ContextManager from ..cache import BaseCache as BaseCache from ..controller import CacheController as CacheController +class _LockClass: + path: str + +_lock_class = ContextManager[_LockClass] + class FileCache(BaseCache): - directory = ... # type: Union[str, PathLike[str]] - forever = ... # type: bool - filemode = ... # type: str - dirmode = ... # type: str - lock_class = ... # type: Callable + directory: str | PathLike[str] + forever: bool + filemode: str + dirmode: str + lock_class: _lock_class def __init__( self, - directory: Union[str, PathLike[str]], - forever=False, - filemode=384, - dirmode=448, - use_dir_lock=None, - lock_class=None, + directory: str | PathLike[str], + forever: bool = ..., + filemode: int = ..., + dirmode: int = ..., + use_dir_lock: bool | None = ..., + lock_class: _lock_class | None = ..., ) -> None: ... @staticmethod - def encode(x): ... - def get(self, key): ... - def set(self, key, value): ... - def delete(self, key): ... - -def url_to_file_path(url, filecache): ... + def encode(x: str) -> str: ... + def get(self, key: str) -> None | str: ... + def set(self, key: str, value: str) -> None: ... + def delete(self, key: str) -> None: ... diff --git a/mypy-stubs/cachecontrol/controller.pyi b/mypy-stubs/cachecontrol/controller.pyi index ce2147ce8..5118fab02 100644 --- a/mypy-stubs/cachecontrol/controller.pyi +++ b/mypy-stubs/cachecontrol/controller.pyi @@ -1,26 +1,17 @@ -# Stubs for cachecontrol.controller (Python 2) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete -from typing import Any - -# from .cache import DictCache as DictCache -# from .serialize import Serializer as Serializer - -logger = ... # type: Any -URI = ... # type: Any - -def parse_uri(uri): ... +logger: Incomplete +URI: Incomplete class CacheController: - cache = ... # type: Any - cache_etags = ... # type: Any - serializer = ... # type: Any - def __init__(self, cache=None, cache_etags=True, serializer=None): ... - @classmethod - def cache_url(cls, uri): ... - def parse_cache_control(self, headers): ... - def cached_request(self, request): ... - def conditional_headers(self, request): ... - def cache_response(self, request, response, body=None): ... - def update_cached_response(self, request, response): ... + cache: Incomplete + cache_etags: Incomplete + serializer: Incomplete + cacheable_status_codes: Incomplete + def __init__( + self, + cache: Incomplete | None = ..., + cache_etags: bool = ..., + serializer: Incomplete | None = ..., + status_codes: Incomplete | None = ..., + ) -> None: ... diff --git a/mypy-stubs/cachecontrol/filewrapper.pyi b/mypy-stubs/cachecontrol/filewrapper.pyi deleted file mode 100644 index d21df1508..000000000 --- a/mypy-stubs/cachecontrol/filewrapper.pyi +++ /dev/null @@ -1,8 +0,0 @@ -# Stubs for cachecontrol.filewrapper (Python 2) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -class CallbackFileWrapper: - def __init__(self, fp, callback): ... - def __getattr__(self, name): ... - def read(self, amt=None): ... diff --git a/mypy-stubs/cachecontrol/serialize.pyi b/mypy-stubs/cachecontrol/serialize.pyi deleted file mode 100644 index bc7939b7e..000000000 --- a/mypy-stubs/cachecontrol/serialize.pyi +++ /dev/null @@ -1,12 +0,0 @@ -# Stubs for cachecontrol.serialize (Python 2) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from .compat import HTTPResponse as HTTPResponse -from .compat import pickle as pickle -from .compat import str as str - -class Serializer: - def dumps(self, request, response, body=None): ... - def loads(self, request, data): ... - def prepare_response(self, request, cached): ... diff --git a/mypy-stubs/cachecontrol/wrapper.pyi b/mypy-stubs/cachecontrol/wrapper.pyi index f1ec68ffa..a4da67289 100644 --- a/mypy-stubs/cachecontrol/wrapper.pyi +++ b/mypy-stubs/cachecontrol/wrapper.pyi @@ -1,16 +1,13 @@ -# Stubs for cachecontrol.wrapper (Python 2) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from .adapter import CacheControlAdapter -from .cache import DictCache +from _typeshed import Incomplete +from requests import Session def CacheControl( - sess: Any, - cache: Optional[Any] = ..., + sess: Session, + cache: Incomplete | None = ..., cache_etags: bool = ..., - serializer: Optional[Any] = ..., - heuristic: Optional[Any] = ..., -): ... + serializer: Incomplete | None = ..., + heuristic: Incomplete | None = ..., + controller_class: Incomplete | None = ..., + adapter_class: Incomplete | None = ..., + cacheable_methods: Incomplete | None = ..., +) -> Session: ... diff --git a/mypy-stubs/coloredlogs/__init__.pyi b/mypy-stubs/coloredlogs/__init__.pyi index 2678a4287..c6842e0d8 100644 --- a/mypy-stubs/coloredlogs/__init__.pyi +++ b/mypy-stubs/coloredlogs/__init__.pyi @@ -45,7 +45,14 @@ class ColoredFormatter(BasicFormatter): log_record_factory: Any = ... level_styles: Any = ... field_styles: Any = ... - def __init__(self, fmt: Optional[Any] = ..., datefmt: Optional[Any] = ..., level_styles: Optional[Any] = ..., field_styles: Optional[Any] = ..., style: Any = ...) -> None: ... + def __init__( + self, + fmt: Optional[Any] = ..., + datefmt: Optional[Any] = ..., + level_styles: Optional[Any] = ..., + field_styles: Optional[Any] = ..., + style: Any = ..., + ) -> None: ... def colorize_format(self, fmt: Any, style: Any = ...): ... def format(self, record: Any): ... @@ -53,14 +60,22 @@ class Empty: ... class HostNameFilter(logging.Filter): @classmethod - def install(cls, handler: Any, fmt: Optional[Any] = ..., use_chroot: bool = ..., style: Any = ...): ... + def install( + cls, + handler: Any, + fmt: Optional[Any] = ..., + use_chroot: bool = ..., + style: Any = ..., + ): ... hostname: Any = ... def __init__(self, use_chroot: bool = ...) -> None: ... def filter(self, record: Any): ... class ProgramNameFilter(logging.Filter): @classmethod - def install(cls, handler: Any, fmt: Any, programname: Optional[Any] = ..., style: Any = ...): ... + def install( + cls, handler: Any, fmt: Any, programname: Optional[Any] = ..., style: Any = ... + ): ... programname: Any = ... def __init__(self, programname: Optional[Any] = ...) -> None: ... def filter(self, record: Any): ... diff --git a/mypy-stubs/galaxy/exceptions/__init__.pyi b/mypy-stubs/galaxy/exceptions/__init__.pyi index e59ac087d..21c935bf8 100644 --- a/mypy-stubs/galaxy/exceptions/__init__.pyi +++ b/mypy-stubs/galaxy/exceptions/__init__.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + from ..exceptions import error_codes as error_codes class MessageException(Exception): @@ -11,7 +12,9 @@ class MessageException(Exception): err_msg = ... # type: Any type = ... # type: Any extra_error_info = ... # type: Any - def __init__(self, err_msg: Optional[Any] = ..., type: str = ..., **extra_error_info) -> None: ... + def __init__( + self, err_msg: Optional[Any] = ..., type: str = ..., **extra_error_info + ) -> None: ... class ItemDeletionException(MessageException): ... class ObjectInvalid(Exception): ... @@ -127,17 +130,36 @@ class ContainerCLIError(Exception): returncode = ... # type: Any command = ... # type: Any subprocess_command = ... # type: Any - def __init__(self, msg: Optional[Any] = ..., stdout: Optional[Any] = ..., stderr: Optional[Any] = ..., returncode: Optional[Any] = ..., command: Optional[Any] = ..., subprocess_command: Optional[Any] = ..., **kwargs) -> None: ... + def __init__( + self, + msg: Optional[Any] = ..., + stdout: Optional[Any] = ..., + stderr: Optional[Any] = ..., + returncode: Optional[Any] = ..., + command: Optional[Any] = ..., + subprocess_command: Optional[Any] = ..., + **kwargs + ) -> None: ... class ContainerNotFound(Exception): container_id = ... # type: Any - def __init__(self, msg: Optional[Any] = ..., container_id: Optional[Any] = ..., **kwargs) -> None: ... + def __init__( + self, msg: Optional[Any] = ..., container_id: Optional[Any] = ..., **kwargs + ) -> None: ... class ContainerImageNotFound(Exception): image = ... # type: Any - def __init__(self, msg: Optional[Any] = ..., image: Optional[Any] = ..., **kwargs) -> None: ... + def __init__( + self, msg: Optional[Any] = ..., image: Optional[Any] = ..., **kwargs + ) -> None: ... class ContainerRunError(Exception): image = ... # type: Any command = ... # type: Any - def __init__(self, msg: Optional[Any] = ..., image: Optional[Any] = ..., command: Optional[Any] = ..., **kwargs) -> None: ... + def __init__( + self, + msg: Optional[Any] = ..., + image: Optional[Any] = ..., + command: Optional[Any] = ..., + **kwargs + ) -> None: ... diff --git a/mypy-stubs/galaxy/jobs/__init__.pyi b/mypy-stubs/galaxy/jobs/__init__.pyi index c65cfb4ee..e3b11dc28 100644 --- a/mypy-stubs/galaxy/jobs/__init__.pyi +++ b/mypy-stubs/galaxy/jobs/__init__.pyi @@ -1,4 +1,3 @@ # Stubs for galaxy.jobs (Python 3.4) # # NOTE: This dynamically typed stub was automatically generated by stubgen. - diff --git a/mypy-stubs/galaxy/jobs/metrics/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/__init__.pyi index 758ddc677..7f494712b 100644 --- a/mypy-stubs/galaxy/jobs/metrics/__init__.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/__init__.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + from ..metrics import formatting as formatting log = ... # type: Any @@ -16,7 +17,9 @@ class JobMetrics: def format(self, plugin, key, value): ... def set_destination_conf_file(self, destination_id, conf_file): ... def set_destination_conf_element(self, destination_id, element): ... - def set_destination_instrumenter(self, destination_id, job_instrumenter: Optional[Any] = ...): ... + def set_destination_instrumenter( + self, destination_id, job_instrumenter: Optional[Any] = ... + ): ... def collect_properties(self, destination_id, job_id, job_directory): ... class NullJobInstrumenter: diff --git a/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi index c58636ec4..ee480022b 100644 --- a/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi @@ -1,4 +1,3 @@ # Stubs for galaxy.jobs.metrics.collectl (Python 3.4) # # NOTE: This dynamically typed stub was automatically generated by stubgen. - diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi index ede6717e0..1a9650669 100644 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + from ...metrics import formatting as formatting INSTRUMENT_FILE_PREFIX = ... # type: str diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi index 080d2e5b4..3ddaaa9e3 100644 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi @@ -3,7 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + import formatting + from ..instrumenters import InstrumentPlugin class CollectlFormatter(formatting.JobMetricFormatter): diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi index 885df5a2b..48d76eedd 100644 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi @@ -3,7 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + import formatting + from ..instrumenters import InstrumentPlugin class CorePluginFormatter(formatting.JobMetricFormatter): diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi index 00744ed68..e17cd1f75 100644 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi @@ -3,7 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + import formatting + from ..instrumenters import InstrumentPlugin class CpuInfoFormatter(formatting.JobMetricFormatter): diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi index 411332205..afbd1a16e 100644 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi @@ -3,7 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + import formatting + from ..instrumenters import InstrumentPlugin class EnvFormatter(formatting.JobMetricFormatter): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi index 344cfa861..252012d92 100644 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi @@ -3,7 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + import formatting + from ..instrumenters import InstrumentPlugin class MemInfoFormatter(formatting.JobMetricFormatter): diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi index b541bd02e..d0c6cff2a 100644 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi +++ b/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi @@ -3,7 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + import formatting + from ..instrumenters import InstrumentPlugin class UnameFormatter(formatting.JobMetricFormatter): diff --git a/mypy-stubs/galaxy/objectstore/__init__.pyi b/mypy-stubs/galaxy/objectstore/__init__.pyi index 82259bceb..8af0e6095 100644 --- a/mypy-stubs/galaxy/objectstore/__init__.pyi +++ b/mypy-stubs/galaxy/objectstore/__init__.pyi @@ -15,21 +15,113 @@ class ObjectStore: check_old_style = ... # type: Any def __init__(self, config, **kwargs) -> None: ... def shutdown(self): ... - def exists(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ...): ... - def file_ready(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... - def create(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... - def empty(self, obj, base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... - def size(self, obj, extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... - def delete(self, obj, entire_dir: bool = ..., base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... - def get_data(self, obj, start: int = ..., count: int = ..., base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... - def get_filename(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... - def update_from_file(self, obj, base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ..., file_name: Optional[Any] = ..., create: bool = ...): ... - def get_object_url(self, obj, extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ... + def exists( + self, + obj, + base_dir: Optional[Any] = ..., + dir_only: bool = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + ): ... + def file_ready( + self, + obj, + base_dir: Optional[Any] = ..., + dir_only: bool = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... + def create( + self, + obj, + base_dir: Optional[Any] = ..., + dir_only: bool = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... + def empty( + self, + obj, + base_dir: Optional[Any] = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... + def size( + self, + obj, + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... + def delete( + self, + obj, + entire_dir: bool = ..., + base_dir: Optional[Any] = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... + def get_data( + self, + obj, + start: int = ..., + count: int = ..., + base_dir: Optional[Any] = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... + def get_filename( + self, + obj, + base_dir: Optional[Any] = ..., + dir_only: bool = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... + def update_from_file( + self, + obj, + base_dir: Optional[Any] = ..., + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + file_name: Optional[Any] = ..., + create: bool = ..., + ): ... + def get_object_url( + self, + obj, + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + obj_dir: bool = ..., + ): ... def get_store_usage_percent(self): ... class DiskObjectStore(ObjectStore): file_path = ... # type: Any - def __init__(self, config, config_xml: Optional[Any] = ..., file_path: Optional[Any] = ..., extra_dirs: Optional[Any] = ...) -> None: ... + def __init__( + self, + config, + config_xml: Optional[Any] = ..., + file_path: Optional[Any] = ..., + extra_dirs: Optional[Any] = ..., + ) -> None: ... def exists(self, obj, **kwargs): ... def create(self, obj, **kwargs): ... def empty(self, obj, **kwargs): ... @@ -37,7 +129,9 @@ class DiskObjectStore(ObjectStore): def delete(self, obj, entire_dir: bool = ..., **kwargs): ... def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... def get_filename(self, obj, **kwargs): ... - def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ... + def update_from_file( + self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs + ): ... def get_object_url(self, obj, **kwargs): ... def get_store_usage_percent(self): ... @@ -65,16 +159,22 @@ class DistributedObjectStore(NestedObjectStore): global_max_percent_full = ... # type: float sleeper = ... # type: Any filesystem_monitor_thread = ... # type: Any - def __init__(self, config, config_xml: Optional[Any] = ..., fsmon: bool = ...) -> None: ... + def __init__( + self, config, config_xml: Optional[Any] = ..., fsmon: bool = ... + ) -> None: ... def shutdown(self): ... def create(self, obj, **kwargs): ... class HierarchicalObjectStore(NestedObjectStore): backends = ... # type: Any - def __init__(self, config, config_xml: Optional[Any] = ..., fsmon: bool = ...) -> None: ... + def __init__( + self, config, config_xml: Optional[Any] = ..., fsmon: bool = ... + ) -> None: ... def exists(self, obj, **kwargs): ... def create(self, obj, **kwargs): ... -def build_object_store_from_config(config, fsmon: bool = ..., config_xml: Optional[Any] = ...): ... +def build_object_store_from_config( + config, fsmon: bool = ..., config_xml: Optional[Any] = ... +): ... def local_extra_dirs(func): ... def convert_bytes(bytes): ... diff --git a/mypy-stubs/galaxy/objectstore/azure_blob.pyi b/mypy-stubs/galaxy/objectstore/azure_blob.pyi index 89b58c1ad..3ab6e9240 100644 --- a/mypy-stubs/galaxy/objectstore/azure_blob.pyi +++ b/mypy-stubs/galaxy/objectstore/azure_blob.pyi @@ -3,7 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional -from ..objectstore import convert_bytes as convert_bytes, ObjectStore as ObjectStore + +from ..objectstore import ObjectStore as ObjectStore +from ..objectstore import convert_bytes as convert_bytes BlockBlobService = ... # type: Any NO_BLOBSERVICE_ERROR_MESSAGE = ... # type: str @@ -24,6 +26,8 @@ class AzureBlobObjectStore(ObjectStore): def delete(self, obj, entire_dir: bool = ..., **kwargs): ... def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... def get_filename(self, obj, **kwargs): ... - def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ... + def update_from_file( + self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs + ): ... def get_object_url(self, obj, **kwargs): ... def get_store_usage_percent(self): ... diff --git a/mypy-stubs/galaxy/objectstore/pulsar.pyi b/mypy-stubs/galaxy/objectstore/pulsar.pyi index bad104522..858800ed2 100644 --- a/mypy-stubs/galaxy/objectstore/pulsar.pyi +++ b/mypy-stubs/galaxy/objectstore/pulsar.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + from ..objectstore import ObjectStore as ObjectStore ObjectStoreClientManager = ... # type: Any @@ -20,5 +21,11 @@ class PulsarObjectStore(ObjectStore): def get_filename(self, obj, **kwds): ... def update_from_file(self, obj, **kwds): ... def get_store_usage_percent(self): ... - def get_object_url(self, obj, extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ...): ... + def get_object_url( + self, + obj, + extra_dir: Optional[Any] = ..., + extra_dir_at_root: bool = ..., + alt_name: Optional[Any] = ..., + ): ... def shutdown(self): ... diff --git a/mypy-stubs/galaxy/objectstore/rods.pyi b/mypy-stubs/galaxy/objectstore/rods.pyi index 125444b20..6e25e17ab 100644 --- a/mypy-stubs/galaxy/objectstore/rods.pyi +++ b/mypy-stubs/galaxy/objectstore/rods.pyi @@ -2,11 +2,13 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from typing import Any, Optional from posixpath import basename as path_basename from posixpath import dirname as path_dirname from posixpath import join as path_join -from ..objectstore import DiskObjectStore as DiskObjectStore, local_extra_dirs as local_extra_dirs +from typing import Any, Optional + +from ..objectstore import DiskObjectStore as DiskObjectStore +from ..objectstore import local_extra_dirs as local_extra_dirs irods = ... # type: Any IRODS_IMPORT_MESSAGE = ... # type: str @@ -17,7 +19,9 @@ class IRODSObjectStore(DiskObjectStore): default_resource = ... # type: Any root_collection_path = ... # type: Any root_collection = ... # type: Any - def __init__(self, config, file_path: Optional[Any] = ..., extra_dirs: Optional[Any] = ...) -> None: ... + def __init__( + self, config, file_path: Optional[Any] = ..., extra_dirs: Optional[Any] = ... + ) -> None: ... def exists(self, obj, **kwargs): ... def create(self, obj, **kwargs): ... def empty(self, obj, **kwargs): ... @@ -25,7 +29,9 @@ class IRODSObjectStore(DiskObjectStore): def delete(self, obj, entire_dir: bool = ..., **kwargs): ... def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... def get_filename(self, obj, **kwargs): ... - def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ... + def update_from_file( + self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs + ): ... def get_object_url(self, obj, **kwargs): ... def get_store_usage_percent(self): ... diff --git a/mypy-stubs/galaxy/objectstore/s3.pyi b/mypy-stubs/galaxy/objectstore/s3.pyi index 8ffbd92c5..34b7c1f88 100644 --- a/mypy-stubs/galaxy/objectstore/s3.pyi +++ b/mypy-stubs/galaxy/objectstore/s3.pyi @@ -3,8 +3,10 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + +from ..objectstore import ObjectStore as ObjectStore +from ..objectstore import convert_bytes as convert_bytes from .s3_multipart_upload import multipart_upload as multipart_upload -from ..objectstore import convert_bytes as convert_bytes, ObjectStore as ObjectStore boto = ... # type: Any NO_BOTO_ERROR_MESSAGE = ... # type: str @@ -27,7 +29,9 @@ class S3ObjectStore(ObjectStore): def delete(self, obj, entire_dir: bool = ..., **kwargs): ... def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... def get_filename(self, obj, **kwargs): ... - def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ... + def update_from_file( + self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs + ): ... def get_object_url(self, obj, **kwargs): ... def get_store_usage_percent(self): ... diff --git a/mypy-stubs/galaxy/tool_util/__init__.pyi b/mypy-stubs/galaxy/tool_util/__init__.pyi index ef883e955..ff77e3d7d 100644 --- a/mypy-stubs/galaxy/tool_util/__init__.pyi +++ b/mypy-stubs/galaxy/tool_util/__init__.pyi @@ -1,4 +1,3 @@ # Stubs for galaxy.tools (Python 3.4) # # NOTE: This dynamically typed stub was automatically generated by stubgen. - diff --git a/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi b/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi index 72bc0494f..9d1473947 100644 --- a/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi +++ b/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi @@ -2,7 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .cwltool_deps import needs_shell_quoting as needs_shell_quoting, shellescape as shellescape -from .parser import tool_proxy as tool_proxy, workflow_proxy as workflow_proxy -from .representation import to_cwl_job as to_cwl_job, to_galaxy_parameters as to_galaxy_parameters +from .cwltool_deps import needs_shell_quoting as needs_shell_quoting +from .cwltool_deps import shellescape as shellescape +from .parser import tool_proxy as tool_proxy +from .parser import workflow_proxy as workflow_proxy +from .representation import to_cwl_job as to_cwl_job +from .representation import to_galaxy_parameters as to_galaxy_parameters from .runtime_actions import handle_outputs as handle_outputs diff --git a/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi b/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi index 351a4208d..767b9a07c 100644 --- a/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi +++ b/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi @@ -3,12 +3,17 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any -from cwltool import main as main, workflow as workflow, process as process, pathmapper as pathmapper -from cwltool import load_tool as load_tool -import shellescape as shellescape + import schema_salad as schema_salad +import shellescape as shellescape from schema_salad import ref_resolver as ref_resolver +from cwltool import load_tool as load_tool +from cwltool import main as main +from cwltool import pathmapper as pathmapper +from cwltool import process as process +from cwltool import workflow as workflow + main = ... # type: Any workflow = ... # type: Any process = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/cwl/parser.pyi b/mypy-stubs/galaxy/tool_util/cwl/parser.pyi index 369b14688..02c0459af 100644 --- a/mypy-stubs/galaxy/tool_util/cwl/parser.pyi +++ b/mypy-stubs/galaxy/tool_util/cwl/parser.pyi @@ -83,7 +83,9 @@ class InputInstance: required = ... # type: bool array = ... # type: Any area = ... # type: Any - def __init__(self, name, label, description, input_type, array: bool = ..., area: bool = ...) -> None: ... + def __init__( + self, name, label, description, input_type, array: bool = ..., area: bool = ... + ) -> None: ... def to_dict(self, itemwise: bool = ...): ... class OutputInstance: @@ -91,4 +93,6 @@ class OutputInstance: output_data_type = ... # type: Any output_type = ... # type: Any path = ... # type: Any - def __init__(self, name, output_data_type, output_type, path: Optional[Any] = ...) -> None: ... + def __init__( + self, name, output_data_type, output_type, path: Optional[Any] = ... + ) -> None: ... diff --git a/mypy-stubs/galaxy/tool_util/cwl/schema.pyi b/mypy-stubs/galaxy/tool_util/cwl/schema.pyi index 1c51ead4e..e801827d3 100644 --- a/mypy-stubs/galaxy/tool_util/cwl/schema.pyi +++ b/mypy-stubs/galaxy/tool_util/cwl/schema.pyi @@ -2,13 +2,26 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from typing import Any -from .cwltool_deps import ensure_cwltool_available as ensure_cwltool_available, load_tool as load_tool, schema_salad as schema_salad, workflow as workflow from collections import namedtuple +from typing import Any + +from .cwltool_deps import ensure_cwltool_available as ensure_cwltool_available +from .cwltool_deps import load_tool as load_tool +from .cwltool_deps import schema_salad as schema_salad +from .cwltool_deps import workflow as workflow -RawProcessReference = namedtuple('RawProcessReference', ['process_object', 'uri']) +RawProcessReference = namedtuple("RawProcessReference", ["process_object", "uri"]) -ProcessDefinition = namedtuple('ProcessDefinition', ['process_object', 'metadata', 'document_loader', 'avsc_names', 'raw_process_reference']) +ProcessDefinition = namedtuple( + "ProcessDefinition", + [ + "process_object", + "metadata", + "document_loader", + "avsc_names", + "raw_process_reference", + ], +) class SchemaLoader: def __init__(self, strict: bool = ...) -> None: ... diff --git a/mypy-stubs/galaxy/tool_util/deps/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/__init__.pyi index 052ba9847..d6cbbd5d8 100644 --- a/mypy-stubs/galaxy/tool_util/deps/__init__.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/__init__.pyi @@ -1,41 +1,20 @@ -# Stubs for galaxy.tools.deps (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from typing import Any, Dict, List, Optional -from typing import Any, Optional, List -from .requirements import ToolRequirement as ToolRequirement, ToolRequirements as ToolRequirements -from .resolvers import NullDependency as NullDependency -from .resolvers.conda import CondaDependencyResolver as CondaDependencyResolver -from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver as GalaxyPackageDependencyResolver -from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver as ToolShedPackageDependencyResolver +from .requirements import ToolRequirement as ToolRequirement +from .requirements import ToolRequirements as ToolRequirements -log = ... # type: Any -CONFIG_VAL_NOT_FOUND = ... # type: Any - -def build_dependency_manager(app_config_dict: Any, resolution_config_dict: Any, conf_file: Any) -> DependencyManager: ... - -class NullDependencyManager: - dependency_resolvers = ... # type: Any - def uses_tool_shed_dependencies(self): ... - def dependency_shell_commands(self, requirements: ToolRequirements, **kwds) -> List[str]: ... - def find_dep(self, name, version: Optional[Any] = ..., type: str = ..., **kwds): ... +def build_dependency_manager( + app_config_dict: Any, resolution_config_dict: Any, conf_file: Any +) -> DependencyManager: ... class DependencyManager: - default_base_path = ... # type: Any - resolver_classes = ... # type: Any - dependency_resolvers = ... # type: Any - def __init__(self, default_base_path, conf_file: Optional[Any] = ..., app_config: Any = ...) -> None: ... - def get_resolver_option(self, resolver, key, explicit_resolver_options: Any = ...): ... - def get_app_option(self, key, default: Optional[Any] = ...): ... - def dependency_shell_commands(self, requirements: ToolRequirements, **kwds) -> List[str]: ... - def requirements_to_dependencies(self, requirements, **kwds): ... - def uses_tool_shed_dependencies(self): ... - def find_dep(self, name, version: Optional[Any] = ..., type: str = ..., **kwds): ... - -class CachedDependencyManager(DependencyManager): - tool_dependency_cache_dir = ... # type: Any - def __init__(self, default_base_path, conf_file: Optional[Any] = ..., app_config: Any = ..., tool_dependency_cache_dir: Optional[Any] = ...) -> None: ... - def build_cache(self, requirements, **kwds): ... - def dependency_shell_commands(self, requirements: ToolRequirements, **kwds) -> List[str]: ... - def hash_dependencies(self, resolved_dependencies): ... - def get_hashed_dependencies_path(self, resolved_dependencies): ... + default_base_path: str + def __init__( + self, + default_base_path: str, + conf_file: Optional[Any] = ..., + app_config: Any = ..., + ) -> None: ... + def dependency_shell_commands( + self, requirements: ToolRequirements, **kwds: Dict[str, str] + ) -> List[str]: ... diff --git a/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi b/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi index c526375e6..b2811528a 100644 --- a/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi @@ -1,74 +1,22 @@ -# Stubs for galaxy.tools.deps.brew_exts (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from collections.abc import Generator -from typing import Any, Optional +from _typeshed import Incomplete -WHITESPACE_PATTERN = ... # type: Any -DESCRIPTION = ... # type: str -DEFAULT_HOMEBREW_ROOT = ... # type: str -NO_BREW_ERROR_MESSAGE = ... # type: str -CANNOT_DETERMINE_TAP_ERROR_MESSAGE = ... # type: str -VERBOSE = ... # type: bool -RELAXED = ... # type: bool -BREW_ARGS = ... # type: Any +WHITESPACE_PATTERN: Incomplete +DESCRIPTION: str +DEFAULT_HOMEBREW_ROOT: Incomplete +NO_BREW_ERROR_MESSAGE: str +CANNOT_DETERMINE_TAP_ERROR_MESSAGE: str +VERBOSE: bool +RELAXED: bool +BREW_ARGS: Incomplete class BrewContext: - homebrew_prefix = ... # type: Any - homebrew_cellar = ... # type: Any - def __init__(self, args: Optional[Any] = ...) -> None: ... + homebrew_prefix: Incomplete + homebrew_cellar: Incomplete + def __init__(self, args: Incomplete | None = ...) -> None: ... -class RecipeContext: - @staticmethod - def from_args(args, brew_context: Optional[Any] = ...): ... - recipe = ... # type: Any - version = ... # type: Any - brew_context = ... # type: Any - def __init__(self, recipe, version, brew_context: Optional[Any] = ...) -> None: ... - @property - def cellar_path(self): ... - @property - def tap_path(self): ... +def main() -> None: ... -def main(): ... - -class CommandLineException(Exception): - command = ... # type: Any - stdout = ... # type: Any - stderr = ... # type: Any - message = ... # type: Any - def __init__(self, command, stdout, stderr) -> None: ... - -def versioned_install(recipe_context, package: Optional[Any] = ..., version: Optional[Any] = ..., installed_deps: Any = ...): ... -def commit_for_version(recipe_context, package, version): ... -def print_versioned_deps(recipe_context, recipe, version): ... -def load_versioned_deps(cellar_path, relaxed: Optional[Any] = ...): ... -def unversioned_install(package): ... -def attempt_unlink_all(package, deps): ... -def attempt_unlink(package): ... -def brew_execute(args, env: Optional[Any] = ...): ... -def build_env_statements_from_recipe_context(recipe_context, **kwds): ... -def build_env_statements(cellar_root, cellar_path, relaxed: Optional[Any] = ..., custom_only: bool = ...): ... -def build_env_actions(deps, cellar_root, cellar_path, relaxed: Optional[Any] = ..., custom_only: bool = ...): ... - -class EnvAction: - variable = ... # type: Any - action = ... # type: Any - value = ... # type: Any - def __init__(self, keg_root, action_description) -> None: ... - @staticmethod - def build_env(env_actions): ... - def modify_environ(self, environ): ... - def to_statements(self): ... - -def brew_head_at_version(recipe_context, package, version): ... -def brew_head_at_commit(commit, tap_path): ... -def git_execute(args): ... -def execute(cmds, env: Optional[Any] = ...): ... -def brew_deps(package): ... -def brew_info(recipe): ... -def extended_brew_info(recipe): ... -def brew_versions_info(package, tap_path): ... -def recipe_cellar_path(cellar_path, recipe, version): ... -def ensure_brew_on_path(args): ... -def which(file): ... +# def execute(cmds, env: Incomplete | None = ...): ... +# def which(file): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi b/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi index c791f1832..b0d1e4b69 100644 --- a/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + from ..deps import brew_exts as brew_exts DEFAULT_TAP = ... # type: str diff --git a/mypy-stubs/galaxy/tool_util/deps/commands.pyi b/mypy-stubs/galaxy/tool_util/deps/commands.pyi index a11b90dc8..1d3c89bcc 100644 --- a/mypy-stubs/galaxy/tool_util/deps/commands.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/commands.pyi @@ -3,20 +3,10 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional -from galaxy.util import which as which -def redirecting_io(sys: Any = ...): ... -def redirect_aware_commmunicate(p, sys: Any = ...): ... -def shell(cmds, env: Optional[Any] = ..., **kwds): ... -def shell_process(cmds, env: Optional[Any] = ..., **kwds): ... -def execute(cmds): ... -def argv_to_str(command_argv, quote: bool = ...): ... -def download_command(url, to: Any = ..., quote_url: bool = ...): ... - -class CommandLineException(Exception): - command = ... # type: Any - stdout = ... # type: Any - stderr = ... # type: Any - returncode = ... # type: Any - message = ... # type: Any - def __init__(self, command, stdout, stderr, returncode) -> None: ... +# def redirecting_io(sys: Any = ...): ... +# def redirect_aware_commmunicate(p, sys: Any = ...): ... +# def shell(cmds, env: Optional[Any] = ..., **kwds): ... +# def shell_process(cmds, env: Optional[Any] = ..., **kwds): ... +# def execute(cmds): ... +# def download_command(url, to: Any = ..., quote_url: bool = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi b/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi index 0cc638263..a61350472 100644 --- a/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + from conda_build.metadata import MetaData as MetaData MetaData = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi b/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi index 1e418baab..ee9102c0a 100644 --- a/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. +from sys import platform as _platform from typing import Any, Optional + import installable -from sys import platform as _platform class CondaContext(installable.InstallableContext): installable_description = ... # type: str @@ -17,7 +18,18 @@ class CondaContext(installable.InstallableContext): ensure_channels = ... # type: Any ensured_channels = ... # type: bool use_local = ... # type: Any - def __init__(self, conda_prefix: Optional[Any] = ..., conda_exec: Optional[Any] = ..., shell_exec: Optional[Any] = ..., debug: bool = ..., ensure_channels: str = ..., condarc_override: Optional[Any] = ..., use_path_exec: Any = ..., copy_dependencies: bool = ..., use_local: Any = ...) -> None: ... + def __init__( + self, + conda_prefix: Optional[Any] = ..., + conda_exec: Optional[Any] = ..., + shell_exec: Optional[Any] = ..., + debug: bool = ..., + ensure_channels: str = ..., + condarc_override: Optional[Any] = ..., + use_path_exec: Any = ..., + copy_dependencies: bool = ..., + use_local: Any = ..., + ) -> None: ... @property def conda_version(self): ... @property @@ -55,7 +67,9 @@ class CondaTarget: package = ... # type: Any version = ... # type: Any channel = ... # type: Any - def __init__(self, package, version: Optional[Any] = ..., channel: Optional[Any] = ...) -> None: ... + def __init__( + self, package, version: Optional[Any] = ..., channel: Optional[Any] = ... + ) -> None: ... @property def package_specifier(self): ... @property @@ -64,6 +78,10 @@ class CondaTarget: def __eq__(self, other): ... def __ne__(self, other): ... -def install_conda(conda_context: Optional[Any] = ..., force_conda_build: bool = ...): ... -def install_conda_target(conda_target, conda_context: Optional[Any] = ..., skip_environment: bool = ...): ... +def install_conda( + conda_context: Optional[Any] = ..., force_conda_build: bool = ... +): ... +def install_conda_target( + conda_target, conda_context: Optional[Any] = ..., skip_environment: bool = ... +): ... def requirements_to_conda_targets(requirements, conda_context: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/container_resolvers/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/container_resolvers/__init__.pyi deleted file mode 100644 index 4e8c8222c..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/container_resolvers/__init__.pyi +++ /dev/null @@ -1,14 +0,0 @@ -# Stubs for galaxy.tools.deps.container_resolvers (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -from galaxy.util.dictifiable import Dictifiable - -class ContainerResolver(Dictifiable): - dict_collection_visible_keys = ... # type: Any - app_info = ... # type: Any - resolver_kwds = ... # type: Any - def __init__(self, app_info: Optional[Any] = ..., **kwds) -> None: ... - def resolve(self, tool_info): ... - def resolver_type(self): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/container_resolvers/explicit.pyi b/mypy-stubs/galaxy/tool_util/deps/container_resolvers/explicit.pyi deleted file mode 100644 index 3f45f9529..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/container_resolvers/explicit.pyi +++ /dev/null @@ -1,9 +0,0 @@ -# Stubs for galaxy.tools.deps.container_resolvers.explicit (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from ..container_resolvers import ContainerResolver - -class ExplicitContainerResolver(ContainerResolver): - resolver_type = ... # type: str - def resolve(self, enabled_container_types, tool_info): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/container_resolvers/mulled.pyi b/mypy-stubs/galaxy/tool_util/deps/container_resolvers/mulled.pyi deleted file mode 100644 index 5f7a6b4ee..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/container_resolvers/mulled.pyi +++ /dev/null @@ -1,55 +0,0 @@ -# Stubs for galaxy.tools.deps.container_resolvers.mulled (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -from ..container_resolvers import ContainerResolver -from collections import namedtuple - -CachedMulledImageSingleTarget = namedtuple('CachedMulledImageSingleTarget', ['package_name', 'version', 'build', 'image_identifier']) - -CachedV1MulledImageMultiTarget = namedtuple('CachedV1MulledImageMultiTarget', ['hash', 'build', 'image_identifier']) - -CachedV2MulledImageMultiTarget = namedtuple('CachedV2MulledImageMultiTarget', ['package_hash', 'version_hash', 'build', 'image_identifier']) - -class CachedMulledDockerContainerResolver(ContainerResolver): - resolver_type = ... # type: str - container_type = ... # type: str - namespace = ... # type: Any - hash_func = ... # type: Any - def __init__(self, app_info: Optional[Any] = ..., namespace: Optional[Any] = ..., hash_func: str = ...) -> None: ... - def resolve(self, enabled_container_types, tool_info): ... - -class CachedMulledSingularityContainerResolver(ContainerResolver): - resolver_type = ... # type: str - container_type = ... # type: str - cache_directory = ... # type: Any - hash_func = ... # type: Any - def __init__(self, app_info: Optional[Any] = ..., hash_func: str = ...) -> None: ... - def resolve(self, enabled_container_types, tool_info): ... - -class MulledDockerContainerResolver(ContainerResolver): - resolver_type = ... # type: str - container_type = ... # type: str - namespace = ... # type: Any - hash_func = ... # type: Any - def __init__(self, app_info: Optional[Any] = ..., namespace: str = ..., hash_func: str = ...) -> None: ... - def resolve(self, enabled_container_types, tool_info): ... - -class BuildMulledDockerContainerResolver(ContainerResolver): - resolver_type = ... # type: str - container_type = ... # type: str - namespace = ... # type: Any - hash_func = ... # type: Any - auto_init = ... # type: Any - def __init__(self, app_info: Optional[Any] = ..., namespace: str = ..., hash_func: str = ..., **kwds) -> None: ... - def resolve(self, enabled_container_types, tool_info): ... - -class BuildMulledSingularityContainerResolver(ContainerResolver): - resolver_type = ... # type: str - container_type = ... # type: str - cache_directory = ... # type: Any - hash_func = ... # type: Any - auto_init = ... # type: Any - def __init__(self, app_info: Optional[Any] = ..., hash_func: str = ..., **kwds) -> None: ... - def resolve(self, enabled_container_types, tool_info): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/containers.pyi b/mypy-stubs/galaxy/tool_util/deps/containers.pyi index bcc023340..3827a0be6 100644 --- a/mypy-stubs/galaxy/tool_util/deps/containers.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/containers.pyi @@ -2,13 +2,14 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from typing import Any, Optional, Text -from .container_resolvers.explicit import ExplicitContainerResolver as ExplicitContainerResolver -from .container_resolvers.mulled import BuildMulledDockerContainerResolver as BuildMulledDockerContainerResolver, BuildMulledSingularityContainerResolver as BuildMulledSingularityContainerResolver, CachedMulledDockerContainerResolver as CachedMulledDockerContainerResolver, CachedMulledSingularityContainerResolver as CachedMulledSingularityContainerResolver, MulledDockerContainerResolver as MulledDockerContainerResolver +from typing import Any, Dict, Optional, Sequence + +from .dependencies import AppInfo, JobInfo, ToolInfo +from .requirements import ( + DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES as DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, +) +from .requirements import DEFAULT_CONTAINER_SHELL as DEFAULT_CONTAINER_SHELL from .requirements import ContainerDescription -from .requirements import DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES as DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, DEFAULT_CONTAINER_SHELL as DEFAULT_CONTAINER_SHELL -from ..deps import docker_util as docker_util -from ..deps import singularity_util as singularity_util log = ... # type: Any DOCKER_CONTAINER_TYPE = ... # type: str @@ -17,30 +18,15 @@ DEFAULT_CONTAINER_TYPE = ... # type: Any ALL_CONTAINER_TYPES = ... # type: Any LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = ... # type: str -class ContainerFinder: - app_info = ... # type: Any - container_registry = ... # type: Any - def __init__(self, app_info) -> None: ... - def find_best_container_description(self, enabled_container_types, tool_info) -> ContainerDescription: ... - def find_container(self, tool_info, destination_info, job_info): ... - -class NullContainerFinder: - def find_container(self, tool_info, destination_info, job_info): ... - class ContainerRegistry: resolver_classes = ... # type: Any enable_beta_mulled_containers = ... # type: Any - app_info = ... # type: Any + app_info: AppInfo container_resolvers = ... # type: Any - def __init__(self, app_info) -> None: ... - def find_best_container_description(self, enabled_container_types, tool_info) -> ContainerDescription: ... - -class JobInfo: - working_directory = ... # type: Any - job_directory = ... # type: Any - tool_directory = ... # type: Any - job_directory_type = ... # type: Any - def __init__(self, working_directory, tool_directory, job_directory, job_directory_type) -> None: ... + def __init__(self, app_info: AppInfo) -> None: ... + def find_best_container_description( + self, enabled_container_types: Sequence[str], tool_info: ToolInfo + ) -> ContainerDescription | None: ... class Container: container_id = ... # type: Any @@ -49,32 +35,19 @@ class Container: destination_info = ... # type: Any job_info = ... # type: Any container_description = ... # type: Any - def __init__(self, container_id, app_info, tool_info, destination_info, job_info, container_description) -> None: ... + def __init__( + self, + container_id: str, + app_info: AppInfo, + tool_info: ToolInfo, + destination_info: Dict[str, str], + job_info: JobInfo, + container_description: ContainerDescription, + ) -> None: ... @property - def resolve_dependencies(self): ... + def resolve_dependencies(self) -> bool: ... @property - def shell(self): ... - def containerize_command(self, command): ... - -def preprocess_volumes(volumes_raw_str, container_type): ... - -class HasDockerLikeVolumes: ... - -class DockerContainer(Container, HasDockerLikeVolumes): - container_type = ... # type: Any - def containerize_command(self, command): ... - -def docker_cache_path(cache_directory, container_id): ... - -class SingularityContainer(Container, HasDockerLikeVolumes): - container_type = ... # type: Any - def containerize_command(self, command): ... - -CONTAINER_CLASSES = ... # type: Any - -class NullContainer: - def __init__(self) -> None: ... - def __bool__(self): ... - __nonzero__ = ... # type: Any + def shell(self) -> str: ... + def containerize_command(self, command: str) -> str: ... -NULL_CONTAINER = ... # type: Any +# def docker_cache_path(cache_directory, container_id): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi b/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi index 83bf63c0b..0ae396c27 100644 --- a/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi @@ -14,19 +14,44 @@ class AppInfo: containers_resolvers_config_file = ... # type: Any involucro_path = ... # type: Any involucro_auto_init = ... # type: Any - def __init__(self, galaxy_root_dir: Optional[Any] = ..., default_file_path: Optional[Any] = ..., outputs_to_working_directory: bool = ..., container_image_cache_path: Optional[Any] = ..., library_import_dir: Optional[Any] = ..., enable_mulled_containers: bool = ..., containers_resolvers_config_file: Optional[Any] = ..., involucro_path: Optional[Any] = ..., involucro_auto_init: bool = ...) -> None: ... - -class DependenciesDescription: - requirements = ... # type: Any - installed_tool_dependencies = ... # type: Any - def __init__(self, requirements: Any = ..., installed_tool_dependencies: Any = ...) -> None: ... - def to_dict(self): ... - @staticmethod - def from_dict(as_dict): ... + def __init__( + self, + galaxy_root_dir: Optional[Any] = ..., + default_file_path: Optional[Any] = ..., + outputs_to_working_directory: bool = ..., + container_image_cache_path: Optional[Any] = ..., + library_import_dir: Optional[Any] = ..., + enable_mulled_containers: bool = ..., + containers_resolvers_config_file: Optional[Any] = ..., + involucro_path: Optional[Any] = ..., + involucro_auto_init: bool = ..., + ) -> None: ... class ToolInfo: container_descriptions = ... # type: Any requirements = ... # type: Any requires_galaxy_python_environment = ... # type: Any env_pass_through = ... # type: Any - def __init__(self, container_descriptions: Any = ..., requirements: Any = ..., requires_galaxy_python_environment: bool = ...) -> None: ... + def __init__( + self, + container_descriptions: Any = ..., + requirements: Any = ..., + requires_galaxy_python_environment: bool = ..., + ) -> None: ... + +class JobInfo: + working_directory: str + tool_directory: str + job_directory: str + tmp_directory: str + home_directory: str + job_directory_type: str + def __init__( + self, + working_directory: str, + tool_directory: str, + job_directory: str, + tmp_directory: str, + home_directory: str, + job_directory_type: str, + ): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/docker_util.pyi b/mypy-stubs/galaxy/tool_util/deps/docker_util.pyi deleted file mode 100644 index e98b338cc..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/docker_util.pyi +++ /dev/null @@ -1,41 +0,0 @@ -# Stubs for galaxy.tools.deps.docker_util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -from .commands import argv_to_str as argv_to_str - -DEFAULT_DOCKER_COMMAND = ... # type: str -DEFAULT_SUDO = ... # type: bool -DEFAULT_SUDO_COMMAND = ... # type: str -DEFAULT_HOST = ... # type: Any -DEFAULT_VOLUME_MOUNT_TYPE = ... # type: str -DEFAULT_WORKING_DIRECTORY = ... # type: Any -DEFAULT_NET = ... # type: Any -DEFAULT_MEMORY = ... # type: Any -DEFAULT_VOLUMES_FROM = ... # type: Any -DEFAULT_AUTO_REMOVE = ... # type: bool -DEFAULT_SET_USER = ... # type: str -DEFAULT_RUN_EXTRA_ARGUMENTS = ... # type: Any - -class DockerVolume: - from_path = ... # type: Any - to_path = ... # type: Any - how = ... # type: Any - def __init__(self, path, to_path: Optional[Any] = ..., how: Any = ...) -> None: ... - @staticmethod - def volumes_from_str(volumes_as_str): ... - @staticmethod - def volume_from_str(as_str): ... - -def kill_command(container, signal: Optional[Any] = ..., **kwds): ... -def logs_command(container, **kwds): ... -def build_command(image, docker_build_path, **kwds): ... -def build_save_image_command(image, destination, **kwds): ... -def build_pull_command(tag, **kwds): ... -def build_docker_cache_command(image, **kwds): ... -def build_docker_images_command(truncate: bool = ..., **kwds): ... -def build_docker_load_command(**kwds): ... -def build_docker_run_command(container_command, image, interactive: bool = ..., terminal: bool = ..., tag: Optional[Any] = ..., volumes: Any = ..., volumes_from: Any = ..., memory: Any = ..., env_directives: Any = ..., working_directory: Any = ..., name: Optional[Any] = ..., net: Any = ..., run_extra_arguments: Any = ..., docker_cmd: Any = ..., sudo: Any = ..., sudo_cmd: Any = ..., auto_rm: Any = ..., set_user: Any = ..., host: Any = ...): ... -def command_list(command, command_args: Any = ..., **kwds): ... -def command_shell(command, command_args: Any = ..., **kwds): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi b/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi index 3cf02d563..880ddab2d 100644 --- a/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi @@ -3,13 +3,17 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + +from ...tools import loader_directory as loader_directory from ..deps import commands as commands -from ..deps import docker_util as docker_util from ..deps.containers import docker_cache_path as docker_cache_path -from ..deps.requirements import parse_requirements_from_xml as parse_requirements_from_xml -from ...tools import loader_directory as loader_directory +from ..deps.requirements import ( + parse_requirements_from_xml as parse_requirements_from_xml, +) log = ... # type: Any def docker_host_args(**kwds): ... -def dockerfile_build(path, dockerfile: Optional[Any] = ..., error: Any = ..., **kwds): ... +def dockerfile_build( + path, dockerfile: Optional[Any] = ..., error: Any = ..., **kwds +): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi index a3f6bf315..2c36270f6 100644 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi @@ -1,4 +1,3 @@ # Stubs for galaxy.tools.deps.mulled (Python 3.4) # # NOTE: This dynamically typed stub was automatically generated by stubgen. - diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi index 25650508b..c4c881a5c 100644 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. +from sys import platform as _platform from typing import Any, Optional + import installable -from sys import platform as _platform class BuildExistsException(Exception): ... @@ -13,7 +14,12 @@ class InvolucroContext(installable.InstallableContext): involucro_bin = ... # type: str shell_exec = ... # type: Any verbose = ... # type: Any - def __init__(self, involucro_bin: Optional[Any] = ..., shell_exec: Optional[Any] = ..., verbose: str = ...) -> None: ... + def __init__( + self, + involucro_bin: Optional[Any] = ..., + shell_exec: Optional[Any] = ..., + verbose: str = ..., + ) -> None: ... def build_command(self, involucro_args): ... def exec_command(self, involucro_args): ... def is_installed(self): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi index 0057d4d8b..5e725df4f 100644 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi @@ -2,9 +2,9 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from typing import Any, Optional from collections import namedtuple +from typing import Any, Optional def main(argv: Optional[Any] = ...): ... -_Line = namedtuple('_Line', ['targets', 'image_build', 'name_override']) +_Line = namedtuple("_Line", ["targets", "image_build", "name_override"]) diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi index 33063c28d..0c7948b60 100644 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi @@ -2,20 +2,29 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from typing import Any, Optional from collections import namedtuple +from typing import Any, Optional def quay_versions(namespace, pkg_name): ... def mulled_tags_for(namespace, image, tag_prefix: Optional[Any] = ...): ... def split_tag(tag): ... def version_sorted(elements): ... -Target = namedtuple('Target', ['package_name', 'version', 'build']) +Target = namedtuple("Target", ["package_name", "version", "build"]) -def build_target(package_name, version: Optional[Any] = ..., build: Optional[Any] = ..., tag: Optional[Any] = ...): ... +def build_target( + package_name, + version: Optional[Any] = ..., + build: Optional[Any] = ..., + tag: Optional[Any] = ..., +): ... def conda_build_target_str(target): ... -def v1_image_name(targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ...): ... -def v2_image_name(targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ...): ... +def v1_image_name( + targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ... +): ... +def v2_image_name( + targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ... +): ... image_name = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/deps/requirements.pyi b/mypy-stubs/galaxy/tool_util/deps/requirements.pyi index 9e6532903..3307bb3fb 100644 --- a/mypy-stubs/galaxy/tool_util/deps/requirements.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/requirements.pyi @@ -1,75 +1,74 @@ -# Stubs for galaxy.tools.deps.requirements (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from typing import Any, Dict, Iterable, List, Union -from typing import Any, Dict, List, Optional, Text +from _typeshed import Incomplete -DEFAULT_REQUIREMENT_TYPE = ... # type: str -DEFAULT_REQUIREMENT_VERSION = ... # type: Any +DEFAULT_REQUIREMENT_TYPE: str +DEFAULT_REQUIREMENT_VERSION: Incomplete class ToolRequirement: - name = ... # type: Any - type = ... # type: Any - version = ... # type: Any - specs = ... # type: Any - def __init__(self, name: Optional[Any] = ..., type: Optional[Any] = ..., version: Optional[Any] = ..., specs: Any = ...) -> None: ... - def to_dict(self) -> Dict[str, Any]: ... - def copy(self): ... + name: Incomplete + type: Incomplete + version: Incomplete + specs: Incomplete + def __init__( + self, + name: Incomplete | None = ..., + type: Incomplete | None = ..., + version: Incomplete | None = ..., + specs: Incomplete | None = ..., + ) -> None: ... + def to_dict(self) -> Dict[str, str]: ... + def copy(self) -> ToolRequirement: ... @staticmethod - def from_dict(dict: Dict[str, Any]) -> ToolRequirement: ... - def __eq__(self, other): ... - def __ne__(self, other): ... - def __hash__(self): ... - -class RequirementSpecification: - uri = ... # type: Any - version = ... # type: Any - def __init__(self, uri, version: Optional[Any] = ...) -> None: ... - @property - def specifies_version(self): ... - @property - def short_name(self): ... - def to_dict(self): ... - @staticmethod - def from_dict(dict: Dict[str, Any]) -> ToolRequirements: ... - def __eq__(self, other): ... - def __ne__(self, other): ... - def __hash__(self): ... + def from_dict(d: Dict[str, str]) -> "ToolRequirement": ... + def __eq__(self, other: Any) -> bool: ... + def __ne__(self, other: Any) -> bool: ... + def __hash__(self) -> int: ... class ToolRequirements: - tool_requirements = ... # type: Any - def __init__(self, tool_requirements: Optional[Any] = ...) -> None: ... + tool_requirements: Incomplete + def __init__( + self, + tool_requirements: List[Union[ToolRequirement, Dict[str, str]]] | None = ..., + ) -> None: ... @staticmethod - def from_list(requirements: List[ToolRequirement]) -> ToolRequirements: ... + def from_list( + requirements: List[Union[ToolRequirement, Dict[str, str]]] + ) -> "ToolRequirements": ... @property - def resolvable(self): ... + def resolvable(self) -> "ToolRequirements": ... @property - def packages(self): ... - def to_list(self) -> List[ToolRequirement]: ... - def append(self, requirement): ... - def __eq__(self, other): ... - def __ne__(self, other): ... - def __iter__(self): ... - def __getitem__(self, ii): ... - def __len__(self): ... - def __hash__(self): ... - -class ToolRequirementsException(Exception): ... + def packages(self) -> "ToolRequirements": ... + def to_list(self) -> List[Dict[str, str]]: ... + def append(self, requirement: Union[ToolRequirement, Dict[str, str]]) -> None: ... + def __eq__(self, other: Any) -> bool: ... + def __ne__(self, other: Any) -> bool: ... + def __iter__(self) -> Iterable[ToolRequirement]: ... + def __getitem__(self, ii: int) -> ToolRequirement: ... + def __len__(self) -> int: ... + def __hash__(self) -> int: ... + def to_dict(self) -> List[Dict[str, str]]: ... -DEFAULT_CONTAINER_TYPE = ... # type: str -DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES = ... # type: bool -DEFAULT_CONTAINER_SHELL = ... # type: str +DEFAULT_CONTAINER_TYPE: str +DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES: bool +DEFAULT_CONTAINER_SHELL: str class ContainerDescription: - identifier = ... # type: Text - type = ... # type: Any - resolve_dependencies = ... # type: Any - shell = ... # type: Any - def __init__(self, identifier: Optional[Any] = ..., type: Any = ..., resolve_dependencies: Any = ..., shell: Any = ...) -> None: ... - def to_dict(self): ... + identifier: str | None + type: str + resolve_dependencies: bool + shell: str + explicit: bool + def __init__( + self, + identifier: str | None = ..., + type: str = ..., + resolve_dependencies: bool = ..., + shell: str = ..., + ) -> None: ... + def to_dict(self, *args: Any, **kwds: Any) -> Dict[str, str]: ... @staticmethod - def from_dict(dict): ... + def from_dict(dict: Dict[str, str]) -> "ContainerDescription": ... -def parse_requirements_from_dict(root_dict): ... -def parse_requirements_from_xml(xml_root): ... -def container_from_element(container_elem): ... +# def parse_requirements_from_dict(root_dict): ... +# def parse_requirements_from_xml(xml_root): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/__init__.pyi deleted file mode 100644 index a1ffb20a5..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/__init__.pyi +++ /dev/null @@ -1,62 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -from galaxy.util.dictifiable import Dictifiable -from ..requirements import ToolRequirement as ToolRequirement - -class DependencyResolver(Dictifiable): - dict_collection_visible_keys = ... # type: Any - disabled = ... # type: bool - resolves_simple_dependencies = ... # type: bool - can_uninstall_dependencies = ... # type: bool - config_options = ... # type: Any - def resolve(self, requirement, **kwds): ... - -class MultipleDependencyResolver: - def resolve_all(self, requirements, **kwds): ... - -class ListableDependencyResolver: - def list_dependencies(self): ... - -class MappableDependencyResolver: ... - -FROM_UNVERSIONED = ... # type: Any - -class RequirementMapping: - from_name = ... # type: Any - from_version = ... # type: Any - to_name = ... # type: Any - to_version = ... # type: Any - def __init__(self, from_name, from_version, to_name, to_version) -> None: ... - def matches_requirement(self, requirement): ... - def apply(self, requirement): ... - @staticmethod - def from_dict(raw_mapping): ... - -class SpecificationAwareDependencyResolver: ... -class SpecificationPatternDependencyResolver: ... - -class InstallableDependencyResolver: - def install_dependency(self, name, version, type, **kwds): ... - -class Dependency(Dictifiable): - dict_collection_visible_keys = ... # type: Any - cacheable = ... # type: bool - def shell_commands(self, requirement): ... - def exact(self): ... - @property - def resolver_msg(self): ... - -class NullDependency(Dependency): - dependency_type = ... # type: Any - exact = ... # type: bool - version = ... # type: Any - name = ... # type: Any - def __init__(self, version: Optional[Any] = ..., name: Optional[Any] = ...) -> None: ... - @property - def resolver_msg(self): ... - def shell_commands(self, requirement): ... - -class DependencyException(Exception): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.pyi deleted file mode 100644 index d581de350..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/brewed_tool_shed_packages.pyi +++ /dev/null @@ -1,33 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.brewed_tool_shed_packages (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any -from xml.etree import ElementTree as ET -from .resolver_mixins import UsesHomebrewMixin, UsesInstalledRepositoriesMixin, UsesToolDependencyDirMixin -from ..resolvers import DependencyResolver - -class HomebrewToolShedDependencyResolver(DependencyResolver, UsesHomebrewMixin, UsesToolDependencyDirMixin, UsesInstalledRepositoriesMixin): - resolver_type = ... # type: str - def __init__(self, dependency_manager, **kwds) -> None: ... - def resolve(self, requirement, **kwds): ... - -class RawDependencies: - root = ... # type: Any - dependencies = ... # type: Any - def __init__(self, dependencies_file) -> None: ... - def find(self, package_name, package_version): ... - -class RawDependency: - dependencies = ... # type: Any - package_el = ... # type: Any - repository_el = ... # type: Any - def __init__(self, dependencies, package_el, repository_el) -> None: ... - @property - def repository_owner(self): ... - @property - def repository_name(self): ... - @property - def package_name(self): ... - @property - def package_version(self): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/conda.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/conda.pyi deleted file mode 100644 index 333954de7..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/conda.pyi +++ /dev/null @@ -1,72 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.conda (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -from ..resolvers import Dependency, DependencyResolver, InstallableDependencyResolver, ListableDependencyResolver, MappableDependencyResolver, MultipleDependencyResolver, SpecificationPatternDependencyResolver - -DEFAULT_ENSURE_CHANNELS = ... # type: str - -class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, ListableDependencyResolver, InstallableDependencyResolver, SpecificationPatternDependencyResolver, MappableDependencyResolver): - dict_collection_visible_keys = ... # type: Any - resolver_type = ... # type: str - config_options = ... # type: Any - can_uninstall_dependencies = ... # type: bool - versionless = ... # type: Any - dependency_manager = ... # type: Any - conda_prefix_parent = ... # type: Any - ensure_channels = ... # type: Any - auto_init = ... # type: Any - conda_context = ... # type: Any - disabled = ... # type: Any - auto_install = ... # type: Any - copy_dependencies = ... # type: Any - def __init__(self, dependency_manager, **kwds) -> None: ... - def clean(self, **kwds): ... - def uninstall(self, requirements): ... - def uninstall_environments(self, environments): ... - def install_all(self, conda_targets): ... - def resolve_all(self, requirements, **kwds): ... - def merged_environment_name(self, conda_targets): ... - def resolve(self, requirement, **kwds): ... - def unused_dependency_paths(self, toolbox_requirements_status): ... - def list_dependencies(self): ... - def install_dependency(self, name, version, type, **kwds): ... - @property - def prefix(self): ... - -class MergedCondaDependency(Dependency): - dict_collection_visible_keys = ... # type: Any - dependency_type = ... # type: str - activate = ... # type: Any - conda_context = ... # type: Any - environment_path = ... # type: Any - cache_path = ... # type: Any - def __init__(self, conda_context, environment_path, exact, name: Optional[Any] = ..., version: Optional[Any] = ..., preserve_python_environment: bool = ...) -> None: ... - @property - def exact(self): ... - @property - def name(self): ... - @property - def version(self): ... - def shell_commands(self, requirement): ... - -class CondaDependency(Dependency): - dict_collection_visible_keys = ... # type: Any - dependency_type = ... # type: str - cacheable = ... # type: bool - activate = ... # type: Any - conda_context = ... # type: Any - environment_path = ... # type: Any - cache_path = ... # type: Any - def __init__(self, conda_context, environment_path, exact, name: Optional[Any] = ..., version: Optional[Any] = ..., preserve_python_environment: bool = ...) -> None: ... - @property - def exact(self): ... - @property - def name(self): ... - @property - def version(self): ... - def build_cache(self, cache_path): ... - def set_cache_path(self, cache_path): ... - def build_environment(self): ... - def shell_commands(self, requirement): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/galaxy_packages.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/galaxy_packages.pyi deleted file mode 100644 index cb4551ffe..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/galaxy_packages.pyi +++ /dev/null @@ -1,35 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.galaxy_packages (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any -from .resolver_mixins import UsesToolDependencyDirMixin -from ..resolvers import Dependency, DependencyResolver, ListableDependencyResolver, MappableDependencyResolver - -class GalaxyPackageDependency(Dependency): - dict_collection_visible_keys = ... # type: Any - dependency_type = ... # type: str - script = ... # type: Any - path = ... # type: Any - version = ... # type: Any - name = ... # type: Any - def __init__(self, script, path, version, name, exact: bool = ...) -> None: ... - @property - def exact(self): ... - def shell_commands(self, requirement): ... - -class ToolShedDependency(GalaxyPackageDependency): - dependency_type = ... # type: str - -class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependencyDirMixin): - dict_collection_visible_keys = ... # type: Any - dependency_type = ... # type: Any - versionless = ... # type: Any - def __init__(self, dependency_manager, **kwds) -> None: ... - def resolve(self, requirement, **kwds): ... - -class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, ListableDependencyResolver, MappableDependencyResolver): - resolver_type = ... # type: str - def __init__(self, dependency_manager, **kwds) -> None: ... - def resolve(self, requirement, **kwds): ... - def list_dependencies(self): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/homebrew.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/homebrew.pyi deleted file mode 100644 index 789617317..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/homebrew.pyi +++ /dev/null @@ -1,14 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.homebrew (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any -from .resolver_mixins import UsesHomebrewMixin -from ..resolvers import DependencyResolver - -class HomebrewDependencyResolver(DependencyResolver, UsesHomebrewMixin): - resolver_type = ... # type: str - versionless = ... # type: Any - prefer_version = ... # type: Any - def __init__(self, dependency_manager, **kwds) -> None: ... - def resolve(self, requirement, **kwds): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/modules.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/modules.pyi deleted file mode 100644 index 5762d957d..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/modules.pyi +++ /dev/null @@ -1,42 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.modules (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -from ..resolvers import Dependency, DependencyResolver, MappableDependencyResolver - -class ModuleDependencyResolver(DependencyResolver, MappableDependencyResolver): - dict_collection_visible_keys = ... # type: Any - resolver_type = ... # type: str - versionless = ... # type: Any - modulecmd = ... # type: Any - modulepath = ... # type: Any - default_indicator = ... # type: Any - module_checker = ... # type: Any - def __init__(self, dependency_manager, **kwds) -> None: ... - def resolve(self, requirement, **kwds): ... - -class DirectoryModuleChecker: - module_dependency_resolver = ... # type: Any - directories = ... # type: Any - def __init__(self, module_dependency_resolver, modulepath, prefetch) -> None: ... - def has_module(self, module, version): ... - -class AvailModuleChecker: - module_dependency_resolver = ... # type: Any - modulepath = ... # type: Any - default_indicator = ... # type: Any - prefetched_modules = ... # type: Any - def __init__(self, module_dependency_resolver, modulepath, prefetch, default_indicator: Any = ...) -> None: ... - def has_module(self, module, version): ... - -class ModuleDependency(Dependency): - dict_collection_visible_keys = ... # type: Any - dependency_type = ... # type: str - module_dependency_resolver = ... # type: Any - module_name = ... # type: Any - module_version = ... # type: Any - def __init__(self, module_dependency_resolver, module_name, module_version: Optional[Any] = ..., exact: bool = ...) -> None: ... - @property - def exact(self): ... - def shell_commands(self, requirement): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/resolver_mixins.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/resolver_mixins.pyi deleted file mode 100644 index 2b90a98d5..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/resolver_mixins.pyi +++ /dev/null @@ -1,18 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.resolver_mixins (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any -from ..brew_exts import build_env_statements as build_env_statements, DEFAULT_HOMEBREW_ROOT as DEFAULT_HOMEBREW_ROOT, recipe_cellar_path as recipe_cellar_path -from ..resolvers import Dependency as Dependency, NullDependency as NullDependency - -class UsesHomebrewMixin: ... -class UsesToolDependencyDirMixin: ... -class UsesInstalledRepositoriesMixin: ... - -class HomebrewDependency(Dependency): - commands = ... # type: Any - def __init__(self, commands, exact: bool = ...) -> None: ... - @property - def exact(self): ... - def shell_commands(self, requirement): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/tool_shed_packages.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/tool_shed_packages.pyi deleted file mode 100644 index 224d377c2..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/tool_shed_packages.pyi +++ /dev/null @@ -1,13 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.tool_shed_packages (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any -from .galaxy_packages import BaseGalaxyPackageDependencyResolver -from .resolver_mixins import UsesInstalledRepositoriesMixin - -class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, UsesInstalledRepositoriesMixin): - resolver_type = ... # type: str - dependency_type = ... # type: Any - resolves_simple_dependencies = ... # type: bool - def __init__(self, dependency_manager, **kwds) -> None: ... diff --git a/mypy-stubs/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.pyi b/mypy-stubs/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.pyi deleted file mode 100644 index ddf2ee041..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.pyi +++ /dev/null @@ -1,25 +0,0 @@ -# Stubs for galaxy.tools.deps.resolvers.unlinked_tool_shed_packages (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any -from .galaxy_packages import BaseGalaxyPackageDependencyResolver -from ..resolvers import Dependency - -class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver): - dict_collection_visible_keys = ... # type: Any - resolver_type = ... # type: str - preferred_owners = ... # type: Any - select_by_owner = ... # type: Any - def __init__(self, dependency_manager, **kwds) -> None: ... - -class CandidateDependency(Dependency): - dict_collection_visible_keys = ... # type: Any - dependency_type = ... # type: str - @property - def exact(self): ... - dependency = ... # type: Any - path = ... # type: Any - owner = ... # type: Any - def __init__(self, dependency, path, owner: Any = ...) -> None: ... - def shell_commands(self, requirement): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/singularity_util.pyi b/mypy-stubs/galaxy/tool_util/deps/singularity_util.pyi deleted file mode 100644 index a701d1fd8..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/singularity_util.pyi +++ /dev/null @@ -1,7 +0,0 @@ -# Stubs for galaxy.tools.deps.singularity_util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -def build_singularity_run_command(container_command, image, volumes: Any = ..., env: Any = ..., working_directory: Any = ..., singularity_cmd: Any = ..., run_extra_arguments: Any = ..., sudo: Any = ..., sudo_cmd: Any = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/views.pyi b/mypy-stubs/galaxy/tool_util/deps/views.pyi index 2f5799018..271f2b57a 100644 --- a/mypy-stubs/galaxy/tool_util/deps/views.pyi +++ b/mypy-stubs/galaxy/tool_util/deps/views.pyi @@ -13,7 +13,9 @@ class DependencyResolversView: def resolver_requirements(self, index): ... def manager_dependency(self, **kwds): ... def resolver_dependency(self, index, **kwds): ... - def show_dependencies(self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ...): ... + def show_dependencies( + self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ... + ): ... def uninstall_dependencies(self, index: Optional[Any] = ..., **payload): ... @property def unused_dependency_paths(self): ... @@ -28,5 +30,7 @@ class DependencyResolversView: def tool_ids_by_requirements(self): ... @property def toolbox_requirements_status(self): ... - def get_requirements_status(self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ...): ... + def get_requirements_status( + self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ... + ): ... def clean(self, index: Optional[Any] = ..., **kwds): ... diff --git a/mypy-stubs/galaxy/tool_util/lint.pyi b/mypy-stubs/galaxy/tool_util/lint.pyi index 9cd7a2631..ddf1a78e5 100644 --- a/mypy-stubs/galaxy/tool_util/lint.pyi +++ b/mypy-stubs/galaxy/tool_util/lint.pyi @@ -3,14 +3,27 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + from .parser import get_tool_source as get_tool_source LEVEL_ALL = ... # type: str LEVEL_WARN = ... # type: str LEVEL_ERROR = ... # type: str -def lint_tool_source(tool_source, level: Any = ..., fail_level: Any = ..., extra_modules: Any = ..., skip_types: Any = ...): ... -def lint_xml(tool_xml, level: Any = ..., fail_level: Any = ..., extra_modules: Any = ..., skip_types: Any = ...): ... +def lint_tool_source( + tool_source, + level: Any = ..., + fail_level: Any = ..., + extra_modules: Any = ..., + skip_types: Any = ..., +): ... +def lint_xml( + tool_xml, + level: Any = ..., + fail_level: Any = ..., + extra_modules: Any = ..., + skip_types: Any = ..., +): ... def lint_tool_source_with(lint_context, tool_source, extra_modules: Any = ...): ... def lint_xml_with(lint_context, tool_xml, extra_modules: Any = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/__init__.pyi b/mypy-stubs/galaxy/tool_util/linters/__init__.pyi index 7f56312cb..725c48e0d 100644 --- a/mypy-stubs/galaxy/tool_util/linters/__init__.pyi +++ b/mypy-stubs/galaxy/tool_util/linters/__init__.pyi @@ -1,4 +1,3 @@ # Stubs for galaxy.tools.linters (Python 3.4) # # NOTE: This dynamically typed stub was automatically generated by stubgen. - diff --git a/mypy-stubs/galaxy/tool_util/loader.pyi b/mypy-stubs/galaxy/tool_util/loader.pyi index 4e7cd7fdd..d7ee04a05 100644 --- a/mypy-stubs/galaxy/tool_util/loader.pyi +++ b/mypy-stubs/galaxy/tool_util/loader.pyi @@ -3,6 +3,9 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any -from galaxy.util.xml_macros import imported_macro_paths as imported_macro_paths, raw_tool_xml_tree as raw_tool_xml_tree, template_macro_params as template_macro_params + +from galaxy.util.xml_macros import imported_macro_paths as imported_macro_paths +from galaxy.util.xml_macros import raw_tool_xml_tree as raw_tool_xml_tree +from galaxy.util.xml_macros import template_macro_params as template_macro_params load_tool = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/loader_directory.pyi b/mypy-stubs/galaxy/tool_util/loader_directory.pyi index 628289f72..b52abdc55 100644 --- a/mypy-stubs/galaxy/tool_util/loader_directory.pyi +++ b/mypy-stubs/galaxy/tool_util/loader_directory.pyi @@ -4,9 +4,21 @@ from typing import Any, Optional -def find_possible_tools_from_path(path, recursive: bool = ..., enable_beta_formats: bool = ...): ... -def load_tool_sources_from_path(path, load_exception_handler: Any = ..., recursive: bool = ..., register_load_errors: bool = ...): ... -def load_tool_elements_from_path(path, load_exception_handler: Any = ..., recursive: bool = ..., register_load_errors: bool = ...): ... +def find_possible_tools_from_path( + path, recursive: bool = ..., enable_beta_formats: bool = ... +): ... +def load_tool_sources_from_path( + path, + load_exception_handler: Any = ..., + recursive: bool = ..., + register_load_errors: bool = ..., +): ... +def load_tool_elements_from_path( + path, + load_exception_handler: Any = ..., + recursive: bool = ..., + register_load_errors: bool = ..., +): ... def is_tool_load_error(obj): ... def looks_like_a_tool_xml(path): ... def is_a_yaml_with_class(path, classes): ... diff --git a/mypy-stubs/galaxy/tool_util/locations/dockstore.pyi b/mypy-stubs/galaxy/tool_util/locations/dockstore.pyi index 3420e1eba..0ef01352e 100644 --- a/mypy-stubs/galaxy/tool_util/locations/dockstore.pyi +++ b/mypy-stubs/galaxy/tool_util/locations/dockstore.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + from ..locations import ToolLocationResolver class DockStoreResolver(ToolLocationResolver): @@ -15,5 +16,7 @@ class _Ga4ghToolClient: def get_tools(self): ... def get_tool(self, tool_id): ... def get_tool_version(self, tool_id, version: str = ...): ... - def get_tool_descriptor(self, tool_id, version: str = ..., tool_type: str = ...): ... + def get_tool_descriptor( + self, tool_id, version: str = ..., tool_type: str = ... + ): ... def get_tool_cwl(self, tool_id, version: str = ..., as_string: bool = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/parser/__init__.pyi b/mypy-stubs/galaxy/tool_util/parser/__init__.pyi index 0b1bc8142..a2e601725 100644 --- a/mypy-stubs/galaxy/tool_util/parser/__init__.pyi +++ b/mypy-stubs/galaxy/tool_util/parser/__init__.pyi @@ -2,6 +2,7 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .factory import get_input_source as get_input_source, get_tool_source as get_tool_source +from .factory import get_input_source as get_input_source +from .factory import get_tool_source as get_tool_source from .interface import ToolSource as ToolSource from .output_objects import ToolOutputCollectionPart as ToolOutputCollectionPart diff --git a/mypy-stubs/galaxy/tool_util/parser/cwl.pyi b/mypy-stubs/galaxy/tool_util/parser/cwl.pyi index 1b754a91b..c9fb631fb 100644 --- a/mypy-stubs/galaxy/tool_util/parser/cwl.pyi +++ b/mypy-stubs/galaxy/tool_util/parser/cwl.pyi @@ -3,6 +3,7 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any + from .interface import PageSource as PageSource from .interface import PagesSource as PagesSource from .interface import ToolSource as ToolSource diff --git a/mypy-stubs/galaxy/tool_util/parser/factory.pyi b/mypy-stubs/galaxy/tool_util/parser/factory.pyi index c6b63d099..d3b4244b0 100644 --- a/mypy-stubs/galaxy/tool_util/parser/factory.pyi +++ b/mypy-stubs/galaxy/tool_util/parser/factory.pyi @@ -3,7 +3,13 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + from galaxy.tools.loader import load_tool as load_tool_xml -def get_tool_source(config_file: Optional[Any] = ..., xml_tree: Optional[Any] = ..., enable_beta_formats: bool = ..., tool_location_fetcher: Optional[Any] = ...): ... +def get_tool_source( + config_file: Optional[Any] = ..., + xml_tree: Optional[Any] = ..., + enable_beta_formats: bool = ..., + tool_location_fetcher: Optional[Any] = ..., +): ... def get_input_source(content): ... diff --git a/mypy-stubs/galaxy/tool_util/parser/output_actions.pyi b/mypy-stubs/galaxy/tool_util/parser/output_actions.pyi index 5945acdcd..a045a4f08 100644 --- a/mypy-stubs/galaxy/tool_util/parser/output_actions.pyi +++ b/mypy-stubs/galaxy/tool_util/parser/output_actions.pyi @@ -31,7 +31,9 @@ class ValueToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen): tag = ... # type: str def is_case(self, output_dataset, other_values): ... -class DatatypeIsInstanceToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen): +class DatatypeIsInstanceToolOutputActionConditionalWhen( + ToolOutputActionConditionalWhen +): tag = ... # type: str value = ... # type: Any def __init__(self, parent, config_elem, value) -> None: ... diff --git a/mypy-stubs/galaxy/tool_util/parser/output_objects.pyi b/mypy-stubs/galaxy/tool_util/parser/output_objects.pyi deleted file mode 100644 index 68f824eaf..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/output_objects.pyi +++ /dev/null @@ -1,68 +0,0 @@ -# Stubs for galaxy.tools.parser.output_objects (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -from galaxy.util.dictifiable import Dictifiable - -class ToolOutputBase(Dictifiable): - name = ... # type: Any - label = ... # type: Any - filters = ... # type: Any - hidden = ... # type: Any - collection = ... # type: bool - def __init__(self, name, label: Optional[Any] = ..., filters: Optional[Any] = ..., hidden: bool = ...) -> None: ... - -class ToolOutput(ToolOutputBase): - dict_collection_visible_keys = ... # type: Any - format = ... # type: Any - format_source = ... # type: Any - metadata_source = ... # type: Any - parent = ... # type: Any - actions = ... # type: Any - change_format = ... # type: Any - implicit = ... # type: Any - from_work_dir = ... # type: Any - def __init__(self, name, format: Optional[Any] = ..., format_source: Optional[Any] = ..., metadata_source: Optional[Any] = ..., parent: Optional[Any] = ..., label: Optional[Any] = ..., filters: Optional[Any] = ..., actions: Optional[Any] = ..., hidden: bool = ..., implicit: bool = ...) -> None: ... - def __len__(self): ... - def __getitem__(self, index): ... - def __iter__(self): ... - def to_dict(self, view: str = ..., value_mapper: Optional[Any] = ..., app: Optional[Any] = ...): ... - -class ToolOutputCollection(ToolOutputBase): - collection = ... # type: bool - default_format = ... # type: Any - structure = ... # type: Any - outputs = ... # type: Any - inherit_format = ... # type: Any - inherit_metadata = ... # type: Any - metadata_source = ... # type: Any - format_source = ... # type: Any - change_format = ... # type: Any - def __init__(self, name, structure, label: Optional[Any] = ..., filters: Optional[Any] = ..., hidden: bool = ..., default_format: str = ..., default_format_source: Optional[Any] = ..., default_metadata_source: Optional[Any] = ..., inherit_format: bool = ..., inherit_metadata: bool = ...) -> None: ... - def known_outputs(self, inputs, type_registry): ... - @property - def dynamic_structure(self): ... - @property - def dataset_collector_descriptions(self): ... - -class ToolOutputCollectionStructure: - collection_type = ... # type: Any - collection_type_source = ... # type: Any - structured_like = ... # type: Any - dataset_collector_descriptions = ... # type: Any - dynamic = ... # type: Any - def __init__(self, collection_type, collection_type_source, structured_like, dataset_collector_descriptions) -> None: ... - -class ToolOutputCollectionPart: - output_collection_def = ... # type: Any - element_identifier = ... # type: Any - output_def = ... # type: Any - parent_ids = ... # type: Any - def __init__(self, output_collection_def, element_identifier, output_def, parent_ids: Any = ...) -> None: ... - @property - def effective_output_name(self): ... - @staticmethod - def is_named_collection_part_name(name): ... - @staticmethod - def split_output_name(name): ... diff --git a/mypy-stubs/galaxy/tool_util/parser/xml.pyi b/mypy-stubs/galaxy/tool_util/parser/xml.pyi index ffdd7e92f..439919eb8 100644 --- a/mypy-stubs/galaxy/tool_util/parser/xml.pyi +++ b/mypy-stubs/galaxy/tool_util/parser/xml.pyi @@ -3,11 +3,26 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional -from .interface import InputSource as InputSource, PageSource as PageSource, PagesSource as PagesSource, TestCollectionDef as TestCollectionDef, TestCollectionOutputDef as TestCollectionOutputDef, ToolSource as ToolSource, ToolStdioExitCode as ToolStdioExitCode, ToolStdioRegex as ToolStdioRegex + +from .interface import InputSource as InputSource +from .interface import PageSource as PageSource +from .interface import PagesSource as PagesSource +from .interface import TestCollectionDef as TestCollectionDef +from .interface import TestCollectionOutputDef as TestCollectionOutputDef +from .interface import ToolSource as ToolSource +from .interface import ToolStdioExitCode as ToolStdioExitCode +from .interface import ToolStdioRegex as ToolStdioRegex from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup -from .output_collection_def import dataset_collector_descriptions_from_elem as dataset_collector_descriptions_from_elem -from .output_objects import ToolOutput as ToolOutput, ToolOutputCollection as ToolOutputCollection, ToolOutputCollectionStructure as ToolOutputCollectionStructure -from .util import aggressive_error_checks as aggressive_error_checks, error_on_exit_code as error_on_exit_code +from .output_collection_def import ( + dataset_collector_descriptions_from_elem as dataset_collector_descriptions_from_elem, +) +from .output_objects import ToolOutput as ToolOutput +from .output_objects import ToolOutputCollection as ToolOutputCollection +from .output_objects import ( + ToolOutputCollectionStructure as ToolOutputCollectionStructure, +) +from .util import aggressive_error_checks as aggressive_error_checks +from .util import error_on_exit_code as error_on_exit_code log = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/parser/yaml.pyi b/mypy-stubs/galaxy/tool_util/parser/yaml.pyi index ccf2afdd7..834451be7 100644 --- a/mypy-stubs/galaxy/tool_util/parser/yaml.pyi +++ b/mypy-stubs/galaxy/tool_util/parser/yaml.pyi @@ -3,13 +3,20 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + from .interface import InputSource as InputSource from .interface import PageSource as PageSource from .interface import PagesSource as PagesSource from .interface import ToolSource as ToolSource from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup -from .output_collection_def import dataset_collector_descriptions_from_list as dataset_collector_descriptions_from_list -from .output_objects import ToolOutput as ToolOutput, ToolOutputCollection as ToolOutputCollection, ToolOutputCollectionStructure as ToolOutputCollectionStructure +from .output_collection_def import ( + dataset_collector_descriptions_from_list as dataset_collector_descriptions_from_list, +) +from .output_objects import ToolOutput as ToolOutput +from .output_objects import ToolOutputCollection as ToolOutputCollection +from .output_objects import ( + ToolOutputCollectionStructure as ToolOutputCollectionStructure, +) from .util import error_on_exit_code as error_on_exit_code class YamlToolSource(ToolSource): diff --git a/mypy-stubs/galaxy/tool_util/verify/__init__.pyi b/mypy-stubs/galaxy/tool_util/verify/__init__.pyi index 624255387..5271b6308 100644 --- a/mypy-stubs/galaxy/tool_util/verify/__init__.pyi +++ b/mypy-stubs/galaxy/tool_util/verify/__init__.pyi @@ -3,13 +3,22 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from typing import Any, Optional + from .asserts import verify_assertions as verify_assertions from .test_data import TestDataResolver as TestDataResolver log = ... # type: Any DEFAULT_TEST_DATA_RESOLVER = ... # type: Any -def verify(item_label, output_content, attributes, filename: Optional[Any] = ..., get_filename: Optional[Any] = ..., keep_outputs_dir: Optional[Any] = ..., verify_extra_files: Optional[Any] = ...): ... +def verify( + item_label, + output_content, + attributes, + filename: Optional[Any] = ..., + get_filename: Optional[Any] = ..., + keep_outputs_dir: Optional[Any] = ..., + verify_extra_files: Optional[Any] = ..., +): ... def make_temp_fname(fname: Optional[Any] = ...): ... def check_command(command, description): ... def files_diff(file1, file2, attributes: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/util/__init__.pyi b/mypy-stubs/galaxy/util/__init__.pyi index d0e0292f3..d97198b21 100644 --- a/mypy-stubs/galaxy/util/__init__.pyi +++ b/mypy-stubs/galaxy/util/__init__.pyi @@ -1,130 +1,102 @@ -# Stubs for galaxy.util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional import collections -from .inflection import English as English, Inflector as Inflector - -grp = ... # type: Any -docutils_core = ... # type: Any -docutils_html4css1 = ... # type: Any -inflector = ... # type: Any -log = ... # type: Any -CHUNK_SIZE = ... # type: int -DATABASE_MAX_STRING_SIZE = ... # type: int -DATABASE_MAX_STRING_SIZE_PRETTY = ... # type: str -gzip_magic = ... # type: str -bz2_magic = ... # type: str -DEFAULT_ENCODING = ... # type: Any -NULL_CHAR = ... # type: str -BINARY_CHARS = ... # type: Any -FILENAME_VALID_CHARS = ... # type: str - -def remove_protocol_from_url(url): ... -def is_binary(value, binary_chars: Optional[Any] = ...): ... -def is_uuid(value): ... -def directory_hash_id(id): ... -def get_charset_from_http_headers(headers, default: Optional[Any] = ...): ... -def synchronized(func): ... -def file_iter(fname, sep: Optional[Any] = ...): ... -def file_reader(fp, chunk_size: Any = ...): ... -def unique_id(KEY_SIZE: int = ...): ... -def parse_xml(fname): ... -def parse_xml_string(xml_string): ... -def xml_to_string(elem, pretty: bool = ...): ... -def xml_element_compare(elem1, elem2): ... -def xml_element_list_compare(elem_list1, elem_list2): ... -def xml_element_to_dict(elem): ... -def pretty_print_xml(elem, level: int = ...): ... -def get_file_size(value, default: Optional[Any] = ...): ... -def shrink_stream_by_size(value, size, join_by: str = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ... -def shrink_string_by_size(value, size, join_by: str = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ... -def pretty_print_time_interval(time: bool = ..., precise: bool = ...): ... -def pretty_print_json(json_data, is_json_string: bool = ...): ... - -valid_chars = ... # type: Any -mapped_chars = ... # type: Any - -def restore_text(text, character_map: Any = ...): ... -def sanitize_text(text, valid_characters: Any = ..., character_map: Any = ..., invalid_character: str = ...): ... -def sanitize_lists_to_string(values, valid_characters: Any = ..., character_map: Any = ..., invalid_character: str = ...): ... -def sanitize_param(value, valid_characters: Any = ..., character_map: Any = ..., invalid_character: str = ...): ... - -valid_filename_chars = ... # type: Any -invalid_filenames = ... # type: Any - -def sanitize_for_filename(text, default: Optional[Any] = ...): ... -def mask_password_from_url(url): ... -def ready_name_for_url(raw_name): ... -def which(file): ... -def safe_makedirs(path): ... -def in_directory(file, directory, local_path_module: Any = ...): ... -def merge_sorted_iterables(operator, *iterables): ... - -class Params: - NEVER_SANITIZE = ... # type: Any - def __init__(self, params, sanitize: bool = ...) -> None: ... - def flatten(self): ... - def __getattr__(self, name): ... - def get(self, key, default): ... - def __len__(self): ... - def __iter__(self): ... - def update(self, values): ... - -def rst_to_html(s): ... -def xml_text(root, name: Optional[Any] = ...): ... - -truthy = ... # type: Any -falsy = ... # type: Any - -def asbool(obj): ... -def string_as_bool(string): ... -def string_as_bool_or_none(string): ... -def listify(item, do_strip: bool = ...): ... -def commaify(amount): ... -def roundify(amount, sfs: int = ...): ... -def unicodify(value, encoding: Any = ..., error: str = ..., default: Optional[Any] = ...): ... -def smart_str(s, encoding: Any = ..., strings_only: bool = ..., errors: str = ...): ... -def object_to_string(obj): ... -def string_to_object(s): ... - -class ParamsWithSpecs(collections.defaultdict): - specs = ... # type: Any - params = ... # type: Any - def __init__(self, specs: Optional[Any] = ..., params: Optional[Any] = ...) -> None: ... - def __missing__(self, name): ... - def __getattr__(self, name): ... - -def compare_urls(url1, url2, compare_scheme: bool = ..., compare_hostname: bool = ..., compare_path: bool = ...): ... -def read_dbnames(filename): ... -def read_build_sites(filename, check_builds: bool = ...): ... -def relativize_symlinks(path, start: Optional[Any] = ..., followlinks: bool = ...): ... -def stringify_dictionary_keys(in_dict): ... -def recursively_stringify_dictionary_keys(d): ... -def mkstemp_ln(src, prefix: str = ...): ... -def umask_fix_perms(path, umask, unmasked_perms, gid: Optional[Any] = ...): ... -def docstring_trim(docstring): ... -def nice_size(size): ... -def size_to_bytes(size): ... -def send_mail(frm, to, subject, body, config, html: Optional[Any] = ...): ... -def force_symlink(source, link_name): ... -def move_merge(source, target): ... -def safe_str_cmp(a, b): ... - -galaxy_root_path = ... # type: Any - -def galaxy_directory(): ... -def config_directories_from_setting(directories_setting, galaxy_root: Any = ...): ... -def parse_int(value, min_val: Optional[Any] = ..., max_val: Optional[Any] = ..., default: Optional[Any] = ..., allow_none: bool = ...): ... -def parse_non_hex_float(s): ... -def build_url(base_url, port: int = ..., scheme: str = ..., pathspec: Optional[Any] = ..., params: Optional[Any] = ..., doseq: bool = ...): ... -def url_get(base_url, password_mgr: Optional[Any] = ..., pathspec: Optional[Any] = ..., params: Optional[Any] = ...): ... -def download_to_file(url, dest_file_path, timeout: int = ..., chunk_size: Any = ...): ... -def safe_relpath(path): ... - -class ExecutionTimer: - begin = ... # type: Any - def __init__(self) -> None: ... - @property - def elapsed(self): ... +from collections.abc import Generator + +from _typeshed import Incomplete + +LXML_AVAILABLE: bool +inflector: Incomplete +log: Incomplete +namedtuple = collections.namedtuple +CHUNK_SIZE: int +DATABASE_MAX_STRING_SIZE: int +DATABASE_MAX_STRING_SIZE_PRETTY: str +gzip_magic: bytes +bz2_magic: bytes +DEFAULT_ENCODING: Incomplete +NULL_CHAR: bytes +BINARY_CHARS: Incomplete +FILENAME_VALID_CHARS: str +RW_R__R__: Incomplete +RWXR_XR_X: Incomplete +RWXRWXRWX: Incomplete +XML: Incomplete +defaultdict = collections.defaultdict + +# def xml_to_string(elem, pretty: bool = ...): ... +# def xml_element_compare(elem1, elem2): ... +# def xml_element_list_compare(elem_list1, elem_list2): ... +# def xml_element_to_dict(elem): ... +# def pretty_print_xml(elem, level: int = ...): ... +# def get_file_size(value, default: Incomplete | None = ...): ... +# def shrink_stream_by_size(value, size, join_by: bytes = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ... +# def shrink_and_unicodify(stream): ... +# def shrink_string_by_size(value, size, join_by: str = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ... +# def pretty_print_time_interval(time: bool = ..., precise: bool = ..., utc: bool = ...): ... +# def pretty_print_json(json_data, is_json_string: bool = ...): ... + +valid_chars: Incomplete +mapped_chars: Incomplete + +# def restore_text(text, character_map=...): ... +# def sanitize_text(text, valid_characters=..., character_map=..., invalid_character: str = ...): ... +# def sanitize_lists_to_string(values, valid_characters=..., character_map=..., invalid_character: str = ...): ... +# def sanitize_param(value, valid_characters=..., character_map=..., invalid_character: str = ...): ... + +valid_filename_chars: Incomplete +invalid_filenames: Incomplete + +# def sanitize_for_filename(text, default: Incomplete | None = ...): ... +# def find_instance_nested(item, instances, match_key: Incomplete | None = ...): ... +# def mask_password_from_url(url): ... +# def ready_name_for_url(raw_name): ... +# def which(file): ... +# def in_directory(file, directory, local_path_module=...): ... +# def merge_sorted_iterables(operator, *iterables) -> None: ... + +# def rst_to_html(s, error: bool = ...): ... +# def xml_text(root, name: Incomplete | None = ...): ... +# def parse_resource_parameters(resource_param_file): ... + +truthy: Incomplete +falsy: Incomplete + +# def asbool(obj): ... +# def string_as_bool(string): ... +# def string_as_bool_or_none(string): ... +# def listify(item, do_strip: bool = ...): ... +# def commaify(amount): ... +# def roundify(amount, sfs: int = ...): ... +# def unicodify(value, encoding=..., error: str = ..., strip_null: bool = ..., log_exception: bool = ...): ... +# def smart_str(s, encoding=..., strings_only: bool = ..., errors: str = ...): ... +# def strip_control_characters(s): ... +# def object_to_string(obj): ... +# def string_to_object(s): ... +# def clean_multiline_string(multiline_string, sep: str = ...): ... + +# def compare_urls(url1, url2, compare_scheme: bool = ..., compare_hostname: bool = ..., compare_path: bool = ...): ... +# def read_build_sites(filename, check_builds: bool = ...): ... +# def relativize_symlinks(path, start: Incomplete | None = ..., followlinks: bool = ...) -> None: ... +# def stringify_dictionary_keys(in_dict): ... +# def mkstemp_ln(src, prefix: str = ...): ... +# def umask_fix_perms(path, umask, unmasked_perms, gid: Incomplete | None = ...) -> None: ... +# def docstring_trim(docstring): ... +# def nice_size(size): ... +# def size_to_bytes(size): ... +# def send_mail(frm, to, subject, body, config, html: Incomplete | None = ...) -> None: ... +# def force_symlink(source, link_name) -> None: ... +# def move_merge(source, target): ... +# def safe_str_cmp(a, b): ... + +galaxy_root_path: Incomplete +galaxy_samples_path: Incomplete + +# def galaxy_directory(): ... +# def galaxy_samples_directory(): ... +# def config_directories_from_setting(directories_setting, galaxy_root=...): ... +# def parse_int(value, min_val: Incomplete | None = ..., max_val: Incomplete | None = ..., default: Incomplete | None = ..., allow_none: bool = ...): ... +# def parse_non_hex_float(s): ... +# def build_url(base_url, port: int = ..., scheme: str = ..., pathspec: Incomplete | None = ..., params: Incomplete | None = ..., doseq: bool = ...): ... +# def url_get(base_url, auth: Incomplete | None = ..., pathspec: Incomplete | None = ..., params: Incomplete | None = ..., max_retries: int = ..., backoff_factor: int = ...): ... +# def download_to_file(url, dest_file_path, timeout: int = ..., chunk_size=...) -> None: ... + +# def get_executable(): ... diff --git a/mypy-stubs/galaxy/util/aliaspickler.pyi b/mypy-stubs/galaxy/util/aliaspickler.pyi index 95c60a9b1..245177634 100644 --- a/mypy-stubs/galaxy/util/aliaspickler.pyi +++ b/mypy-stubs/galaxy/util/aliaspickler.pyi @@ -1,18 +1,14 @@ -# Stubs for galaxy.util.aliaspickler (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any import pickle -from six.moves import cStringIO as StringIO + +from _typeshed import Incomplete class AliasUnpickler(pickle.Unpickler): - aliases = ... # type: Any + aliases: Incomplete def __init__(self, aliases, *args, **kw) -> None: ... def find_class(self, module, name): ... class AliasPickleModule: - aliases = ... # type: Any + aliases: Incomplete def __init__(self, aliases) -> None: ... def dump(self, obj, fileobj, protocol: int = ...): ... def dumps(self, obj, protocol: int = ...): ... diff --git a/mypy-stubs/galaxy/util/bunch.pyi b/mypy-stubs/galaxy/util/bunch.pyi index 87dc09bd0..424097035 100644 --- a/mypy-stubs/galaxy/util/bunch.pyi +++ b/mypy-stubs/galaxy/util/bunch.pyi @@ -1,17 +1,14 @@ -# Stubs for galaxy.util.bunch (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional +from _typeshed import Incomplete class Bunch: def __init__(self, **kwds) -> None: ... def dict(self): ... - def get(self, key, default: Optional[Any] = ...): ... + def get(self, key, default: Incomplete | None = ...): ... def __iter__(self): ... def items(self): ... def keys(self): ... def values(self): ... - def __nonzero__(self): ... - def __setitem__(self, k, v): ... + def __bool__(self): ... + __nonzero__: Incomplete + def __setitem__(self, k, v) -> None: ... def __contains__(self, item): ... diff --git a/mypy-stubs/galaxy/util/bytesize.pyi b/mypy-stubs/galaxy/util/bytesize.pyi new file mode 100644 index 000000000..d6b923350 --- /dev/null +++ b/mypy-stubs/galaxy/util/bytesize.pyi @@ -0,0 +1,10 @@ +from _typeshed import Incomplete + +SUFFIX_TO_BYTES: Incomplete + +class ByteSize: + value: Incomplete + def __init__(self, value) -> None: ... + def to_unit(self, unit: Incomplete | None = ..., as_string: bool = ...): ... + +def parse_bytesize(value): ... diff --git a/mypy-stubs/galaxy/util/checkers.pyi b/mypy-stubs/galaxy/util/checkers.pyi index cdcb3efb6..eedae9b05 100644 --- a/mypy-stubs/galaxy/util/checkers.pyi +++ b/mypy-stubs/galaxy/util/checkers.pyi @@ -1,14 +1,9 @@ -# Stubs for galaxy.util.checkers (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -def check_html(file_path, chunk: Optional[Any] = ...): ... +def check_html(name, file_path: bool = ...): ... def check_binary(name, file_path: bool = ...): ... -def check_gzip(file_path): ... -def check_bz2(file_path): ... -def check_zip(file_path): ... +def check_gzip(file_path, check_content: bool = ...): ... +def check_bz2(file_path, check_content: bool = ...): ... +def check_zip(file_path, check_content: bool = ..., files: int = ...): ... def is_bz2(file_path): ... def is_gzip(file_path): ... +def is_zip(file_path): ... def check_image(file_path): ... diff --git a/mypy-stubs/galaxy/util/commands.pyi b/mypy-stubs/galaxy/util/commands.pyi new file mode 100644 index 000000000..0210333bd --- /dev/null +++ b/mypy-stubs/galaxy/util/commands.pyi @@ -0,0 +1,18 @@ +from _typeshed import Incomplete +from galaxy.util import which as which + +def redirecting_io(sys=...): ... +def redirect_aware_commmunicate(p, sys=...): ... +def shell(cmds, env: Incomplete | None = ..., **kwds): ... +def shell_process(cmds, env: Incomplete | None = ..., **kwds): ... +def execute(cmds, input: Incomplete | None = ...): ... +def argv_to_str(command_argv, quote: bool = ...): ... +def download_command(url, to=...): ... + +class CommandLineException(Exception): + command: Incomplete + stdout: Incomplete + stderr: Incomplete + returncode: Incomplete + message: Incomplete + def __init__(self, command, stdout, stderr, returncode) -> None: ... diff --git a/mypy-stubs/galaxy/util/compression_utils.pyi b/mypy-stubs/galaxy/util/compression_utils.pyi index 0c6ca3a79..d2b9d4ccb 100644 --- a/mypy-stubs/galaxy/util/compression_utils.pyi +++ b/mypy-stubs/galaxy/util/compression_utils.pyi @@ -1,7 +1,46 @@ -# Stubs for galaxy.util.compression_utils (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from collections.abc import Generator -from .checkers import is_bz2 as is_bz2, is_gzip as is_gzip +from _typeshed import Incomplete -def get_fileobj(filename, mode: str = ..., gzip_only: bool = ..., bz2_only: bool = ..., zip_only: bool = ...): ... +from .checkers import bz2 as bz2 +from .checkers import is_bz2 as is_bz2 +from .checkers import is_gzip as is_gzip + +log: Incomplete + +def get_fileobj( + filename, mode: str = ..., compressed_formats: Incomplete | None = ... +): ... +def get_fileobj_raw( + filename, mode: str = ..., compressed_formats: Incomplete | None = ... +): ... +def file_iter( + fname, sep: Incomplete | None = ... +) -> Generator[Incomplete, None, None]: ... + +class CompressedFile: + @staticmethod + def can_decompress(file_path): ... + file_type: str + file_name: Incomplete + type: Incomplete + archive: Incomplete + def __init__(self, file_path, mode: str = ...) -> None: ... + @property + def common_prefix_dir(self): ... + def extract(self, path): ... + def safemembers(self) -> Generator[Incomplete, None, None]: ... + def getmembers_tar(self): ... + def getmembers_zip(self): ... + def getname_tar(self, item): ... + def getname_zip(self, item): ... + def getmember(self, name): ... + def getmembers(self): ... + def getname(self, member): ... + def isdir(self, member): ... + def isdir_tar(self, member): ... + def isdir_zip(self, member): ... + def isfile(self, member): ... + def open_tar(self, filepath, mode): ... + def open_zip(self, filepath, mode): ... + def zipfile_ok(self, path_to_archive): ... diff --git a/mypy-stubs/galaxy/util/dbkeys.pyi b/mypy-stubs/galaxy/util/dbkeys.pyi new file mode 100644 index 000000000..f5337dd61 --- /dev/null +++ b/mypy-stubs/galaxy/util/dbkeys.pyi @@ -0,0 +1,23 @@ +from _typeshed import Incomplete +from galaxy.util import galaxy_directory as galaxy_directory, unicodify as unicodify +from galaxy.util.object_wrapper import ( + sanitize_lists_to_string as sanitize_lists_to_string, +) + +log: Incomplete + +def read_dbnames(filename): ... + +class GenomeBuilds: + default_value: str + default_name: str + def __init__( + self, app, data_table_name: str = ..., load_old_style: bool = ... + ) -> None: ... + def get_genome_build_names(self, trans: Incomplete | None = ...): ... + def get_chrom_info( + self, + dbkey, + trans: Incomplete | None = ..., + custom_build_hack_get_len_from_fasta_conversion: bool = ..., + ): ... diff --git a/mypy-stubs/galaxy/util/dictifiable.pyi b/mypy-stubs/galaxy/util/dictifiable.pyi deleted file mode 100644 index babdeb4d3..000000000 --- a/mypy-stubs/galaxy/util/dictifiable.pyi +++ /dev/null @@ -1,8 +0,0 @@ -# Stubs for galaxy.util.dictifiable (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -class Dictifiable: - def to_dict(self, view: str = ..., value_mapper: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/util/expressions.pyi b/mypy-stubs/galaxy/util/expressions.pyi index f1eca5ee8..1dcde253d 100644 --- a/mypy-stubs/galaxy/util/expressions.pyi +++ b/mypy-stubs/galaxy/util/expressions.pyi @@ -1,18 +1,16 @@ -# Stubs for galaxy.util.expressions (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from collections.abc import MutableMapping -from typing import Any, Optional -from collections import MutableMapping +from _typeshed import Incomplete class ExpressionContext(MutableMapping): - dict = ... # type: Any - parent = ... # type: Any - def __init__(self, dict, parent: Optional[Any] = ...) -> None: ... - def __delitem__(self, key): ... + dict: Incomplete + parent: Incomplete + def __init__(self, dict, parent: Incomplete | None = ...) -> None: ... + def __delitem__(self, key) -> None: ... def __iter__(self): ... def __len__(self): ... def __getitem__(self, key): ... - def __setitem__(self, key, value): ... + def __setitem__(self, key, value) -> None: ... def __contains__(self, key): ... - def __nonzero__(self): ... + def __bool__(self): ... + __nonzero__: Incomplete diff --git a/mypy-stubs/galaxy/util/facts.pyi b/mypy-stubs/galaxy/util/facts.pyi new file mode 100644 index 000000000..497dadf6b --- /dev/null +++ b/mypy-stubs/galaxy/util/facts.pyi @@ -0,0 +1,13 @@ +from _typeshed import Incomplete +from collections.abc import MutableMapping + +class Facts(MutableMapping): + __dict__: Incomplete + def __init__(self, config: Incomplete | None = ..., **kwargs) -> None: ... + def __getitem__(self, key): ... + def __setitem__(self, key, value): ... + def __delitem__(self, key): ... + def __iter__(self): ... + def __len__(self): ... + +def get_facts(config: Incomplete | None = ..., **kwargs): ... diff --git a/mypy-stubs/galaxy/util/filelock.pyi b/mypy-stubs/galaxy/util/filelock.pyi index f74dd9a4c..55a3ecaab 100644 --- a/mypy-stubs/galaxy/util/filelock.pyi +++ b/mypy-stubs/galaxy/util/filelock.pyi @@ -1,21 +1,17 @@ -# Stubs for galaxy.util.filelock (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any +from _typeshed import Incomplete class FileLockException(Exception): ... class FileLock: - is_locked = ... # type: bool - lockfile = ... # type: Any - file_name = ... # type: Any - timeout = ... # type: Any - delay = ... # type: Any + is_locked: bool + lockfile: Incomplete + file_name: Incomplete + timeout: Incomplete + delay: Incomplete def __init__(self, file_name, timeout: int = ..., delay: float = ...) -> None: ... - fd = ... # type: Any - def acquire(self): ... - def release(self): ... + fd: Incomplete + def acquire(self) -> None: ... + def release(self) -> None: ... def __enter__(self): ... - def __exit__(self, type, value, traceback): ... - def __del__(self): ... + def __exit__(self, type, value, traceback) -> None: ... + def __del__(self) -> None: ... diff --git a/mypy-stubs/galaxy/util/form_builder.pyi b/mypy-stubs/galaxy/util/form_builder.pyi new file mode 100644 index 000000000..dbd6ea2ed --- /dev/null +++ b/mypy-stubs/galaxy/util/form_builder.pyi @@ -0,0 +1,110 @@ +from _typeshed import Incomplete +from galaxy.util import asbool as asbool + +log: Incomplete + +class BaseField: + name: Incomplete + label: Incomplete + value: Incomplete + disabled: Incomplete + optional: Incomplete + help: Incomplete + def __init__( + self, + name, + value: Incomplete | None = ..., + label: Incomplete | None = ..., + **kwds + ) -> None: ... + def to_dict(self): ... + +class TextField(BaseField): + def to_dict(self): ... + +class PasswordField(BaseField): + def to_dict(self): ... + +class TextArea(BaseField): + def to_dict(self): ... + +class CheckboxField(BaseField): + @staticmethod + def is_checked(value): ... + def to_dict(self): ... + +class SelectField(BaseField): + field_id: Incomplete + multiple: Incomplete + refresh_on_change: Incomplete + selectlist: Incomplete + options: Incomplete + display: Incomplete + def __init__( + self, + name, + multiple: Incomplete | None = ..., + display: Incomplete | None = ..., + field_id: Incomplete | None = ..., + value: Incomplete | None = ..., + selectlist: Incomplete | None = ..., + refresh_on_change: bool = ..., + **kwds + ) -> None: ... + def add_option(self, text, value, selected: bool = ...) -> None: ... + def to_dict(self): ... + +class AddressField(BaseField): + @staticmethod + def fields(): ... + user: Incomplete + security: Incomplete + def __init__( + self, + name, + user: Incomplete | None = ..., + value: Incomplete | None = ..., + security: Incomplete | None = ..., + **kwds + ) -> None: ... + def to_dict(self): ... + +class WorkflowField(BaseField): + user: Incomplete + value: Incomplete + security: Incomplete + def __init__( + self, + name, + user: Incomplete | None = ..., + value: Incomplete | None = ..., + security: Incomplete | None = ..., + **kwds + ) -> None: ... + def to_dict(self): ... + +class WorkflowMappingField(BaseField): + user: Incomplete + def __init__( + self, + name, + user: Incomplete | None = ..., + value: Incomplete | None = ..., + **kwds + ) -> None: ... + +class HistoryField(BaseField): + user: Incomplete + value: Incomplete + security: Incomplete + def __init__( + self, + name, + user: Incomplete | None = ..., + value: Incomplete | None = ..., + security: Incomplete | None = ..., + **kwds + ) -> None: ... + def to_dict(self): ... + +def get_suite(): ... diff --git a/mypy-stubs/galaxy/util/getargspec.pyi b/mypy-stubs/galaxy/util/getargspec.pyi new file mode 100644 index 000000000..d0c74c235 --- /dev/null +++ b/mypy-stubs/galaxy/util/getargspec.pyi @@ -0,0 +1 @@ +def getfullargspec(func): ... diff --git a/mypy-stubs/galaxy/util/hash_util.pyi b/mypy-stubs/galaxy/util/hash_util.pyi index 1a81a16aa..b9e737db4 100644 --- a/mypy-stubs/galaxy/util/hash_util.pyi +++ b/mypy-stubs/galaxy/util/hash_util.pyi @@ -1,14 +1,11 @@ -# Stubs for galaxy.util.hash_util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional import hashlib as hashlib -sha1 = ... # type: Any -sha = ... # type: Any -md5 = ... # type: Any +sha1 = hashlib.sha1 +sha256 = hashlib.sha256 +sha512 = hashlib.sha512 +sha = sha1 +md5 = hashlib.md5 -def new_secure_hash(text_type: Optional[Any] = ...): ... +def new_secure_hash(text_type): ... def hmac_new(key, value): ... def is_hashable(value): ... diff --git a/mypy-stubs/galaxy/util/heartbeat.pyi b/mypy-stubs/galaxy/util/heartbeat.pyi index e7152ae9a..fea3aa044 100644 --- a/mypy-stubs/galaxy/util/heartbeat.pyi +++ b/mypy-stubs/galaxy/util/heartbeat.pyi @@ -1,30 +1,29 @@ -# Stubs for galaxy.util.heartbeat (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any import threading +from _typeshed import Incomplete + def get_current_thread_object_dict(): ... class Heartbeat(threading.Thread): - config = ... # type: Any - should_stop = ... # type: bool - period = ... # type: Any - fname = ... # type: Any - file = ... # type: Any - fname_nonsleeping = ... # type: Any - file_nonsleeping = ... # type: Any - pid = ... # type: Any - nonsleeping_heartbeats = ... # type: Any - wait_event = ... # type: Any - def __init__(self, config, name: str = ..., period: int = ..., fname: str = ...) -> None: ... - def run(self): ... - def open_logs(self): ... - def close_logs(self): ... - def dump(self): ... - def shutdown(self): ... + config: Incomplete + should_stop: bool + period: Incomplete + fname: Incomplete + file: Incomplete + fname_nonsleeping: Incomplete + file_nonsleeping: Incomplete + pid: Incomplete + nonsleeping_heartbeats: Incomplete + wait_event: Incomplete + def __init__( + self, config, name: str = ..., period: int = ..., fname: str = ... + ) -> None: ... + def run(self) -> None: ... + def open_logs(self) -> None: ... + def close_logs(self) -> None: ... + def dump(self) -> None: ... + def shutdown(self) -> None: ... def thread_is_sleeping(self, last_stack_frame): ... def get_interesting_stack_frame(self, stack_frames): ... - def print_nonsleeping(self, threads_object_dict): ... - def dump_signal_handler(self, signum, frame): ... + def print_nonsleeping(self, threads_object_dict) -> None: ... + def dump_signal_handler(self, signum, frame) -> None: ... diff --git a/mypy-stubs/galaxy/util/image_util.pyi b/mypy-stubs/galaxy/util/image_util.pyi index ce04019bf..59a3e3a6c 100644 --- a/mypy-stubs/galaxy/util/image_util.pyi +++ b/mypy-stubs/galaxy/util/image_util.pyi @@ -1,13 +1,6 @@ -# Stubs for galaxy.util.image_util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete -from typing import Any -from PIL import Image as PIL - -PIL = ... # type: Any -log = ... # type: Any +log: Incomplete def image_type(filename): ... def check_image_type(filename, types): ... -def get_image_ext(file_path): ... diff --git a/mypy-stubs/galaxy/util/inflection.pyi b/mypy-stubs/galaxy/util/inflection.pyi deleted file mode 100644 index 92f01cb91..000000000 --- a/mypy-stubs/galaxy/util/inflection.pyi +++ /dev/null @@ -1,46 +0,0 @@ -# Stubs for galaxy.util.inflection (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -class Base: - def cond_plural(self, number_of_records, word): ... - def titleize(self, word, uppercase: str = ...): ... - def camelize(self, word): ... - def underscore(self, word): ... - def humanize(self, word, uppercase: str = ...): ... - def variablize(self, word): ... - def tableize(self, class_name): ... - def classify(self, table_name): ... - def ordinalize(self, number): ... - def unaccent(self, text): ... - def string_replace(self, word, find, replace): ... - def urlize(self, text): ... - def demodulize(self, module_name): ... - def modulize(self, module_description): ... - def foreignKey(self, class_name, separate_class_name_and_id_with_underscore: int = ...): ... - -class English(Base): - def pluralize(self, word): ... - def singularize(self, word): ... - -class Inflector: - Inflector = ... # type: Any - def __init__(self, Inflector: Any = ...) -> None: ... - def pluralize(self, word): ... - def singularize(self, word): ... - def cond_plural(self, number_of_records, word): ... - def titleize(self, word, uppercase: str = ...): ... - def camelize(self, word): ... - def underscore(self, word): ... - def humanize(self, word, uppercase: str = ...): ... - def variablize(self, word): ... - def tableize(self, class_name): ... - def classify(self, table_name): ... - def ordinalize(self, number): ... - def unaccent(self, text): ... - def urlize(self, text): ... - def demodulize(self, module_name): ... - def modulize(self, module_description): ... - def foreignKey(self, class_name, separate_class_name_and_id_with_underscore: int = ...): ... diff --git a/mypy-stubs/galaxy/util/json.pyi b/mypy-stubs/galaxy/util/json.pyi index d124bd660..be04dffe3 100644 --- a/mypy-stubs/galaxy/util/json.pyi +++ b/mypy-stubs/galaxy/util/json.pyi @@ -1,12 +1,23 @@ -# Stubs for galaxy.util.json (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +import json -from typing import Any, Optional +from _typeshed import Incomplete + +to_json_string = json.dumps +from_json_string = json.loads -def json_fix(val): ... def safe_dumps(*args, **kwargs): ... def validate_jsonrpc_request(request, regular_methods, notification_methods): ... -def validate_jsonrpc_response(response, id: Optional[Any] = ...): ... -def jsonrpc_request(method, params: Optional[Any] = ..., id: Optional[Any] = ..., jsonrpc: str = ...): ... -def jsonrpc_response(request: Optional[Any] = ..., id: Optional[Any] = ..., result: Optional[Any] = ..., error: Optional[Any] = ..., jsonrpc: str = ...): ... +def validate_jsonrpc_response(response, id: Incomplete | None = ...): ... +def jsonrpc_request( + method, + params: Incomplete | None = ..., + id: Incomplete | None = ..., + jsonrpc: str = ..., +): ... +def jsonrpc_response( + request: Incomplete | None = ..., + id: Incomplete | None = ..., + result: Incomplete | None = ..., + error: Incomplete | None = ..., + jsonrpc: str = ..., +): ... diff --git a/mypy-stubs/galaxy/util/jstree.pyi b/mypy-stubs/galaxy/util/jstree.pyi new file mode 100644 index 000000000..3106df4d8 --- /dev/null +++ b/mypy-stubs/galaxy/util/jstree.pyi @@ -0,0 +1,19 @@ +import dictobj +from _typeshed import Incomplete +from typing import NamedTuple + +class Path(NamedTuple): + path: Incomplete + id: Incomplete + options: Incomplete + +class Node(dictobj.DictionaryObject): + def __init__(self, path, oid, **kwargs) -> None: ... + def jsonData(self): ... + +class JSTree(dictobj.DictionaryObject): + def __init__(self, paths, **kwargs) -> None: ... + def pretty( + self, root: Incomplete | None = ..., depth: int = ..., spacing: int = ... + ): ... + def jsonData(self): ... diff --git a/mypy-stubs/galaxy/util/lazy_process.pyi b/mypy-stubs/galaxy/util/lazy_process.pyi index 045e42f44..6831c8375 100644 --- a/mypy-stubs/galaxy/util/lazy_process.pyi +++ b/mypy-stubs/galaxy/util/lazy_process.pyi @@ -1,22 +1,18 @@ -# Stubs for galaxy.util.lazy_process (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any +from _typeshed import Incomplete class LazyProcess: - command_and_args = ... # type: Any - thread_lock = ... # type: Any - allow_process_request = ... # type: bool - process = ... # type: Any + command_and_args: Incomplete + thread_lock: Incomplete + allow_process_request: bool + process: Incomplete def __init__(self, command_and_args) -> None: ... - def start_process(self): ... - def shutdown(self): ... + def start_process(self) -> None: ... + def shutdown(self) -> None: ... @property def running(self): ... class NoOpLazyProcess: - def start_process(self): ... - def shutdown(self): ... + def start_process(self) -> None: ... + def shutdown(self) -> None: ... @property def running(self): ... diff --git a/mypy-stubs/galaxy/util/monitors.pyi b/mypy-stubs/galaxy/util/monitors.pyi new file mode 100644 index 000000000..1e1128e76 --- /dev/null +++ b/mypy-stubs/galaxy/util/monitors.pyi @@ -0,0 +1,12 @@ +from .sleeper import Sleeper as Sleeper +from .web_compat import register_postfork_function as register_postfork_function +from _typeshed import Incomplete + +log: Incomplete +DEFAULT_MONITOR_THREAD_JOIN_TIMEOUT: int + +class Monitors: + def start_monitoring(self) -> None: ... + monitor_running: bool + def stop_monitoring(self) -> None: ... + def shutdown_monitor(self) -> None: ... diff --git a/mypy-stubs/galaxy/util/object_wrapper.pyi b/mypy-stubs/galaxy/util/object_wrapper.pyi index 8a5cda6e6..8d320674b 100644 --- a/mypy-stubs/galaxy/util/object_wrapper.pyi +++ b/mypy-stubs/galaxy/util/object_wrapper.pyi @@ -1,42 +1,37 @@ -# Stubs for galaxy.util.object_wrapper (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete -from typing import Any, Optional -from six.moves import copyreg as copy_reg -from galaxy.util import sanitize_lists_to_string as _sanitize_lists_to_string - -NoneType = ... # type: Any -NotImplementedType = ... # type: Any -EllipsisType = ... # type: Any -XRangeType = ... # type: Any -SliceType = ... # type: Any -BufferType = ... # type: Any -DictProxyType = ... # type: Any -log = ... # type: Any -__CALLABLE_TYPES__ = ... # type: Any -__WRAP_NO_SUBCLASS__ = ... # type: Any -__DONT_SANITIZE_TYPES__ = ... # type: Any -__DONT_WRAP_TYPES__ = ... # type: Any -__WRAP_SEQUENCES__ = ... # type: Any -__WRAP_SETS__ = ... # type: Any -__WRAP_MAPPINGS__ = ... # type: Any -VALID_CHARACTERS = ... # type: Any -CHARACTER_MAP = ... # type: Any -INVALID_CHARACTER = ... # type: str +NoneType: Incomplete +NotImplementedType: Incomplete +EllipsisType: Incomplete +XRangeType = range +SliceType = slice +BufferType = SliceType +DictProxyType = SliceType +log: Incomplete +__CALLABLE_TYPES__: Incomplete +__WRAP_NO_SUBCLASS__: Incomplete +__DONT_SANITIZE_TYPES__: Incomplete +__WRAP_SEQUENCES__: Incomplete +__WRAP_SETS__: Incomplete +__WRAP_MAPPINGS__: Incomplete +VALID_CHARACTERS: Incomplete +CHARACTER_MAP: Incomplete +INVALID_CHARACTER: str def coerce(x, y): ... def cmp(x, y): ... -def sanitize_lists_to_string(values, valid_characters: Any = ..., character_map: Any = ..., invalid_character: Any = ...): ... -def wrap_with_safe_string(value, no_wrap_classes: Optional[Any] = ...): ... +def sanitize_lists_to_string( + values, valid_characters=..., character_map=..., invalid_character=... +): ... +def wrap_with_safe_string(value, no_wrap_classes: Incomplete | None = ...): ... class SafeStringWrapper: - __UNSANITIZED_ATTRIBUTE_NAME__ = ... # type: str - __NO_WRAP_NAMES__ = ... # type: Any + __UNSANITIZED_ATTRIBUTE_NAME__: str + __NO_WRAP_NAMES__: Incomplete def __new__(cls, *arg, **kwd): ... - unsanitized = ... # type: Any - __safe_string_wrapper_function__ = ... # type: Any - def __init__(self, value, safe_string_wrapper_function: Any = ...) -> None: ... + unsanitized: Incomplete + __safe_string_wrapper_function__: Incomplete + def __init__(self, value, safe_string_wrapper_function=...) -> None: ... def __lt__(self, other): ... def __le__(self, other): ... def __eq__(self, other): ... @@ -46,20 +41,20 @@ class SafeStringWrapper: def __cmp__(self, other): ... def __hash__(self): ... def __bool__(self): ... - __nonzero__ = ... # type: Any + __nonzero__: Incomplete def __getattr__(self, name): ... def __setattr__(self, name, value): ... def __delattr__(self, name): ... def __getattribute__(self, name): ... def __len__(self): ... def __getitem__(self, key): ... - def __setitem__(self, key, value): ... - def __delitem__(self, key): ... + def __setitem__(self, key, value) -> None: ... + def __delitem__(self, key) -> None: ... def __iter__(self): ... def __contains__(self, item): ... def __getslice__(self, i, j): ... - def __setslice__(self, i, j, value): ... - def __delslice__(self, i, j): ... + def __setslice__(self, i, j, value) -> None: ... + def __delslice__(self, i, j) -> None: ... def __add__(self, other): ... def __sub__(self, other): ... def __mul__(self, other): ... diff --git a/mypy-stubs/galaxy/util/odict.pyi b/mypy-stubs/galaxy/util/odict.pyi index 459e30699..ecbd4969f 100644 --- a/mypy-stubs/galaxy/util/odict.pyi +++ b/mypy-stubs/galaxy/util/odict.pyi @@ -1,27 +1,25 @@ -# Stubs for galaxy.util.odict (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from collections import UserDict +from collections.abc import Generator -from typing import Any, Optional -from six.moves import UserDict +from _typeshed import Incomplete -dict_alias = ... # type: Any +dict_alias = dict class odict(UserDict): - def __init__(self, dict: Optional[Any] = ...) -> None: ... - def __delitem__(self, key): ... - def __setitem__(self, key, item): ... - def clear(self): ... + def __init__(self, dict: Incomplete | None = ...) -> None: ... + def __delitem__(self, key) -> None: ... + def __setitem__(self, key, item) -> None: ... + def clear(self) -> None: ... def copy(self): ... def items(self): ... def keys(self): ... def popitem(self): ... - def setdefault(self, key, failobj: Optional[Any] = ...): ... - def update(self, dict): ... + def setdefault(self, key, failobj: Incomplete | None = ...): ... + def update(self, dict) -> None: ... def values(self): ... def iterkeys(self): ... - def itervalues(self): ... - def iteritems(self): ... + def itervalues(self) -> Generator[Incomplete, None, None]: ... + def iteritems(self) -> Generator[Incomplete, None, None]: ... def __iter__(self): ... - def reverse(self): ... - def insert(self, index, key, item): ... + def reverse(self) -> None: ... + def insert(self, index, key, item) -> None: ... diff --git a/mypy-stubs/galaxy/util/oset.pyi b/mypy-stubs/galaxy/util/oset.pyi deleted file mode 100644 index 1d1f7bd80..000000000 --- a/mypy-stubs/galaxy/util/oset.pyi +++ /dev/null @@ -1,19 +0,0 @@ -# Stubs for galaxy.util.oset (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional -import collections - -class OrderedSet(collections.MutableSet): - end = ... # type: Any - map = ... # type: Any - def __init__(self, iterable: Optional[Any] = ...) -> None: ... - def __len__(self): ... - def __contains__(self, key): ... - def add(self, key): ... - def discard(self, key): ... - def __iter__(self): ... - def __reversed__(self): ... - def pop(self, last: bool = ...): ... - def __eq__(self, other): ... diff --git a/mypy-stubs/galaxy/util/pastescript/__init__.pyi b/mypy-stubs/galaxy/util/pastescript/__init__.pyi new file mode 100644 index 000000000..e69de29bb diff --git a/mypy-stubs/galaxy/util/pastescript/loadwsgi.pyi b/mypy-stubs/galaxy/util/pastescript/loadwsgi.pyi new file mode 100644 index 000000000..4037dceea --- /dev/null +++ b/mypy-stubs/galaxy/util/pastescript/loadwsgi.pyi @@ -0,0 +1,129 @@ +from _typeshed import Incomplete +from typing import List, Optional, Union + +class _ObjectType: + name: Optional[str] + egg_protocols: Optional[List[Union[str, List[str]]]] + config_prefixes: Optional[List[Union[List[str], str]]] + def __init__(self) -> None: ... + def invoke(self, context): ... + +class _App(_ObjectType): + name: str + egg_protocols: Incomplete + config_prefixes: Incomplete + def invoke(self, context): ... + +class _Filter(_ObjectType): + name: str + egg_protocols: Incomplete + config_prefixes: Incomplete + def invoke(self, context): ... + +class _Server(_ObjectType): + name: str + egg_protocols: Incomplete + config_prefixes: Incomplete + def invoke(self, context): ... + +class _PipeLine(_ObjectType): + name: str + def invoke(self, context): ... + +class _FilterApp(_ObjectType): + name: str + def invoke(self, context): ... + +class _FilterWith(_App): + name: str + def invoke(self, context): ... + +def loadapp(uri, name: Incomplete | None = ..., **kw): ... +def loadfilter(uri, name: Incomplete | None = ..., **kw): ... +def loadserver(uri, name: Incomplete | None = ..., **kw): ... +def appconfig( + uri, + name: Incomplete | None = ..., + relative_to: Incomplete | None = ..., + global_conf: Incomplete | None = ..., +): ... + +class _Loader: + def get_app( + self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... + ): ... + def get_filter( + self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... + ): ... + def get_server( + self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... + ): ... + def app_context( + self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... + ): ... + def filter_context( + self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... + ): ... + def server_context( + self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... + ): ... + def absolute_name(self, name): ... + +class ConfigLoader(_Loader): + filename: Incomplete + parser: Incomplete + def __init__(self, filename) -> None: ... + def update_defaults(self, new_defaults, overwrite: bool = ...) -> None: ... + def get_context( + self, + object_type, + name: Incomplete | None = ..., + global_conf: Incomplete | None = ..., + ): ... + def find_config_section(self, object_type, name: Incomplete | None = ...): ... + +class EggLoader(_Loader): + spec: Incomplete + def __init__(self, spec) -> None: ... + def get_context( + self, + object_type, + name: Incomplete | None = ..., + global_conf: Incomplete | None = ..., + ): ... + def find_egg_entry_point(self, object_type, name: Incomplete | None = ...): ... + +class FuncLoader(_Loader): + spec: Incomplete + def __init__(self, spec) -> None: ... + def get_context( + self, + object_type, + name: Incomplete | None = ..., + global_conf: Incomplete | None = ..., + ): ... + +class LoaderContext: + object: Incomplete + object_type: Incomplete + protocol: Incomplete + global_conf: Incomplete + local_conf: Incomplete + loader: Incomplete + distribution: Incomplete + entry_point_name: Incomplete + def __init__( + self, + obj, + object_type, + protocol, + global_conf, + local_conf, + loader, + distribution: Incomplete | None = ..., + entry_point_name: Incomplete | None = ..., + ) -> None: ... + def create(self): ... + def config(self): ... + +class AttrDict(dict): ... diff --git a/mypy-stubs/galaxy/util/pastescript/serve.pyi b/mypy-stubs/galaxy/util/pastescript/serve.pyi new file mode 100644 index 000000000..ea9d9f3b9 --- /dev/null +++ b/mypy-stubs/galaxy/util/pastescript/serve.pyi @@ -0,0 +1,94 @@ +import optparse +from .loadwsgi import loadapp as loadapp, loadserver as loadserver +from _typeshed import Incomplete +from typing import Optional + +difflib: Incomplete + +class BoolOptionParser(optparse.OptionParser): ... + +class BadCommand(Exception): + message: Incomplete + exit_code: Incomplete + def __init__(self, message, exit_code: int = ...) -> None: ... + +class NoDefault: ... + +class Command: + command_name: Incomplete + def __init__(self, name) -> None: ... + max_args: Incomplete + max_args_error: str + min_args: Optional[int] + min_args_error: str + required_args: Incomplete + takes_config_file: Optional[int] + group_name: str + description: Optional[str] + usage: str + hidden: bool + default_verbosity: int + default_interactive: int + return_code: int + BadCommand: Incomplete + interactive: Incomplete + verbose: Incomplete + simulate: Incomplete + def run(self, args): ... + def parse_args(self, args) -> None: ... + def pad(self, s, length, dir: str = ...): ... + standard_parser: Incomplete + def quote_first_command_arg(self, arg): ... + def parse_vars(self, args): ... + def logging_file_config(self, config_file) -> None: ... + +class NotFoundCommand(Command): + def run(self, args): ... + +MAXFD: int +jython: Incomplete + +class DaemonizeException(Exception): ... + +class ServeCommand(Command): + min_args: int + usage: str + takes_config_file: int + summary: str + description: Optional[str] + requires_config_file: bool + parser: Incomplete + default_verbosity: int + possible_subcommands: Incomplete + def command(self): ... + def daemonize(self) -> None: ... + def record_pid(self, pid_file) -> None: ... + def stop_daemon(self): ... + def show_status(self): ... + def restart_with_reloader(self) -> None: ... + def restart_with_monitor(self, reloader: bool = ...): ... + def change_user_group(self, user, group) -> None: ... + +class LazyWriter: + filename: Incomplete + fileobj: Incomplete + lock: Incomplete + mode: Incomplete + def __init__(self, filename, mode: str = ...) -> None: ... + def open(self): ... + def write(self, text) -> None: ... + def writelines(self, text) -> None: ... + def flush(self) -> None: ... + +def live_pidfile(pidfile): ... +def read_pidfile(filename): ... +def ensure_port_cleanup( + bound_addresses, maxtries: int = ..., sleeptime: int = ... +) -> None: ... + +python_version: Incomplete +parser: Incomplete +commands: Incomplete + +def run(args: Incomplete | None = ...) -> None: ... +def invoke(command, command_name, options, args) -> None: ... diff --git a/mypy-stubs/galaxy/util/path/__init__.pyi b/mypy-stubs/galaxy/util/path/__init__.pyi new file mode 100644 index 000000000..5f49b9785 --- /dev/null +++ b/mypy-stubs/galaxy/util/path/__init__.pyi @@ -0,0 +1,19 @@ +from collections.abc import Generator + +from _typeshed import Incomplete + +def safe_walk( + path, allowlist: Incomplete | None = ... +) -> Generator[Incomplete, None, None]: ... +def unsafe_walk( + path, allowlist: Incomplete | None = ..., username: Incomplete | None = ... +): ... +def joinext(root, ext): ... +def has_ext(path, ext, aliases: bool = ..., ignore: Incomplete | None = ...): ... +def get_ext(path, ignore: Incomplete | None = ..., canonicalize: bool = ...): ... + +class Extensions(dict): + def __missing__(self, key): ... + def canonicalize(self, ext): ... + +extensions: Incomplete diff --git a/mypy-stubs/galaxy/util/path/ntpath.pyi b/mypy-stubs/galaxy/util/path/ntpath.pyi new file mode 100644 index 000000000..e69de29bb diff --git a/mypy-stubs/galaxy/util/path/posixpath.pyi b/mypy-stubs/galaxy/util/path/posixpath.pyi new file mode 100644 index 000000000..e69de29bb diff --git a/mypy-stubs/galaxy/util/permutations.pyi b/mypy-stubs/galaxy/util/permutations.pyi new file mode 100644 index 000000000..d3f6e3139 --- /dev/null +++ b/mypy-stubs/galaxy/util/permutations.pyi @@ -0,0 +1,9 @@ +from _typeshed import Incomplete +from galaxy.exceptions import MessageException as MessageException +from galaxy.util.bunch import Bunch as Bunch + +input_classification: Incomplete + +class InputMatchedException(MessageException): ... + +def expand_multi_inputs(inputs, classifier, key_filter: Incomplete | None = ...): ... diff --git a/mypy-stubs/galaxy/util/plugin_config.pyi b/mypy-stubs/galaxy/util/plugin_config.pyi index 887a82b7b..4c9a5e123 100644 --- a/mypy-stubs/galaxy/util/plugin_config.pyi +++ b/mypy-stubs/galaxy/util/plugin_config.pyi @@ -1,11 +1,19 @@ -# Stubs for galaxy.util.plugin_config (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from typing import NamedTuple -from typing import Any +from _typeshed import Incomplete +from galaxy.util.submodules import import_submodules as import_submodules -yaml = ... # type: Any +class PluginConfigSource(NamedTuple): + type: Incomplete + source: Incomplete def plugins_dict(module, plugin_type_identifier): ... -def load_plugins(plugins_dict, plugin_source, extra_kwds: Any = ...): ... +def load_plugins( + plugins_dict, + plugin_source, + extra_kwds: Incomplete | None = ..., + plugin_type_keys=..., + dict_to_list_key: Incomplete | None = ..., +): ... def plugin_source_from_path(path): ... +def plugin_source_from_dict(as_dict): ... diff --git a/mypy-stubs/galaxy/util/properties.pyi b/mypy-stubs/galaxy/util/properties.pyi index b59fdd0c8..0b66754ed 100644 --- a/mypy-stubs/galaxy/util/properties.pyi +++ b/mypy-stubs/galaxy/util/properties.pyi @@ -1,19 +1,33 @@ -# Stubs for galaxy.util.properties (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from configparser import ConfigParser -from typing import Any, Optional -from six.moves.configparser import ConfigParser +from _typeshed import Incomplete -def find_config_file(default, old_default, explicit, cwd: Optional[Any] = ...): ... -def load_app_properties(kwds: Any = ..., ini_file: Optional[Any] = ..., ini_section: str = ..., config_prefix: str = ...): ... +def find_config_file( + names, + exts: Incomplete | None = ..., + dirs: Incomplete | None = ..., + include_samples: bool = ..., +): ... +def load_app_properties( + kwds: Incomplete | None = ..., + ini_file: Incomplete | None = ..., + ini_section: Incomplete | None = ..., + config_file: Incomplete | None = ..., + config_section: Incomplete | None = ..., + config_prefix: str = ..., +): ... class NicerConfigParser(ConfigParser): - filename = ... # type: Any + filename: Incomplete def __init__(self, filename, *args, **kw) -> None: ... - read_file = ... # type: Any + read_file: Incomplete def defaults(self): ... + class InterpolateWrapper: def __init__(self, original) -> None: ... def __getattr__(self, name): ... def before_get(self, parser, section, option, value, defaults): ... + +running_from_source: Incomplete + +def get_data_dir(properties): ... diff --git a/mypy-stubs/galaxy/util/renamed_temporary_file.pyi b/mypy-stubs/galaxy/util/renamed_temporary_file.pyi new file mode 100644 index 000000000..afdf5701d --- /dev/null +++ b/mypy-stubs/galaxy/util/renamed_temporary_file.pyi @@ -0,0 +1,9 @@ +from _typeshed import Incomplete + +class RenamedTemporaryFile: + tmpfile: Incomplete + final_path: Incomplete + def __init__(self, final_path, **kwargs) -> None: ... + def __getattr__(self, attr): ... + def __enter__(self): ... + def __exit__(self, exc_type, exc_val, exc_tb): ... diff --git a/mypy-stubs/galaxy/util/rules_dsl.pyi b/mypy-stubs/galaxy/util/rules_dsl.pyi new file mode 100644 index 000000000..d9f0fa1ec --- /dev/null +++ b/mypy-stubs/galaxy/util/rules_dsl.pyi @@ -0,0 +1,129 @@ +import abc +from _typeshed import Incomplete +from typing import List, Type + +def get_rules_specification(): ... +def apply_regex( + regex, + target, + data, + replacement: Incomplete | None = ..., + group_count: Incomplete | None = ..., +): ... + +class BaseRuleDefinition(metaclass=abc.ABCMeta): + @property + @abc.abstractmethod + def rule_type(self): ... + @abc.abstractmethod + def validate_rule(self, rule): ... + @abc.abstractmethod + def apply(self, rule, data, sources): ... + +class AddColumnMetadataRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddColumnGroupTagValueRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddColumnConcatenateRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddColumnBasenameRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddColumnRegexRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddColumnRownumRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddColumnValueRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddColumnSubstrRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class RemoveColumnsRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddFilterRegexRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddFilterCountRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddFilterEmptyRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddFilterMatchesRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class AddFilterCompareRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class SortRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class SwapColumnsRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +class SplitColumnsRuleDefinition(BaseRuleDefinition): + rule_type: str + def validate_rule(self, rule) -> None: ... + def apply(self, rule, data, sources): ... + +def flat_map(f, items): ... + +class RuleSet: + raw_rules: Incomplete + raw_mapping: Incomplete + def __init__(self, rule_set_as_dict) -> None: ... + @property + def rules(self): ... + def apply(self, data, sources): ... + @property + def has_errors(self): ... + @property + def mapping_as_dict(self): ... + @property + def identifier_columns(self): ... + @property + def collection_type(self): ... + @property + def display(self): ... + +RULES_DEFINITION_CLASSES: List[Type[BaseRuleDefinition]] +RULES_DEFINITIONS: Incomplete diff --git a/mypy-stubs/galaxy/util/sanitize_html.pyi b/mypy-stubs/galaxy/util/sanitize_html.pyi new file mode 100644 index 000000000..a68479c22 --- /dev/null +++ b/mypy-stubs/galaxy/util/sanitize_html.pyi @@ -0,0 +1,3 @@ +from galaxy.util import unicodify as unicodify + +def sanitize_html(htmlSource, allow_data_urls: bool = ...): ... diff --git a/mypy-stubs/galaxy/util/script.pyi b/mypy-stubs/galaxy/util/script.pyi new file mode 100644 index 000000000..7461cd81a --- /dev/null +++ b/mypy-stubs/galaxy/util/script.pyi @@ -0,0 +1,29 @@ +from _typeshed import Incomplete +from galaxy.util.properties import ( + find_config_file as find_config_file, + load_app_properties as load_app_properties, +) + +DESCRIPTION: Incomplete +ACTIONS: Incomplete +ARGUMENTS: Incomplete +DEFAULT_ACTION: Incomplete +ARG_HELP_CONFIG_FILE: str + +def main_factory( + description: Incomplete | None = ..., + actions: Incomplete | None = ..., + arguments: Incomplete | None = ..., + default_action: Incomplete | None = ..., +): ... +def main(argv: Incomplete | None = ...) -> None: ... +def app_properties_from_args( + args, legacy_config_override: Incomplete | None = ..., app: Incomplete | None = ... +): ... +def config_file_from_args( + args, legacy_config_override: Incomplete | None = ..., app: Incomplete | None = ... +): ... +def populate_config_args(parser) -> None: ... +def set_log_handler( + filename: Incomplete | None = ..., stream: Incomplete | None = ... +): ... diff --git a/mypy-stubs/galaxy/util/search.pyi b/mypy-stubs/galaxy/util/search.pyi new file mode 100644 index 000000000..5c3c4a7a0 --- /dev/null +++ b/mypy-stubs/galaxy/util/search.pyi @@ -0,0 +1 @@ +def parse_filters(search_term, filters): ... diff --git a/mypy-stubs/galaxy/util/simplegraph.pyi b/mypy-stubs/galaxy/util/simplegraph.pyi index b1aba1a6e..e057eb455 100644 --- a/mypy-stubs/galaxy/util/simplegraph.pyi +++ b/mypy-stubs/galaxy/util/simplegraph.pyi @@ -1,26 +1,26 @@ -# Stubs for galaxy.util.simplegraph (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from collections.abc import Generator -from typing import Any, Optional +from _typeshed import Incomplete class SimpleGraphNode: - index = ... # type: Any - data = ... # type: Any + index: Incomplete + data: Incomplete def __init__(self, index, **data) -> None: ... class SimpleGraphEdge: - source_index = ... # type: Any - target_index = ... # type: Any - data = ... # type: Any + source_index: Incomplete + target_index: Incomplete + data: Incomplete def __init__(self, source_index, target_index, **data) -> None: ... class SimpleGraph: - nodes = ... # type: Any - edges = ... # type: Any - def __init__(self, nodes: Optional[Any] = ..., edges: Optional[Any] = ...) -> None: ... + nodes: Incomplete + edges: Incomplete + def __init__( + self, nodes: Incomplete | None = ..., edges: Incomplete | None = ... + ) -> None: ... def add_node(self, node_id, **data): ... def add_edge(self, source_id, target_id, **data): ... - def gen_node_dicts(self): ... - def gen_edge_dicts(self): ... + def gen_node_dicts(self) -> Generator[Incomplete, None, None]: ... + def gen_edge_dicts(self) -> Generator[Incomplete, None, None]: ... def as_dict(self): ... diff --git a/mypy-stubs/galaxy/util/sleeper.pyi b/mypy-stubs/galaxy/util/sleeper.pyi index 600adf989..47b04fe80 100644 --- a/mypy-stubs/galaxy/util/sleeper.pyi +++ b/mypy-stubs/galaxy/util/sleeper.pyi @@ -1,11 +1,7 @@ -# Stubs for galaxy.util.sleeper (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any +from _typeshed import Incomplete class Sleeper: - condition = ... # type: Any + condition: Incomplete def __init__(self) -> None: ... - def sleep(self, seconds): ... - def wake(self): ... + def sleep(self, seconds) -> None: ... + def wake(self) -> None: ... diff --git a/mypy-stubs/galaxy/util/sockets.pyi b/mypy-stubs/galaxy/util/sockets.pyi index 100aba9a9..401c1d60a 100644 --- a/mypy-stubs/galaxy/util/sockets.pyi +++ b/mypy-stubs/galaxy/util/sockets.pyi @@ -1,7 +1,5 @@ -# Stubs for galaxy.util.sockets (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete +from galaxy.util import commands as commands -from typing import Any, Optional - -def unused_port(range: Optional[Any] = ...): ... +def get_ip(): ... +def unused_port(range: Incomplete | None = ...): ... diff --git a/mypy-stubs/galaxy/util/specs.pyi b/mypy-stubs/galaxy/util/specs.pyi index e3a95b9de..3727d149c 100644 --- a/mypy-stubs/galaxy/util/specs.pyi +++ b/mypy-stubs/galaxy/util/specs.pyi @@ -1,6 +1,4 @@ -# Stubs for galaxy.util.specs (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from galaxy import util as util def to_str_or_none(value): ... def to_bool_or_none(value): ... diff --git a/mypy-stubs/galaxy/util/sqlite.pyi b/mypy-stubs/galaxy/util/sqlite.pyi index 53c7eaeaf..d190ccb49 100644 --- a/mypy-stubs/galaxy/util/sqlite.pyi +++ b/mypy-stubs/galaxy/util/sqlite.pyi @@ -1,6 +1,2 @@ -# Stubs for galaxy.util.sqlite (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - def is_read_only_query(query): ... def connect(path): ... diff --git a/mypy-stubs/galaxy/util/submodules.pyi b/mypy-stubs/galaxy/util/submodules.pyi index dbae0501f..370654d1a 100644 --- a/mypy-stubs/galaxy/util/submodules.pyi +++ b/mypy-stubs/galaxy/util/submodules.pyi @@ -1,9 +1,5 @@ -# Stubs for galaxy.util.submodules (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete -from typing import Any +log: Incomplete -log = ... # type: Any - -def submodules(module): ... +def import_submodules(module, ordered: bool = ..., recursive: bool = ...): ... diff --git a/mypy-stubs/galaxy/util/template.pyi b/mypy-stubs/galaxy/util/template.pyi new file mode 100644 index 000000000..89012e9ac --- /dev/null +++ b/mypy-stubs/galaxy/util/template.pyi @@ -0,0 +1,22 @@ +from . import unicodify as unicodify +from Cheetah.Compiler import Compiler +from _typeshed import Incomplete + +refactoring_tool: Incomplete + +class FixedModuleCodeCompiler(Compiler): + module_code: Incomplete + def getModuleCode(self): ... + +def create_compiler_class(module_code): ... +def fill_template( + template_text, + context: Incomplete | None = ..., + retry: int = ..., + compiler_class=..., + first_exception: Incomplete | None = ..., + futurized: bool = ..., + python_template_version: str = ..., + **kwargs +): ... +def futurize_preprocessor(source): ... diff --git a/mypy-stubs/galaxy/util/tool_shed/__init__.pyi b/mypy-stubs/galaxy/util/tool_shed/__init__.pyi new file mode 100644 index 000000000..e69de29bb diff --git a/mypy-stubs/galaxy/util/tool_shed/common_util.pyi b/mypy-stubs/galaxy/util/tool_shed/common_util.pyi new file mode 100644 index 000000000..c972c1593 --- /dev/null +++ b/mypy-stubs/galaxy/util/tool_shed/common_util.pyi @@ -0,0 +1,41 @@ +from _typeshed import Incomplete +from galaxy import util as util +from galaxy.util.tool_shed import encoding_util as encoding_util, xml_util as xml_util + +log: Incomplete +REPOSITORY_OWNER: str +MIGRATE_DIR: Incomplete +TOOL_MIGRATION_SCRIPTS_DIR: Incomplete +TOOL_MIGRATION_VERSIONS_DIR: Incomplete + +def accumulate_tool_dependencies( + tool_shed_accessible, tool_dependencies, all_tool_dependencies +): ... +def check_for_missing_tools( + app, tool_panel_configs, latest_tool_migration_script_number +): ... +def check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict): ... +def generate_clone_url_for_installed_repository(app, repository): ... +def generate_clone_url_for_repository_in_tool_shed(user, repository): ... +def generate_clone_url_from_repo_info_tup(app, repo_info_tup): ... +def get_non_shed_tool_panel_configs(app): ... +def get_repository_dependencies( + app, tool_shed_url, repository_name, repository_owner, changeset_revision +): ... +def get_protocol_from_tool_shed_url(tool_shed_url): ... +def get_tool_dependencies( + app, tool_shed_url, repository_name, repository_owner, changeset_revision +): ... +def get_tool_shed_repository_ids(as_string: bool = ..., **kwd): ... +def get_tool_shed_url_from_tool_shed_registry(app, tool_shed): ... +def get_tool_shed_repository_url(app, tool_shed, owner, name): ... +def get_user_by_username(app, username): ... +def handle_galaxy_url(trans, **kwd): ... +def handle_tool_shed_url_protocol(app, shed_url): ... +def parse_repository_dependency_tuple( + repository_dependency_tuple, contains_error: bool = ... +): ... +def remove_port_from_tool_shed_url(tool_shed_url): ... +def remove_protocol_and_port_from_tool_shed_url(tool_shed_url): ... +def remove_protocol_and_user_from_clone_url(repository_clone_url): ... +def remove_protocol_from_tool_shed_url(tool_shed_url): ... diff --git a/mypy-stubs/galaxy/util/tool_shed/encoding_util.pyi b/mypy-stubs/galaxy/util/tool_shed/encoding_util.pyi new file mode 100644 index 000000000..9dfeeb282 --- /dev/null +++ b/mypy-stubs/galaxy/util/tool_shed/encoding_util.pyi @@ -0,0 +1,8 @@ +from galaxy.util import smart_str as smart_str, unicodify as unicodify +from galaxy.util.hash_util import hmac_new as hmac_new + +encoding_sep: str +encoding_sep2: str + +def tool_shed_decode(value): ... +def tool_shed_encode(val): ... diff --git a/mypy-stubs/galaxy/util/tool_shed/xml_util.pyi b/mypy-stubs/galaxy/util/tool_shed/xml_util.pyi new file mode 100644 index 000000000..e0958b4e3 --- /dev/null +++ b/mypy-stubs/galaxy/util/tool_shed/xml_util.pyi @@ -0,0 +1,14 @@ +from _typeshed import Incomplete +from galaxy.util import ( + etree as etree, + unicodify as unicodify, + xml_to_string as xml_to_string, +) + +log: Incomplete + +def create_and_write_tmp_file(elem): ... +def create_element( + tag, attributes: Incomplete | None = ..., sub_elements: Incomplete | None = ... +): ... +def parse_xml(file_name, check_exists: bool = ...): ... diff --git a/mypy-stubs/galaxy/util/tool_version.pyi b/mypy-stubs/galaxy/util/tool_version.pyi new file mode 100644 index 000000000..4c6e6b690 --- /dev/null +++ b/mypy-stubs/galaxy/util/tool_version.pyi @@ -0,0 +1 @@ +def remove_version_from_guid(guid): ... diff --git a/mypy-stubs/galaxy/util/topsort.pyi b/mypy-stubs/galaxy/util/topsort.pyi index 79396d98a..b6a74be87 100644 --- a/mypy-stubs/galaxy/util/topsort.pyi +++ b/mypy-stubs/galaxy/util/topsort.pyi @@ -1,12 +1,7 @@ -# Stubs for galaxy.util.topsort (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any -from galaxy.util.odict import odict as OrderedDict +from _typeshed import Incomplete class CycleError(Exception): - preds = ... # type: Any + preds: Incomplete def __init__(self, sofar, numpreds, succs) -> None: ... def get_partial(self): ... def get_pred_counts(self): ... diff --git a/mypy-stubs/galaxy/util/ucsc.pyi b/mypy-stubs/galaxy/util/ucsc.pyi new file mode 100644 index 000000000..b291ef8c6 --- /dev/null +++ b/mypy-stubs/galaxy/util/ucsc.pyi @@ -0,0 +1,12 @@ +from _typeshed import Incomplete + +class UCSCLimitException(Exception): ... + +class UCSCOutWrapper: + other: Incomplete + lookahead: Incomplete + def __init__(self, other) -> None: ... + def __iter__(self): ... + def __next__(self): ... + def next(self): ... + def readline(self): ... diff --git a/mypy-stubs/galaxy/util/validation.pyi b/mypy-stubs/galaxy/util/validation.pyi new file mode 100644 index 000000000..6bb0b7c35 --- /dev/null +++ b/mypy-stubs/galaxy/util/validation.pyi @@ -0,0 +1,6 @@ +from galaxy import exceptions as exceptions +from galaxy.util.sanitize_html import sanitize_html as sanitize_html + +def validate_and_sanitize_basestring(key, val): ... +def validate_and_sanitize_basestring_list(key, val): ... +def validate_boolean(key, val): ... diff --git a/mypy-stubs/galaxy/util/watcher.pyi b/mypy-stubs/galaxy/util/watcher.pyi new file mode 100644 index 000000000..b9d03f338 --- /dev/null +++ b/mypy-stubs/galaxy/util/watcher.pyi @@ -0,0 +1,58 @@ +from _typeshed import Incomplete +from galaxy.util.hash_util import md5_hash_file as md5_hash_file +from watchdog.events import FileSystemEventHandler + +can_watch: bool +FileSystemEventHandler = object +log: Incomplete + +def get_observer_class(config_name, config_value, default, monitor_what_str): ... +def get_watcher( + config, + config_name, + default: str = ..., + monitor_what_str: Incomplete | None = ..., + watcher_class: Incomplete | None = ..., + event_handler_class: Incomplete | None = ..., + **kwargs +): ... + +class BaseWatcher: + observer: Incomplete + observer_class: Incomplete + event_handler: Incomplete + monitored_dirs: Incomplete + def __init__(self, observer_class, even_handler_class, **kwargs) -> None: ... + def start(self) -> None: ... + def monitor(self, dir_path, recursive: bool = ...) -> None: ... + def resume_watching(self) -> None: ... + def shutdown(self) -> None: ... + +class Watcher(BaseWatcher): + path_hash: Incomplete + file_callbacks: Incomplete + dir_callbacks: Incomplete + ignore_extensions: Incomplete + require_extensions: Incomplete + event_handler: Incomplete + def __init__(self, observer_class, event_handler_class, **kwargs) -> None: ... + def watch_file(self, file_path, callback: Incomplete | None = ...) -> None: ... + def watch_directory( + self, + dir_path, + callback: Incomplete | None = ..., + recursive: bool = ..., + ignore_extensions: Incomplete | None = ..., + require_extensions: Incomplete | None = ..., + ) -> None: ... + +class EventHandler(FileSystemEventHandler): + watcher: Incomplete + def __init__(self, watcher) -> None: ... + def on_any_event(self, event) -> None: ... + +class NullWatcher: + def start(self) -> None: ... + def shutdown(self) -> None: ... + def watch_file(self, *args, **kwargs) -> None: ... + def watch_directory(self, *args, **kwargs) -> None: ... diff --git a/mypy-stubs/galaxy/util/web_compat.pyi b/mypy-stubs/galaxy/util/web_compat.pyi new file mode 100644 index 000000000..5feb5dd94 --- /dev/null +++ b/mypy-stubs/galaxy/util/web_compat.pyi @@ -0,0 +1 @@ +from galaxy.web_stack import register_postfork_function as register_postfork_function diff --git a/mypy-stubs/galaxy/util/xml_macros.pyi b/mypy-stubs/galaxy/util/xml_macros.pyi index 27607dfd1..98b85f006 100644 --- a/mypy-stubs/galaxy/util/xml_macros.pyi +++ b/mypy-stubs/galaxy/util/xml_macros.pyi @@ -1,18 +1,13 @@ -# Stubs for galaxy.util.xml_macros (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -REQUIRED_PARAMETER = ... # type: Any +from _typeshed import Incomplete +def load_with_references(path): ... def load(path): ... def template_macro_params(root): ... -def raw_tool_xml_tree(path): ... +def raw_xml_tree(path): ... def imported_macro_paths(root): ... class XmlMacroDef: - elements = ... # type: Any - parameters = ... # type: Any + elements: Incomplete + parameters: Incomplete def __init__(self, el) -> None: ... def macro_tokens(self, expand_el): ... diff --git a/mypy-stubs/galaxy/util/yaml_util.pyi b/mypy-stubs/galaxy/util/yaml_util.pyi new file mode 100644 index 000000000..a05e98ffa --- /dev/null +++ b/mypy-stubs/galaxy/util/yaml_util.pyi @@ -0,0 +1,11 @@ +from _typeshed import Incomplete +from yaml import SafeLoader + +log: Incomplete + +class OrderedLoader(SafeLoader): + def __init__(self, stream) -> None: ... + def include(self, node): ... + +def ordered_load(stream, merge_duplicate_keys: bool = ...): ... +def ordered_dump(data, stream: Incomplete | None = ..., Dumper=..., **kwds): ... diff --git a/mypy-stubs/galaxy/util/zipstream.pyi b/mypy-stubs/galaxy/util/zipstream.pyi new file mode 100644 index 000000000..53b5be5fb --- /dev/null +++ b/mypy-stubs/galaxy/util/zipstream.pyi @@ -0,0 +1,20 @@ +from .path import safe_walk as safe_walk +from _typeshed import Incomplete +from collections.abc import Generator + +class ZipstreamWrapper: + upstream_mod_zip: Incomplete + archive_name: Incomplete + archive: Incomplete + files: Incomplete + size: int + def __init__( + self, + archive_name: Incomplete | None = ..., + upstream_mod_zip: bool = ..., + upstream_gzip: bool = ..., + ) -> None: ... + def response(self) -> Generator[Incomplete, None, None]: ... + def get_headers(self): ... + def add_path(self, path, archive_name) -> None: ... + def write(self, path, archive_name: Incomplete | None = ...) -> None: ... diff --git a/mypy-stubs/graphviz/_compat.pyi b/mypy-stubs/graphviz/_compat.pyi index ce4b27131..4308df0ad 100644 --- a/mypy-stubs/graphviz/_compat.pyi +++ b/mypy-stubs/graphviz/_compat.pyi @@ -11,4 +11,5 @@ text_type = unicode def iteritems(d): ... def makedirs(name, mode: int = ..., exist_ok: bool = ...): ... def stderr_write_binary(data): ... + text_type = str diff --git a/mypy-stubs/graphviz/dot.pyi b/mypy-stubs/graphviz/dot.pyi index 1616346b4..01b81ea0f 100644 --- a/mypy-stubs/graphviz/dot.pyi +++ b/mypy-stubs/graphviz/dot.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from . import files from typing import Any, Optional +from . import files + class Dot(files.File): name: Any = ... comment: Any = ... @@ -13,15 +14,53 @@ class Dot(files.File): edge_attr: Any = ... body: Any = ... strict: Any = ... - def __init__(self, name: Optional[Any] = ..., comment: Optional[Any] = ..., filename: Optional[Any] = ..., directory: Optional[Any] = ..., format: Optional[Any] = ..., engine: Optional[Any] = ..., encoding: Any = ..., graph_attr: Optional[Any] = ..., node_attr: Optional[Any] = ..., edge_attr: Optional[Any] = ..., body: Optional[Any] = ..., strict: bool = ...) -> None: ... + def __init__( + self, + name: Optional[Any] = ..., + comment: Optional[Any] = ..., + filename: Optional[Any] = ..., + directory: Optional[Any] = ..., + format: Optional[Any] = ..., + engine: Optional[Any] = ..., + encoding: Any = ..., + graph_attr: Optional[Any] = ..., + node_attr: Optional[Any] = ..., + edge_attr: Optional[Any] = ..., + body: Optional[Any] = ..., + strict: bool = ..., + ) -> None: ... def clear(self, keep_attrs: bool = ...): ... def __iter__(self, subgraph: bool = ...): ... source: Any = ... - def node(self, name, label: Optional[Any] = ..., _attributes: Optional[Any] = ..., **attrs): ... - def edge(self, tail_name, head_name, label: Optional[Any] = ..., _attributes: Optional[Any] = ..., **attrs): ... + def node( + self, + name, + label: Optional[Any] = ..., + _attributes: Optional[Any] = ..., + **attrs + ): ... + def edge( + self, + tail_name, + head_name, + label: Optional[Any] = ..., + _attributes: Optional[Any] = ..., + **attrs + ): ... def edges(self, tail_head_iter): ... - def attr(self, kw: Optional[Any] = ..., _attributes: Optional[Any] = ..., **attrs): ... - def subgraph(self, graph: Optional[Any] = ..., name: Optional[Any] = ..., comment: Optional[Any] = ..., graph_attr: Optional[Any] = ..., node_attr: Optional[Any] = ..., edge_attr: Optional[Any] = ..., body: Optional[Any] = ...): ... + def attr( + self, kw: Optional[Any] = ..., _attributes: Optional[Any] = ..., **attrs + ): ... + def subgraph( + self, + graph: Optional[Any] = ..., + name: Optional[Any] = ..., + comment: Optional[Any] = ..., + graph_attr: Optional[Any] = ..., + node_attr: Optional[Any] = ..., + edge_attr: Optional[Any] = ..., + body: Optional[Any] = ..., + ): ... class SubgraphContext: parent: Any = ... diff --git a/mypy-stubs/graphviz/files.pyi b/mypy-stubs/graphviz/files.pyi index f8951640d..b0b8bdedc 100644 --- a/mypy-stubs/graphviz/files.pyi +++ b/mypy-stubs/graphviz/files.pyi @@ -25,16 +25,49 @@ class File(Base): format: Any = ... engine: Any = ... encoding: Any = ... - def __init__(self, filename: Optional[Any] = ..., directory: Optional[Any] = ..., format: Optional[Any] = ..., engine: Optional[Any] = ..., encoding: Any = ...) -> None: ... + def __init__( + self, + filename: Optional[Any] = ..., + directory: Optional[Any] = ..., + format: Optional[Any] = ..., + engine: Optional[Any] = ..., + encoding: Any = ..., + ) -> None: ... def pipe(self, format: Optional[Any] = ...): ... @property def filepath(self): ... def save(self, filename: Optional[Any] = ..., directory: Optional[Any] = ...): ... - def render(self, filename: Optional[Any] = ..., directory: Optional[Any] = ..., view: bool = ..., cleanup: bool = ...): ... - def view(self, filename: Optional[Any] = ..., directory: Optional[Any] = ..., cleanup: bool = ...): ... + def render( + self, + filename: Optional[Any] = ..., + directory: Optional[Any] = ..., + view: bool = ..., + cleanup: bool = ..., + ): ... + def view( + self, + filename: Optional[Any] = ..., + directory: Optional[Any] = ..., + cleanup: bool = ..., + ): ... class Source(File): @classmethod - def from_file(cls, filename, directory: Optional[Any] = ..., format: Optional[Any] = ..., engine: Optional[Any] = ..., encoding: Any = ...): ... + def from_file( + cls, + filename, + directory: Optional[Any] = ..., + format: Optional[Any] = ..., + engine: Optional[Any] = ..., + encoding: Any = ..., + ): ... source: Any = ... - def __init__(self, source, filename: Optional[Any] = ..., directory: Optional[Any] = ..., format: Optional[Any] = ..., engine: Optional[Any] = ..., encoding: Any = ...) -> None: ... + def __init__( + self, + source, + filename: Optional[Any] = ..., + directory: Optional[Any] = ..., + format: Optional[Any] = ..., + engine: Optional[Any] = ..., + encoding: Any = ..., + ) -> None: ... diff --git a/mypy-stubs/graphviz/lang.pyi b/mypy-stubs/graphviz/lang.pyi index 4429b02b4..9613c5c50 100644 --- a/mypy-stubs/graphviz/lang.pyi +++ b/mypy-stubs/graphviz/lang.pyi @@ -4,9 +4,19 @@ from typing import Any, Optional -def quote(identifier, html: Any = ..., valid_id: Any = ..., dot_keywords: Any = ...): ... +def quote( + identifier, html: Any = ..., valid_id: Any = ..., dot_keywords: Any = ... +): ... def quote_edge(identifier): ... -def a_list(label: Optional[Any] = ..., kwargs: Optional[Any] = ..., attributes: Optional[Any] = ...): ... -def attr_list(label: Optional[Any] = ..., kwargs: Optional[Any] = ..., attributes: Optional[Any] = ...): ... +def a_list( + label: Optional[Any] = ..., + kwargs: Optional[Any] = ..., + attributes: Optional[Any] = ..., +): ... +def attr_list( + label: Optional[Any] = ..., + kwargs: Optional[Any] = ..., + attributes: Optional[Any] = ..., +): ... class NoHtml: ... diff --git a/mypy-stubs/mistune.pyi b/mypy-stubs/mistune.pyi index 3c4279b0f..b4fe10213 100644 --- a/mypy-stubs/mistune.pyi +++ b/mypy-stubs/mistune.pyi @@ -10,187 +10,188 @@ from typing import ( Optional, Pattern, Sequence, - Text, Tuple, Type, ) -Tokens = List[Dict[Text, Any]] +Tokens = List[Dict[str, Any]] # There are too much levels of optional unions of lists of text in cell and align 385 and 396 lines in mistune -def escape(text: Text, quote: bool = ..., smart_amp: bool = ...) -> Text: ... +def escape(text: str, quote: bool = ..., smart_amp: bool = ...) -> str: ... class BlockGrammar: - def_links = ... # type: Pattern - def_footnotes = ... # type: Pattern - newline = ... # type: Pattern - block_code = ... # type: Pattern - fences = ... # type: Pattern - hrule = ... # type: Pattern - heading = ... # type: Pattern - lheading = ... # type: Pattern - block_quote = ... # type: Pattern - list_block = ... # type: Pattern - list_item = ... # type: Pattern - list_bullet = ... # type: Pattern - paragraph = ... # type: Pattern - block_html = ... # type: Pattern - table = ... # type: Pattern - nptable = ... # type: Pattern - text = ... # type: Pattern + def_links: Pattern[str] + def_footnotes: Pattern[str] + newline: Pattern[str] + block_code: Pattern[str] + fences: Pattern[str] + hrule: Pattern[str] + heading: Pattern[str] + lheading: Pattern[str] + block_quote: Pattern[str] + list_block: Pattern[str] + list_item: Pattern[str] + list_bullet: Pattern[str] + paragraph: Pattern[str] + block_html: Pattern[str] + table: Pattern[str] + nptable: Pattern[str] + text: Pattern[str] class BlockLexer: - grammar_class = ... # type: Type[BlockGrammar] - default_rules = ... # type: List[Text] - list_rules = ... # type: Tuple[Text] - footnote_rules = ... # type: Tuple[Text] - tokens = ... # type: Tokens - def_links = ... # type: Dict[Text, Dict[Text, Text]] - def_footnotes = ... # type: Dict[Text, int] + grammar_class: Type[BlockGrammar] + default_rules: List[str] + list_rules: Tuple[str] + footnote_rules: Tuple[str] + tokens: Tokens + def_links: Dict[str, Dict[str, str]] + def_footnotes: Dict[str, int] rules = ... # type: BlockGrammar - def __init__(self, rules: Optional[BlockGrammar] = ..., **kwargs) -> None: ... - def __call__(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Tokens: ... - def parse(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Tokens: ... - def parse_newline(self, m: Match) -> None: ... - def parse_block_code(self, m: Match) -> None: ... - def parse_fences(self, m: Match) -> None: ... - def parse_heading(self, m: Match) -> None: ... - def parse_lheading(self, m: Match) -> None: ... - def parse_hrule(self, m: Match) -> None: ... - def parse_list_block(self, m: Match) -> None: ... - def parse_block_quote(self, m: Match) -> None: ... - def parse_def_links(self, m: Match) -> None: ... - def parse_def_footnotes(self, m: Match) -> None: ... - def parse_table(self, m: Match) -> None: ... - def parse_nptable(self, m: Match) -> None: ... - def parse_block_html(self, m: Match) -> None: ... - def parse_paragraph(self, m: Match) -> None: ... - def parse_text(self, m: Match) -> None: ... + def __init__(self, rules: Optional[BlockGrammar] = ..., **kwargs: Any) -> None: ... + def __call__(self, text: str, rules: Optional[Sequence[str]] = ...) -> Tokens: ... + def parse(self, text: str, rules: Optional[Sequence[str]] = ...) -> Tokens: ... + def parse_newline(self, m: Match[str]) -> None: ... + def parse_block_code(self, m: Match[str]) -> None: ... + def parse_fences(self, m: Match[str]) -> None: ... + def parse_heading(self, m: Match[str]) -> None: ... + def parse_lheading(self, m: Match[str]) -> None: ... + def parse_hrule(self, m: Match[str]) -> None: ... + def parse_list_block(self, m: Match[str]) -> None: ... + def parse_block_quote(self, m: Match[str]) -> None: ... + def parse_def_links(self, m: Match[str]) -> None: ... + def parse_def_footnotes(self, m: Match[str]) -> None: ... + def parse_table(self, m: Match[str]) -> None: ... + def parse_nptable(self, m: Match[str]) -> None: ... + def parse_block_html(self, m: Match[str]) -> None: ... + def parse_paragraph(self, m: Match[str]) -> None: ... + def parse_text(self, m: Match[str]) -> None: ... class InlineGrammar: - escape = ... # type: Pattern - inline_html = ... # type: Pattern - autolink = ... # type: Pattern - link = ... # type: Pattern - reflink = ... # type: Pattern - nolink = ... # type: Pattern - url = ... # type: Pattern - double_emphasis = ... # type: Pattern - emphasis = ... # type: Pattern - code = ... # type: Pattern - linebreak = ... # type: Pattern - strikethrough = ... # type: Pattern - footnote = ... # type: Pattern - text = ... # type: Pattern + escape: Pattern[str] + inline_html: Pattern[str] + autolink: Pattern[str] + link: Pattern[str] + reflink: Pattern[str] + nolink: Pattern[str] + url: Pattern[str] + double_emphasis: Pattern[str] + emphasis: Pattern[str] + code: Pattern[str] + linebreak: Pattern[str] + strikethrough: Pattern[str] + footnote: Pattern[str] + text: Pattern[str] def hard_wrap(self) -> None: ... class InlineLexer: - grammar_class = ... # type: Type[InlineGrammar] - default_rules = ... # type: List[Text] - inline_html_rules = ... # type: List[Text] - renderer = ... # type: Renderer - links = ... # type: Dict[Any, Dict] - footnotes = ... # type: Dict[Text, int] - footnote_index = ... # type: int - _in_link = ... # type: bool - _in_footnote = ... # type: bool - _parse_inline_html = ... # type: bool - rules = ... # type: InlineGrammar + grammar_class: Type[InlineGrammar] + default_rules: List[str] + inline_html_rules: List[str] + renderer: Renderer + links: Dict[str, Dict[str, str]] + footnotes: Dict[str, int] + footnote_index: int + _in_link: bool + _in_footnote: bool + _parse_inline_html: bool + rules: InlineGrammar def __init__( - self, renderer: Renderer, rules: Optional[InlineGrammar] = ..., **kwargs + self, renderer: Renderer, rules: Optional[InlineGrammar] = ..., **kwargs: Any ) -> None: ... - def __call__(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Text: ... + def __call__(self, text: str, rules: Optional[Sequence[str]] = ...) -> str: ... def setup( - self, links: Optional[Dict[Any, Dict]], footnotes: Optional[Dict[Text, int]] + self, + links: Optional[Dict[str, Dict[str, str]]], + footnotes: Optional[Dict[str, int]], ) -> None: ... - line_match = ... # type: Match - line_started = ... # type: bool - def output(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Text: ... - def output_escape(self, m: Match) -> Text: ... - def output_autolink(self, m: Match) -> Text: ... - def output_url(self, m: Match) -> Text: ... - def output_inline_html(self, m: Match) -> Text: ... - def output_footnote(self, m: Match) -> Optional[Text]: ... - def output_link(self, m: Match) -> Text: ... - def output_reflink(self, m: Match) -> Optional[Text]: ... - def output_nolink(self, m: Match) -> Optional[Text]: ... - def output_double_emphasis(self, m: Match) -> Text: ... - def output_emphasis(self, m: Match) -> Text: ... - def output_code(self, m: Match) -> Text: ... - def output_linebreak(self, m: Match) -> Text: ... - def output_strikethrough(self, m: Match) -> Text: ... - def output_text(self, m: Match) -> Text: ... + line_match: Match[str] + line_started: bool + def output(self, text: str, rules: Optional[Sequence[str]] = ...) -> str: ... + def output_escape(self, m: Match[str]) -> str: ... + def output_autolink(self, m: Match[str]) -> str: ... + def output_url(self, m: Match[str]) -> str: ... + def output_inline_html(self, m: Match[str]) -> str: ... + def output_footnote(self, m: Match[str]) -> Optional[str]: ... + def output_link(self, m: Match[str]) -> str: ... + def output_reflink(self, m: Match[str]) -> Optional[str]: ... + def output_nolink(self, m: Match[str]) -> Optional[str]: ... + def output_double_emphasis(self, m: Match[str]) -> str: ... + def output_emphasis(self, m: Match[str]) -> str: ... + def output_code(self, m: Match[str]) -> str: ... + def output_linebreak(self, m: Match[str]) -> str: ... + def output_strikethrough(self, m: Match[str]) -> str: ... + def output_text(self, m: Match[str]) -> str: ... class Renderer: - options = ... # type: Dict - def __init__(self, **kwargs) -> None: ... - def placeholder(self) -> Text: ... + options: Dict[str, str] + def __init__(self, **kwargs: Any) -> None: ... + def placeholder(self) -> str: ... def block_code( - self, code: Text, lang: Any = ... - ) -> Text: ... # It seems that lang should be string, however other types are valid as well - def block_quote(self, text: Text) -> Text: ... - def block_html(self, html: Text) -> Text: ... - def header(self, text: Text, level: int, raw: Optional[Text] = ...) -> Text: ... - def hrule(self) -> Text: ... + self, code: str, lang: Any = ... + ) -> str: ... # It seems that lang should be string, however other types are valid as well + def block_quote(self, text: str) -> str: ... + def block_html(self, html: str) -> str: ... + def header(self, text: str, level: int, raw: Optional[str] = ...) -> str: ... + def hrule(self) -> str: ... def list( self, body: Any, ordered: bool = ... - ) -> Text: ... # body - same reason as for lang above, and for other Any in this class - def list_item(self, text: Any) -> Text: ... - def paragraph(self, text: Text) -> Text: ... - def table(self, header: Any, body: Any) -> Text: ... - def table_row(self, content: Any) -> Text: ... - def table_cell(self, content: Any, **flags) -> Text: ... - def double_emphasis(self, text: Any) -> Text: ... - def emphasis(self, text: Any) -> Text: ... - def codespan(self, text: Text) -> Text: ... - def linebreak(self) -> Text: ... - def strikethrough(self, text: Any) -> Text: ... - def text(self, text: Any) -> Text: ... - def escape(self, text: Any) -> Text: ... - def autolink(self, link: Any, is_email: bool = ...) -> Text: ... - def link(self, link: Any, title: Any, text: Any) -> Text: ... - def image(self, src: Any, title: Any, text: Any) -> Text: ... - def inline_html(self, html: Any) -> Text: ... - def newline(self) -> Text: ... - def footnote_ref(self, key: Any, index: int) -> Text: ... - def footnote_item(self, key: Any, text: Text) -> Text: ... - def footnotes(self, text: Any) -> Text: ... + ) -> str: ... # body - same reason as for lang above, and for other Any in this class + def list_item(self, text: Any) -> str: ... + def paragraph(self, text: str) -> str: ... + def table(self, header: Any, body: Any) -> str: ... + def table_row(self, content: Any) -> str: ... + def table_cell(self, content: Any, **flags: Dict[str, Any]) -> str: ... + def double_emphasis(self, text: Any) -> str: ... + def emphasis(self, text: Any) -> str: ... + def codespan(self, text: str) -> str: ... + def linebreak(self) -> str: ... + def strikethrough(self, text: Any) -> str: ... + def text(self, text: Any) -> str: ... + def escape(self, text: Any) -> str: ... + def autolink(self, link: Any, is_email: bool = ...) -> str: ... + def link(self, link: Any, title: Any, text: Any) -> str: ... + def image(self, src: Any, title: Any, text: Any) -> str: ... + def inline_html(self, html: Any) -> str: ... + def newline(self) -> str: ... + def footnote_ref(self, key: Any, index: int) -> str: ... + def footnote_item(self, key: Any, text: str) -> str: ... + def footnotes(self, text: Any) -> str: ... class Markdown: renderer = ... # type: Renderer inline = ... # type: InlineLexer block = ... # type: BlockLexer - footnotes = ... # type: List[Dict[Text, Any]] + footnotes = ... # type: List[Dict[str, Any]] tokens = ... # type: Tokens def __init__( self, renderer: Optional[Renderer] = ..., inline: Optional[InlineLexer] = ..., block: Optional[BlockLexer] = ..., - **kwargs + **kwargs: Any ) -> None: ... - def __call__(self, text: Text) -> Text: ... - def render(self, text: Text) -> Text: ... - def parse(self, text: Text) -> Text: ... - token = ... # type: Dict[Text, Any] - def pop(self) -> Optional[Dict[Text, Any]]: ... - def peek(self) -> Optional[Dict[Text, Any]]: ... - def output(self, text: Text, rules: Optional[Sequence[Text]] = ...): ... - def tok(self) -> Text: ... - def tok_text(self) -> Text: ... - def output_newline(self) -> Text: ... - def output_hrule(self) -> Text: ... - def output_heading(self) -> Text: ... - def output_code(self) -> Text: ... - def output_table(self) -> Text: ... - def output_block_quote(self) -> Text: ... - def output_list(self) -> Text: ... - def output_list_item(self) -> Text: ... - def output_loose_item(self) -> Text: ... - def output_footnote(self) -> Text: ... - def output_close_html(self) -> Text: ... - def output_open_html(self) -> Text: ... - def output_paragraph(self) -> Text: ... - def output_text(self) -> Text: ... + def __call__(self, text: str) -> str: ... + def render(self, text: str) -> str: ... + def parse(self, text: str) -> str: ... + token = ... # type: Dict[str, Any] + def pop(self) -> Optional[Dict[str, Any]]: ... + def peek(self) -> Optional[Dict[str, Any]]: ... + def output(self, text: str, rules: Optional[Sequence[str]] = ...) -> str: ... + def tok(self) -> str: ... + def tok_text(self) -> str: ... + def output_newline(self) -> str: ... + def output_hrule(self) -> str: ... + def output_heading(self) -> str: ... + def output_code(self) -> str: ... + def output_table(self) -> str: ... + def output_block_quote(self) -> str: ... + def output_list(self) -> str: ... + def output_list_item(self) -> str: ... + def output_loose_item(self) -> str: ... + def output_footnote(self) -> str: ... + def output_close_html(self) -> str: ... + def output_open_html(self) -> str: ... + def output_paragraph(self) -> str: ... + def output_text(self) -> str: ... -def markdown(text: Text, escape: bool = ..., **kwargs) -> Text: ... +def markdown(text: str, escape: bool = ..., **kwargs: Any) -> str: ... diff --git a/mypy-stubs/networkx/algorithms/__init__.pyi b/mypy-stubs/networkx/algorithms/__init__.pyi index bf5ef35b0..d4579ee00 100644 --- a/mypy-stubs/networkx/algorithms/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/__init__.pyi @@ -5,18 +5,18 @@ from networkx.algorithms.assortativity import * from networkx.algorithms.boundary import * from networkx.algorithms.bridges import * -from networkx.algorithms.chains import * from networkx.algorithms.centrality import * +from networkx.algorithms.chains import * from networkx.algorithms.chordal import * -from networkx.algorithms.cluster import * from networkx.algorithms.clique import * +from networkx.algorithms.cluster import * +from networkx.algorithms.coloring import * from networkx.algorithms.communicability_alg import * from networkx.algorithms.components import * -from networkx.algorithms.coloring import * from networkx.algorithms.core import * from networkx.algorithms.covering import * -from networkx.algorithms.cycles import * from networkx.algorithms.cuts import * +from networkx.algorithms.cycles import * from networkx.algorithms.dag import * from networkx.algorithms.distance_measures import * from networkx.algorithms.distance_regular import * @@ -27,10 +27,10 @@ from networkx.algorithms.euler import * from networkx.algorithms.graphical import * from networkx.algorithms.hierarchy import * from networkx.algorithms.hybrid import * +from networkx.algorithms.isolate import * from networkx.algorithms.link_analysis import * from networkx.algorithms.link_prediction import * from networkx.algorithms.lowest_common_ancestors import * -from networkx.algorithms.isolate import * from networkx.algorithms.matching import * from networkx.algorithms.minors import * from networkx.algorithms.mis import * @@ -42,13 +42,13 @@ from networkx.algorithms.similarity import * from networkx.algorithms.simple_paths import * from networkx.algorithms.smetric import * from networkx.algorithms.structuralholes import * -from networkx.algorithms.triads import * from networkx.algorithms.swap import * from networkx.algorithms.traversal import * -from networkx.algorithms.vitality import * -from networkx.algorithms.voronoi import * -from networkx.algorithms.wiener import * from networkx.algorithms.tree.coding import * +from networkx.algorithms.tree.mst import * from networkx.algorithms.tree.operations import * from networkx.algorithms.tree.recognition import * -from networkx.algorithms.tree.mst import * +from networkx.algorithms.triads import * +from networkx.algorithms.vitality import * +from networkx.algorithms.voronoi import * +from networkx.algorithms.wiener import * diff --git a/mypy-stubs/networkx/algorithms/approximation/__init__.pyi b/mypy-stubs/networkx/algorithms/approximation/__init__.pyi index b320de64d..24da5b4c0 100644 --- a/mypy-stubs/networkx/algorithms/approximation/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/approximation/__init__.pyi @@ -2,12 +2,12 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.approximation.clustering_coefficient import * from networkx.algorithms.approximation.clique import * +from networkx.algorithms.approximation.clustering_coefficient import * from networkx.algorithms.approximation.connectivity import * from networkx.algorithms.approximation.dominating_set import * -from networkx.algorithms.approximation.kcomponents import * from networkx.algorithms.approximation.independent_set import * +from networkx.algorithms.approximation.kcomponents import * from networkx.algorithms.approximation.matching import * from networkx.algorithms.approximation.ramsey import * from networkx.algorithms.approximation.steinertree import * diff --git a/mypy-stubs/networkx/algorithms/approximation/connectivity.pyi b/mypy-stubs/networkx/algorithms/approximation/connectivity.pyi index d10a99c6e..e7723ca0f 100644 --- a/mypy-stubs/networkx/algorithms/approximation/connectivity.pyi +++ b/mypy-stubs/networkx/algorithms/approximation/connectivity.pyi @@ -6,4 +6,6 @@ from typing import Any, Optional def local_node_connectivity(G, source, target, cutoff: Optional[Any] = ...): ... def node_connectivity(G, s: Optional[Any] = ..., t: Optional[Any] = ...): ... -def all_pairs_node_connectivity(G, nbunch: Optional[Any] = ..., cutoff: Optional[Any] = ...): ... +def all_pairs_node_connectivity( + G, nbunch: Optional[Any] = ..., cutoff: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/approximation/kcomponents.pyi b/mypy-stubs/networkx/algorithms/approximation/kcomponents.pyi index 61b5efe0a..0fb63e819 100644 --- a/mypy-stubs/networkx/algorithms/approximation/kcomponents.pyi +++ b/mypy-stubs/networkx/algorithms/approximation/kcomponents.pyi @@ -2,10 +2,11 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -import networkx as nx from collections import Mapping from typing import Any +import networkx as nx + def k_components(G, min_density: float = ...): ... class _AntiGraph(nx.Graph): @@ -14,22 +15,27 @@ class _AntiGraph(nx.Graph): edge_attr_dict_factory: Any = ... def __getitem__(self, n): ... def neighbors(self, n): ... + class AntiAtlasView(Mapping): def __init__(self, graph, node) -> None: ... def __len__(self): ... def __iter__(self): ... def __getitem__(self, nbr): ... + class AntiAdjacencyView(AntiAtlasView): def __init__(self, graph) -> None: ... def __len__(self): ... def __iter__(self): ... def __getitem__(self, node): ... + @property def adj(self): ... def subgraph(self, nodes): ... + class AntiDegreeView(nx.reportviews.DegreeView): def __iter__(self): ... def __getitem__(self, n): ... + @property def degree(self): ... def adjacency(self): ... diff --git a/mypy-stubs/networkx/algorithms/assortativity/connectivity.pyi b/mypy-stubs/networkx/algorithms/assortativity/connectivity.pyi index 7f3ea3d7a..c9bf01116 100644 --- a/mypy-stubs/networkx/algorithms/assortativity/connectivity.pyi +++ b/mypy-stubs/networkx/algorithms/assortativity/connectivity.pyi @@ -4,5 +4,12 @@ from typing import Any, Optional -def average_degree_connectivity(G, source: str = ..., target: str = ..., nodes: Optional[Any] = ..., weight: Optional[Any] = ...): ... +def average_degree_connectivity( + G, + source: str = ..., + target: str = ..., + nodes: Optional[Any] = ..., + weight: Optional[Any] = ..., +): ... + k_nearest_neighbors = average_degree_connectivity diff --git a/mypy-stubs/networkx/algorithms/assortativity/correlation.pyi b/mypy-stubs/networkx/algorithms/assortativity/correlation.pyi index 23a19a4d9..35774b514 100644 --- a/mypy-stubs/networkx/algorithms/assortativity/correlation.pyi +++ b/mypy-stubs/networkx/algorithms/assortativity/correlation.pyi @@ -4,7 +4,19 @@ from typing import Any, Optional -def degree_assortativity_coefficient(G, x: str = ..., y: str = ..., weight: Optional[Any] = ..., nodes: Optional[Any] = ...): ... -def degree_pearson_correlation_coefficient(G, x: str = ..., y: str = ..., weight: Optional[Any] = ..., nodes: Optional[Any] = ...): ... +def degree_assortativity_coefficient( + G, + x: str = ..., + y: str = ..., + weight: Optional[Any] = ..., + nodes: Optional[Any] = ..., +): ... +def degree_pearson_correlation_coefficient( + G, + x: str = ..., + y: str = ..., + weight: Optional[Any] = ..., + nodes: Optional[Any] = ..., +): ... def attribute_assortativity_coefficient(G, attribute, nodes: Optional[Any] = ...): ... def numeric_assortativity_coefficient(G, attribute, nodes: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/assortativity/mixing.pyi b/mypy-stubs/networkx/algorithms/assortativity/mixing.pyi index c7cd71dfa..2b938b7ba 100644 --- a/mypy-stubs/networkx/algorithms/assortativity/mixing.pyi +++ b/mypy-stubs/networkx/algorithms/assortativity/mixing.pyi @@ -4,9 +4,33 @@ from typing import Any, Optional -def attribute_mixing_dict(G, attribute, nodes: Optional[Any] = ..., normalized: bool = ...): ... -def attribute_mixing_matrix(G, attribute, nodes: Optional[Any] = ..., mapping: Optional[Any] = ..., normalized: bool = ...): ... -def degree_mixing_dict(G, x: str = ..., y: str = ..., weight: Optional[Any] = ..., nodes: Optional[Any] = ..., normalized: bool = ...): ... -def degree_mixing_matrix(G, x: str = ..., y: str = ..., weight: Optional[Any] = ..., nodes: Optional[Any] = ..., normalized: bool = ...): ... -def numeric_mixing_matrix(G, attribute, nodes: Optional[Any] = ..., normalized: bool = ...): ... +def attribute_mixing_dict( + G, attribute, nodes: Optional[Any] = ..., normalized: bool = ... +): ... +def attribute_mixing_matrix( + G, + attribute, + nodes: Optional[Any] = ..., + mapping: Optional[Any] = ..., + normalized: bool = ..., +): ... +def degree_mixing_dict( + G, + x: str = ..., + y: str = ..., + weight: Optional[Any] = ..., + nodes: Optional[Any] = ..., + normalized: bool = ..., +): ... +def degree_mixing_matrix( + G, + x: str = ..., + y: str = ..., + weight: Optional[Any] = ..., + nodes: Optional[Any] = ..., + normalized: bool = ..., +): ... +def numeric_mixing_matrix( + G, attribute, nodes: Optional[Any] = ..., normalized: bool = ... +): ... def mixing_dict(xy, normalized: bool = ...): ... diff --git a/mypy-stubs/networkx/algorithms/assortativity/neighbor_degree.pyi b/mypy-stubs/networkx/algorithms/assortativity/neighbor_degree.pyi index 21ddd0b30..212c18e66 100644 --- a/mypy-stubs/networkx/algorithms/assortativity/neighbor_degree.pyi +++ b/mypy-stubs/networkx/algorithms/assortativity/neighbor_degree.pyi @@ -4,4 +4,10 @@ from typing import Any, Optional -def average_neighbor_degree(G, source: str = ..., target: str = ..., nodes: Optional[Any] = ..., weight: Optional[Any] = ...): ... +def average_neighbor_degree( + G, + source: str = ..., + target: str = ..., + nodes: Optional[Any] = ..., + weight: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/assortativity/pairs.pyi b/mypy-stubs/networkx/algorithms/assortativity/pairs.pyi index 701f6d989..d5c9cd8d7 100644 --- a/mypy-stubs/networkx/algorithms/assortativity/pairs.pyi +++ b/mypy-stubs/networkx/algorithms/assortativity/pairs.pyi @@ -5,4 +5,10 @@ from typing import Any, Optional def node_attribute_xy(G, attribute, nodes: Optional[Any] = ...): ... -def node_degree_xy(G, x: str = ..., y: str = ..., weight: Optional[Any] = ..., nodes: Optional[Any] = ...): ... +def node_degree_xy( + G, + x: str = ..., + y: str = ..., + weight: Optional[Any] = ..., + nodes: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/bipartite/__init__.pyi b/mypy-stubs/networkx/algorithms/bipartite/__init__.pyi index 7dfa994f4..34c5b33f9 100644 --- a/mypy-stubs/networkx/algorithms/bipartite/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/bipartite/__init__.pyi @@ -7,9 +7,9 @@ from networkx.algorithms.bipartite.centrality import * from networkx.algorithms.bipartite.cluster import * from networkx.algorithms.bipartite.covering import * from networkx.algorithms.bipartite.edgelist import * +from networkx.algorithms.bipartite.generators import * from networkx.algorithms.bipartite.matching import * from networkx.algorithms.bipartite.matrix import * from networkx.algorithms.bipartite.projection import * from networkx.algorithms.bipartite.redundancy import * from networkx.algorithms.bipartite.spectral import * -from networkx.algorithms.bipartite.generators import * diff --git a/mypy-stubs/networkx/algorithms/bipartite/cluster.pyi b/mypy-stubs/networkx/algorithms/bipartite/cluster.pyi index c420e043b..ec4796faf 100644 --- a/mypy-stubs/networkx/algorithms/bipartite/cluster.pyi +++ b/mypy-stubs/networkx/algorithms/bipartite/cluster.pyi @@ -5,6 +5,7 @@ from typing import Any, Optional def latapy_clustering(G, nodes: Optional[Any] = ..., mode: str = ...): ... + clustering = latapy_clustering def average_clustering(G, nodes: Optional[Any] = ..., mode: str = ...): ... diff --git a/mypy-stubs/networkx/algorithms/bipartite/edgelist.pyi b/mypy-stubs/networkx/algorithms/bipartite/edgelist.pyi index 33f4aa4e7..c3ee3d82d 100644 --- a/mypy-stubs/networkx/algorithms/bipartite/edgelist.pyi +++ b/mypy-stubs/networkx/algorithms/bipartite/edgelist.pyi @@ -4,7 +4,30 @@ from typing import Any, Optional -def write_edgelist(G, path, comments: str = ..., delimiter: str = ..., data: bool = ..., encoding: str = ...): ... +def write_edgelist( + G, + path, + comments: str = ..., + delimiter: str = ..., + data: bool = ..., + encoding: str = ..., +): ... def generate_edgelist(G, delimiter: str = ..., data: bool = ...): ... -def parse_edgelist(lines, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., data: bool = ...): ... -def read_edgelist(path, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., data: bool = ..., edgetype: Optional[Any] = ..., encoding: str = ...): ... +def parse_edgelist( + lines, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + data: bool = ..., +): ... +def read_edgelist( + path, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + data: bool = ..., + edgetype: Optional[Any] = ..., + encoding: str = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/bipartite/generators.pyi b/mypy-stubs/networkx/algorithms/bipartite/generators.pyi index f8dd9ba2f..e1a85a260 100644 --- a/mypy-stubs/networkx/algorithms/bipartite/generators.pyi +++ b/mypy-stubs/networkx/algorithms/bipartite/generators.pyi @@ -5,10 +5,14 @@ from typing import Any, Optional def complete_bipartite_graph(n1, n2, create_using: Optional[Any] = ...): ... -def configuration_model(aseq, bseq, create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... +def configuration_model( + aseq, bseq, create_using: Optional[Any] = ..., seed: Optional[Any] = ... +): ... def havel_hakimi_graph(aseq, bseq, create_using: Optional[Any] = ...): ... def reverse_havel_hakimi_graph(aseq, bseq, create_using: Optional[Any] = ...): ... def alternating_havel_hakimi_graph(aseq, bseq, create_using: Optional[Any] = ...): ... -def preferential_attachment_graph(aseq, p, create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... +def preferential_attachment_graph( + aseq, p, create_using: Optional[Any] = ..., seed: Optional[Any] = ... +): ... def random_graph(n, m, p, seed: Optional[Any] = ..., directed: bool = ...): ... def gnmk_random_graph(n, m, k, seed: Optional[Any] = ..., directed: bool = ...): ... diff --git a/mypy-stubs/networkx/algorithms/bipartite/matching.pyi b/mypy-stubs/networkx/algorithms/bipartite/matching.pyi index dd6a81b68..8652e20e6 100644 --- a/mypy-stubs/networkx/algorithms/bipartite/matching.pyi +++ b/mypy-stubs/networkx/algorithms/bipartite/matching.pyi @@ -7,4 +7,5 @@ from typing import Any, Optional def hopcroft_karp_matching(G, top_nodes: Optional[Any] = ...): ... def eppstein_matching(G, top_nodes: Optional[Any] = ...): ... def to_vertex_cover(G, matching, top_nodes: Optional[Any] = ...): ... + maximum_matching = hopcroft_karp_matching diff --git a/mypy-stubs/networkx/algorithms/bipartite/matrix.pyi b/mypy-stubs/networkx/algorithms/bipartite/matrix.pyi index c673f7608..56588c7b1 100644 --- a/mypy-stubs/networkx/algorithms/bipartite/matrix.pyi +++ b/mypy-stubs/networkx/algorithms/bipartite/matrix.pyi @@ -4,5 +4,14 @@ from typing import Any, Optional -def biadjacency_matrix(G, row_order, column_order: Optional[Any] = ..., dtype: Optional[Any] = ..., weight: str = ..., format: str = ...): ... -def from_biadjacency_matrix(A, create_using: Optional[Any] = ..., edge_attribute: str = ...): ... +def biadjacency_matrix( + G, + row_order, + column_order: Optional[Any] = ..., + dtype: Optional[Any] = ..., + weight: str = ..., + format: str = ..., +): ... +def from_biadjacency_matrix( + A, create_using: Optional[Any] = ..., edge_attribute: str = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/bipartite/projection.pyi b/mypy-stubs/networkx/algorithms/bipartite/projection.pyi index f5b72a9f0..9f7825752 100644 --- a/mypy-stubs/networkx/algorithms/bipartite/projection.pyi +++ b/mypy-stubs/networkx/algorithms/bipartite/projection.pyi @@ -8,5 +8,7 @@ def projected_graph(B, nodes, multigraph: bool = ...): ... def weighted_projected_graph(B, nodes, ratio: bool = ...): ... def collaboration_weighted_projected_graph(B, nodes): ... def overlap_weighted_projected_graph(B, nodes, jaccard: bool = ...): ... -def generic_weighted_projected_graph(B, nodes, weight_function: Optional[Any] = ...): ... +def generic_weighted_projected_graph( + B, nodes, weight_function: Optional[Any] = ... +): ... def project(B, nodes, create_using: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/boundary.pyi b/mypy-stubs/networkx/algorithms/boundary.pyi index 679e9977a..44991875c 100644 --- a/mypy-stubs/networkx/algorithms/boundary.pyi +++ b/mypy-stubs/networkx/algorithms/boundary.pyi @@ -4,5 +4,12 @@ from typing import Any, Optional -def edge_boundary(G, nbunch1, nbunch2: Optional[Any] = ..., data: bool = ..., keys: bool = ..., default: Optional[Any] = ...): ... +def edge_boundary( + G, + nbunch1, + nbunch2: Optional[Any] = ..., + data: bool = ..., + keys: bool = ..., + default: Optional[Any] = ..., +): ... def node_boundary(G, nbunch1, nbunch2: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/betweenness.pyi b/mypy-stubs/networkx/algorithms/centrality/betweenness.pyi index 5441ed1f1..5a4be1a4a 100644 --- a/mypy-stubs/networkx/algorithms/centrality/betweenness.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/betweenness.pyi @@ -4,6 +4,25 @@ from typing import Any, Optional -def betweenness_centrality(G, k: Optional[Any] = ..., normalized: bool = ..., weight: Optional[Any] = ..., endpoints: bool = ..., seed: Optional[Any] = ...): ... -def edge_betweenness_centrality(G, k: Optional[Any] = ..., normalized: bool = ..., weight: Optional[Any] = ..., seed: Optional[Any] = ...): ... -def edge_betweenness(G, k: Optional[Any] = ..., normalized: bool = ..., weight: Optional[Any] = ..., seed: Optional[Any] = ...): ... +def betweenness_centrality( + G, + k: Optional[Any] = ..., + normalized: bool = ..., + weight: Optional[Any] = ..., + endpoints: bool = ..., + seed: Optional[Any] = ..., +): ... +def edge_betweenness_centrality( + G, + k: Optional[Any] = ..., + normalized: bool = ..., + weight: Optional[Any] = ..., + seed: Optional[Any] = ..., +): ... +def edge_betweenness( + G, + k: Optional[Any] = ..., + normalized: bool = ..., + weight: Optional[Any] = ..., + seed: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/betweenness_subset.pyi b/mypy-stubs/networkx/algorithms/centrality/betweenness_subset.pyi index 93aa14707..fa6316801 100644 --- a/mypy-stubs/networkx/algorithms/centrality/betweenness_subset.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/betweenness_subset.pyi @@ -4,6 +4,12 @@ from typing import Any, Optional -def betweenness_centrality_subset(G, sources, targets, normalized: bool = ..., weight: Optional[Any] = ...): ... -def edge_betweenness_centrality_subset(G, sources, targets, normalized: bool = ..., weight: Optional[Any] = ...): ... -def betweenness_centrality_source(G, normalized: bool = ..., weight: Optional[Any] = ..., sources: Optional[Any] = ...): ... +def betweenness_centrality_subset( + G, sources, targets, normalized: bool = ..., weight: Optional[Any] = ... +): ... +def edge_betweenness_centrality_subset( + G, sources, targets, normalized: bool = ..., weight: Optional[Any] = ... +): ... +def betweenness_centrality_source( + G, normalized: bool = ..., weight: Optional[Any] = ..., sources: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/closeness.pyi b/mypy-stubs/networkx/algorithms/centrality/closeness.pyi index fbbe89e9d..e1abeecfc 100644 --- a/mypy-stubs/networkx/algorithms/centrality/closeness.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/closeness.pyi @@ -4,4 +4,10 @@ from typing import Any, Optional -def closeness_centrality(G, u: Optional[Any] = ..., distance: Optional[Any] = ..., wf_improved: bool = ..., reverse: bool = ...): ... +def closeness_centrality( + G, + u: Optional[Any] = ..., + distance: Optional[Any] = ..., + wf_improved: bool = ..., + reverse: bool = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness.pyi b/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness.pyi index 85f907d2a..4e01428dd 100644 --- a/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness.pyi @@ -2,9 +2,30 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.centrality.flow_matrix import * from typing import Any, Optional -def approximate_current_flow_betweenness_centrality(G, normalized: bool = ..., weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ..., epsilon: float = ..., kmax: int = ...): ... -def current_flow_betweenness_centrality(G, normalized: bool = ..., weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ...): ... -def edge_current_flow_betweenness_centrality(G, normalized: bool = ..., weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ...): ... +from networkx.algorithms.centrality.flow_matrix import * + +def approximate_current_flow_betweenness_centrality( + G, + normalized: bool = ..., + weight: Optional[Any] = ..., + dtype: Any = ..., + solver: str = ..., + epsilon: float = ..., + kmax: int = ..., +): ... +def current_flow_betweenness_centrality( + G, + normalized: bool = ..., + weight: Optional[Any] = ..., + dtype: Any = ..., + solver: str = ..., +): ... +def edge_current_flow_betweenness_centrality( + G, + normalized: bool = ..., + weight: Optional[Any] = ..., + dtype: Any = ..., + solver: str = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness_subset.pyi b/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness_subset.pyi index fb7bf28db..7b9c3eaec 100644 --- a/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness_subset.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/current_flow_betweenness_subset.pyi @@ -2,8 +2,25 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.centrality.flow_matrix import * from typing import Any, Optional -def current_flow_betweenness_centrality_subset(G, sources, targets, normalized: bool = ..., weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ...): ... -def edge_current_flow_betweenness_centrality_subset(G, sources, targets, normalized: bool = ..., weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ...): ... +from networkx.algorithms.centrality.flow_matrix import * + +def current_flow_betweenness_centrality_subset( + G, + sources, + targets, + normalized: bool = ..., + weight: Optional[Any] = ..., + dtype: Any = ..., + solver: str = ..., +): ... +def edge_current_flow_betweenness_centrality_subset( + G, + sources, + targets, + normalized: bool = ..., + weight: Optional[Any] = ..., + dtype: Any = ..., + solver: str = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/current_flow_closeness.pyi b/mypy-stubs/networkx/algorithms/centrality/current_flow_closeness.pyi index eddf4d444..1555cf8f4 100644 --- a/mypy-stubs/networkx/algorithms/centrality/current_flow_closeness.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/current_flow_closeness.pyi @@ -2,8 +2,12 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.centrality.flow_matrix import * from typing import Any, Optional -def current_flow_closeness_centrality(G, weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ...): ... +from networkx.algorithms.centrality.flow_matrix import * + +def current_flow_closeness_centrality( + G, weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ... +): ... + information_centrality = current_flow_closeness_centrality diff --git a/mypy-stubs/networkx/algorithms/centrality/dispersion.pyi b/mypy-stubs/networkx/algorithms/centrality/dispersion.pyi index 79657bcd7..032d455de 100644 --- a/mypy-stubs/networkx/algorithms/centrality/dispersion.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/dispersion.pyi @@ -4,4 +4,12 @@ from typing import Any, Optional -def dispersion(G, u: Optional[Any] = ..., v: Optional[Any] = ..., normalized: bool = ..., alpha: float = ..., b: float = ..., c: float = ...): ... +def dispersion( + G, + u: Optional[Any] = ..., + v: Optional[Any] = ..., + normalized: bool = ..., + alpha: float = ..., + b: float = ..., + c: float = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/eigenvector.pyi b/mypy-stubs/networkx/algorithms/centrality/eigenvector.pyi index cf0dde768..df5313cd8 100644 --- a/mypy-stubs/networkx/algorithms/centrality/eigenvector.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/eigenvector.pyi @@ -4,5 +4,13 @@ from typing import Any, Optional -def eigenvector_centrality(G, max_iter: int = ..., tol: float = ..., nstart: Optional[Any] = ..., weight: Optional[Any] = ...): ... -def eigenvector_centrality_numpy(G, weight: Optional[Any] = ..., max_iter: int = ..., tol: int = ...): ... +def eigenvector_centrality( + G, + max_iter: int = ..., + tol: float = ..., + nstart: Optional[Any] = ..., + weight: Optional[Any] = ..., +): ... +def eigenvector_centrality_numpy( + G, weight: Optional[Any] = ..., max_iter: int = ..., tol: int = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/flow_matrix.pyi b/mypy-stubs/networkx/algorithms/centrality/flow_matrix.pyi index 3aaa39261..1a6009919 100644 --- a/mypy-stubs/networkx/algorithms/centrality/flow_matrix.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/flow_matrix.pyi @@ -4,7 +4,9 @@ from typing import Any, Optional -def flow_matrix_row(G, weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ...): ... +def flow_matrix_row( + G, weight: Optional[Any] = ..., dtype: Any = ..., solver: str = ... +): ... class InverseLaplacian: dtype: Any = ... @@ -12,7 +14,9 @@ class InverseLaplacian: w: Any = ... C: Any = ... L1: Any = ... - def __init__(self, L, width: Optional[Any] = ..., dtype: Optional[Any] = ...) -> None: ... + def __init__( + self, L, width: Optional[Any] = ..., dtype: Optional[Any] = ... + ) -> None: ... def init_solver(self, L): ... def solve(self, r): ... def solve_inverse(self, r): ... @@ -38,4 +42,10 @@ class CGInverseLaplacian(InverseLaplacian): def solve(self, rhs): ... def solve_inverse(self, r): ... -def laplacian_sparse_matrix(G, nodelist: Optional[Any] = ..., weight: Optional[Any] = ..., dtype: Optional[Any] = ..., format: str = ...): ... +def laplacian_sparse_matrix( + G, + nodelist: Optional[Any] = ..., + weight: Optional[Any] = ..., + dtype: Optional[Any] = ..., + format: str = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/harmonic.pyi b/mypy-stubs/networkx/algorithms/centrality/harmonic.pyi index 723e2c919..521de798a 100644 --- a/mypy-stubs/networkx/algorithms/centrality/harmonic.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/harmonic.pyi @@ -4,4 +4,6 @@ from typing import Any, Optional -def harmonic_centrality(G, nbunch: Optional[Any] = ..., distance: Optional[Any] = ...): ... +def harmonic_centrality( + G, nbunch: Optional[Any] = ..., distance: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/katz.pyi b/mypy-stubs/networkx/algorithms/centrality/katz.pyi index 9a843dcf3..b576d4295 100644 --- a/mypy-stubs/networkx/algorithms/centrality/katz.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/katz.pyi @@ -4,5 +4,20 @@ from typing import Any, Optional -def katz_centrality(G, alpha: float = ..., beta: float = ..., max_iter: int = ..., tol: float = ..., nstart: Optional[Any] = ..., normalized: bool = ..., weight: Optional[Any] = ...): ... -def katz_centrality_numpy(G, alpha: float = ..., beta: float = ..., normalized: bool = ..., weight: Optional[Any] = ...): ... +def katz_centrality( + G, + alpha: float = ..., + beta: float = ..., + max_iter: int = ..., + tol: float = ..., + nstart: Optional[Any] = ..., + normalized: bool = ..., + weight: Optional[Any] = ..., +): ... +def katz_centrality_numpy( + G, + alpha: float = ..., + beta: float = ..., + normalized: bool = ..., + weight: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/centrality/reaching.pyi b/mypy-stubs/networkx/algorithms/centrality/reaching.pyi index 675b36c0e..c6f4cd02f 100644 --- a/mypy-stubs/networkx/algorithms/centrality/reaching.pyi +++ b/mypy-stubs/networkx/algorithms/centrality/reaching.pyi @@ -4,5 +4,13 @@ from typing import Any, Optional -def global_reaching_centrality(G, weight: Optional[Any] = ..., normalized: bool = ...): ... -def local_reaching_centrality(G, v, paths: Optional[Any] = ..., weight: Optional[Any] = ..., normalized: bool = ...): ... +def global_reaching_centrality( + G, weight: Optional[Any] = ..., normalized: bool = ... +): ... +def local_reaching_centrality( + G, + v, + paths: Optional[Any] = ..., + weight: Optional[Any] = ..., + normalized: bool = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/chordal.pyi b/mypy-stubs/networkx/algorithms/chordal.pyi index 5bc34ff02..4c6042db7 100644 --- a/mypy-stubs/networkx/algorithms/chordal.pyi +++ b/mypy-stubs/networkx/algorithms/chordal.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -import networkx as nx from typing import Any +import networkx as nx + class NetworkXTreewidthBoundExceeded(nx.NetworkXException): ... def is_chordal(G): ... diff --git a/mypy-stubs/networkx/algorithms/clique.pyi b/mypy-stubs/networkx/algorithms/clique.pyi index df7cda816..ef1a7faa6 100644 --- a/mypy-stubs/networkx/algorithms/clique.pyi +++ b/mypy-stubs/networkx/algorithms/clique.pyi @@ -8,9 +8,16 @@ def enumerate_all_cliques(G): ... def find_cliques(G): ... def find_cliques_recursive(G): ... def make_max_clique_graph(G, create_using: Optional[Any] = ...): ... -def make_clique_bipartite(G, fpos: Optional[Any] = ..., create_using: Optional[Any] = ..., name: Optional[Any] = ...): ... +def make_clique_bipartite( + G, + fpos: Optional[Any] = ..., + create_using: Optional[Any] = ..., + name: Optional[Any] = ..., +): ... def graph_clique_number(G, cliques: Optional[Any] = ...): ... def graph_number_of_cliques(G, cliques: Optional[Any] = ...): ... def node_clique_number(G, nodes: Optional[Any] = ..., cliques: Optional[Any] = ...): ... def number_of_cliques(G, nodes: Optional[Any] = ..., cliques: Optional[Any] = ...): ... -def cliques_containing_node(G, nodes: Optional[Any] = ..., cliques: Optional[Any] = ...): ... +def cliques_containing_node( + G, nodes: Optional[Any] = ..., cliques: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/cluster.pyi b/mypy-stubs/networkx/algorithms/cluster.pyi index f9eb6b227..3e87622eb 100644 --- a/mypy-stubs/networkx/algorithms/cluster.pyi +++ b/mypy-stubs/networkx/algorithms/cluster.pyi @@ -5,7 +5,9 @@ from typing import Any, Optional def triangles(G, nodes: Optional[Any] = ...): ... -def average_clustering(G, nodes: Optional[Any] = ..., weight: Optional[Any] = ..., count_zeros: bool = ...): ... +def average_clustering( + G, nodes: Optional[Any] = ..., weight: Optional[Any] = ..., count_zeros: bool = ... +): ... def clustering(G, nodes: Optional[Any] = ..., weight: Optional[Any] = ...): ... def transitivity(G): ... def square_clustering(G, nodes: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/community/__init__.pyi b/mypy-stubs/networkx/algorithms/community/__init__.pyi index 66a855768..5b7c52e00 100644 --- a/mypy-stubs/networkx/algorithms/community/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/community/__init__.pyi @@ -5,8 +5,8 @@ from networkx.algorithms.community.asyn_fluidc import * from networkx.algorithms.community.centrality import * from networkx.algorithms.community.community_generators import * +from networkx.algorithms.community.community_utils import * from networkx.algorithms.community.kclique import * from networkx.algorithms.community.kernighan_lin import * from networkx.algorithms.community.label_propagation import * from networkx.algorithms.community.quality import * -from networkx.algorithms.community.community_utils import * diff --git a/mypy-stubs/networkx/algorithms/community/community_generators.pyi b/mypy-stubs/networkx/algorithms/community/community_generators.pyi index b6ff9c7cf..37248edb1 100644 --- a/mypy-stubs/networkx/algorithms/community/community_generators.pyi +++ b/mypy-stubs/networkx/algorithms/community/community_generators.pyi @@ -4,4 +4,17 @@ from typing import Any, Optional -def LFR_benchmark_graph(n, tau1, tau2, mu, average_degree: Optional[Any] = ..., min_degree: Optional[Any] = ..., max_degree: Optional[Any] = ..., min_community: Optional[Any] = ..., max_community: Optional[Any] = ..., tol: float = ..., max_iters: int = ..., seed: Optional[Any] = ...): ... +def LFR_benchmark_graph( + n, + tau1, + tau2, + mu, + average_degree: Optional[Any] = ..., + min_degree: Optional[Any] = ..., + max_degree: Optional[Any] = ..., + min_community: Optional[Any] = ..., + max_community: Optional[Any] = ..., + tol: float = ..., + max_iters: int = ..., + seed: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/community/kernighan_lin.pyi b/mypy-stubs/networkx/algorithms/community/kernighan_lin.pyi index 167b4cded..a68349552 100644 --- a/mypy-stubs/networkx/algorithms/community/kernighan_lin.pyi +++ b/mypy-stubs/networkx/algorithms/community/kernighan_lin.pyi @@ -4,4 +4,6 @@ from typing import Any, Optional -def kernighan_lin_bisection(G, partition: Optional[Any] = ..., max_iter: int = ..., weight: str = ...): ... +def kernighan_lin_bisection( + G, partition: Optional[Any] = ..., max_iter: int = ..., weight: str = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/components/__init__.pyi b/mypy-stubs/networkx/algorithms/components/__init__.pyi index 9f197dbe9..8894f98d2 100644 --- a/mypy-stubs/networkx/algorithms/components/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/components/__init__.pyi @@ -2,9 +2,9 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .connected import * -from .strongly_connected import * -from .weakly_connected import * from .attracting import * from .biconnected import * +from .connected import * from .semiconnected import * +from .strongly_connected import * +from .weakly_connected import * diff --git a/mypy-stubs/networkx/algorithms/connectivity/__init__.pyi b/mypy-stubs/networkx/algorithms/connectivity/__init__.pyi index d77737ef1..3ca76bd89 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/__init__.pyi @@ -4,9 +4,9 @@ from .connectivity import * from .cuts import * +from .disjoint_paths import * from .edge_augmentation import * from .edge_kcomponents import * -from .disjoint_paths import * from .kcomponents import * from .kcutsets import * from .stoerwagner import * diff --git a/mypy-stubs/networkx/algorithms/connectivity/connectivity.pyi b/mypy-stubs/networkx/algorithms/connectivity/connectivity.pyi index 67f4a289e..9d8780294 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/connectivity.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/connectivity.pyi @@ -2,14 +2,41 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.flow import edmonds_karp from typing import Any, Optional +from networkx.algorithms.flow import edmonds_karp + default_flow_func = edmonds_karp -def local_node_connectivity(G, s, t, flow_func: Optional[Any] = ..., auxiliary: Optional[Any] = ..., residual: Optional[Any] = ..., cutoff: Optional[Any] = ...): ... -def node_connectivity(G, s: Optional[Any] = ..., t: Optional[Any] = ..., flow_func: Optional[Any] = ...): ... +def local_node_connectivity( + G, + s, + t, + flow_func: Optional[Any] = ..., + auxiliary: Optional[Any] = ..., + residual: Optional[Any] = ..., + cutoff: Optional[Any] = ..., +): ... +def node_connectivity( + G, s: Optional[Any] = ..., t: Optional[Any] = ..., flow_func: Optional[Any] = ... +): ... def average_node_connectivity(G, flow_func: Optional[Any] = ...): ... -def all_pairs_node_connectivity(G, nbunch: Optional[Any] = ..., flow_func: Optional[Any] = ...): ... -def local_edge_connectivity(G, s, t, flow_func: Optional[Any] = ..., auxiliary: Optional[Any] = ..., residual: Optional[Any] = ..., cutoff: Optional[Any] = ...): ... -def edge_connectivity(G, s: Optional[Any] = ..., t: Optional[Any] = ..., flow_func: Optional[Any] = ..., cutoff: Optional[Any] = ...): ... +def all_pairs_node_connectivity( + G, nbunch: Optional[Any] = ..., flow_func: Optional[Any] = ... +): ... +def local_edge_connectivity( + G, + s, + t, + flow_func: Optional[Any] = ..., + auxiliary: Optional[Any] = ..., + residual: Optional[Any] = ..., + cutoff: Optional[Any] = ..., +): ... +def edge_connectivity( + G, + s: Optional[Any] = ..., + t: Optional[Any] = ..., + flow_func: Optional[Any] = ..., + cutoff: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/connectivity/cuts.pyi b/mypy-stubs/networkx/algorithms/connectivity/cuts.pyi index be7a69a01..8e9f371c5 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/cuts.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/cuts.pyi @@ -2,12 +2,31 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.flow import edmonds_karp from typing import Any, Optional +from networkx.algorithms.flow import edmonds_karp + default_flow_func = edmonds_karp -def minimum_st_edge_cut(G, s, t, flow_func: Optional[Any] = ..., auxiliary: Optional[Any] = ..., residual: Optional[Any] = ...): ... -def minimum_st_node_cut(G, s, t, flow_func: Optional[Any] = ..., auxiliary: Optional[Any] = ..., residual: Optional[Any] = ...): ... -def minimum_node_cut(G, s: Optional[Any] = ..., t: Optional[Any] = ..., flow_func: Optional[Any] = ...): ... -def minimum_edge_cut(G, s: Optional[Any] = ..., t: Optional[Any] = ..., flow_func: Optional[Any] = ...): ... +def minimum_st_edge_cut( + G, + s, + t, + flow_func: Optional[Any] = ..., + auxiliary: Optional[Any] = ..., + residual: Optional[Any] = ..., +): ... +def minimum_st_node_cut( + G, + s, + t, + flow_func: Optional[Any] = ..., + auxiliary: Optional[Any] = ..., + residual: Optional[Any] = ..., +): ... +def minimum_node_cut( + G, s: Optional[Any] = ..., t: Optional[Any] = ..., flow_func: Optional[Any] = ... +): ... +def minimum_edge_cut( + G, s: Optional[Any] = ..., t: Optional[Any] = ..., flow_func: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/connectivity/disjoint_paths.pyi b/mypy-stubs/networkx/algorithms/connectivity/disjoint_paths.pyi index 437d9a0a7..197aefd81 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/disjoint_paths.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/disjoint_paths.pyi @@ -2,10 +2,27 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.flow import edmonds_karp from typing import Any, Optional +from networkx.algorithms.flow import edmonds_karp + default_flow_func = edmonds_karp -def edge_disjoint_paths(G, s, t, flow_func: Optional[Any] = ..., cutoff: Optional[Any] = ..., auxiliary: Optional[Any] = ..., residual: Optional[Any] = ...): ... -def node_disjoint_paths(G, s, t, flow_func: Optional[Any] = ..., cutoff: Optional[Any] = ..., auxiliary: Optional[Any] = ..., residual: Optional[Any] = ...): ... +def edge_disjoint_paths( + G, + s, + t, + flow_func: Optional[Any] = ..., + cutoff: Optional[Any] = ..., + auxiliary: Optional[Any] = ..., + residual: Optional[Any] = ..., +): ... +def node_disjoint_paths( + G, + s, + t, + flow_func: Optional[Any] = ..., + cutoff: Optional[Any] = ..., + auxiliary: Optional[Any] = ..., + residual: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/connectivity/kcomponents.pyi b/mypy-stubs/networkx/algorithms/connectivity/kcomponents.pyi index 951ecba38..ebf249683 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/kcomponents.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/kcomponents.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.flow import edmonds_karp from typing import Any, Optional +from networkx.algorithms.flow import edmonds_karp + default_flow_func = edmonds_karp def k_components(G, flow_func: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/connectivity/kcutsets.pyi b/mypy-stubs/networkx/algorithms/connectivity/kcutsets.pyi index 7fc0d3bf0..0cba1963c 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/kcutsets.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/kcutsets.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.flow import edmonds_karp from typing import Any, Optional +from networkx.algorithms.flow import edmonds_karp + default_flow_func = edmonds_karp def all_node_cuts(G, k: Optional[Any] = ..., flow_func: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/core.pyi b/mypy-stubs/networkx/algorithms/core.pyi index 9e133591a..3c01a6a7c 100644 --- a/mypy-stubs/networkx/algorithms/core.pyi +++ b/mypy-stubs/networkx/algorithms/core.pyi @@ -5,6 +5,7 @@ from typing import Any, Optional def core_number(G): ... + find_cores = core_number def k_core(G, k: Optional[Any] = ..., core_number: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/flow/__init__.pyi b/mypy-stubs/networkx/algorithms/flow/__init__.pyi index 5fd243bb6..c8b739a9c 100644 --- a/mypy-stubs/networkx/algorithms/flow/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/flow/__init__.pyi @@ -2,14 +2,14 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .maxflow import * -from .mincost import * from .boykovkolmogorov import * +from .capacityscaling import * from .dinitz_alg import * from .edmondskarp import * from .gomory_hu import * +from .maxflow import * +from .mincost import * +from .networksimplex import * from .preflowpush import * from .shortestaugmentingpath import * -from .capacityscaling import * -from .networksimplex import * from .utils import build_flow_dict, build_residual_network diff --git a/mypy-stubs/networkx/algorithms/flow/boykovkolmogorov.pyi b/mypy-stubs/networkx/algorithms/flow/boykovkolmogorov.pyi index 094456a60..cea4e5e87 100644 --- a/mypy-stubs/networkx/algorithms/flow/boykovkolmogorov.pyi +++ b/mypy-stubs/networkx/algorithms/flow/boykovkolmogorov.pyi @@ -4,4 +4,12 @@ from typing import Any, Optional -def boykov_kolmogorov(G, s, t, capacity: str = ..., residual: Optional[Any] = ..., value_only: bool = ..., cutoff: Optional[Any] = ...): ... +def boykov_kolmogorov( + G, + s, + t, + capacity: str = ..., + residual: Optional[Any] = ..., + value_only: bool = ..., + cutoff: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/flow/capacityscaling.pyi b/mypy-stubs/networkx/algorithms/flow/capacityscaling.pyi index 121428e84..62151938e 100644 --- a/mypy-stubs/networkx/algorithms/flow/capacityscaling.pyi +++ b/mypy-stubs/networkx/algorithms/flow/capacityscaling.pyi @@ -4,4 +4,6 @@ from typing import Any -def capacity_scaling(G, demand: str = ..., capacity: str = ..., weight: str = ..., heap: Any = ...): ... +def capacity_scaling( + G, demand: str = ..., capacity: str = ..., weight: str = ..., heap: Any = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/flow/dinitz_alg.pyi b/mypy-stubs/networkx/algorithms/flow/dinitz_alg.pyi index a0cbd8d1f..ccfb48e4d 100644 --- a/mypy-stubs/networkx/algorithms/flow/dinitz_alg.pyi +++ b/mypy-stubs/networkx/algorithms/flow/dinitz_alg.pyi @@ -4,4 +4,12 @@ from typing import Any, Optional -def dinitz(G, s, t, capacity: str = ..., residual: Optional[Any] = ..., value_only: bool = ..., cutoff: Optional[Any] = ...): ... +def dinitz( + G, + s, + t, + capacity: str = ..., + residual: Optional[Any] = ..., + value_only: bool = ..., + cutoff: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/flow/edmondskarp.pyi b/mypy-stubs/networkx/algorithms/flow/edmondskarp.pyi index ab4876551..96d92b927 100644 --- a/mypy-stubs/networkx/algorithms/flow/edmondskarp.pyi +++ b/mypy-stubs/networkx/algorithms/flow/edmondskarp.pyi @@ -2,7 +2,16 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.flow.utils import * from typing import Any, Optional -def edmonds_karp(G, s, t, capacity: str = ..., residual: Optional[Any] = ..., value_only: bool = ..., cutoff: Optional[Any] = ...): ... +from networkx.algorithms.flow.utils import * + +def edmonds_karp( + G, + s, + t, + capacity: str = ..., + residual: Optional[Any] = ..., + value_only: bool = ..., + cutoff: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/flow/gomory_hu.pyi b/mypy-stubs/networkx/algorithms/flow/gomory_hu.pyi index da26cd17f..a548e83c7 100644 --- a/mypy-stubs/networkx/algorithms/flow/gomory_hu.pyi +++ b/mypy-stubs/networkx/algorithms/flow/gomory_hu.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .edmondskarp import edmonds_karp from typing import Any, Optional +from .edmondskarp import edmonds_karp + default_flow_func = edmonds_karp def gomory_hu_tree(G, capacity: str = ..., flow_func: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/flow/maxflow.pyi b/mypy-stubs/networkx/algorithms/flow/maxflow.pyi index 97f5e0ff4..e0ebab1f7 100644 --- a/mypy-stubs/networkx/algorithms/flow/maxflow.pyi +++ b/mypy-stubs/networkx/algorithms/flow/maxflow.pyi @@ -2,12 +2,21 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .preflowpush import preflow_push from typing import Any, Optional +from .preflowpush import preflow_push + default_flow_func = preflow_push -def maximum_flow(flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs): ... -def maximum_flow_value(flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs): ... -def minimum_cut(flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs): ... -def minimum_cut_value(flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs): ... +def maximum_flow( + flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs +): ... +def maximum_flow_value( + flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs +): ... +def minimum_cut( + flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs +): ... +def minimum_cut_value( + flowG, _s, _t, capacity: str = ..., flow_func: Optional[Any] = ..., **kwargs +): ... diff --git a/mypy-stubs/networkx/algorithms/flow/mincost.pyi b/mypy-stubs/networkx/algorithms/flow/mincost.pyi index 8de9f4835..93c4e6904 100644 --- a/mypy-stubs/networkx/algorithms/flow/mincost.pyi +++ b/mypy-stubs/networkx/algorithms/flow/mincost.pyi @@ -2,7 +2,9 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -def min_cost_flow_cost(G, demand: str = ..., capacity: str = ..., weight: str = ...): ... +def min_cost_flow_cost( + G, demand: str = ..., capacity: str = ..., weight: str = ... +): ... def min_cost_flow(G, demand: str = ..., capacity: str = ..., weight: str = ...): ... def cost_of_flow(G, flowDict, weight: str = ...): ... def max_flow_min_cost(G, s, t, capacity: str = ..., weight: str = ...): ... diff --git a/mypy-stubs/networkx/algorithms/flow/preflowpush.pyi b/mypy-stubs/networkx/algorithms/flow/preflowpush.pyi index 4d8566093..181bf72b7 100644 --- a/mypy-stubs/networkx/algorithms/flow/preflowpush.pyi +++ b/mypy-stubs/networkx/algorithms/flow/preflowpush.pyi @@ -4,4 +4,12 @@ from typing import Any, Optional -def preflow_push(G, s, t, capacity: str = ..., residual: Optional[Any] = ..., global_relabel_freq: int = ..., value_only: bool = ...): ... +def preflow_push( + G, + s, + t, + capacity: str = ..., + residual: Optional[Any] = ..., + global_relabel_freq: int = ..., + value_only: bool = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/flow/shortestaugmentingpath.pyi b/mypy-stubs/networkx/algorithms/flow/shortestaugmentingpath.pyi index 9c2d2d253..5112e85c7 100644 --- a/mypy-stubs/networkx/algorithms/flow/shortestaugmentingpath.pyi +++ b/mypy-stubs/networkx/algorithms/flow/shortestaugmentingpath.pyi @@ -2,7 +2,17 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .utils import * from typing import Any, Optional -def shortest_augmenting_path(G, s, t, capacity: str = ..., residual: Optional[Any] = ..., value_only: bool = ..., two_phase: bool = ..., cutoff: Optional[Any] = ...): ... +from .utils import * + +def shortest_augmenting_path( + G, + s, + t, + capacity: str = ..., + residual: Optional[Any] = ..., + value_only: bool = ..., + two_phase: bool = ..., + cutoff: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/hybrid.pyi b/mypy-stubs/networkx/algorithms/hybrid.pyi index e6a6f14a6..020479b17 100644 --- a/mypy-stubs/networkx/algorithms/hybrid.pyi +++ b/mypy-stubs/networkx/algorithms/hybrid.pyi @@ -2,5 +2,7 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -def kl_connected_subgraph(G, k, l, low_memory: bool = ..., same_as_graph: bool = ...): ... +def kl_connected_subgraph( + G, k, l, low_memory: bool = ..., same_as_graph: bool = ... +): ... def is_kl_connected(G, k, l, low_memory: bool = ...): ... diff --git a/mypy-stubs/networkx/algorithms/isomorphism/__init__.pyi b/mypy-stubs/networkx/algorithms/isomorphism/__init__.pyi index df1779d1a..00c077680 100644 --- a/mypy-stubs/networkx/algorithms/isomorphism/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/isomorphism/__init__.pyi @@ -3,6 +3,6 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from networkx.algorithms.isomorphism.isomorph import * -from networkx.algorithms.isomorphism.vf2userfunc import * from networkx.algorithms.isomorphism.matchhelpers import * from networkx.algorithms.isomorphism.temporalisomorphvf2 import * +from networkx.algorithms.isomorphism.vf2userfunc import * diff --git a/mypy-stubs/networkx/algorithms/isomorphism/isomorph.pyi b/mypy-stubs/networkx/algorithms/isomorphism/isomorph.pyi index e7d971eab..25e42d410 100644 --- a/mypy-stubs/networkx/algorithms/isomorphism/isomorph.pyi +++ b/mypy-stubs/networkx/algorithms/isomorphism/isomorph.pyi @@ -5,12 +5,17 @@ from typing import Any, Optional def could_be_isomorphic(G1, G2): ... + graph_could_be_isomorphic = could_be_isomorphic def fast_could_be_isomorphic(G1, G2): ... + fast_graph_could_be_isomorphic = fast_could_be_isomorphic def faster_could_be_isomorphic(G1, G2): ... + faster_graph_could_be_isomorphic = faster_could_be_isomorphic -def is_isomorphic(G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ...): ... +def is_isomorphic( + G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/isomorphism/isomorphvf2.pyi b/mypy-stubs/networkx/algorithms/isomorphism/isomorphvf2.pyi index caec90325..30a2d51e1 100644 --- a/mypy-stubs/networkx/algorithms/isomorphism/isomorphvf2.pyi +++ b/mypy-stubs/networkx/algorithms/isomorphism/isomorphvf2.pyi @@ -48,7 +48,9 @@ class GMState: G1_node: Any = ... G2_node: Any = ... depth: Any = ... - def __init__(self, GM, G1_node: Optional[Any] = ..., G2_node: Optional[Any] = ...) -> None: ... + def __init__( + self, GM, G1_node: Optional[Any] = ..., G2_node: Optional[Any] = ... + ) -> None: ... def restore(self): ... class DiGMState: @@ -56,5 +58,7 @@ class DiGMState: G1_node: Any = ... G2_node: Any = ... depth: Any = ... - def __init__(self, GM, G1_node: Optional[Any] = ..., G2_node: Optional[Any] = ...) -> None: ... + def __init__( + self, GM, G1_node: Optional[Any] = ..., G2_node: Optional[Any] = ... + ) -> None: ... def restore(self): ... diff --git a/mypy-stubs/networkx/algorithms/isomorphism/temporalisomorphvf2.pyi b/mypy-stubs/networkx/algorithms/isomorphism/temporalisomorphvf2.pyi index 7fcbb8c68..d79e96c22 100644 --- a/mypy-stubs/networkx/algorithms/isomorphism/temporalisomorphvf2.pyi +++ b/mypy-stubs/networkx/algorithms/isomorphism/temporalisomorphvf2.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .isomorphvf2 import DiGraphMatcher, GraphMatcher from typing import Any, Optional +from .isomorphvf2 import DiGraphMatcher, GraphMatcher + class TimeRespectingGraphMatcher(GraphMatcher): temporal_attribute_name: Any = ... delta: Any = ... diff --git a/mypy-stubs/networkx/algorithms/isomorphism/vf2userfunc.pyi b/mypy-stubs/networkx/algorithms/isomorphism/vf2userfunc.pyi index 6a0d2353f..43f5ec19b 100644 --- a/mypy-stubs/networkx/algorithms/isomorphism/vf2userfunc.pyi +++ b/mypy-stubs/networkx/algorithms/isomorphism/vf2userfunc.pyi @@ -2,15 +2,18 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from . import isomorphvf2 as vf2 from typing import Any, Optional +from . import isomorphvf2 as vf2 + class GraphMatcher(vf2.GraphMatcher): node_match: Any = ... edge_match: Any = ... G1_adj: Any = ... G2_adj: Any = ... - def __init__(self, G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ...) -> None: ... + def __init__( + self, G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ... + ) -> None: ... semantic_feasibility: Any = ... class DiGraphMatcher(vf2.DiGraphMatcher): @@ -18,7 +21,9 @@ class DiGraphMatcher(vf2.DiGraphMatcher): edge_match: Any = ... G1_adj: Any = ... G2_adj: Any = ... - def __init__(self, G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ...) -> None: ... + def __init__( + self, G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ... + ) -> None: ... def semantic_feasibility(self, G1_node, G2_node): ... class MultiGraphMatcher(GraphMatcher): ... diff --git a/mypy-stubs/networkx/algorithms/link_analysis/__init__.pyi b/mypy-stubs/networkx/algorithms/link_analysis/__init__.pyi index f2bc2c751..5c7882e12 100644 --- a/mypy-stubs/networkx/algorithms/link_analysis/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/link_analysis/__init__.pyi @@ -2,5 +2,5 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.algorithms.link_analysis.pagerank_alg import * from networkx.algorithms.link_analysis.hits_alg import * +from networkx.algorithms.link_analysis.pagerank_alg import * diff --git a/mypy-stubs/networkx/algorithms/link_analysis/hits_alg.pyi b/mypy-stubs/networkx/algorithms/link_analysis/hits_alg.pyi index f1b971c03..b48e767ad 100644 --- a/mypy-stubs/networkx/algorithms/link_analysis/hits_alg.pyi +++ b/mypy-stubs/networkx/algorithms/link_analysis/hits_alg.pyi @@ -4,7 +4,13 @@ from typing import Any, Optional -def hits(G, max_iter: int = ..., tol: float = ..., nstart: Optional[Any] = ..., normalized: bool = ...): ... +def hits( + G, + max_iter: int = ..., + tol: float = ..., + nstart: Optional[Any] = ..., + normalized: bool = ..., +): ... def authority_matrix(G, nodelist: Optional[Any] = ...): ... def hub_matrix(G, nodelist: Optional[Any] = ...): ... def hits_numpy(G, normalized: bool = ...): ... diff --git a/mypy-stubs/networkx/algorithms/link_analysis/pagerank_alg.pyi b/mypy-stubs/networkx/algorithms/link_analysis/pagerank_alg.pyi index 6e8e1eb31..9beccabd6 100644 --- a/mypy-stubs/networkx/algorithms/link_analysis/pagerank_alg.pyi +++ b/mypy-stubs/networkx/algorithms/link_analysis/pagerank_alg.pyi @@ -4,7 +4,37 @@ from typing import Any, Optional -def pagerank(G, alpha: float = ..., personalization: Optional[Any] = ..., max_iter: int = ..., tol: float = ..., nstart: Optional[Any] = ..., weight: str = ..., dangling: Optional[Any] = ...): ... -def google_matrix(G, alpha: float = ..., personalization: Optional[Any] = ..., nodelist: Optional[Any] = ..., weight: str = ..., dangling: Optional[Any] = ...): ... -def pagerank_numpy(G, alpha: float = ..., personalization: Optional[Any] = ..., weight: str = ..., dangling: Optional[Any] = ...): ... -def pagerank_scipy(G, alpha: float = ..., personalization: Optional[Any] = ..., max_iter: int = ..., tol: float = ..., weight: str = ..., dangling: Optional[Any] = ...): ... +def pagerank( + G, + alpha: float = ..., + personalization: Optional[Any] = ..., + max_iter: int = ..., + tol: float = ..., + nstart: Optional[Any] = ..., + weight: str = ..., + dangling: Optional[Any] = ..., +): ... +def google_matrix( + G, + alpha: float = ..., + personalization: Optional[Any] = ..., + nodelist: Optional[Any] = ..., + weight: str = ..., + dangling: Optional[Any] = ..., +): ... +def pagerank_numpy( + G, + alpha: float = ..., + personalization: Optional[Any] = ..., + weight: str = ..., + dangling: Optional[Any] = ..., +): ... +def pagerank_scipy( + G, + alpha: float = ..., + personalization: Optional[Any] = ..., + max_iter: int = ..., + tol: float = ..., + weight: str = ..., + dangling: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/link_prediction.pyi b/mypy-stubs/networkx/algorithms/link_prediction.pyi index 57ce8989b..1d9a5813b 100644 --- a/mypy-stubs/networkx/algorithms/link_prediction.pyi +++ b/mypy-stubs/networkx/algorithms/link_prediction.pyi @@ -9,5 +9,9 @@ def jaccard_coefficient(G, ebunch: Optional[Any] = ...): ... def adamic_adar_index(G, ebunch: Optional[Any] = ...): ... def preferential_attachment(G, ebunch: Optional[Any] = ...): ... def cn_soundarajan_hopcroft(G, ebunch: Optional[Any] = ..., community: str = ...): ... -def ra_index_soundarajan_hopcroft(G, ebunch: Optional[Any] = ..., community: str = ...): ... -def within_inter_cluster(G, ebunch: Optional[Any] = ..., delta: float = ..., community: str = ...): ... +def ra_index_soundarajan_hopcroft( + G, ebunch: Optional[Any] = ..., community: str = ... +): ... +def within_inter_cluster( + G, ebunch: Optional[Any] = ..., delta: float = ..., community: str = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/lowest_common_ancestors.pyi b/mypy-stubs/networkx/algorithms/lowest_common_ancestors.pyi index e643a3190..edcf10148 100644 --- a/mypy-stubs/networkx/algorithms/lowest_common_ancestors.pyi +++ b/mypy-stubs/networkx/algorithms/lowest_common_ancestors.pyi @@ -4,6 +4,8 @@ from typing import Any, Optional -def tree_all_pairs_lowest_common_ancestor(G, root: Optional[Any] = ..., pairs: Optional[Any] = ...): ... +def tree_all_pairs_lowest_common_ancestor( + G, root: Optional[Any] = ..., pairs: Optional[Any] = ... +): ... def lowest_common_ancestor(G, node1, node2, default: Optional[Any] = ...): ... def all_pairs_lowest_common_ancestor(G, pairs: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/minors.pyi b/mypy-stubs/networkx/algorithms/minors.pyi index 8f2e60625..b7e296112 100644 --- a/mypy-stubs/networkx/algorithms/minors.pyi +++ b/mypy-stubs/networkx/algorithms/minors.pyi @@ -4,8 +4,17 @@ from typing import Any, Optional -def quotient_graph(G, partition, edge_relation: Optional[Any] = ..., node_data: Optional[Any] = ..., edge_data: Optional[Any] = ..., relabel: bool = ..., create_using: Optional[Any] = ...): ... +def quotient_graph( + G, + partition, + edge_relation: Optional[Any] = ..., + node_data: Optional[Any] = ..., + edge_data: Optional[Any] = ..., + relabel: bool = ..., + create_using: Optional[Any] = ..., +): ... def contracted_nodes(G, u, v, self_loops: bool = ...): ... + identified_nodes = contracted_nodes def contracted_edge(G, edge, self_loops: bool = ...): ... diff --git a/mypy-stubs/networkx/algorithms/shortest_paths/__init__.pyi b/mypy-stubs/networkx/algorithms/shortest_paths/__init__.pyi index 060ec4cff..0f156904d 100644 --- a/mypy-stubs/networkx/algorithms/shortest_paths/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/shortest_paths/__init__.pyi @@ -2,8 +2,8 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. +from networkx.algorithms.shortest_paths.astar import * +from networkx.algorithms.shortest_paths.dense import * from networkx.algorithms.shortest_paths.generic import * from networkx.algorithms.shortest_paths.unweighted import * from networkx.algorithms.shortest_paths.weighted import * -from networkx.algorithms.shortest_paths.astar import * -from networkx.algorithms.shortest_paths.dense import * diff --git a/mypy-stubs/networkx/algorithms/shortest_paths/astar.pyi b/mypy-stubs/networkx/algorithms/shortest_paths/astar.pyi index 37b2fdd6a..abe9be2dc 100644 --- a/mypy-stubs/networkx/algorithms/shortest_paths/astar.pyi +++ b/mypy-stubs/networkx/algorithms/shortest_paths/astar.pyi @@ -4,5 +4,9 @@ from typing import Any, Optional -def astar_path(G, source, target, heuristic: Optional[Any] = ..., weight: str = ...): ... -def astar_path_length(G, source, target, heuristic: Optional[Any] = ..., weight: str = ...): ... +def astar_path( + G, source, target, heuristic: Optional[Any] = ..., weight: str = ... +): ... +def astar_path_length( + G, source, target, heuristic: Optional[Any] = ..., weight: str = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/shortest_paths/generic.pyi b/mypy-stubs/networkx/algorithms/shortest_paths/generic.pyi index 4d79c613d..c177663eb 100644 --- a/mypy-stubs/networkx/algorithms/shortest_paths/generic.pyi +++ b/mypy-stubs/networkx/algorithms/shortest_paths/generic.pyi @@ -5,7 +5,17 @@ from typing import Any, Optional def has_path(G, source, target): ... -def shortest_path(G, source: Optional[Any] = ..., target: Optional[Any] = ..., weight: Optional[Any] = ...): ... -def shortest_path_length(G, source: Optional[Any] = ..., target: Optional[Any] = ..., weight: Optional[Any] = ...): ... +def shortest_path( + G, + source: Optional[Any] = ..., + target: Optional[Any] = ..., + weight: Optional[Any] = ..., +): ... +def shortest_path_length( + G, + source: Optional[Any] = ..., + target: Optional[Any] = ..., + weight: Optional[Any] = ..., +): ... def average_shortest_path_length(G, weight: Optional[Any] = ...): ... def all_shortest_paths(G, source, target, weight: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/algorithms/shortest_paths/unweighted.pyi b/mypy-stubs/networkx/algorithms/shortest_paths/unweighted.pyi index 1d403755b..50b441237 100644 --- a/mypy-stubs/networkx/algorithms/shortest_paths/unweighted.pyi +++ b/mypy-stubs/networkx/algorithms/shortest_paths/unweighted.pyi @@ -11,4 +11,10 @@ def bidirectional_shortest_path(G, source, target): ... def single_source_shortest_path(G, source, cutoff: Optional[Any] = ...): ... def single_target_shortest_path(G, target, cutoff: Optional[Any] = ...): ... def all_pairs_shortest_path(G, cutoff: Optional[Any] = ...): ... -def predecessor(G, source, target: Optional[Any] = ..., cutoff: Optional[Any] = ..., return_seen: Optional[Any] = ...): ... +def predecessor( + G, + source, + target: Optional[Any] = ..., + cutoff: Optional[Any] = ..., + return_seen: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/shortest_paths/weighted.pyi b/mypy-stubs/networkx/algorithms/shortest_paths/weighted.pyi index e5777a2ef..52e388360 100644 --- a/mypy-stubs/networkx/algorithms/shortest_paths/weighted.pyi +++ b/mypy-stubs/networkx/algorithms/shortest_paths/weighted.pyi @@ -6,23 +6,65 @@ from typing import Any, Optional def dijkstra_path(G, source, target, weight: str = ...): ... def dijkstra_path_length(G, source, target, weight: str = ...): ... -def single_source_dijkstra_path(G, source, cutoff: Optional[Any] = ..., weight: str = ...): ... -def single_source_dijkstra_path_length(G, source, cutoff: Optional[Any] = ..., weight: str = ...): ... -def single_source_dijkstra(G, source, target: Optional[Any] = ..., cutoff: Optional[Any] = ..., weight: str = ...): ... -def multi_source_dijkstra_path(G, sources, cutoff: Optional[Any] = ..., weight: str = ...): ... -def multi_source_dijkstra_path_length(G, sources, cutoff: Optional[Any] = ..., weight: str = ...): ... -def multi_source_dijkstra(G, sources, target: Optional[Any] = ..., cutoff: Optional[Any] = ..., weight: str = ...): ... -def dijkstra_predecessor_and_distance(G, source, cutoff: Optional[Any] = ..., weight: str = ...): ... +def single_source_dijkstra_path( + G, source, cutoff: Optional[Any] = ..., weight: str = ... +): ... +def single_source_dijkstra_path_length( + G, source, cutoff: Optional[Any] = ..., weight: str = ... +): ... +def single_source_dijkstra( + G, + source, + target: Optional[Any] = ..., + cutoff: Optional[Any] = ..., + weight: str = ..., +): ... +def multi_source_dijkstra_path( + G, sources, cutoff: Optional[Any] = ..., weight: str = ... +): ... +def multi_source_dijkstra_path_length( + G, sources, cutoff: Optional[Any] = ..., weight: str = ... +): ... +def multi_source_dijkstra( + G, + sources, + target: Optional[Any] = ..., + cutoff: Optional[Any] = ..., + weight: str = ..., +): ... +def dijkstra_predecessor_and_distance( + G, source, cutoff: Optional[Any] = ..., weight: str = ... +): ... def all_pairs_dijkstra(G, cutoff: Optional[Any] = ..., weight: str = ...): ... -def all_pairs_dijkstra_path_length(G, cutoff: Optional[Any] = ..., weight: str = ...): ... +def all_pairs_dijkstra_path_length( + G, cutoff: Optional[Any] = ..., weight: str = ... +): ... def all_pairs_dijkstra_path(G, cutoff: Optional[Any] = ..., weight: str = ...): ... -def bellman_ford_predecessor_and_distance(G, source, target: Optional[Any] = ..., cutoff: Optional[Any] = ..., weight: str = ...): ... +def bellman_ford_predecessor_and_distance( + G, + source, + target: Optional[Any] = ..., + cutoff: Optional[Any] = ..., + weight: str = ..., +): ... def bellman_ford_path(G, source, target, weight: str = ...): ... def bellman_ford_path_length(G, source, target, weight: str = ...): ... -def single_source_bellman_ford_path(G, source, cutoff: Optional[Any] = ..., weight: str = ...): ... -def single_source_bellman_ford_path_length(G, source, cutoff: Optional[Any] = ..., weight: str = ...): ... -def single_source_bellman_ford(G, source, target: Optional[Any] = ..., cutoff: Optional[Any] = ..., weight: str = ...): ... -def all_pairs_bellman_ford_path_length(G, cutoff: Optional[Any] = ..., weight: str = ...): ... +def single_source_bellman_ford_path( + G, source, cutoff: Optional[Any] = ..., weight: str = ... +): ... +def single_source_bellman_ford_path_length( + G, source, cutoff: Optional[Any] = ..., weight: str = ... +): ... +def single_source_bellman_ford( + G, + source, + target: Optional[Any] = ..., + cutoff: Optional[Any] = ..., + weight: str = ..., +): ... +def all_pairs_bellman_ford_path_length( + G, cutoff: Optional[Any] = ..., weight: str = ... +): ... def all_pairs_bellman_ford_path(G, cutoff: Optional[Any] = ..., weight: str = ...): ... def goldberg_radzik(G, source, weight: str = ...): ... def negative_edge_cycle(G, weight: str = ...): ... diff --git a/mypy-stubs/networkx/algorithms/similarity.pyi b/mypy-stubs/networkx/algorithms/similarity.pyi index 2192aba2c..ce5ab447b 100644 --- a/mypy-stubs/networkx/algorithms/similarity.pyi +++ b/mypy-stubs/networkx/algorithms/similarity.pyi @@ -5,7 +5,56 @@ from operator import * from typing import Any, Optional -def graph_edit_distance(G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ..., node_subst_cost: Optional[Any] = ..., node_del_cost: Optional[Any] = ..., node_ins_cost: Optional[Any] = ..., edge_subst_cost: Optional[Any] = ..., edge_del_cost: Optional[Any] = ..., edge_ins_cost: Optional[Any] = ..., upper_bound: Optional[Any] = ...): ... -def optimal_edit_paths(G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ..., node_subst_cost: Optional[Any] = ..., node_del_cost: Optional[Any] = ..., node_ins_cost: Optional[Any] = ..., edge_subst_cost: Optional[Any] = ..., edge_del_cost: Optional[Any] = ..., edge_ins_cost: Optional[Any] = ..., upper_bound: Optional[Any] = ...): ... -def optimize_graph_edit_distance(G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ..., node_subst_cost: Optional[Any] = ..., node_del_cost: Optional[Any] = ..., node_ins_cost: Optional[Any] = ..., edge_subst_cost: Optional[Any] = ..., edge_del_cost: Optional[Any] = ..., edge_ins_cost: Optional[Any] = ..., upper_bound: Optional[Any] = ...): ... -def optimize_edit_paths(G1, G2, node_match: Optional[Any] = ..., edge_match: Optional[Any] = ..., node_subst_cost: Optional[Any] = ..., node_del_cost: Optional[Any] = ..., node_ins_cost: Optional[Any] = ..., edge_subst_cost: Optional[Any] = ..., edge_del_cost: Optional[Any] = ..., edge_ins_cost: Optional[Any] = ..., upper_bound: Optional[Any] = ..., strictly_decreasing: bool = ...): ... +def graph_edit_distance( + G1, + G2, + node_match: Optional[Any] = ..., + edge_match: Optional[Any] = ..., + node_subst_cost: Optional[Any] = ..., + node_del_cost: Optional[Any] = ..., + node_ins_cost: Optional[Any] = ..., + edge_subst_cost: Optional[Any] = ..., + edge_del_cost: Optional[Any] = ..., + edge_ins_cost: Optional[Any] = ..., + upper_bound: Optional[Any] = ..., +): ... +def optimal_edit_paths( + G1, + G2, + node_match: Optional[Any] = ..., + edge_match: Optional[Any] = ..., + node_subst_cost: Optional[Any] = ..., + node_del_cost: Optional[Any] = ..., + node_ins_cost: Optional[Any] = ..., + edge_subst_cost: Optional[Any] = ..., + edge_del_cost: Optional[Any] = ..., + edge_ins_cost: Optional[Any] = ..., + upper_bound: Optional[Any] = ..., +): ... +def optimize_graph_edit_distance( + G1, + G2, + node_match: Optional[Any] = ..., + edge_match: Optional[Any] = ..., + node_subst_cost: Optional[Any] = ..., + node_del_cost: Optional[Any] = ..., + node_ins_cost: Optional[Any] = ..., + edge_subst_cost: Optional[Any] = ..., + edge_del_cost: Optional[Any] = ..., + edge_ins_cost: Optional[Any] = ..., + upper_bound: Optional[Any] = ..., +): ... +def optimize_edit_paths( + G1, + G2, + node_match: Optional[Any] = ..., + edge_match: Optional[Any] = ..., + node_subst_cost: Optional[Any] = ..., + node_del_cost: Optional[Any] = ..., + node_ins_cost: Optional[Any] = ..., + edge_subst_cost: Optional[Any] = ..., + edge_del_cost: Optional[Any] = ..., + edge_ins_cost: Optional[Any] = ..., + upper_bound: Optional[Any] = ..., + strictly_decreasing: bool = ..., +): ... diff --git a/mypy-stubs/networkx/algorithms/traversal/depth_first_search.pyi b/mypy-stubs/networkx/algorithms/traversal/depth_first_search.pyi index dc8fecf60..554accd1c 100644 --- a/mypy-stubs/networkx/algorithms/traversal/depth_first_search.pyi +++ b/mypy-stubs/networkx/algorithms/traversal/depth_first_search.pyi @@ -6,8 +6,18 @@ from typing import Any, Optional def dfs_edges(G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ...): ... def dfs_tree(G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ...): ... -def dfs_predecessors(G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ...): ... -def dfs_successors(G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ...): ... -def dfs_postorder_nodes(G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ...): ... -def dfs_preorder_nodes(G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ...): ... -def dfs_labeled_edges(G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ...): ... +def dfs_predecessors( + G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ... +): ... +def dfs_successors( + G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ... +): ... +def dfs_postorder_nodes( + G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ... +): ... +def dfs_preorder_nodes( + G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ... +): ... +def dfs_labeled_edges( + G, source: Optional[Any] = ..., depth_limit: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/tree/__init__.pyi b/mypy-stubs/networkx/algorithms/tree/__init__.pyi index dfe3cc6ce..db314da6b 100644 --- a/mypy-stubs/networkx/algorithms/tree/__init__.pyi +++ b/mypy-stubs/networkx/algorithms/tree/__init__.pyi @@ -5,5 +5,5 @@ from .branchings import * from .coding import * from .mst import * -from .recognition import * from .operations import * +from .recognition import * diff --git a/mypy-stubs/networkx/algorithms/tree/branchings.pyi b/mypy-stubs/networkx/algorithms/tree/branchings.pyi index 563bd4382..2dff70833 100644 --- a/mypy-stubs/networkx/algorithms/tree/branchings.pyi +++ b/mypy-stubs/networkx/algorithms/tree/branchings.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .recognition import * from typing import Any, Optional +from .recognition import * + def branching_weight(G, attr: str = ..., default: int = ...): ... def greedy_branching(G, attr: str = ..., default: int = ..., kind: str = ...): ... @@ -25,7 +26,9 @@ class Edmonds: edges: Any = ... template: Any = ... def __init__(self, G, seed: Optional[Any] = ...) -> None: ... - def find_optimum(self, attr: str = ..., default: int = ..., kind: str = ..., style: str = ...): ... + def find_optimum( + self, attr: str = ..., default: int = ..., kind: str = ..., style: str = ... + ): ... def maximum_branching(G, attr: str = ..., default: int = ...): ... def minimum_branching(G, attr: str = ..., default: int = ...): ... diff --git a/mypy-stubs/networkx/algorithms/tree/mst.pyi b/mypy-stubs/networkx/algorithms/tree/mst.pyi index e268af33e..13a819bc1 100644 --- a/mypy-stubs/networkx/algorithms/tree/mst.pyi +++ b/mypy-stubs/networkx/algorithms/tree/mst.pyi @@ -2,7 +2,25 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -def minimum_spanning_edges(G, algorithm: str = ..., weight: str = ..., keys: bool = ..., data: bool = ..., ignore_nan: bool = ...): ... -def maximum_spanning_edges(G, algorithm: str = ..., weight: str = ..., keys: bool = ..., data: bool = ..., ignore_nan: bool = ...): ... -def minimum_spanning_tree(G, weight: str = ..., algorithm: str = ..., ignore_nan: bool = ...): ... -def maximum_spanning_tree(G, weight: str = ..., algorithm: str = ..., ignore_nan: bool = ...): ... +def minimum_spanning_edges( + G, + algorithm: str = ..., + weight: str = ..., + keys: bool = ..., + data: bool = ..., + ignore_nan: bool = ..., +): ... +def maximum_spanning_edges( + G, + algorithm: str = ..., + weight: str = ..., + keys: bool = ..., + data: bool = ..., + ignore_nan: bool = ..., +): ... +def minimum_spanning_tree( + G, weight: str = ..., algorithm: str = ..., ignore_nan: bool = ... +): ... +def maximum_spanning_tree( + G, weight: str = ..., algorithm: str = ..., ignore_nan: bool = ... +): ... diff --git a/mypy-stubs/networkx/algorithms/vitality.pyi b/mypy-stubs/networkx/algorithms/vitality.pyi index 5cec0c8f2..6a6e452fa 100644 --- a/mypy-stubs/networkx/algorithms/vitality.pyi +++ b/mypy-stubs/networkx/algorithms/vitality.pyi @@ -4,4 +4,9 @@ from typing import Any, Optional -def closeness_vitality(G, node: Optional[Any] = ..., weight: Optional[Any] = ..., wiener_index: Optional[Any] = ...): ... +def closeness_vitality( + G, + node: Optional[Any] = ..., + weight: Optional[Any] = ..., + wiener_index: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/classes/__init__.pyi b/mypy-stubs/networkx/classes/__init__.pyi index c35bc875c..e5869d172 100644 --- a/mypy-stubs/networkx/classes/__init__.pyi +++ b/mypy-stubs/networkx/classes/__init__.pyi @@ -2,9 +2,9 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from .ordered import * -from .function import * from .digraph import DiGraph +from .function import * from .graph import Graph from .multidigraph import MultiDiGraph from .multigraph import MultiGraph +from .ordered import * diff --git a/mypy-stubs/networkx/classes/digraph.pyi b/mypy-stubs/networkx/classes/digraph.pyi index c77bb721b..bbe371e94 100644 --- a/mypy-stubs/networkx/classes/digraph.pyi +++ b/mypy-stubs/networkx/classes/digraph.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.classes.graph import Graph from typing import Any, Optional +from networkx.classes.graph import Graph + class DiGraph(Graph): node_dict_factory: Any = ... adjlist_outer_dict_factory: Any = ... diff --git a/mypy-stubs/networkx/classes/function.pyi b/mypy-stubs/networkx/classes/function.pyi index d93da4395..4de47f5f1 100644 --- a/mypy-stubs/networkx/classes/function.pyi +++ b/mypy-stubs/networkx/classes/function.pyi @@ -39,5 +39,7 @@ def is_weighted(G, edge: Optional[Any] = ..., weight: str = ...): ... def is_negatively_weighted(G, edge: Optional[Any] = ..., weight: str = ...): ... def is_empty(G): ... def nodes_with_selfloops(G): ... -def selfloop_edges(G, data: bool = ..., keys: bool = ..., default: Optional[Any] = ...): ... +def selfloop_edges( + G, data: bool = ..., keys: bool = ..., default: Optional[Any] = ... +): ... def number_of_selfloops(G): ... diff --git a/mypy-stubs/networkx/classes/graph.pyi b/mypy-stubs/networkx/classes/graph.pyi index 9692b5110..302b25351 100644 --- a/mypy-stubs/networkx/classes/graph.pyi +++ b/mypy-stubs/networkx/classes/graph.pyi @@ -34,7 +34,9 @@ class Graph: def add_star(self, nodes, **attr): ... def nodes_with_selfloops(self): ... def number_of_selfloops(self): ... - def selfloop_edges(self, data: bool = ..., keys: bool = ..., default: Optional[Any] = ...): ... + def selfloop_edges( + self, data: bool = ..., keys: bool = ..., default: Optional[Any] = ... + ): ... def number_of_nodes(self): ... def order(self): ... def has_node(self, n): ... diff --git a/mypy-stubs/networkx/classes/graphviews.pyi b/mypy-stubs/networkx/classes/graphviews.pyi index 308ddc93d..064a80f44 100644 --- a/mypy-stubs/networkx/classes/graphviews.pyi +++ b/mypy-stubs/networkx/classes/graphviews.pyi @@ -2,29 +2,38 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. +from typing import Any + from networkx.classes import DiGraph, Graph, MultiDiGraph, MultiGraph from networkx.classes.coreviews import ReadOnlyGraph -from typing import Any class SubGraph(ReadOnlyGraph, Graph): root_graph: Any = ... graph: Any = ... - def __init__(self, graph, filter_node: Any = ..., filter_edge: Any = ...) -> None: ... + def __init__( + self, graph, filter_node: Any = ..., filter_edge: Any = ... + ) -> None: ... class SubDiGraph(ReadOnlyGraph, DiGraph): root_graph: Any = ... graph: Any = ... - def __init__(self, graph, filter_node: Any = ..., filter_edge: Any = ...) -> None: ... + def __init__( + self, graph, filter_node: Any = ..., filter_edge: Any = ... + ) -> None: ... class SubMultiGraph(ReadOnlyGraph, MultiGraph): root_graph: Any = ... graph: Any = ... - def __init__(self, graph, filter_node: Any = ..., filter_edge: Any = ...) -> None: ... + def __init__( + self, graph, filter_node: Any = ..., filter_edge: Any = ... + ) -> None: ... class SubMultiDiGraph(ReadOnlyGraph, MultiDiGraph): root_graph: Any = ... graph: Any = ... - def __init__(self, graph, filter_node: Any = ..., filter_edge: Any = ...) -> None: ... + def __init__( + self, graph, filter_node: Any = ..., filter_edge: Any = ... + ) -> None: ... class ReverseView(ReadOnlyGraph, DiGraph): root_graph: Any = ... diff --git a/mypy-stubs/networkx/classes/multidigraph.pyi b/mypy-stubs/networkx/classes/multidigraph.pyi index 4962ae051..7ccf4f2d0 100644 --- a/mypy-stubs/networkx/classes/multidigraph.pyi +++ b/mypy-stubs/networkx/classes/multidigraph.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. +from typing import Any, Optional + from networkx.classes.digraph import DiGraph from networkx.classes.multigraph import MultiGraph -from typing import Any, Optional class MultiDiGraph(MultiGraph, DiGraph): edge_key_dict_factory: Any = ... diff --git a/mypy-stubs/networkx/classes/multigraph.pyi b/mypy-stubs/networkx/classes/multigraph.pyi index a4864c962..18c4329da 100644 --- a/mypy-stubs/networkx/classes/multigraph.pyi +++ b/mypy-stubs/networkx/classes/multigraph.pyi @@ -2,9 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.classes.graph import Graph from typing import Any, Optional +from networkx.classes.graph import Graph + class MultiGraph(Graph): edge_key_dict_factory: Any = ... def __init__(self, incoming_graph_data: Optional[Any] = ..., **attr) -> None: ... @@ -18,7 +19,9 @@ class MultiGraph(Graph): def has_edge(self, u, v, key: Optional[Any] = ...): ... @property def edges(self): ... - def get_edge_data(self, u, v, key: Optional[Any] = ..., default: Optional[Any] = ...): ... + def get_edge_data( + self, u, v, key: Optional[Any] = ..., default: Optional[Any] = ... + ): ... @property def degree(self): ... def is_multigraph(self): ... diff --git a/mypy-stubs/networkx/classes/ordered.pyi b/mypy-stubs/networkx/classes/ordered.pyi index de61f1af0..af305388a 100644 --- a/mypy-stubs/networkx/classes/ordered.pyi +++ b/mypy-stubs/networkx/classes/ordered.pyi @@ -2,11 +2,12 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. +from typing import Any + from .digraph import DiGraph from .graph import Graph from .multidigraph import MultiDiGraph from .multigraph import MultiGraph -from typing import Any class OrderedGraph(Graph): node_dict_factory: Any = ... diff --git a/mypy-stubs/networkx/classes/reportviews.pyi b/mypy-stubs/networkx/classes/reportviews.pyi index 1df9786dc..41d409d77 100644 --- a/mypy-stubs/networkx/classes/reportviews.pyi +++ b/mypy-stubs/networkx/classes/reportviews.pyi @@ -15,14 +15,18 @@ class NodeView(Mapping, Set): def data(self, data: bool = ..., default: Optional[Any] = ...): ... class NodeDataView(Set): - def __init__(self, nodedict, data: bool = ..., default: Optional[Any] = ...) -> None: ... + def __init__( + self, nodedict, data: bool = ..., default: Optional[Any] = ... + ) -> None: ... def __len__(self): ... def __iter__(self): ... def __contains__(self, n): ... def __getitem__(self, n): ... class DiDegreeView: - def __init__(self, G, nbunch: Optional[Any] = ..., weight: Optional[Any] = ...) -> None: ... + def __init__( + self, G, nbunch: Optional[Any] = ..., weight: Optional[Any] = ... + ) -> None: ... def __call__(self, nbunch: Optional[Any] = ..., weight: Optional[Any] = ...): ... def __getitem__(self, n): ... def __iter__(self): ... @@ -57,7 +61,13 @@ class OutMultiDegreeView(DiDegreeView): def __iter__(self): ... class OutEdgeDataView: - def __init__(self, viewer, nbunch: Optional[Any] = ..., data: bool = ..., default: Optional[Any] = ...) -> None: ... + def __init__( + self, + viewer, + nbunch: Optional[Any] = ..., + data: bool = ..., + default: Optional[Any] = ..., + ) -> None: ... def __len__(self): ... def __iter__(self): ... def __contains__(self, e): ... @@ -73,7 +83,14 @@ class InEdgeDataView(OutEdgeDataView): class OutMultiEdgeDataView(OutEdgeDataView): keys: Any = ... - def __init__(self, viewer, nbunch: Optional[Any] = ..., data: bool = ..., keys: bool = ..., default: Optional[Any] = ...) -> None: ... + def __init__( + self, + viewer, + nbunch: Optional[Any] = ..., + data: bool = ..., + keys: bool = ..., + default: Optional[Any] = ..., + ) -> None: ... def __len__(self): ... def __iter__(self): ... def __contains__(self, e): ... @@ -93,8 +110,18 @@ class OutEdgeView(Set, Mapping): def __iter__(self): ... def __contains__(self, e): ... def __getitem__(self, e): ... - def __call__(self, nbunch: Optional[Any] = ..., data: bool = ..., default: Optional[Any] = ...): ... - def data(self, data: bool = ..., default: Optional[Any] = ..., nbunch: Optional[Any] = ...): ... + def __call__( + self, + nbunch: Optional[Any] = ..., + data: bool = ..., + default: Optional[Any] = ..., + ): ... + def data( + self, + data: bool = ..., + default: Optional[Any] = ..., + nbunch: Optional[Any] = ..., + ): ... class EdgeView(OutEdgeView): dataview: Any = ... @@ -115,8 +142,20 @@ class OutMultiEdgeView(OutEdgeView): def __iter__(self): ... def __contains__(self, e): ... def __getitem__(self, e): ... - def __call__(self, nbunch: Optional[Any] = ..., data: bool = ..., keys: bool = ..., default: Optional[Any] = ...): ... - def data(self, data: bool = ..., keys: bool = ..., default: Optional[Any] = ..., nbunch: Optional[Any] = ...): ... + def __call__( + self, + nbunch: Optional[Any] = ..., + data: bool = ..., + keys: bool = ..., + default: Optional[Any] = ..., + ): ... + def data( + self, + data: bool = ..., + keys: bool = ..., + default: Optional[Any] = ..., + nbunch: Optional[Any] = ..., + ): ... class MultiEdgeView(OutMultiEdgeView): dataview: Any = ... diff --git a/mypy-stubs/networkx/convert.pyi b/mypy-stubs/networkx/convert.pyi index cc98a3e9d..ac3868c1b 100644 --- a/mypy-stubs/networkx/convert.pyi +++ b/mypy-stubs/networkx/convert.pyi @@ -4,10 +4,16 @@ from typing import Any, Optional -def to_networkx_graph(data, create_using: Optional[Any] = ..., multigraph_input: bool = ...): ... +def to_networkx_graph( + data, create_using: Optional[Any] = ..., multigraph_input: bool = ... +): ... def to_dict_of_lists(G, nodelist: Optional[Any] = ...): ... def from_dict_of_lists(d, create_using: Optional[Any] = ...): ... -def to_dict_of_dicts(G, nodelist: Optional[Any] = ..., edge_data: Optional[Any] = ...): ... -def from_dict_of_dicts(d, create_using: Optional[Any] = ..., multigraph_input: bool = ...): ... +def to_dict_of_dicts( + G, nodelist: Optional[Any] = ..., edge_data: Optional[Any] = ... +): ... +def from_dict_of_dicts( + d, create_using: Optional[Any] = ..., multigraph_input: bool = ... +): ... def to_edgelist(G, nodelist: Optional[Any] = ...): ... def from_edgelist(edgelist, create_using: Optional[Any] = ...): ... diff --git a/mypy-stubs/networkx/convert_matrix.pyi b/mypy-stubs/networkx/convert_matrix.pyi index fa379ae0b..c991bddb6 100644 --- a/mypy-stubs/networkx/convert_matrix.pyi +++ b/mypy-stubs/networkx/convert_matrix.pyi @@ -4,14 +4,71 @@ from typing import Any, Optional -def to_pandas_adjacency(G, nodelist: Optional[Any] = ..., dtype: Optional[Any] = ..., order: Optional[Any] = ..., multigraph_weight: Any = ..., weight: str = ..., nonedge: float = ...): ... +def to_pandas_adjacency( + G, + nodelist: Optional[Any] = ..., + dtype: Optional[Any] = ..., + order: Optional[Any] = ..., + multigraph_weight: Any = ..., + weight: str = ..., + nonedge: float = ..., +): ... def from_pandas_adjacency(df, create_using: Optional[Any] = ...): ... -def to_pandas_edgelist(G, source: str = ..., target: str = ..., nodelist: Optional[Any] = ..., dtype: Optional[Any] = ..., order: Optional[Any] = ...): ... -def from_pandas_edgelist(df, source: str = ..., target: str = ..., edge_attr: Optional[Any] = ..., create_using: Optional[Any] = ...): ... -def to_numpy_matrix(G, nodelist: Optional[Any] = ..., dtype: Optional[Any] = ..., order: Optional[Any] = ..., multigraph_weight: Any = ..., weight: str = ..., nonedge: float = ...): ... -def from_numpy_matrix(A, parallel_edges: bool = ..., create_using: Optional[Any] = ...): ... -def to_numpy_recarray(G, nodelist: Optional[Any] = ..., dtype: Optional[Any] = ..., order: Optional[Any] = ...): ... -def to_scipy_sparse_matrix(G, nodelist: Optional[Any] = ..., dtype: Optional[Any] = ..., weight: str = ..., format: str = ...): ... -def from_scipy_sparse_matrix(A, parallel_edges: bool = ..., create_using: Optional[Any] = ..., edge_attribute: str = ...): ... -def to_numpy_array(G, nodelist: Optional[Any] = ..., dtype: Optional[Any] = ..., order: Optional[Any] = ..., multigraph_weight: Any = ..., weight: str = ..., nonedge: float = ...): ... -def from_numpy_array(A, parallel_edges: bool = ..., create_using: Optional[Any] = ...): ... +def to_pandas_edgelist( + G, + source: str = ..., + target: str = ..., + nodelist: Optional[Any] = ..., + dtype: Optional[Any] = ..., + order: Optional[Any] = ..., +): ... +def from_pandas_edgelist( + df, + source: str = ..., + target: str = ..., + edge_attr: Optional[Any] = ..., + create_using: Optional[Any] = ..., +): ... +def to_numpy_matrix( + G, + nodelist: Optional[Any] = ..., + dtype: Optional[Any] = ..., + order: Optional[Any] = ..., + multigraph_weight: Any = ..., + weight: str = ..., + nonedge: float = ..., +): ... +def from_numpy_matrix( + A, parallel_edges: bool = ..., create_using: Optional[Any] = ... +): ... +def to_numpy_recarray( + G, + nodelist: Optional[Any] = ..., + dtype: Optional[Any] = ..., + order: Optional[Any] = ..., +): ... +def to_scipy_sparse_matrix( + G, + nodelist: Optional[Any] = ..., + dtype: Optional[Any] = ..., + weight: str = ..., + format: str = ..., +): ... +def from_scipy_sparse_matrix( + A, + parallel_edges: bool = ..., + create_using: Optional[Any] = ..., + edge_attribute: str = ..., +): ... +def to_numpy_array( + G, + nodelist: Optional[Any] = ..., + dtype: Optional[Any] = ..., + order: Optional[Any] = ..., + multigraph_weight: Any = ..., + weight: str = ..., + nonedge: float = ..., +): ... +def from_numpy_array( + A, parallel_edges: bool = ..., create_using: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/drawing/layout.pyi b/mypy-stubs/networkx/drawing/layout.pyi index 9d8917c49..63863ff00 100644 --- a/mypy-stubs/networkx/drawing/layout.pyi +++ b/mypy-stubs/networkx/drawing/layout.pyi @@ -4,12 +4,45 @@ from typing import Any, Optional -def random_layout(G, center: Optional[Any] = ..., dim: int = ..., random_state: Optional[Any] = ...): ... -def circular_layout(G, scale: int = ..., center: Optional[Any] = ..., dim: int = ...): ... -def shell_layout(G, nlist: Optional[Any] = ..., scale: int = ..., center: Optional[Any] = ..., dim: int = ...): ... -def fruchterman_reingold_layout(G, k: Optional[Any] = ..., pos: Optional[Any] = ..., fixed: Optional[Any] = ..., iterations: int = ..., threshold: float = ..., weight: str = ..., scale: int = ..., center: Optional[Any] = ..., dim: int = ..., random_state: Optional[Any] = ...): ... +def random_layout( + G, center: Optional[Any] = ..., dim: int = ..., random_state: Optional[Any] = ... +): ... +def circular_layout( + G, scale: int = ..., center: Optional[Any] = ..., dim: int = ... +): ... +def shell_layout( + G, + nlist: Optional[Any] = ..., + scale: int = ..., + center: Optional[Any] = ..., + dim: int = ..., +): ... +def fruchterman_reingold_layout( + G, + k: Optional[Any] = ..., + pos: Optional[Any] = ..., + fixed: Optional[Any] = ..., + iterations: int = ..., + threshold: float = ..., + weight: str = ..., + scale: int = ..., + center: Optional[Any] = ..., + dim: int = ..., + random_state: Optional[Any] = ..., +): ... + spring_layout = fruchterman_reingold_layout -def kamada_kawai_layout(G, dist: Optional[Any] = ..., pos: Optional[Any] = ..., weight: str = ..., scale: int = ..., center: Optional[Any] = ..., dim: int = ...): ... -def spectral_layout(G, weight: str = ..., scale: int = ..., center: Optional[Any] = ..., dim: int = ...): ... +def kamada_kawai_layout( + G, + dist: Optional[Any] = ..., + pos: Optional[Any] = ..., + weight: str = ..., + scale: int = ..., + center: Optional[Any] = ..., + dim: int = ..., +): ... +def spectral_layout( + G, weight: str = ..., scale: int = ..., center: Optional[Any] = ..., dim: int = ... +): ... def rescale_layout(pos, scale: int = ...): ... diff --git a/mypy-stubs/networkx/drawing/nx_agraph.pyi b/mypy-stubs/networkx/drawing/nx_agraph.pyi index 806f2923a..2e9900dd1 100644 --- a/mypy-stubs/networkx/drawing/nx_agraph.pyi +++ b/mypy-stubs/networkx/drawing/nx_agraph.pyi @@ -9,5 +9,14 @@ def to_agraph(N): ... def write_dot(G, path): ... def read_dot(path): ... def graphviz_layout(G, prog: str = ..., root: Optional[Any] = ..., args: str = ...): ... -def pygraphviz_layout(G, prog: str = ..., root: Optional[Any] = ..., args: str = ...): ... -def view_pygraphviz(G, edgelabel: Optional[Any] = ..., prog: str = ..., args: str = ..., suffix: str = ..., path: Optional[Any] = ...): ... +def pygraphviz_layout( + G, prog: str = ..., root: Optional[Any] = ..., args: str = ... +): ... +def view_pygraphviz( + G, + edgelabel: Optional[Any] = ..., + prog: str = ..., + args: str = ..., + suffix: str = ..., + path: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/drawing/nx_pylab.pyi b/mypy-stubs/networkx/drawing/nx_pylab.pyi index 5c2487265..72bf69163 100644 --- a/mypy-stubs/networkx/drawing/nx_pylab.pyi +++ b/mypy-stubs/networkx/drawing/nx_pylab.pyi @@ -5,11 +5,75 @@ from typing import Any, Optional def draw(G, pos: Optional[Any] = ..., ax: Optional[Any] = ..., **kwds): ... -def draw_networkx(G, pos: Optional[Any] = ..., arrows: bool = ..., with_labels: bool = ..., **kwds): ... -def draw_networkx_nodes(G, pos, nodelist: Optional[Any] = ..., node_size: int = ..., node_color: str = ..., node_shape: str = ..., alpha: float = ..., cmap: Optional[Any] = ..., vmin: Optional[Any] = ..., vmax: Optional[Any] = ..., ax: Optional[Any] = ..., linewidths: Optional[Any] = ..., edgecolors: Optional[Any] = ..., label: Optional[Any] = ..., **kwds): ... -def draw_networkx_edges(G, pos, edgelist: Optional[Any] = ..., width: float = ..., edge_color: str = ..., style: str = ..., alpha: float = ..., arrowstyle: str = ..., arrowsize: int = ..., edge_cmap: Optional[Any] = ..., edge_vmin: Optional[Any] = ..., edge_vmax: Optional[Any] = ..., ax: Optional[Any] = ..., arrows: bool = ..., label: Optional[Any] = ..., node_size: int = ..., nodelist: Optional[Any] = ..., node_shape: str = ..., **kwds): ... -def draw_networkx_labels(G, pos, labels: Optional[Any] = ..., font_size: int = ..., font_color: str = ..., font_family: str = ..., font_weight: str = ..., alpha: float = ..., bbox: Optional[Any] = ..., ax: Optional[Any] = ..., **kwds): ... -def draw_networkx_edge_labels(G, pos, edge_labels: Optional[Any] = ..., label_pos: float = ..., font_size: int = ..., font_color: str = ..., font_family: str = ..., font_weight: str = ..., alpha: float = ..., bbox: Optional[Any] = ..., ax: Optional[Any] = ..., rotate: bool = ..., **kwds): ... +def draw_networkx( + G, pos: Optional[Any] = ..., arrows: bool = ..., with_labels: bool = ..., **kwds +): ... +def draw_networkx_nodes( + G, + pos, + nodelist: Optional[Any] = ..., + node_size: int = ..., + node_color: str = ..., + node_shape: str = ..., + alpha: float = ..., + cmap: Optional[Any] = ..., + vmin: Optional[Any] = ..., + vmax: Optional[Any] = ..., + ax: Optional[Any] = ..., + linewidths: Optional[Any] = ..., + edgecolors: Optional[Any] = ..., + label: Optional[Any] = ..., + **kwds +): ... +def draw_networkx_edges( + G, + pos, + edgelist: Optional[Any] = ..., + width: float = ..., + edge_color: str = ..., + style: str = ..., + alpha: float = ..., + arrowstyle: str = ..., + arrowsize: int = ..., + edge_cmap: Optional[Any] = ..., + edge_vmin: Optional[Any] = ..., + edge_vmax: Optional[Any] = ..., + ax: Optional[Any] = ..., + arrows: bool = ..., + label: Optional[Any] = ..., + node_size: int = ..., + nodelist: Optional[Any] = ..., + node_shape: str = ..., + **kwds +): ... +def draw_networkx_labels( + G, + pos, + labels: Optional[Any] = ..., + font_size: int = ..., + font_color: str = ..., + font_family: str = ..., + font_weight: str = ..., + alpha: float = ..., + bbox: Optional[Any] = ..., + ax: Optional[Any] = ..., + **kwds +): ... +def draw_networkx_edge_labels( + G, + pos, + edge_labels: Optional[Any] = ..., + label_pos: float = ..., + font_size: int = ..., + font_color: str = ..., + font_family: str = ..., + font_weight: str = ..., + alpha: float = ..., + bbox: Optional[Any] = ..., + ax: Optional[Any] = ..., + rotate: bool = ..., + **kwds +): ... def draw_circular(G, **kwargs): ... def draw_kamada_kawai(G, **kwargs): ... def draw_random(G, **kwargs): ... diff --git a/mypy-stubs/networkx/generators/community.pyi b/mypy-stubs/networkx/generators/community.pyi index 87676ee3c..71dd2e603 100644 --- a/mypy-stubs/networkx/generators/community.pyi +++ b/mypy-stubs/networkx/generators/community.pyi @@ -7,8 +7,14 @@ from typing import Any, Optional def caveman_graph(l, k): ... def connected_caveman_graph(l, k): ... def relaxed_caveman_graph(l, k, p, seed: Optional[Any] = ...): ... -def random_partition_graph(sizes, p_in, p_out, seed: Optional[Any] = ..., directed: bool = ...): ... -def planted_partition_graph(l, k, p_in, p_out, seed: Optional[Any] = ..., directed: bool = ...): ... -def gaussian_random_partition_graph(n, s, v, p_in, p_out, directed: bool = ..., seed: Optional[Any] = ...): ... +def random_partition_graph( + sizes, p_in, p_out, seed: Optional[Any] = ..., directed: bool = ... +): ... +def planted_partition_graph( + l, k, p_in, p_out, seed: Optional[Any] = ..., directed: bool = ... +): ... +def gaussian_random_partition_graph( + n, s, v, p_in, p_out, directed: bool = ..., seed: Optional[Any] = ... +): ... def ring_of_cliques(num_cliques, clique_size): ... def windmill_graph(n, k): ... diff --git a/mypy-stubs/networkx/generators/degree_seq.pyi b/mypy-stubs/networkx/generators/degree_seq.pyi index c6a316a28..85d846470 100644 --- a/mypy-stubs/networkx/generators/degree_seq.pyi +++ b/mypy-stubs/networkx/generators/degree_seq.pyi @@ -4,13 +4,24 @@ from typing import Any, Optional -def configuration_model(deg_sequence, create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... -def directed_configuration_model(in_degree_sequence, out_degree_sequence, create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... +def configuration_model( + deg_sequence, create_using: Optional[Any] = ..., seed: Optional[Any] = ... +): ... +def directed_configuration_model( + in_degree_sequence, + out_degree_sequence, + create_using: Optional[Any] = ..., + seed: Optional[Any] = ..., +): ... def expected_degree_graph(w, seed: Optional[Any] = ..., selfloops: bool = ...): ... def havel_hakimi_graph(deg_sequence, create_using: Optional[Any] = ...): ... -def directed_havel_hakimi_graph(in_deg_sequence, out_deg_sequence, create_using: Optional[Any] = ...): ... +def directed_havel_hakimi_graph( + in_deg_sequence, out_deg_sequence, create_using: Optional[Any] = ... +): ... def degree_sequence_tree(deg_sequence, create_using: Optional[Any] = ...): ... -def random_degree_sequence_graph(sequence, seed: Optional[Any] = ..., tries: int = ...): ... +def random_degree_sequence_graph( + sequence, seed: Optional[Any] = ..., tries: int = ... +): ... class DegreeSequenceRandomGraph: degree: Any = ... diff --git a/mypy-stubs/networkx/generators/directed.pyi b/mypy-stubs/networkx/generators/directed.pyi index ab2784f1d..41015ef79 100644 --- a/mypy-stubs/networkx/generators/directed.pyi +++ b/mypy-stubs/networkx/generators/directed.pyi @@ -4,8 +4,24 @@ from typing import Any, Optional -def gn_graph(n, kernel: Optional[Any] = ..., create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... +def gn_graph( + n, + kernel: Optional[Any] = ..., + create_using: Optional[Any] = ..., + seed: Optional[Any] = ..., +): ... def gnr_graph(n, p, create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... def gnc_graph(n, create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... -def scale_free_graph(n, alpha: float = ..., beta: float = ..., gamma: float = ..., delta_in: float = ..., delta_out: int = ..., create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... -def random_k_out_graph(n, k, alpha, self_loops: bool = ..., seed: Optional[Any] = ...): ... +def scale_free_graph( + n, + alpha: float = ..., + beta: float = ..., + gamma: float = ..., + delta_in: float = ..., + delta_out: int = ..., + create_using: Optional[Any] = ..., + seed: Optional[Any] = ..., +): ... +def random_k_out_graph( + n, k, alpha, self_loops: bool = ..., seed: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/generators/ego.pyi b/mypy-stubs/networkx/generators/ego.pyi index 7999ae0a8..3322b0848 100644 --- a/mypy-stubs/networkx/generators/ego.pyi +++ b/mypy-stubs/networkx/generators/ego.pyi @@ -4,4 +4,11 @@ from typing import Any, Optional -def ego_graph(G, n, radius: int = ..., center: bool = ..., undirected: bool = ..., distance: Optional[Any] = ...): ... +def ego_graph( + G, + n, + radius: int = ..., + center: bool = ..., + undirected: bool = ..., + distance: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/generators/geometric.pyi b/mypy-stubs/networkx/generators/geometric.pyi index a904eb8e1..051b8e5be 100644 --- a/mypy-stubs/networkx/generators/geometric.pyi +++ b/mypy-stubs/networkx/generators/geometric.pyi @@ -4,9 +4,48 @@ from typing import Any, Optional -def random_geometric_graph(n, radius, dim: int = ..., pos: Optional[Any] = ..., p: int = ...): ... -def soft_random_geometric_graph(n, radius, dim: int = ..., pos: Optional[Any] = ..., p: int = ..., p_dist: Optional[Any] = ...): ... -def geographical_threshold_graph(n, theta, dim: int = ..., pos: Optional[Any] = ..., weight: Optional[Any] = ..., metric: Optional[Any] = ..., p_dist: Optional[Any] = ...): ... -def waxman_graph(n, beta: float = ..., alpha: float = ..., L: Optional[Any] = ..., domain: Any = ..., metric: Optional[Any] = ...): ... -def navigable_small_world_graph(n, p: int = ..., q: int = ..., r: int = ..., dim: int = ..., seed: Optional[Any] = ...): ... -def thresholded_random_geometric_graph(n, radius, theta, dim: int = ..., pos: Optional[Any] = ..., weight: Optional[Any] = ..., p: int = ...): ... +def random_geometric_graph( + n, radius, dim: int = ..., pos: Optional[Any] = ..., p: int = ... +): ... +def soft_random_geometric_graph( + n, + radius, + dim: int = ..., + pos: Optional[Any] = ..., + p: int = ..., + p_dist: Optional[Any] = ..., +): ... +def geographical_threshold_graph( + n, + theta, + dim: int = ..., + pos: Optional[Any] = ..., + weight: Optional[Any] = ..., + metric: Optional[Any] = ..., + p_dist: Optional[Any] = ..., +): ... +def waxman_graph( + n, + beta: float = ..., + alpha: float = ..., + L: Optional[Any] = ..., + domain: Any = ..., + metric: Optional[Any] = ..., +): ... +def navigable_small_world_graph( + n, + p: int = ..., + q: int = ..., + r: int = ..., + dim: int = ..., + seed: Optional[Any] = ..., +): ... +def thresholded_random_geometric_graph( + n, + radius, + theta, + dim: int = ..., + pos: Optional[Any] = ..., + weight: Optional[Any] = ..., + p: int = ..., +): ... diff --git a/mypy-stubs/networkx/generators/lattice.pyi b/mypy-stubs/networkx/generators/lattice.pyi index d426e6bb3..25d726a95 100644 --- a/mypy-stubs/networkx/generators/lattice.pyi +++ b/mypy-stubs/networkx/generators/lattice.pyi @@ -7,5 +7,17 @@ from typing import Any, Optional def grid_2d_graph(m, n, periodic: bool = ..., create_using: Optional[Any] = ...): ... def grid_graph(dim, periodic: bool = ...): ... def hypercube_graph(n): ... -def triangular_lattice_graph(m, n, periodic: bool = ..., with_positions: bool = ..., create_using: Optional[Any] = ...): ... -def hexagonal_lattice_graph(m, n, periodic: bool = ..., with_positions: bool = ..., create_using: Optional[Any] = ...): ... +def triangular_lattice_graph( + m, + n, + periodic: bool = ..., + with_positions: bool = ..., + create_using: Optional[Any] = ..., +): ... +def hexagonal_lattice_graph( + m, + n, + periodic: bool = ..., + with_positions: bool = ..., + create_using: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/generators/line.pyi b/mypy-stubs/networkx/generators/line.pyi index 394858581..339d8682c 100644 --- a/mypy-stubs/networkx/generators/line.pyi +++ b/mypy-stubs/networkx/generators/line.pyi @@ -2,8 +2,9 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.utils.decorators import * from typing import Any, Optional +from networkx.utils.decorators import * + def line_graph(G, create_using: Optional[Any] = ...): ... def inverse_line_graph(G): ... diff --git a/mypy-stubs/networkx/generators/random_clustered.pyi b/mypy-stubs/networkx/generators/random_clustered.pyi index ec9bab32e..ae7bf5c3d 100644 --- a/mypy-stubs/networkx/generators/random_clustered.pyi +++ b/mypy-stubs/networkx/generators/random_clustered.pyi @@ -4,4 +4,6 @@ from typing import Any, Optional -def random_clustered_graph(joint_degree_sequence, create_using: Optional[Any] = ..., seed: Optional[Any] = ...): ... +def random_clustered_graph( + joint_degree_sequence, create_using: Optional[Any] = ..., seed: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/generators/random_graphs.pyi b/mypy-stubs/networkx/generators/random_graphs.pyi index 067c54c85..16fc313df 100644 --- a/mypy-stubs/networkx/generators/random_graphs.pyi +++ b/mypy-stubs/networkx/generators/random_graphs.pyi @@ -6,6 +6,7 @@ from typing import Any, Optional def fast_gnp_random_graph(n, p, seed: Optional[Any] = ..., directed: bool = ...): ... def gnp_random_graph(n, p, seed: Optional[Any] = ..., directed: bool = ...): ... + binomial_graph = gnp_random_graph erdos_renyi_graph = gnp_random_graph @@ -13,13 +14,21 @@ def dense_gnm_random_graph(n, m, seed: Optional[Any] = ...): ... def gnm_random_graph(n, m, seed: Optional[Any] = ..., directed: bool = ...): ... def newman_watts_strogatz_graph(n, k, p, seed: Optional[Any] = ...): ... def watts_strogatz_graph(n, k, p, seed: Optional[Any] = ...): ... -def connected_watts_strogatz_graph(n, k, p, tries: int = ..., seed: Optional[Any] = ...): ... +def connected_watts_strogatz_graph( + n, k, p, tries: int = ..., seed: Optional[Any] = ... +): ... def random_regular_graph(d, n, seed: Optional[Any] = ...): ... def barabasi_albert_graph(n, m, seed: Optional[Any] = ...): ... def extended_barabasi_albert_graph(n, m, p, q, seed: Optional[Any] = ...): ... def powerlaw_cluster_graph(n, m, p, seed: Optional[Any] = ...): ... def random_lobster(n, p1, p2, seed: Optional[Any] = ...): ... def random_shell_graph(constructor, seed: Optional[Any] = ...): ... -def random_powerlaw_tree(n, gamma: int = ..., seed: Optional[Any] = ..., tries: int = ...): ... -def random_powerlaw_tree_sequence(n, gamma: int = ..., seed: Optional[Any] = ..., tries: int = ...): ... -def random_kernel_graph(n, kernel_integral, kernel_root: Optional[Any] = ..., seed: Optional[Any] = ...): ... +def random_powerlaw_tree( + n, gamma: int = ..., seed: Optional[Any] = ..., tries: int = ... +): ... +def random_powerlaw_tree_sequence( + n, gamma: int = ..., seed: Optional[Any] = ..., tries: int = ... +): ... +def random_kernel_graph( + n, kernel_integral, kernel_root: Optional[Any] = ..., seed: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/linalg/__init__.pyi b/mypy-stubs/networkx/linalg/__init__.pyi index 5ef948643..f0e2c3064 100644 --- a/mypy-stubs/networkx/linalg/__init__.pyi +++ b/mypy-stubs/networkx/linalg/__init__.pyi @@ -2,9 +2,9 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. +from networkx.linalg.algebraicconnectivity import * from networkx.linalg.attrmatrix import * -from networkx.linalg.spectrum import * from networkx.linalg.graphmatrix import * from networkx.linalg.laplacianmatrix import * -from networkx.linalg.algebraicconnectivity import * from networkx.linalg.modularitymatrix import * +from networkx.linalg.spectrum import * diff --git a/mypy-stubs/networkx/linalg/algebraicconnectivity.pyi b/mypy-stubs/networkx/linalg/algebraicconnectivity.pyi index 974280bd7..12b5a7ffa 100644 --- a/mypy-stubs/networkx/linalg/algebraicconnectivity.pyi +++ b/mypy-stubs/networkx/linalg/algebraicconnectivity.pyi @@ -16,7 +16,13 @@ class _LUSolver: def __init__(self, A) -> None: ... def solve(self, B, tol: Optional[Any] = ...): ... -def algebraic_connectivity(G, weight: str = ..., normalized: bool = ..., tol: float = ..., method: str = ...): ... -def fiedler_vector(G, weight: str = ..., normalized: bool = ..., tol: float = ..., method: str = ...): ... -def spectral_ordering(G, weight: str = ..., normalized: bool = ..., tol: float = ..., method: str = ...): ... +def algebraic_connectivity( + G, weight: str = ..., normalized: bool = ..., tol: float = ..., method: str = ... +): ... +def fiedler_vector( + G, weight: str = ..., normalized: bool = ..., tol: float = ..., method: str = ... +): ... +def spectral_ordering( + G, weight: str = ..., normalized: bool = ..., tol: float = ..., method: str = ... +): ... def setup_module(module): ... diff --git a/mypy-stubs/networkx/linalg/attrmatrix.pyi b/mypy-stubs/networkx/linalg/attrmatrix.pyi index e10548bc5..e4a404015 100644 --- a/mypy-stubs/networkx/linalg/attrmatrix.pyi +++ b/mypy-stubs/networkx/linalg/attrmatrix.pyi @@ -4,5 +4,20 @@ from typing import Any, Optional -def attr_matrix(G, edge_attr: Optional[Any] = ..., node_attr: Optional[Any] = ..., normalized: bool = ..., rc_order: Optional[Any] = ..., dtype: Optional[Any] = ..., order: Optional[Any] = ...): ... -def attr_sparse_matrix(G, edge_attr: Optional[Any] = ..., node_attr: Optional[Any] = ..., normalized: bool = ..., rc_order: Optional[Any] = ..., dtype: Optional[Any] = ...): ... +def attr_matrix( + G, + edge_attr: Optional[Any] = ..., + node_attr: Optional[Any] = ..., + normalized: bool = ..., + rc_order: Optional[Any] = ..., + dtype: Optional[Any] = ..., + order: Optional[Any] = ..., +): ... +def attr_sparse_matrix( + G, + edge_attr: Optional[Any] = ..., + node_attr: Optional[Any] = ..., + normalized: bool = ..., + rc_order: Optional[Any] = ..., + dtype: Optional[Any] = ..., +): ... diff --git a/mypy-stubs/networkx/linalg/graphmatrix.pyi b/mypy-stubs/networkx/linalg/graphmatrix.pyi index 0b30f3602..2081fb906 100644 --- a/mypy-stubs/networkx/linalg/graphmatrix.pyi +++ b/mypy-stubs/networkx/linalg/graphmatrix.pyi @@ -4,6 +4,13 @@ from typing import Any, Optional -def incidence_matrix(G, nodelist: Optional[Any] = ..., edgelist: Optional[Any] = ..., oriented: bool = ..., weight: Optional[Any] = ...): ... +def incidence_matrix( + G, + nodelist: Optional[Any] = ..., + edgelist: Optional[Any] = ..., + oriented: bool = ..., + weight: Optional[Any] = ..., +): ... def adjacency_matrix(G, nodelist: Optional[Any] = ..., weight: str = ...): ... + adj_matrix = adjacency_matrix diff --git a/mypy-stubs/networkx/linalg/laplacianmatrix.pyi b/mypy-stubs/networkx/linalg/laplacianmatrix.pyi index f02f21051..70b758f3b 100644 --- a/mypy-stubs/networkx/linalg/laplacianmatrix.pyi +++ b/mypy-stubs/networkx/linalg/laplacianmatrix.pyi @@ -5,5 +5,13 @@ from typing import Any, Optional def laplacian_matrix(G, nodelist: Optional[Any] = ..., weight: str = ...): ... -def normalized_laplacian_matrix(G, nodelist: Optional[Any] = ..., weight: str = ...): ... -def directed_laplacian_matrix(G, nodelist: Optional[Any] = ..., weight: str = ..., walk_type: Optional[Any] = ..., alpha: float = ...): ... +def normalized_laplacian_matrix( + G, nodelist: Optional[Any] = ..., weight: str = ... +): ... +def directed_laplacian_matrix( + G, + nodelist: Optional[Any] = ..., + weight: str = ..., + walk_type: Optional[Any] = ..., + alpha: float = ..., +): ... diff --git a/mypy-stubs/networkx/linalg/modularitymatrix.pyi b/mypy-stubs/networkx/linalg/modularitymatrix.pyi index 05b07df19..5e91a0993 100644 --- a/mypy-stubs/networkx/linalg/modularitymatrix.pyi +++ b/mypy-stubs/networkx/linalg/modularitymatrix.pyi @@ -4,5 +4,9 @@ from typing import Any, Optional -def modularity_matrix(G, nodelist: Optional[Any] = ..., weight: Optional[Any] = ...): ... -def directed_modularity_matrix(G, nodelist: Optional[Any] = ..., weight: Optional[Any] = ...): ... +def modularity_matrix( + G, nodelist: Optional[Any] = ..., weight: Optional[Any] = ... +): ... +def directed_modularity_matrix( + G, nodelist: Optional[Any] = ..., weight: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/readwrite/__init__.pyi b/mypy-stubs/networkx/readwrite/__init__.pyi index 177f56a9f..d16702b25 100644 --- a/mypy-stubs/networkx/readwrite/__init__.pyi +++ b/mypy-stubs/networkx/readwrite/__init__.pyi @@ -3,16 +3,16 @@ # NOTE: This dynamically typed stub was automatically generated by stubgen. from networkx.readwrite.adjlist import * -from networkx.readwrite.multiline_adjlist import * from networkx.readwrite.edgelist import * +from networkx.readwrite.gexf import * +from networkx.readwrite.gml import * from networkx.readwrite.gpickle import * -from networkx.readwrite.pajek import * -from networkx.readwrite.leda import * -from networkx.readwrite.sparse6 import * from networkx.readwrite.graph6 import * -from networkx.readwrite.nx_yaml import * -from networkx.readwrite.gml import * from networkx.readwrite.graphml import * -from networkx.readwrite.gexf import * -from networkx.readwrite.nx_shp import * from networkx.readwrite.json_graph import * +from networkx.readwrite.leda import * +from networkx.readwrite.multiline_adjlist import * +from networkx.readwrite.nx_shp import * +from networkx.readwrite.nx_yaml import * +from networkx.readwrite.pajek import * +from networkx.readwrite.sparse6 import * diff --git a/mypy-stubs/networkx/readwrite/adjlist.pyi b/mypy-stubs/networkx/readwrite/adjlist.pyi index c59eb8504..eb9cb374e 100644 --- a/mypy-stubs/networkx/readwrite/adjlist.pyi +++ b/mypy-stubs/networkx/readwrite/adjlist.pyi @@ -5,6 +5,21 @@ from typing import Any, Optional def generate_adjlist(G, delimiter: str = ...): ... -def write_adjlist(G, path, comments: str = ..., delimiter: str = ..., encoding: str = ...): ... -def parse_adjlist(lines, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ...): ... -def read_adjlist(path, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., encoding: str = ...): ... +def write_adjlist( + G, path, comments: str = ..., delimiter: str = ..., encoding: str = ... +): ... +def parse_adjlist( + lines, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., +): ... +def read_adjlist( + path, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + encoding: str = ..., +): ... diff --git a/mypy-stubs/networkx/readwrite/edgelist.pyi b/mypy-stubs/networkx/readwrite/edgelist.pyi index 3b3414961..2b50c0dd2 100644 --- a/mypy-stubs/networkx/readwrite/edgelist.pyi +++ b/mypy-stubs/networkx/readwrite/edgelist.pyi @@ -5,8 +5,40 @@ from typing import Any, Optional def generate_edgelist(G, delimiter: str = ..., data: bool = ...): ... -def write_edgelist(G, path, comments: str = ..., delimiter: str = ..., data: bool = ..., encoding: str = ...): ... -def parse_edgelist(lines, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., data: bool = ...): ... -def read_edgelist(path, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., data: bool = ..., edgetype: Optional[Any] = ..., encoding: str = ...): ... -def write_weighted_edgelist(G, path, comments: str = ..., delimiter: str = ..., encoding: str = ...): ... -def read_weighted_edgelist(path, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., encoding: str = ...): ... +def write_edgelist( + G, + path, + comments: str = ..., + delimiter: str = ..., + data: bool = ..., + encoding: str = ..., +): ... +def parse_edgelist( + lines, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + data: bool = ..., +): ... +def read_edgelist( + path, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + data: bool = ..., + edgetype: Optional[Any] = ..., + encoding: str = ..., +): ... +def write_weighted_edgelist( + G, path, comments: str = ..., delimiter: str = ..., encoding: str = ... +): ... +def read_weighted_edgelist( + path, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + encoding: str = ..., +): ... diff --git a/mypy-stubs/networkx/readwrite/gexf.pyi b/mypy-stubs/networkx/readwrite/gexf.pyi index eaffccbac..ee02cb295 100644 --- a/mypy-stubs/networkx/readwrite/gexf.pyi +++ b/mypy-stubs/networkx/readwrite/gexf.pyi @@ -4,9 +4,15 @@ from typing import Any, Optional -def write_gexf(G, path, encoding: str = ..., prettyprint: bool = ..., version: str = ...): ... -def generate_gexf(G, encoding: str = ..., prettyprint: bool = ..., version: str = ...): ... -def read_gexf(path, node_type: Optional[Any] = ..., relabel: bool = ..., version: str = ...): ... +def write_gexf( + G, path, encoding: str = ..., prettyprint: bool = ..., version: str = ... +): ... +def generate_gexf( + G, encoding: str = ..., prettyprint: bool = ..., version: str = ... +): ... +def read_gexf( + path, node_type: Optional[Any] = ..., relabel: bool = ..., version: str = ... +): ... class GEXF: versions: Any = ... @@ -31,7 +37,13 @@ class GEXFWriter(GEXF): edge_id: Any = ... attr_id: Any = ... attr: Any = ... - def __init__(self, graph: Optional[Any] = ..., encoding: str = ..., prettyprint: bool = ..., version: str = ...) -> None: ... + def __init__( + self, + graph: Optional[Any] = ..., + encoding: str = ..., + prettyprint: bool = ..., + version: str = ..., + ) -> None: ... graph_element: Any = ... def add_graph(self, G): ... def add_meta(self, G, graph_element): ... diff --git a/mypy-stubs/networkx/readwrite/graphml.pyi b/mypy-stubs/networkx/readwrite/graphml.pyi index 267c95a9d..b227aa864 100644 --- a/mypy-stubs/networkx/readwrite/graphml.pyi +++ b/mypy-stubs/networkx/readwrite/graphml.pyi @@ -4,8 +4,20 @@ from typing import Any, Optional -def write_graphml_xml(G, path, encoding: str = ..., prettyprint: bool = ..., infer_numeric_types: bool = ...): ... -def write_graphml_lxml(G, path, encoding: str = ..., prettyprint: bool = ..., infer_numeric_types: bool = ...): ... +def write_graphml_xml( + G, + path, + encoding: str = ..., + prettyprint: bool = ..., + infer_numeric_types: bool = ..., +): ... +def write_graphml_lxml( + G, + path, + encoding: str = ..., + prettyprint: bool = ..., + infer_numeric_types: bool = ..., +): ... def generate_graphml(G, encoding: str = ..., prettyprint: bool = ...): ... def read_graphml(path, node_type: Any = ..., edge_key_type: Any = ...): ... def parse_graphml(graphml_string, node_type: Any = ...): ... @@ -31,10 +43,18 @@ class GraphMLWriter(GraphML): keys: Any = ... attributes: Any = ... attribute_types: Any = ... - def __init__(self, graph: Optional[Any] = ..., encoding: str = ..., prettyprint: bool = ..., infer_numeric_types: bool = ...) -> None: ... + def __init__( + self, + graph: Optional[Any] = ..., + encoding: str = ..., + prettyprint: bool = ..., + infer_numeric_types: bool = ..., + ) -> None: ... def attr_type(self, name, scope, value): ... def get_key(self, name, attr_type, scope, default): ... - def add_data(self, name, element_type, value, scope: str = ..., default: Optional[Any] = ...): ... + def add_data( + self, name, element_type, value, scope: str = ..., default: Optional[Any] = ... + ): ... def add_attributes(self, scope, xml_obj, data, default): ... def add_nodes(self, G, graph_element): ... def add_edges(self, G, graph_element): ... @@ -55,10 +75,18 @@ class GraphMLWriterLxml(GraphMLWriter): xml: Any = ... keys: Any = ... attribute_types: Any = ... - def __init__(self, path, graph: Optional[Any] = ..., encoding: str = ..., prettyprint: bool = ..., infer_numeric_types: bool = ...) -> None: ... + def __init__( + self, + path, + graph: Optional[Any] = ..., + encoding: str = ..., + prettyprint: bool = ..., + infer_numeric_types: bool = ..., + ) -> None: ... def add_graph_element(self, G): ... def add_attributes(self, scope, xml_obj, data, default): ... def dump(self): ... + write_graphml = write_graphml_xml write_graphml = write_graphml_lxml diff --git a/mypy-stubs/networkx/readwrite/json_graph/__init__.pyi b/mypy-stubs/networkx/readwrite/json_graph/__init__.pyi index f10bb040b..ddb956c03 100644 --- a/mypy-stubs/networkx/readwrite/json_graph/__init__.pyi +++ b/mypy-stubs/networkx/readwrite/json_graph/__init__.pyi @@ -2,8 +2,8 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.readwrite.json_graph.node_link import * from networkx.readwrite.json_graph.adjacency import * -from networkx.readwrite.json_graph.tree import * -from networkx.readwrite.json_graph.jit import * from networkx.readwrite.json_graph.cytoscape import * +from networkx.readwrite.json_graph.jit import * +from networkx.readwrite.json_graph.node_link import * +from networkx.readwrite.json_graph.tree import * diff --git a/mypy-stubs/networkx/readwrite/json_graph/adjacency.pyi b/mypy-stubs/networkx/readwrite/json_graph/adjacency.pyi index c540eb8a3..82a05102e 100644 --- a/mypy-stubs/networkx/readwrite/json_graph/adjacency.pyi +++ b/mypy-stubs/networkx/readwrite/json_graph/adjacency.pyi @@ -5,4 +5,6 @@ from typing import Any def adjacency_data(G, attrs: Any = ...): ... -def adjacency_graph(data, directed: bool = ..., multigraph: bool = ..., attrs: Any = ...): ... +def adjacency_graph( + data, directed: bool = ..., multigraph: bool = ..., attrs: Any = ... +): ... diff --git a/mypy-stubs/networkx/readwrite/json_graph/node_link.pyi b/mypy-stubs/networkx/readwrite/json_graph/node_link.pyi index eb183509e..4024f94c3 100644 --- a/mypy-stubs/networkx/readwrite/json_graph/node_link.pyi +++ b/mypy-stubs/networkx/readwrite/json_graph/node_link.pyi @@ -5,4 +5,6 @@ from typing import Any, Optional def node_link_data(G, attrs: Optional[Any] = ...): ... -def node_link_graph(data, directed: bool = ..., multigraph: bool = ..., attrs: Optional[Any] = ...): ... +def node_link_graph( + data, directed: bool = ..., multigraph: bool = ..., attrs: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/readwrite/multiline_adjlist.pyi b/mypy-stubs/networkx/readwrite/multiline_adjlist.pyi index db2522392..c228feb2a 100644 --- a/mypy-stubs/networkx/readwrite/multiline_adjlist.pyi +++ b/mypy-stubs/networkx/readwrite/multiline_adjlist.pyi @@ -5,6 +5,23 @@ from typing import Any, Optional def generate_multiline_adjlist(G, delimiter: str = ...): ... -def write_multiline_adjlist(G, path, delimiter: str = ..., comments: str = ..., encoding: str = ...): ... -def parse_multiline_adjlist(lines, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., edgetype: Optional[Any] = ...): ... -def read_multiline_adjlist(path, comments: str = ..., delimiter: Optional[Any] = ..., create_using: Optional[Any] = ..., nodetype: Optional[Any] = ..., edgetype: Optional[Any] = ..., encoding: str = ...): ... +def write_multiline_adjlist( + G, path, delimiter: str = ..., comments: str = ..., encoding: str = ... +): ... +def parse_multiline_adjlist( + lines, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + edgetype: Optional[Any] = ..., +): ... +def read_multiline_adjlist( + path, + comments: str = ..., + delimiter: Optional[Any] = ..., + create_using: Optional[Any] = ..., + nodetype: Optional[Any] = ..., + edgetype: Optional[Any] = ..., + encoding: str = ..., +): ... diff --git a/mypy-stubs/networkx/readwrite/nx_shp.pyi b/mypy-stubs/networkx/readwrite/nx_shp.pyi index c2d9deb67..a9109b51c 100644 --- a/mypy-stubs/networkx/readwrite/nx_shp.pyi +++ b/mypy-stubs/networkx/readwrite/nx_shp.pyi @@ -2,5 +2,7 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -def read_shp(path, simplify: bool = ..., geom_attrs: bool = ..., strict: bool = ...): ... +def read_shp( + path, simplify: bool = ..., geom_attrs: bool = ..., strict: bool = ... +): ... def write_shp(G, outdir): ... diff --git a/mypy-stubs/networkx/relabel.pyi b/mypy-stubs/networkx/relabel.pyi index 6b43fd996..eeb7ebf13 100644 --- a/mypy-stubs/networkx/relabel.pyi +++ b/mypy-stubs/networkx/relabel.pyi @@ -5,4 +5,6 @@ from typing import Any, Optional def relabel_nodes(G, mapping, copy: bool = ...): ... -def convert_node_labels_to_integers(G, first_label: int = ..., ordering: str = ..., label_attribute: Optional[Any] = ...): ... +def convert_node_labels_to_integers( + G, first_label: int = ..., ordering: str = ..., label_attribute: Optional[Any] = ... +): ... diff --git a/mypy-stubs/networkx/tests/__init__.pyi b/mypy-stubs/networkx/tests/__init__.pyi index ca7451852..11a6b20ca 100644 --- a/mypy-stubs/networkx/tests/__init__.pyi +++ b/mypy-stubs/networkx/tests/__init__.pyi @@ -1,4 +1,3 @@ # Stubs for networkx.tests (Python 3.5) # # NOTE: This dynamically typed stub was automatically generated by stubgen. - diff --git a/mypy-stubs/networkx/utils/__init__.pyi b/mypy-stubs/networkx/utils/__init__.pyi index c8caeefe2..04da9c71c 100644 --- a/mypy-stubs/networkx/utils/__init__.pyi +++ b/mypy-stubs/networkx/utils/__init__.pyi @@ -2,10 +2,10 @@ # # NOTE: This dynamically typed stub was automatically generated by stubgen. -from networkx.utils.misc import * +from networkx.utils.contextmanagers import * from networkx.utils.decorators import * +from networkx.utils.heaps import * +from networkx.utils.misc import * from networkx.utils.random_sequence import * -from networkx.utils.union_find import * from networkx.utils.rcm import * -from networkx.utils.heaps import * -from networkx.utils.contextmanagers import * +from networkx.utils.union_find import * diff --git a/mypy-stubs/networkx/utils/heaps.pyi b/mypy-stubs/networkx/utils/heaps.pyi index ffe6cb5be..4e53dddb1 100644 --- a/mypy-stubs/networkx/utils/heaps.pyi +++ b/mypy-stubs/networkx/utils/heaps.pyi @@ -9,6 +9,7 @@ class MinHeap: key: Any = ... value: Any = ... def __init__(self, key, value) -> None: ... + def __init__(self) -> None: ... def min(self): ... def pop(self): ... @@ -26,6 +27,7 @@ class PairingHeap(MinHeap): prev: Any = ... parent: Any = ... def __init__(self, key, value) -> None: ... + def __init__(self) -> None: ... def min(self): ... def pop(self): ... diff --git a/mypy-stubs/networkx/utils/random_sequence.pyi b/mypy-stubs/networkx/utils/random_sequence.pyi index b90e8219b..7ff56e9ee 100644 --- a/mypy-stubs/networkx/utils/random_sequence.pyi +++ b/mypy-stubs/networkx/utils/random_sequence.pyi @@ -7,6 +7,8 @@ from typing import Any, Optional def powerlaw_sequence(n, exponent: float = ...): ... def zipf_rv(alpha, xmin: int = ..., seed: Optional[Any] = ...): ... def cumulative_distribution(distribution): ... -def discrete_sequence(n, distribution: Optional[Any] = ..., cdistribution: Optional[Any] = ...): ... +def discrete_sequence( + n, distribution: Optional[Any] = ..., cdistribution: Optional[Any] = ... +): ... def random_weighted_sample(mapping, k): ... def weighted_choice(mapping): ... diff --git a/mypy-stubs/prov/__init__.pyi b/mypy-stubs/prov/__init__.pyi index 8518ac7f0..3f8d5df47 100644 --- a/mypy-stubs/prov/__init__.pyi +++ b/mypy-stubs/prov/__init__.pyi @@ -1,12 +1,8 @@ -# Stubs for prov (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional +from _typeshed import Incomplete class Error(Exception): ... -def read(source: Any, format: Optional[Any] = ...): ... +# def read(source, format: Incomplete | None = ...): ... # Names in __all__ with no definition: # model diff --git a/mypy-stubs/prov/constants.pyi b/mypy-stubs/prov/constants.pyi index 7481b7e25..ac0d7582d 100644 --- a/mypy-stubs/prov/constants.pyi +++ b/mypy-stubs/prov/constants.pyi @@ -1,94 +1,90 @@ -# Stubs for prov.constants (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete +from prov.identifier import Namespace as Namespace -from typing import Any - -__email__: str -XSD: Any -PROV: Any -XSI: Any -PROV_ENTITY: Any -PROV_ACTIVITY: Any -PROV_GENERATION: Any -PROV_USAGE: Any -PROV_COMMUNICATION: Any -PROV_START: Any -PROV_END: Any -PROV_INVALIDATION: Any -PROV_DERIVATION: Any -PROV_AGENT: Any -PROV_ATTRIBUTION: Any -PROV_ASSOCIATION: Any -PROV_DELEGATION: Any -PROV_INFLUENCE: Any -PROV_BUNDLE: Any -PROV_ALTERNATE: Any -PROV_SPECIALIZATION: Any -PROV_MENTION: Any -PROV_MEMBERSHIP: Any -PROV_N_MAP: Any -ADDITIONAL_N_MAP: Any -PROV_BASE_CLS: Any -PROV_ATTR_ENTITY: Any -PROV_ATTR_ACTIVITY: Any -PROV_ATTR_TRIGGER: Any -PROV_ATTR_INFORMED: Any -PROV_ATTR_INFORMANT: Any -PROV_ATTR_STARTER: Any -PROV_ATTR_ENDER: Any -PROV_ATTR_AGENT: Any -PROV_ATTR_PLAN: Any -PROV_ATTR_DELEGATE: Any -PROV_ATTR_RESPONSIBLE: Any -PROV_ATTR_GENERATED_ENTITY: Any -PROV_ATTR_USED_ENTITY: Any -PROV_ATTR_GENERATION: Any -PROV_ATTR_USAGE: Any -PROV_ATTR_SPECIFIC_ENTITY: Any -PROV_ATTR_GENERAL_ENTITY: Any -PROV_ATTR_ALTERNATE1: Any -PROV_ATTR_ALTERNATE2: Any -PROV_ATTR_BUNDLE: Any -PROV_ATTR_INFLUENCEE: Any -PROV_ATTR_INFLUENCER: Any -PROV_ATTR_COLLECTION: Any -PROV_ATTR_TIME: Any -PROV_ATTR_STARTTIME: Any -PROV_ATTR_ENDTIME: Any -PROV_ATTRIBUTE_QNAMES: Any -PROV_ATTRIBUTE_LITERALS: Any -PROV_ATTRIBUTES: Any -PROV_RECORD_ATTRIBUTES: Any -PROV_RECORD_IDS_MAP: Any -PROV_ID_ATTRIBUTES_MAP: Any -PROV_ATTRIBUTES_ID_MAP: Any -PROV_TYPE: Any -PROV_LABEL: Any -PROV_VALUE: Any -PROV_LOCATION: Any -PROV_ROLE: Any -PROV_QUALIFIEDNAME: Any -XSD_ANYURI: Any -XSD_QNAME: Any -XSD_DATETIME: Any -XSD_TIME: Any -XSD_DATE: Any -XSD_STRING: Any -XSD_BOOLEAN: Any -XSD_INTEGER: Any -XSD_LONG: Any -XSD_INT: Any -XSD_SHORT: Any -XSD_BYTE: Any -XSD_NONNEGATIVEINTEGER: Any -XSD_UNSIGNEDLONG: Any -XSD_UNSIGNEDINT: Any -XSD_UNSIGNEDSHORT: Any -XSD_UNSIGNEDBYTE: Any -XSD_POSITIVEINTEGER: Any -XSD_NONPOSITIVEINTEGER: Any -XSD_NEGATIVEINTEGER: Any -XSD_FLOAT: Any -XSD_DOUBLE: Any -XSD_DECIMAL: Any +XSD: Incomplete +PROV: Incomplete +XSI: Incomplete +PROV_ENTITY: Incomplete +PROV_ACTIVITY: Incomplete +PROV_GENERATION: Incomplete +PROV_USAGE: Incomplete +PROV_COMMUNICATION: Incomplete +PROV_START: Incomplete +PROV_END: Incomplete +PROV_INVALIDATION: Incomplete +PROV_DERIVATION: Incomplete +PROV_AGENT: Incomplete +PROV_ATTRIBUTION: Incomplete +PROV_ASSOCIATION: Incomplete +PROV_DELEGATION: Incomplete +PROV_INFLUENCE: Incomplete +PROV_BUNDLE: Incomplete +PROV_ALTERNATE: Incomplete +PROV_SPECIALIZATION: Incomplete +PROV_MENTION: Incomplete +PROV_MEMBERSHIP: Incomplete +PROV_N_MAP: Incomplete +ADDITIONAL_N_MAP: Incomplete +PROV_BASE_CLS: Incomplete +PROV_ATTR_ENTITY: Incomplete +PROV_ATTR_ACTIVITY: Incomplete +PROV_ATTR_TRIGGER: Incomplete +PROV_ATTR_INFORMED: Incomplete +PROV_ATTR_INFORMANT: Incomplete +PROV_ATTR_STARTER: Incomplete +PROV_ATTR_ENDER: Incomplete +PROV_ATTR_AGENT: Incomplete +PROV_ATTR_PLAN: Incomplete +PROV_ATTR_DELEGATE: Incomplete +PROV_ATTR_RESPONSIBLE: Incomplete +PROV_ATTR_GENERATED_ENTITY: Incomplete +PROV_ATTR_USED_ENTITY: Incomplete +PROV_ATTR_GENERATION: Incomplete +PROV_ATTR_USAGE: Incomplete +PROV_ATTR_SPECIFIC_ENTITY: Incomplete +PROV_ATTR_GENERAL_ENTITY: Incomplete +PROV_ATTR_ALTERNATE1: Incomplete +PROV_ATTR_ALTERNATE2: Incomplete +PROV_ATTR_BUNDLE: Incomplete +PROV_ATTR_INFLUENCEE: Incomplete +PROV_ATTR_INFLUENCER: Incomplete +PROV_ATTR_COLLECTION: Incomplete +PROV_ATTR_TIME: Incomplete +PROV_ATTR_STARTTIME: Incomplete +PROV_ATTR_ENDTIME: Incomplete +PROV_ATTRIBUTE_QNAMES: Incomplete +PROV_ATTRIBUTE_LITERALS: Incomplete +PROV_ATTRIBUTES: Incomplete +PROV_RECORD_ATTRIBUTES: Incomplete +PROV_RECORD_IDS_MAP: Incomplete +PROV_ID_ATTRIBUTES_MAP: Incomplete +PROV_ATTRIBUTES_ID_MAP: Incomplete +PROV_TYPE: Incomplete +PROV_LABEL: Incomplete +PROV_VALUE: Incomplete +PROV_LOCATION: Incomplete +PROV_ROLE: Incomplete +PROV_QUALIFIEDNAME: Incomplete +XSD_ANYURI: Incomplete +XSD_QNAME: Incomplete +XSD_DATETIME: Incomplete +XSD_TIME: Incomplete +XSD_DATE: Incomplete +XSD_STRING: Incomplete +XSD_BOOLEAN: Incomplete +XSD_INTEGER: Incomplete +XSD_LONG: Incomplete +XSD_INT: Incomplete +XSD_SHORT: Incomplete +XSD_BYTE: Incomplete +XSD_NONNEGATIVEINTEGER: Incomplete +XSD_UNSIGNEDLONG: Incomplete +XSD_UNSIGNEDINT: Incomplete +XSD_UNSIGNEDSHORT: Incomplete +XSD_UNSIGNEDBYTE: Incomplete +XSD_POSITIVEINTEGER: Incomplete +XSD_NONPOSITIVEINTEGER: Incomplete +XSD_NEGATIVEINTEGER: Incomplete +XSD_FLOAT: Incomplete +XSD_DOUBLE: Incomplete +XSD_DECIMAL: Incomplete diff --git a/mypy-stubs/prov/dot.pyi b/mypy-stubs/prov/dot.pyi new file mode 100644 index 000000000..9ac52aee0 --- /dev/null +++ b/mypy-stubs/prov/dot.pyi @@ -0,0 +1,43 @@ +from _typeshed import Incomplete +from prov.model import ( + Identifier as Identifier, + PROV_ACTIVITY as PROV_ACTIVITY, + PROV_AGENT as PROV_AGENT, + PROV_ALTERNATE as PROV_ALTERNATE, + PROV_ASSOCIATION as PROV_ASSOCIATION, + PROV_ATTRIBUTE_QNAMES as PROV_ATTRIBUTE_QNAMES, + PROV_ATTRIBUTION as PROV_ATTRIBUTION, + PROV_BUNDLE as PROV_BUNDLE, + PROV_COMMUNICATION as PROV_COMMUNICATION, + PROV_DELEGATION as PROV_DELEGATION, + PROV_DERIVATION as PROV_DERIVATION, + PROV_END as PROV_END, + PROV_ENTITY as PROV_ENTITY, + PROV_GENERATION as PROV_GENERATION, + PROV_INFLUENCE as PROV_INFLUENCE, + PROV_INVALIDATION as PROV_INVALIDATION, + PROV_MEMBERSHIP as PROV_MEMBERSHIP, + PROV_MENTION as PROV_MENTION, + PROV_SPECIALIZATION as PROV_SPECIALIZATION, + PROV_START as PROV_START, + PROV_USAGE as PROV_USAGE, + ProvException as ProvException, + sorted_attributes as sorted_attributes, +) + +DOT_PROV_STYLE: Incomplete +ANNOTATION_STYLE: Incomplete +ANNOTATION_LINK_STYLE: Incomplete +ANNOTATION_START_ROW: str +ANNOTATION_ROW_TEMPLATE: str +ANNOTATION_END_ROW: str + +def htlm_link_if_uri(value): ... +def prov_to_dot( + bundle, + show_nary: bool = ..., + use_labels: bool = ..., + direction: str = ..., + show_element_attributes: bool = ..., + show_relation_attributes: bool = ..., +): ... diff --git a/mypy-stubs/prov/graph.pyi b/mypy-stubs/prov/graph.pyi index cfd94ccb3..ad8a3c493 100644 --- a/mypy-stubs/prov/graph.pyi +++ b/mypy-stubs/prov/graph.pyi @@ -1,11 +1,28 @@ -# Stubs for prov.graph (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete +from prov.model import PROV_ATTR_ACTIVITY as PROV_ATTR_ACTIVITY +from prov.model import PROV_ATTR_AGENT as PROV_ATTR_AGENT +from prov.model import PROV_ATTR_ALTERNATE1 as PROV_ATTR_ALTERNATE1 +from prov.model import PROV_ATTR_ALTERNATE2 as PROV_ATTR_ALTERNATE2 +from prov.model import PROV_ATTR_COLLECTION as PROV_ATTR_COLLECTION +from prov.model import PROV_ATTR_DELEGATE as PROV_ATTR_DELEGATE +from prov.model import PROV_ATTR_ENTITY as PROV_ATTR_ENTITY +from prov.model import PROV_ATTR_GENERAL_ENTITY as PROV_ATTR_GENERAL_ENTITY +from prov.model import PROV_ATTR_GENERATED_ENTITY as PROV_ATTR_GENERATED_ENTITY +from prov.model import PROV_ATTR_INFORMANT as PROV_ATTR_INFORMANT +from prov.model import PROV_ATTR_INFORMED as PROV_ATTR_INFORMED +from prov.model import PROV_ATTR_RESPONSIBLE as PROV_ATTR_RESPONSIBLE +from prov.model import PROV_ATTR_SPECIFIC_ENTITY as PROV_ATTR_SPECIFIC_ENTITY +from prov.model import PROV_ATTR_TRIGGER as PROV_ATTR_TRIGGER +from prov.model import PROV_ATTR_USED_ENTITY as PROV_ATTR_USED_ENTITY +from prov.model import ProvActivity as ProvActivity +from prov.model import ProvAgent as ProvAgent +from prov.model import ProvDocument as ProvDocument +from prov.model import ProvElement as ProvElement +from prov.model import ProvEntity as ProvEntity +from prov.model import ProvRecord as ProvRecord +from prov.model import ProvRelation as ProvRelation -from typing import Any +INFERRED_ELEMENT_CLASS: Incomplete -__email__: str -INFERRED_ELEMENT_CLASS: Any - -def prov_to_graph(prov_document: Any): ... -def graph_to_prov(g: Any): ... +def prov_to_graph(prov_document): ... +def graph_to_prov(g): ... diff --git a/mypy-stubs/prov/identifier.pyi b/mypy-stubs/prov/identifier.pyi index f8c2c6a8c..c0d79d912 100644 --- a/mypy-stubs/prov/identifier.pyi +++ b/mypy-stubs/prov/identifier.pyi @@ -1,37 +1,31 @@ -# Stubs for prov.identifier (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -__email__: str +from typing import Any, Union class Identifier: - def __init__(self, uri: Any) -> None: ... + def __init__(self, uri: str) -> None: ... @property - def uri(self): ... - def __eq__(self, other: Any): ... - def __hash__(self): ... - def provn_representation(self): ... + def uri(self) -> str: ... + def __eq__(self, other: Any) -> bool: ... + def __hash__(self) -> int: ... + def provn_representation(self) -> str: ... class QualifiedName(Identifier): - def __init__(self, namespace: Any, localpart: Any) -> None: ... + def __init__(self, namespace: str, localpart: str) -> None: ... @property - def namespace(self): ... + def namespace(self) -> str: ... @property - def localpart(self): ... - def __hash__(self): ... - def provn_representation(self): ... + def localpart(self) -> str: ... + def __hash__(self) -> int: ... + def provn_representation(self) -> str: ... class Namespace: - def __init__(self, prefix: Any, uri: Any) -> None: ... + def __init__(self, prefix: str, uri: str) -> None: ... @property - def uri(self): ... + def uri(self) -> str: ... @property - def prefix(self): ... - def contains(self, identifier: Any): ... - def qname(self, identifier: Any): ... - def __eq__(self, other: Any): ... - def __ne__(self, other: Any): ... - def __hash__(self): ... - def __getitem__(self, localpart: Any): ... + def prefix(self) -> str: ... + def contains(self, identifier: Union[Identifier, str]) -> bool: ... + def qname(self, identifier: Union[Identifier, str]) -> QualifiedName: ... + def __eq__(self, other: Any) -> bool: ... + def __ne__(self, other: Any) -> bool: ... + def __hash__(self) -> int: ... + def __getitem__(self, localpart: str) -> QualifiedName: ... diff --git a/mypy-stubs/prov/model.pyi b/mypy-stubs/prov/model.pyi index e27637146..28595adca 100644 --- a/mypy-stubs/prov/model.pyi +++ b/mypy-stubs/prov/model.pyi @@ -1,170 +1,206 @@ -# Stubs for prov.model (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from datetime import datetime +from typing import Any, Dict, List, Set, Tuple +from _typeshed import Incomplete from prov.constants import * -from prov import Error -from typing import Any, List, Optional +# from prov import Error as Error, serializers as serializers +from prov.identifier import Identifier as Identifier +from prov.identifier import Namespace as Namespace -__email__: str -logger: Any +logger: Incomplete -def parse_xsd_datetime(value: Any): ... -def parse_boolean(value: Any): ... +# def parse_xsd_datetime(value): ... -DATATYPE_PARSERS: Any -XSD_DATATYPE_PARSERS: Any +DATATYPE_PARSERS: Incomplete +XSD_DATATYPE_PARSERS: Incomplete -def parse_xsd_types(value: Any, datatype: Any): ... -def first(a_set: Any): ... -def encoding_provn_value(value: Any): ... - -class Literal: - def __init__(self, value: Any, datatype: Optional[Any] = ..., langtag: Optional[Any] = ...) -> None: ... - def __eq__(self, other: Any): ... - def __ne__(self, other: Any): ... - def __hash__(self): ... - @property - def value(self): ... - @property - def datatype(self): ... - @property - def langtag(self): ... - def has_no_langtag(self): ... - def provn_representation(self): ... - -class ProvException(Error): ... -class ProvWarning(Warning): ... - -class ProvExceptionInvalidQualifiedName(ProvException): - qname: Any = ... - def __init__(self, qname: Any) -> None: ... - -class ProvElementIdentifierRequired(ProvException): ... +# def first(a_set): ... class ProvRecord: - FORMAL_ATTRIBUTES: Any = ... - def __init__(self, bundle: Any, identifier: Any, attributes: Optional[Any] = ...) -> None: ... - def __hash__(self): ... - def copy(self): ... - def get_type(self): ... - def get_asserted_types(self): ... - def add_asserted_type(self, type_identifier: Any) -> None: ... - def get_attribute(self, attr_name: Any): ... + FORMAL_ATTRIBUTES: Incomplete + def __init__( + self, bundle: str, identifier: str, attributes: Dict[str, str] | None = ... + ) -> None: ... + def __hash__(self) -> int: ... + def copy(self) -> ProvRecord: ... + def get_type(self) -> str: ... + def get_asserted_types(self) -> Set[str]: ... + def add_asserted_type(self, type_identifier: str) -> None: ... + def get_attribute(self, attr_name: str) -> Set[str]: ... @property - def identifier(self): ... + def identifier(self) -> str: ... @property - def attributes(self): ... + def attributes(self) -> List[Tuple[str, str]]: ... @property - def args(self): ... + def args(self) -> Tuple[str, ...]: ... @property - def formal_attributes(self): ... + def formal_attributes(self) -> Tuple[Tuple[str, str], ...]: ... @property - def extra_attributes(self): ... + def extra_attributes(self) -> Tuple[Tuple[str, str], ...]: ... @property - def bundle(self): ... + def bundle(self) -> "ProvBundle": ... @property - def label(self): ... + def label(self) -> str: ... @property - def value(self): ... - def add_attributes(self, attributes: Any) -> None: ... - def __eq__(self, other: Any): ... - def get_provn(self): ... - def is_element(self): ... - def is_relation(self): ... + def value(self) -> str: ... + def add_attributes(self, attributes: Dict[str, str]) -> None: ... + def __eq__(self, other: Any) -> bool: ... + def get_provn(self) -> str: ... + def is_element(self) -> bool: ... + def is_relation(self) -> bool: ... class ProvElement(ProvRecord): - def __init__(self, bundle: Any, identifier: Any, attributes: Optional[Any] = ...) -> None: ... - def is_element(self): ... + def __init__( + self, + bundle: "ProvBundle", + identifier: str, + attributes: Dict[str, str] | None = ..., + ) -> None: ... + def is_element(self) -> bool: ... class ProvRelation(ProvRecord): - def is_relation(self): ... + def is_relation(self) -> bool: ... class ProvEntity(ProvElement): - def wasGeneratedBy(self, activity: Any, time: Optional[Any] = ..., attributes: Optional[Any] = ...): ... - def wasInvalidatedBy(self, activity: Any, time: Optional[Any] = ..., attributes: Optional[Any] = ...): ... - def wasDerivedFrom(self, usedEntity: Any, activity: Optional[Any] = ..., generation: Optional[Any] = ..., usage: Optional[Any] = ..., attributes: Optional[Any] = ...): ... - def wasAttributedTo(self, agent: Any, attributes: Optional[Any] = ...): ... - def alternateOf(self, alternate2: Any): ... - def specializationOf(self, generalEntity: Any): ... - def hadMember(self, entity: Any): ... + def wasGeneratedBy( + self, + activity: str, + time: datetime | str | None = ..., + attributes: Dict[str, str] | List[Tuple[str, str]] | None = ..., + ) -> ProvGeneration: ... + def wasInvalidatedBy( + self, + activity: str, + time: datetime | str | None = ..., + attributes: Dict[str, str] | List[Tuple[str, str]] | None = ..., + ) -> ProvInvalidation: ... + def wasDerivedFrom( + self, + usedEntity: str, + activity: str | None = ..., + generation: Incomplete | None = ..., + usage: Incomplete | None = ..., + attributes: Incomplete | None = ..., + ) -> ProvDerivation: ... + def wasAttributedTo( + self, + agent: str, + attributes: Dict[str, str] | List[Tuple[str, str]] | None = ..., + ) -> ProvAttribution: ... + def alternateOf(self, alternate2: str) -> ProvElement: ... + def specializationOf(self, generalEntity: str) -> ProvSpecialization: ... + def hadMember(self, entity: str) -> ProvMembership: ... class ProvActivity(ProvElement): - FORMAL_ATTRIBUTES: Any = ... - def set_time(self, startTime: Optional[Any] = ..., endTime: Optional[Any] = ...) -> None: ... + FORMAL_ATTRIBUTES: Incomplete + def set_time( + self, startTime: Incomplete | None = ..., endTime: Incomplete | None = ... + ) -> None: ... def get_startTime(self): ... def get_endTime(self): ... - def used(self, entity: Any, time: Optional[Any] = ..., attributes: Optional[Any] = ...): ... - def wasInformedBy(self, informant: Any, attributes: Optional[Any] = ...): ... - def wasStartedBy(self, trigger: Any, starter: Optional[Any] = ..., time: Optional[Any] = ..., attributes: Optional[Any] = ...): ... - def wasEndedBy(self, trigger: Any, ender: Optional[Any] = ..., time: Optional[Any] = ..., attributes: Optional[Any] = ...): ... - def wasAssociatedWith(self, agent: Any, plan: Optional[Any] = ..., attributes: Optional[Any] = ...): ... + def used( + self, entity, time: Incomplete | None = ..., attributes: Incomplete | None = ... + ): ... + def wasInformedBy(self, informant, attributes: Incomplete | None = ...): ... + def wasStartedBy( + self, + trigger, + starter: Incomplete | None = ..., + time: Incomplete | None = ..., + attributes: Incomplete | None = ..., + ): ... + def wasEndedBy( + self, + trigger, + ender: Incomplete | None = ..., + time: Incomplete | None = ..., + attributes: Incomplete | None = ..., + ): ... + def wasAssociatedWith( + self, agent, plan: Incomplete | None = ..., attributes: Incomplete | None = ... + ): ... class ProvGeneration(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvUsage(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvCommunication(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvStart(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvEnd(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvInvalidation(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvDerivation(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvAgent(ProvElement): - def actedOnBehalfOf(self, responsible: Any, activity: Optional[Any] = ..., attributes: Optional[Any] = ...): ... + def actedOnBehalfOf( + self, + responsible, + activity: Incomplete | None = ..., + attributes: Incomplete | None = ..., + ): ... class ProvAttribution(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvAssociation(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvDelegation(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvInfluence(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvSpecialization(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvAlternate(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvMention(ProvSpecialization): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete class ProvMembership(ProvRelation): - FORMAL_ATTRIBUTES: Any = ... + FORMAL_ATTRIBUTES: Incomplete -PROV_REC_CLS: Any -DEFAULT_NAMESPACES: Any +PROV_REC_CLS: Incomplete +DEFAULT_NAMESPACES: Incomplete class NamespaceManager(dict): - parent: Any = ... - def __init__(self, namespaces: Optional[Any] = ..., default: Optional[Any] = ..., parent: Optional[Any] = ...) -> None: ... - def get_namespace(self, uri: Any): ... + parent: Incomplete + def __init__( + self, + namespaces: Incomplete | None = ..., + default: Incomplete | None = ..., + parent: Incomplete | None = ..., + ) -> None: ... + def get_namespace(self, uri): ... def get_registered_namespaces(self): ... - def set_default_namespace(self, uri: Any) -> None: ... + def set_default_namespace(self, uri) -> None: ... def get_default_namespace(self): ... - def add_namespace(self, namespace: Any): ... - def add_namespaces(self, namespaces: Any) -> None: ... - def valid_qualified_name(self, qname: Any): ... + def add_namespace(self, namespace): ... + def add_namespaces(self, namespaces) -> None: ... + def valid_qualified_name(self, qname): ... def get_anonymous_identifier(self, local_prefix: str = ...): ... class ProvBundle: - def __init__(self, records: Optional[Any] = ..., identifier: Optional[Any] = ..., namespaces: Optional[Any] = ..., document: Optional[Any] = ...) -> None: ... + def __init__( + self, + records: Incomplete | None = ..., + identifier: Incomplete | None = ..., + namespaces: Incomplete | None = ..., + document: Incomplete | None = ..., + ) -> None: ... @property def namespaces(self): ... @property @@ -175,83 +211,216 @@ class ProvBundle: def identifier(self): ... @property def records(self): ... - def set_default_namespace(self, uri: Any) -> None: ... + def set_default_namespace(self, uri) -> None: ... def get_default_namespace(self): ... - def add_namespace(self, namespace_or_prefix: Any, uri: Optional[Any] = ...): ... + def add_namespace(self, namespace_or_prefix, uri: Incomplete | None = ...): ... def get_registered_namespaces(self): ... - def valid_qualified_name(self, identifier: Any): ... - def get_records(self, class_or_type_or_tuple: Optional[Any] = ...): ... - def get_record(self, identifier: Any) -> Optional[List[ProvEntity]]: ... + def valid_qualified_name(self, identifier): ... + def get_records(self, class_or_type_or_tuple: Incomplete | None = ...): ... + def get_record(self, identifier): ... def is_document(self): ... def is_bundle(self): ... def has_bundles(self): ... @property def bundles(self): ... def get_provn(self, _indent_level: int = ...): ... - def __eq__(self, other: Any): ... - def __ne__(self, other: Any): ... - __hash__: Any = ... + def __eq__(self, other): ... + def __ne__(self, other): ... + __hash__: Incomplete def unified(self): ... - def update(self, other: Any) -> None: ... - def new_record(self, record_type: Any, identifier: Any, attributes: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def add_record(self, record: Any): ... - def entity(self, identifier: Any, other_attributes: Optional[Any] = ...) -> ProvEntity: ... - def activity(self, identifier: Any, startTime: Optional[Any] = ..., endTime: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def generation(self, entity: Any, activity: Optional[Any] = ..., time: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def usage(self, activity: Any, entity: Optional[Any] = ..., time: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def start(self, activity: Any, trigger: Optional[Any] = ..., starter: Optional[Any] = ..., time: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def end(self, activity: Any, trigger: Optional[Any] = ..., ender: Optional[Any] = ..., time: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def invalidation(self, entity: Any, activity: Optional[Any] = ..., time: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def communication(self, informed: Any, informant: Any, identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def agent(self, identifier: Any, other_attributes: Optional[Any] = ...): ... - def attribution(self, entity: Any, agent: Any, identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def association(self, activity: Any, agent: Optional[Any] = ..., plan: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def delegation(self, delegate: Any, responsible: Any, activity: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def influence(self, influencee: Any, influencer: Any, identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def derivation(self, generatedEntity: Any, usedEntity: Any, activity: Optional[Any] = ..., generation: Optional[Any] = ..., usage: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def revision(self, generatedEntity: Any, usedEntity: Any, activity: Optional[Any] = ..., generation: Optional[Any] = ..., usage: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def quotation(self, generatedEntity: Any, usedEntity: Any, activity: Optional[Any] = ..., generation: Optional[Any] = ..., usage: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def primary_source(self, generatedEntity: Any, usedEntity: Any, activity: Optional[Any] = ..., generation: Optional[Any] = ..., usage: Optional[Any] = ..., identifier: Optional[Any] = ..., other_attributes: Optional[Any] = ...): ... - def specialization(self, specificEntity: Any, generalEntity: Any): ... - def alternate(self, alternate1: Any, alternate2: Any): ... - def mention(self, specificEntity: Any, generalEntity: Any, bundle: Any): ... - def collection(self, identifier: Any, other_attributes: Optional[Any] = ...): ... - def membership(self, collection: Any, entity: Any): ... - def plot(self, filename: Optional[Any] = ..., show_nary: bool = ..., use_labels: bool = ..., show_element_attributes: bool = ..., show_relation_attributes: bool = ...) -> None: ... - wasGeneratedBy: Any = ... - used: Any = ... - wasStartedBy: Any = ... - wasEndedBy: Any = ... - wasInvalidatedBy: Any = ... - wasInformedBy: Any = ... - wasAttributedTo: Any = ... - wasAssociatedWith: Any = ... - actedOnBehalfOf: Any = ... - wasInfluencedBy: Any = ... - wasDerivedFrom: Any = ... - wasRevisionOf: Any = ... - wasQuotedFrom: Any = ... - hadPrimarySource: Any = ... - alternateOf: Any = ... - specializationOf: Any = ... - mentionOf: Any = ... - hadMember: Any = ... + def update(self, other) -> None: ... + def new_record( + self, + record_type, + identifier, + attributes: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def add_record(self, record): ... + def entity(self, identifier, other_attributes: Incomplete | None = ...): ... + def activity( + self, + identifier, + startTime: Incomplete | None = ..., + endTime: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def generation( + self, + entity, + activity: Incomplete | None = ..., + time: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def usage( + self, + activity, + entity: Incomplete | None = ..., + time: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def start( + self, + activity, + trigger: Incomplete | None = ..., + starter: Incomplete | None = ..., + time: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def end( + self, + activity, + trigger: Incomplete | None = ..., + ender: Incomplete | None = ..., + time: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def invalidation( + self, + entity, + activity: Incomplete | None = ..., + time: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def communication( + self, + informed, + informant, + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def agent(self, identifier, other_attributes: Incomplete | None = ...): ... + def attribution( + self, + entity, + agent, + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def association( + self, + activity, + agent: Incomplete | None = ..., + plan: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def delegation( + self, + delegate, + responsible, + activity: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def influence( + self, + influencee, + influencer, + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def derivation( + self, + generatedEntity, + usedEntity, + activity: Incomplete | None = ..., + generation: Incomplete | None = ..., + usage: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def revision( + self, + generatedEntity, + usedEntity, + activity: Incomplete | None = ..., + generation: Incomplete | None = ..., + usage: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def quotation( + self, + generatedEntity, + usedEntity, + activity: Incomplete | None = ..., + generation: Incomplete | None = ..., + usage: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def primary_source( + self, + generatedEntity, + usedEntity, + activity: Incomplete | None = ..., + generation: Incomplete | None = ..., + usage: Incomplete | None = ..., + identifier: Incomplete | None = ..., + other_attributes: Incomplete | None = ..., + ): ... + def specialization(self, specificEntity, generalEntity): ... + def alternate(self, alternate1, alternate2): ... + def mention(self, specificEntity, generalEntity, bundle): ... + def collection(self, identifier, other_attributes: Incomplete | None = ...): ... + def membership(self, collection, entity): ... + def plot( + self, + filename: Incomplete | None = ..., + show_nary: bool = ..., + use_labels: bool = ..., + show_element_attributes: bool = ..., + show_relation_attributes: bool = ..., + ) -> None: ... + wasGeneratedBy: Incomplete + used: Incomplete + wasStartedBy: Incomplete + wasEndedBy: Incomplete + wasInvalidatedBy: Incomplete + wasInformedBy: Incomplete + wasAttributedTo: Incomplete + wasAssociatedWith: Incomplete + actedOnBehalfOf: Incomplete + wasInfluencedBy: Incomplete + wasDerivedFrom: Incomplete + wasRevisionOf: Incomplete + wasQuotedFrom: Incomplete + hadPrimarySource: Incomplete + alternateOf: Incomplete + specializationOf: Incomplete + mentionOf: Incomplete + hadMember: Incomplete class ProvDocument(ProvBundle): - def __init__(self, records: Optional[Any] = ..., namespaces: Optional[Any] = ...) -> None: ... - def __eq__(self, other: Any): ... + def __init__( + self, records: Incomplete | None = ..., namespaces: Incomplete | None = ... + ) -> None: ... + def __eq__(self, other): ... def is_document(self): ... def is_bundle(self): ... def has_bundles(self): ... @property def bundles(self): ... - def flattened(self) -> ProvDocument: ... + def flattened(self): ... def unified(self): ... - def update(self, other: Any) -> None: ... - def add_bundle(self, bundle: Any, identifier: Optional[Any] = ...) -> None: ... - def bundle(self, identifier: Any): ... - def serialize(self, destination: Optional[Any] = ..., format: str = ..., **args: Any): ... + def update(self, other) -> None: ... + def add_bundle(self, bundle, identifier: Incomplete | None = ...) -> None: ... + def bundle(self, identifier): ... + def serialize( + self, destination: Incomplete | None = ..., format: str = ..., **args + ): ... @staticmethod - def deserialize(source: Optional[Any] = ..., content: Optional[Any] = ..., format: str = ..., **args: Any): ... - -def sorted_attributes(element: Any, attributes: Any): ... + def deserialize( + source: Incomplete | None = ..., + content: Incomplete | None = ..., + format: str = ..., + **args + ): ... + +def sorted_attributes(element, attributes): ... diff --git a/mypy-stubs/prov/serializers/__init__.pyi b/mypy-stubs/prov/serializers/__init__.pyi deleted file mode 100644 index ffddb709c..000000000 --- a/mypy-stubs/prov/serializers/__init__.pyi +++ /dev/null @@ -1,21 +0,0 @@ -# Stubs for prov.serializers (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from prov import Error -from typing import Any, Optional - -class Serializer: - document: Any = ... - def __init__(self, document: Optional[Any] = ...) -> None: ... - def serialize(self, stream: Any, **kwargs: Any) -> None: ... - def deserialize(self, stream: Any, **kwargs: Any) -> None: ... - -class DoNotExist(Error): ... - -class Registry: - serializers: Any = ... - @staticmethod - def load_serializers() -> None: ... - -def get(format_name: Any): ... diff --git a/mypy-stubs/prov/serializers/provjson.pyi b/mypy-stubs/prov/serializers/provjson.pyi index 9ae7c5d2c..723c2d413 100644 --- a/mypy-stubs/prov/serializers/provjson.pyi +++ b/mypy-stubs/prov/serializers/provjson.pyi @@ -1,38 +1,42 @@ -# Stubs for prov.serializers.provjson (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from prov.constants import * import json -from prov.serializers import Error, Serializer -from typing import Any -logger: Any -__email__: str +from _typeshed import Incomplete +from prov.constants import * +from prov.model import Identifier as Identifier +from prov.model import Literal as Literal +from prov.model import Namespace as Namespace +from prov.model import ProvBundle as ProvBundle +from prov.model import ProvDocument as ProvDocument +from prov.model import first as first +from prov.model import parse_xsd_datetime as parse_xsd_datetime +from prov.serializers import Error as Error +from prov.serializers import Serializer as Serializer + +logger: Incomplete class ProvJSONException(Error): ... class AnonymousIDGenerator: def __init__(self) -> None: ... - def get_anon_id(self, obj: Any, local_prefix: str = ...): ... + def get_anon_id(self, obj, local_prefix: str = ...): ... -LITERAL_XSDTYPE_MAP: Any +LITERAL_XSDTYPE_MAP: Incomplete class ProvJSONSerializer(Serializer): - def serialize(self, stream: Any, **kwargs: Any) -> None: ... - def deserialize(self, stream: Any, **kwargs: Any): ... + def serialize(self, stream, **kwargs) -> None: ... + def deserialize(self, stream, **kwargs): ... class ProvJSONEncoder(json.JSONEncoder): - def default(self, o: Any): ... + def default(self, o): ... class ProvJSONDecoder(json.JSONDecoder): - def decode(self, s: Any, *args: Any, **kwargs: Any): ... - -def valid_qualified_name(bundle: Any, value: Any): ... -def encode_json_document(document: Any): ... -def encode_json_container(bundle: Any): ... -def decode_json_document(content: Any, document: Any) -> None: ... -def decode_json_container(jc: Any, bundle: Any) -> None: ... -def encode_json_representation(value: Any): ... -def decode_json_representation(literal: Any, bundle: Any): ... -def literal_json_representation(literal: Any): ... + def decode(self, s, *args, **kwargs): ... + +def valid_qualified_name(bundle, value): ... +def encode_json_document(document): ... +def encode_json_container(bundle): ... +def decode_json_document(content, document) -> None: ... +def decode_json_container(jc, bundle) -> None: ... +def encode_json_representation(value): ... +def decode_json_representation(literal, bundle): ... +def literal_json_representation(literal): ... diff --git a/mypy-stubs/prov/serializers/provn.pyi b/mypy-stubs/prov/serializers/provn.pyi index 31762b068..fa6ac78c7 100644 --- a/mypy-stubs/prov/serializers/provn.pyi +++ b/mypy-stubs/prov/serializers/provn.pyi @@ -1,13 +1,8 @@ -# Stubs for prov.serializers.provn (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from _typeshed import Incomplete +from prov.serializers import Serializer as Serializer -from prov.serializers import Serializer -from typing import Any - -__email__: str -logger: Any +logger: Incomplete class ProvNSerializer(Serializer): - def serialize(self, stream: Any, **kwargs: Any) -> None: ... - def deserialize(self, stream: Any, **kwargs: Any) -> None: ... + def serialize(self, stream, **kwargs) -> None: ... + def deserialize(self, stream, **kwargs) -> None: ... diff --git a/mypy-stubs/prov/serializers/provrdf.pyi b/mypy-stubs/prov/serializers/provrdf.pyi index 9683a2e3f..11e438f6b 100644 --- a/mypy-stubs/prov/serializers/provrdf.pyi +++ b/mypy-stubs/prov/serializers/provrdf.pyi @@ -1,34 +1,67 @@ -# Stubs for prov.serializers.provrdf (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. +from collections.abc import Generator -from prov.serializers import Error, Serializer -from typing import Any, Optional - -__email__: str +from _typeshed import Incomplete +from prov.constants import PROV as PROV +from prov.constants import PROV_ACTIVITY as PROV_ACTIVITY +from prov.constants import PROV_ALTERNATE as PROV_ALTERNATE +from prov.constants import PROV_ATTR_ENDER as PROV_ATTR_ENDER +from prov.constants import PROV_ATTR_ENDTIME as PROV_ATTR_ENDTIME +from prov.constants import PROV_ATTR_INFORMANT as PROV_ATTR_INFORMANT +from prov.constants import PROV_ATTR_RESPONSIBLE as PROV_ATTR_RESPONSIBLE +from prov.constants import PROV_ATTR_STARTER as PROV_ATTR_STARTER +from prov.constants import PROV_ATTR_STARTTIME as PROV_ATTR_STARTTIME +from prov.constants import PROV_ATTR_TIME as PROV_ATTR_TIME +from prov.constants import PROV_ATTR_TRIGGER as PROV_ATTR_TRIGGER +from prov.constants import PROV_ATTR_USED_ENTITY as PROV_ATTR_USED_ENTITY +from prov.constants import PROV_BASE_CLS as PROV_BASE_CLS +from prov.constants import PROV_COMMUNICATION as PROV_COMMUNICATION +from prov.constants import PROV_DELEGATION as PROV_DELEGATION +from prov.constants import PROV_DERIVATION as PROV_DERIVATION +from prov.constants import PROV_END as PROV_END +from prov.constants import PROV_GENERATION as PROV_GENERATION +from prov.constants import PROV_ID_ATTRIBUTES_MAP as PROV_ID_ATTRIBUTES_MAP +from prov.constants import PROV_INVALIDATION as PROV_INVALIDATION +from prov.constants import PROV_LOCATION as PROV_LOCATION +from prov.constants import PROV_MENTION as PROV_MENTION +from prov.constants import PROV_N_MAP as PROV_N_MAP +from prov.constants import PROV_ROLE as PROV_ROLE +from prov.constants import PROV_START as PROV_START +from prov.constants import PROV_USAGE as PROV_USAGE +from prov.constants import XSD_QNAME as XSD_QNAME +from prov.serializers import Error as Error +from prov.serializers import Serializer as Serializer class ProvRDFException(Error): ... class AnonymousIDGenerator: def __init__(self) -> None: ... - def get_anon_id(self, obj: Any, local_prefix: str = ...): ... + def get_anon_id(self, obj, local_prefix: str = ...): ... -LITERAL_XSDTYPE_MAP: Any +LITERAL_XSDTYPE_MAP: Incomplete -def attr2rdf(attr: Any): ... -def valid_qualified_name(bundle: Any, value: Any, xsd_qname: bool = ...): ... +def attr2rdf(attr): ... +def valid_qualified_name(bundle, value, xsd_qname: bool = ...): ... class ProvRDFSerializer(Serializer): - def serialize(self, stream: Optional[Any] = ..., rdf_format: str = ..., **kwargs: Any) -> None: ... - document: Any = ... - def deserialize(self, stream: Any, rdf_format: str = ..., **kwargs: Any): ... - def valid_identifier(self, value: Any): ... - def encode_rdf_representation(self, value: Any): ... - def decode_rdf_representation(self, literal: Any, graph: Any): ... - def encode_document(self, document: Any): ... - def encode_container(self, bundle: Any, container: Optional[Any] = ..., identifier: Optional[Any] = ...): ... - def decode_document(self, content: Any, document: Any) -> None: ... - def decode_container(self, graph: Any, bundle: Any) -> None: ... + def serialize( + self, stream: Incomplete | None = ..., rdf_format: str = ..., **kwargs + ) -> None: ... + document: Incomplete + def deserialize(self, stream, rdf_format: str = ..., **kwargs): ... + def valid_identifier(self, value): ... + def encode_rdf_representation(self, value): ... + def decode_rdf_representation(self, literal, graph): ... + def encode_document(self, document): ... + def encode_container( + self, + bundle, + container: Incomplete | None = ..., + identifier: Incomplete | None = ..., + ): ... + def decode_document(self, content, document) -> None: ... + def decode_container(self, graph, bundle) -> None: ... -def walk(children: Any, level: int = ..., path: Optional[Any] = ..., usename: bool = ...): ... -def literal_rdf_representation(literal: Any): ... +def walk( + children, level: int = ..., path: Incomplete | None = ..., usename: bool = ... +) -> Generator[Incomplete, None, None]: ... +def literal_rdf_representation(literal): ... diff --git a/mypy-stubs/prov/serializers/provxml.pyi b/mypy-stubs/prov/serializers/provxml.pyi index bf95af4c5..693d7f484 100644 --- a/mypy-stubs/prov/serializers/provxml.pyi +++ b/mypy-stubs/prov/serializers/provxml.pyi @@ -1,23 +1,22 @@ -# Stubs for prov.serializers.provxml (Python 3.6) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from prov.constants import * import prov.identifier -from typing import Any, Optional +from _typeshed import Incomplete +from prov.constants import * +from prov.model import DEFAULT_NAMESPACES as DEFAULT_NAMESPACES +from prov.model import sorted_attributes as sorted_attributes -__email__: str -logger: Any -FULL_NAMES_MAP: Any -FULL_PROV_RECORD_IDS_MAP: Any +logger: Incomplete +FULL_NAMES_MAP: Incomplete +FULL_PROV_RECORD_IDS_MAP: Incomplete XML_XSD_URI: str class ProvXMLException(prov.Error): ... class ProvXMLSerializer(prov.serializers.Serializer): - def serialize(self, stream: Any, force_types: bool = ..., **kwargs: Any) -> None: ... - def serialize_bundle(self, bundle: Any, element: Optional[Any] = ..., force_types: bool = ...): ... - def deserialize(self, stream: Any, **kwargs: Any): ... - def deserialize_subtree(self, xml_doc: Any, bundle: Any): ... + def serialize(self, stream, force_types: bool = ..., **kwargs) -> None: ... + def serialize_bundle( + self, bundle, element: Incomplete | None = ..., force_types: bool = ... + ): ... + def deserialize(self, stream, **kwargs): ... + def deserialize_subtree(self, xml_doc, bundle): ... -def xml_qname_to_QualifiedName(element: Any, qname_str: Any): ... +def xml_qname_to_QualifiedName(element, qname_str): ... diff --git a/mypy-stubs/pydot.pyi b/mypy-stubs/pydot.pyi index e836da853..871b3ba80 100644 --- a/mypy-stubs/pydot.pyi +++ b/mypy-stubs/pydot.pyi @@ -1,4 +1,4 @@ -from typing import Any, List +from typing import Any, Dict, List, Sequence, Union PY3: Any str_type = str @@ -11,125 +11,142 @@ DEFAULT_PROGRAMS: Any def is_windows() -> bool: ... def is_anaconda() -> bool: ... def get_executable_extension() -> str: ... -def call_graphviz(program, arguments, working_dir, **kwargs): ... - -class frozendict(dict): - __delitem__: Any - __setitem__: Any - clear: Any - pop: Any - popitem: Any - setdefault: Any - update: Any - def __new__(cls, *args, **kw): ... - def __init__(self, *args, **kw) -> None: ... - def __hash__(self): ... - -dot_keywords: Any -id_re_alpha_nums: Any -id_re_alpha_nums_with_ports: Any -id_re_num: Any -id_re_with_port: Any -id_re_dbl_quoted: Any -id_re_html: Any - -def needs_quotes(s): ... -def quote_if_necessary(s): ... -def graph_from_dot_data(s) -> List['Dot']: ... -def graph_from_dot_file(path, encoding: Any | None = ...): ... -def graph_from_edges(edge_list, node_prefix: str = ..., directed: bool = ...): ... -def graph_from_adjacency_matrix(matrix, node_prefix: str = ..., directed: bool = ...): ... -def graph_from_incidence_matrix(matrix, node_prefix: str = ..., directed: bool = ...): ... +def graph_from_dot_data(s: str) -> List["Dot"]: ... class Common: - def __get_attribute__(self, attr): ... - def set_parent_graph(self, parent_graph) -> None: ... - def get_parent_graph(self): ... - def set(self, name, value) -> None: ... - def get(self, name): ... - def get_attributes(self): ... - def set_sequence(self, seq) -> None: ... - def get_sequence(self): ... - def create_attribute_methods(self, obj_attributes: List[str]): ... + def set_parent_graph(self, parent_graph: "Graph") -> None: ... + def get_parent_graph(self) -> "Graph": ... + def set(self, name: str, value: str) -> None: ... + def get(self, name: str) -> str: ... + def get_attributes(self) -> Dict[str, str]: ... + def set_sequence(self, seq: str) -> None: ... + def get_sequence(self) -> str: ... + def create_attribute_methods(self, obj_attributes: List[str]) -> None: ... class Error(Exception): value: Any - def __init__(self, value) -> None: ... + def __init__(self, value: str) -> None: ... class InvocationException(Exception): value: Any - def __init__(self, value) -> None: ... + def __init__(self, value: str) -> None: ... class Node(Common): obj_dict: Any - def __init__(self, name: str = ..., obj_dict: Any | None = ..., **attrs) -> None: ... - def set_name(self, node_name) -> None: ... - def get_name(self): ... - def get_port(self): ... - def add_style(self, style) -> None: ... + def __init__( + self, name: str = ..., obj_dict: Any | None = ..., **attrs: Dict[str, str] + ) -> None: ... + def set_name(self, node_name: str) -> None: ... + def get_name(self) -> str: ... + def get_port(self) -> str: ... + def add_style(self, style: str) -> None: ... def to_string(self) -> str: ... class Edge(Common): obj_dict: Any - def __init__(self, src: str = ..., dst: str = ..., obj_dict: Any | None = ..., **attrs) -> None: ... - def get_source(self): ... - def get_destination(self): ... - def __hash__(self): ... - def __eq__(self, edge): ... - def parse_node_ref(self, node_str): ... + def __init__( + self, + src: str = ..., + dst: str = ..., + obj_dict: Any | None = ..., + **attrs: Dict[str, str] + ) -> None: ... + def get_source(self) -> str: ... + def get_destination(self) -> str: ... + def __hash__(self) -> int: ... + def __eq__(self, edge: Any) -> bool: ... + def parse_node_ref(self, node_str: str) -> str: ... def to_string(self) -> str: ... class Graph(Common): obj_dict: Any - def __init__(self, graph_name: str = ..., obj_dict: Any | None = ..., graph_type: str = ..., strict: bool = ..., suppress_disconnected: bool = ..., simplify: bool = ..., **attrs) -> None: ... - def get_graph_type(self): ... - def get_top_graph_type(self): ... - def set_graph_defaults(self, **attrs) -> None: ... - def get_graph_defaults(self, **attrs): ... - def set_node_defaults(self, **attrs) -> None: ... - def get_node_defaults(self, **attrs): ... - def set_edge_defaults(self, **attrs) -> None: ... - def get_edge_defaults(self, **attrs): ... - def set_simplify(self, simplify) -> None: ... - def get_simplify(self): ... - def set_type(self, graph_type) -> None: ... - def get_type(self): ... - def set_name(self, graph_name) -> None: ... - def get_name(self): ... - def set_strict(self, val) -> None: ... - def get_strict(self, val): ... - def set_suppress_disconnected(self, val) -> None: ... - def get_suppress_disconnected(self, val): ... - def get_next_sequence_number(self): ... - def add_node(self, graph_node) -> None: ... - def del_node(self, name, index: Any | None = ...): ... - def get_node(self, name): ... - def get_nodes(self): ... - def get_node_list(self): ... - def add_edge(self, graph_edge) -> None: ... - def del_edge(self, src_or_list, dst: Any | None = ..., index: Any | None = ...): ... - def get_edge(self, src_or_list, dst: Any | None = ...): ... - def get_edges(self): ... - def get_edge_list(self): ... - def add_subgraph(self, sgraph) -> None: ... - def get_subgraph(self, name): ... - def get_subgraphs(self): ... - def get_subgraph_list(self): ... - def set_parent_graph(self, parent_graph) -> None: ... + def __init__( + self, + graph_name: str = ..., + obj_dict: Any | None = ..., + graph_type: str = ..., + strict: bool = ..., + suppress_disconnected: bool = ..., + simplify: bool = ..., + **attrs: Dict[str, str] + ) -> None: ... + def get_graph_type(self) -> str: ... + def get_top_graph_type(self) -> str: ... + def set_graph_defaults(self, **attrs: Dict[str, str]) -> None: ... + def get_graph_defaults(self, **attrs: Dict[str, str]) -> Dict[str, str]: ... + def set_node_defaults(self, **attrs: Dict[str, str]) -> None: ... + def get_node_defaults(self, **attrs: Dict[str, str]) -> Dict[str, str]: ... + def set_edge_defaults(self, **attrs: Dict[str, str]) -> None: ... + def get_edge_defaults(self, **attrs: Dict[str, str]) -> Dict[str, str]: ... + def set_simplify(self, simplify: bool) -> None: ... + def get_simplify(self) -> bool: ... + def set_type(self, graph_type: str) -> None: ... + def get_type(self) -> str: ... + def set_name(self, graph_name: str) -> None: ... + def get_name(self) -> str: ... + def set_strict(self, val: bool) -> None: ... + def get_strict(self, val: Any) -> bool: ... + def set_suppress_disconnected(self, val: bool) -> None: ... + def get_suppress_disconnected(self, val: Any) -> None: ... + def get_next_sequence_number(self) -> int: ... + def add_node(self, graph_node: Node) -> None: ... + def del_node(self, name: Union[str, Node], index: int | None = ...) -> bool: ... + def get_node(self, name: str) -> Node: ... + def get_nodes(self) -> List[Node]: ... + def get_node_list(self) -> List[Node]: ... + def add_edge(self, graph_edge: Edge) -> None: ... + def del_edge( + self, + src_or_list: Union[Sequence[Node], Node], + dst: str | int | None = ..., + index: int | None = ..., + ) -> bool: ... + def get_edge( + self, src_or_list: Union[Sequence[Node], Node], dst: Any | None = ... + ) -> List[Edge]: ... + def get_edges(self) -> List[Edge]: ... + def get_edge_list(self) -> List[Edge]: ... + def add_subgraph(self, sgraph: Union["Subgraph", "Cluster"]) -> None: ... + def get_subgraph(self, name: str) -> List["Subgraph"]: ... + def get_subgraphs(self) -> List["Subgraph"]: ... + def get_subgraph_list(self) -> List["Subgraph"]: ... + def set_parent_graph(self, parent_graph: "Graph") -> None: ... def to_string(self) -> str: ... class Subgraph(Graph): - def __init__(self, graph_name: str = ..., obj_dict: Any | None = ..., suppress_disconnected: bool = ..., simplify: bool = ..., **attrs) -> None: ... + def __init__( + self, + graph_name: str = ..., + obj_dict: Any | Dict[str, str] = ..., + suppress_disconnected: bool = ..., + simplify: bool = ..., + **attrs: Dict[str, str] + ) -> None: ... class Cluster(Graph): - def __init__(self, graph_name: str = ..., obj_dict: Any | None = ..., suppress_disconnected: bool = ..., simplify: bool = ..., **attrs) -> None: ... + def __init__( + self, + graph_name: str = ..., + obj_dict: Any | Dict[str, str] = ..., + suppress_disconnected: bool = ..., + simplify: bool = ..., + **attrs: Dict[str, str] + ) -> None: ... class Dot(Graph): shape_files: Any formats: Any prog: str - def __init__(self, *argsl, **argsd): ... - def set_shape_files(self, file_paths) -> None: ... - def set_prog(self, prog) -> None: ... - def write(self, path, prog: Any | None = ..., format: str = ..., encoding: Any | None = ...): ... - def create(self, prog: Any | None = ..., format: str = ..., encoding: Any | None = ...): ... + def __init__(self, *argsl: Any, **argsd: Dict[str, str]): ... + def set_shape_files(self, file_paths: Union[str, Sequence[str]]) -> None: ... + def set_prog(self, prog: str) -> None: ... + def write( + self, + path: str, + prog: Any | str = ..., + format: str = ..., + encoding: Any | str = ..., + ) -> bool: ... + def create( + self, prog: Any | str = ..., format: str = ..., encoding: Any | str = ... + ) -> bytes: ... diff --git a/mypy-stubs/rdflib/__init__.pyi b/mypy-stubs/rdflib/__init__.pyi index 83d9d0ed5..03d8e9090 100644 --- a/mypy-stubs/rdflib/__init__.pyi +++ b/mypy-stubs/rdflib/__init__.pyi @@ -1,7 +1,4 @@ -from rdflib import util as util -from rdflib.container import * from rdflib.graph import ConjunctiveGraph as ConjunctiveGraph -from rdflib.graph import Dataset as Dataset from rdflib.graph import Graph as Graph from rdflib.namespace import CSVW as CSVW from rdflib.namespace import DC as DC diff --git a/mypy-stubs/rdflib/collection.pyi b/mypy-stubs/rdflib/collection.pyi new file mode 100644 index 000000000..0bee98429 --- /dev/null +++ b/mypy-stubs/rdflib/collection.pyi @@ -0,0 +1,19 @@ +from typing import Any, Iterator + +from rdflib.graph import Graph +from rdflib.term import Node + +class Collection: + graph: Graph + uri: Node + def __init__(self, graph: Graph, uri: Node, seq: Any = ...) -> None: ... + def n3(self) -> str: ... + def __len__(self) -> int: ... + def index(self, item: Any) -> int: ... + def __getitem__(self, key: str) -> Any: ... + def __setitem__(self, key: str, value: Any) -> None: ... + def __delitem__(self, key: str) -> None: ... + def __iter__(self) -> Iterator[Any]: ... + def append(self, item: Any) -> Collection: ... + def __iadd__(self, other: Any) -> Collection: ... + def clear(self) -> Collection: ... diff --git a/mypy-stubs/rdflib/exceptions.pyi b/mypy-stubs/rdflib/exceptions.pyi index 4066f6854..06366c971 100644 --- a/mypy-stubs/rdflib/exceptions.pyi +++ b/mypy-stubs/rdflib/exceptions.pyi @@ -7,27 +7,27 @@ class Error(Exception): class TypeCheckError(Error): type: Any node: Any - def __init__(self, node) -> None: ... + def __init__(self, node: Any) -> None: ... class SubjectTypeError(TypeCheckError): msg: Any - def __init__(self, node) -> None: ... + def __init__(self, node: Any) -> None: ... class PredicateTypeError(TypeCheckError): msg: Any - def __init__(self, node) -> None: ... + def __init__(self, node: Any) -> None: ... class ObjectTypeError(TypeCheckError): msg: Any - def __init__(self, node) -> None: ... + def __init__(self, node: Any) -> None: ... class ContextTypeError(TypeCheckError): msg: Any - def __init__(self, node) -> None: ... + def __init__(self, node: Any) -> None: ... class ParserError(Error): msg: Any - def __init__(self, msg) -> None: ... + def __init__(self, msg: Any) -> None: ... class UniquenessError(Error): - def __init__(self, values) -> None: ... + def __init__(self, values: Any) -> None: ... diff --git a/mypy-stubs/rdflib/graph.pyi b/mypy-stubs/rdflib/graph.pyi index 04c921f09..7852c81c6 100644 --- a/mypy-stubs/rdflib/graph.pyi +++ b/mypy-stubs/rdflib/graph.pyi @@ -1,5 +1,8 @@ -from typing import Any, Iterator, List, Optional, Tuple, Union, overload +from typing import Any, Iterable, Iterator, List, Optional, Set, Tuple, Union, overload +from rdflib import query +from rdflib.collection import Collection +from rdflib.resource import Resource from rdflib.term import BNode, Identifier, Node class Graph(Node): @@ -17,11 +20,11 @@ class Graph(Node): store: Any = ... identifier: Any = ... namespace_manager: Any = ... - def toPython(self): ... + def toPython(self) -> str: ... def destroy(self, configuration: Any) -> None: ... def commit(self) -> None: ... def rollback(self) -> None: ... - def open(self, configuration: Any, create: bool = ...): ... + def open(self, configuration: Any, create: bool = ...) -> Any: ... def close(self, commit_pending_transaction: bool = ...) -> None: ... def add(self, triple: Any) -> None: ... def addN(self, quads: Any) -> None: ... @@ -34,35 +37,17 @@ class Graph(Node): Optional[Identifier], ], ) -> Iterator[Tuple[Identifier, Identifier, Identifier]]: ... - def __getitem__(self, item: Any): ... - def __len__(self): ... - def __iter__(self) -> Any: ... - def __contains__(self, triple: Any): ... - def __hash__(self) -> Any: ... - def __cmp__(self, other: Any): ... - def __eq__(self, other: Any) -> Any: ... - def __lt__(self, other: Any) -> Any: ... - def __le__(self, other: Any) -> Any: ... - def __gt__(self, other: Any) -> Any: ... - def __ge__(self, other: Any) -> Any: ... - def __iadd__(self, other: Any): ... - def __isub__(self, other: Any): ... - def __add__(self, other: Any): ... - def __mul__(self, other: Any): ... - def __sub__(self, other: Any): ... - def __xor__(self, other: Any): ... - __or__: Any = ... - __and__: Any = ... + def __add__(self, other: Any) -> Graph: ... def set(self, triple: Any) -> None: ... def subjects( self, predicate: Optional[Any] = ..., object: Optional[Any] = ... - ) -> List[str]: ... + ) -> Iterable[Node]: ... def predicates( self, subject: Optional[Any] = ..., object: Optional[Any] = ... - ) -> None: ... + ) -> Iterable[Node]: ... def objects( self, subject: Optional[Any] = ..., predicate: Optional[Any] = ... - ) -> List[str]: ... + ) -> Iterable[Node]: ... def subject_predicates(self, object: Optional[Any] = ...) -> None: ... def subject_objects(self, predicate: Optional[Any] = ...) -> None: ... def predicate_objects(self, subject: Optional[Any] = ...) -> None: ... @@ -74,34 +59,34 @@ class Graph(Node): object: Optional[Any] = ..., default: Optional[Any] = ..., any: bool = ..., - ): ... - def label(self, subject: Any, default: str = ...): ... + ) -> Any: ... + def label(self, subject: Any, default: str = ...) -> Any: ... def preferredLabel( self, subject: Any, lang: Optional[Any] = ..., default: Optional[Any] = ..., labelProperties: Any = ..., - ): ... - def comment(self, subject: Any, default: str = ...): ... - def items(self, list: Any) -> None: ... + ) -> List[Tuple[Any, Any]]: ... + def comment(self, subject: Any, default: str = ...) -> Any: ... + def items(self, list: Any) -> Iterator[Any]: ... def transitiveClosure( self, func: Any, arg: Any, seen: Optional[Any] = ... - ) -> None: ... + ) -> Iterator[Any]: ... def transitive_objects( self, subject: Any, property: Any, remember: Optional[Any] = ... - ) -> None: ... + ) -> Iterator[Any]: ... def transitive_subjects( self, predicate: Any, object: Any, remember: Optional[Any] = ... - ) -> None: ... - def seq(self, subject: Any): ... - def qname(self, uri: Any): ... - def compute_qname(self, uri: Any, generate: bool = ...): ... + ) -> Iterator[Any]: ... + def seq(self, subject: Any) -> Seq | None: ... + def qname(self, uri: Any) -> Any: ... + def compute_qname(self, uri: Any, generate: bool = ...) -> Any: ... def bind( self, prefix: Any, namespace: Any, override: bool = ..., replace: bool = ... - ): ... - def namespaces(self) -> None: ... - def absolutize(self, uri: Any, defrag: int = ...): ... + ) -> Any: ... + def namespaces(self) -> Iterator[Tuple[Any, Any]]: ... + def absolutize(self, uri: Any, defrag: int = ...) -> Any: ... def serialize( self, destination: Optional[Any] = ..., @@ -109,7 +94,7 @@ class Graph(Node): base: Optional[Any] = ..., encoding: Optional[Any] = ..., **args: Any - ): ... + ) -> Union[bytes, str, "Graph"]: ... def parse( self, source: Optional[Any] = ..., @@ -119,10 +104,10 @@ class Graph(Node): file: Optional[Any] = ..., data: Optional[Any] = ..., **args: Any - ): ... + ) -> "Graph": ... def load( self, source: Any, publicID: Optional[Any] = ..., format: str = ... - ) -> None: ... + ) -> "Graph": ... def query( self, query_object: Any, @@ -132,7 +117,7 @@ class Graph(Node): initBindings: Optional[Any] = ..., use_store_provided: bool = ..., **kwargs: Any - ): ... + ) -> query.Result: ... def update( self, update_object: Any, @@ -141,24 +126,23 @@ class Graph(Node): initBindings: Optional[Any] = ..., use_store_provided: bool = ..., **kwargs: Any - ): ... - def n3(self): ... - def __reduce__(self): ... - def isomorphic(self, other: Any): ... - def connected(self): ... - def all_nodes(self): ... - def collection(self, identifier: Any): ... - def resource(self, identifier: Any): ... + ) -> Any: ... + def n3(self) -> str: ... + def isomorphic(self, other: Any) -> bool: ... + def connected(self) -> bool: ... + def all_nodes(self) -> Set[Any]: ... + def collection(self, identifier: Any) -> Collection: ... + def resource(self, identifier: Any) -> Resource: ... def skolemize( self, new_graph: Optional[Any] = ..., bnode: Optional[Any] = ..., authority: Optional[Any] = ..., basepath: Optional[Any] = ..., - ): ... + ) -> Graph: ... def de_skolemize( self, new_graph: Optional[Any] = ..., uriref: Optional[Any] = ... - ): ... + ) -> Graph: ... class ConjunctiveGraph(Graph): context_aware: bool = ... @@ -170,43 +154,21 @@ class ConjunctiveGraph(Graph): identifier: Optional[Any] = ..., default_graph_base: Optional[Any] = ..., ) -> None: ... - def __contains__(self, triple_or_quad: Any): ... def add(self, triple_or_quad: Any) -> None: ... def addN(self, quads: Any) -> None: ... def remove(self, triple_or_quad: Any) -> None: ... # def triples(self, triple_or_quad: Tuple[Optional[Union[str, BNode]], Optional[Union[str, BNode]], Optional[BNode]], context: Tuple[Optional[Union[str, BNode]], Optional[Union[str, BNode]], Optional[BNode]]) -> Iterator[Tuple[Identifier, Identifier, Identifier]]: ... def quads(self, triple_or_quad: Optional[Any] = ...) -> None: ... def triples_choices(self, triple: Any, context: Optional[Any] = ...) -> None: ... - def __len__(self): ... def contexts(self, triple: Optional[Any] = ...) -> None: ... def get_context( - self, identifier: Any, quoted: bool = ..., base: Optional[Any] = ... - ): ... - def remove_context(self, context: Any) -> None: ... - def context_id(self, uri: Any, context_id: Optional[Any] = ...): ... - def parse( - self, - source: Optional[Any] = ..., - publicID: Optional[Any] = ..., - format: Optional[str] = ..., - location: Optional[Any] = ..., - file: Optional[Any] = ..., - data: Optional[Any] = ..., - **args: Any - ): ... - def __reduce__(self): ... - -class Dataset(ConjunctiveGraph): - __doc__: str = ... - default_context: Any = ... - default_union: Any = ... - def __init__( self, - store: str = ..., - default_union: bool = ..., - default_graph_base: Optional[Any] = ..., - ) -> None: ... - def graph(self, identifier: Optional[Any] = ..., base: Optional[Any] = ...): ... + identifier: Node | str | None, + quoted: bool = ..., + base: Optional[str] = ..., + ) -> Graph: ... + def remove_context(self, context: Any) -> None: ... + def context_id(self, uri: Any, context_id: Optional[Any] = ...) -> Any: ... def parse( self, source: Optional[Any] = ..., @@ -216,59 +178,8 @@ class Dataset(ConjunctiveGraph): file: Optional[Any] = ..., data: Optional[Any] = ..., **args: Any - ): ... - def add_graph(self, g: Any): ... - def remove_graph(self, g: Any) -> None: ... - def contexts(self, triple: Optional[Any] = ...) -> None: ... - graphs: Any = ... - -class QuotedGraph(Graph): - def __init__(self, store: Any, identifier: Any) -> None: ... - def add(self, triple: Any) -> None: ... - def addN(self, quads: Any) -> None: ... - def n3(self): ... - def __reduce__(self): ... + ) -> Graph: ... class Seq: - def __init__(self, graph: Any, subject: Any) -> None: ... - def toPython(self): ... - def __iter__(self) -> Any: ... - def __len__(self): ... - def __getitem__(self, index: Any): ... - -class ModificationException(Exception): - def __init__(self) -> None: ... - -class UnSupportedAggregateOperation(Exception): - def __init__(self) -> None: ... - -class ReadOnlyGraphAggregate(ConjunctiveGraph): - graphs: Any = ... - def __init__(self, graphs: Any, store: str = ...) -> None: ... - def destroy(self, configuration: Any) -> None: ... - def commit(self) -> None: ... - def rollback(self) -> None: ... - def open(self, configuration: Any, create: bool = ...) -> None: ... - def add(self, triple: Any) -> None: ... - def addN(self, quads: Any) -> None: ... - def remove(self, triple: Any) -> None: ... - def triples( - self, - triple: Tuple[ - Optional[Union[str, Identifier]], - Optional[Union[str, Identifier]], - Optional[Identifier], - ], - ) -> Iterator[Tuple[Identifier, Identifier, Identifier]]: ... - def __contains__(self, triple_or_quad: Any): ... - def __len__(self): ... - def __hash__(self) -> Any: ... - def __cmp__(self, other: Any): ... - def __iadd__(self, other: Any) -> None: ... - def __isub__(self, other: Any) -> None: ... - def triples_choices(self, triple: Any, context: Optional[Any] = ...) -> None: ... - def qname(self, uri: Any): ... - def compute_qname(self, uri: Any, generate: bool = ...): ... - def namespaces(self) -> None: ... - def absolutize(self, uri: Any, defrag: int = ...) -> None: ... - def n3(self) -> None: ... + def __init__(self, graph: Graph, subject: Any) -> None: ... + def toPython(self) -> Seq: ... diff --git a/mypy-stubs/rdflib/namespace/__init__.pyi b/mypy-stubs/rdflib/namespace/__init__.pyi index 6803addd8..2ecbc29db 100644 --- a/mypy-stubs/rdflib/namespace/__init__.pyi +++ b/mypy-stubs/rdflib/namespace/__init__.pyi @@ -1,13 +1,11 @@ -from typing import Any +from typing import Any, Tuple from rdflib.term import URIRef __all__ = [ - "is_ncname", "split_uri", "Namespace", "ClosedNamespace", - "NamespaceManager", "RDF", "RDFS", "CSVW", @@ -34,64 +32,30 @@ __all__ = [ ] class Namespace(str): - def __new__(cls, value: Any): ... @property - def title(self): ... - def term(self, name: Any): ... - def __getitem__(self, key: Any): ... - def __getattr__(self, name: Any): ... - def __contains__(self, ref): ... + def title(self) -> URIRef: ... + def term(self, name: Any) -> URIRef: ... + def __getitem__(self, key: Any) -> URIRef: ... class URIPattern(str): - def __new__(cls, value: Any): ... - def __mod__(self, *args: Any, **kwargs: Any): ... - def format(self, *args: Any, **kwargs: Any): ... + def format(self, *args: Any, **kwargs: Any) -> str: ... -class DefinedNamespaceMeta(type): - def __getitem__(cls, name, default: Any | None = ...): ... - def __getattr__(cls, name): ... - def __add__(cls, other): ... - def __contains__(cls, item): ... +class DefinedNamespaceMeta(type): ... class DefinedNamespace(metaclass=DefinedNamespaceMeta): def __init__(self) -> None: ... class ClosedNamespace(Namespace): - def __new__(cls, uri: Any, terms: Any): ... + def __new__(cls, uri: Any, terms: Any) -> ClosedNamespace: ... @property - def uri(self): ... - def term(self, name: Any): ... - def __getitem__(self, key: Any): ... - def __getattr__(self, name: Any): ... - def __dir__(self): ... - def __contains__(self, ref): ... + def uri(self) -> str: ... NAME_START_CATEGORIES = ["Ll", "Lu", "Lo", "Lt", "Nl"] SPLIT_START_CATEGORIES = NAME_START_CATEGORIES + ["Nd"] -class NamespaceManager: - graph: Any - def __init__(self, graph) -> None: ... - def __contains__(self, ref): ... - def reset(self) -> None: ... - @property - def store(self): ... - def qname(self, uri): ... - def qname_strict(self, uri): ... - def normalizeUri(self, rdfTerm) -> str: ... - def compute_qname(self, uri, generate: bool = ...): ... - def compute_qname_strict(self, uri, generate: bool = ...): ... - def bind( - self, prefix, namespace, override: bool = ..., replace: bool = ... - ) -> None: ... - def namespaces(self) -> None: ... - def absolutize(self, uri, defrag: int = ...): ... - -def is_ncname(name): ... - XMLNS = "http://www.w3.org/XML/1998/namespace" -def split_uri(uri: Any, split_start: Any = ...): ... +def split_uri(uri: Any, split_start: Any = ...) -> Tuple[str, str]: ... from rdflib.namespace._CSVW import CSVW from rdflib.namespace._DC import DC diff --git a/mypy-stubs/rdflib/parser.pyi b/mypy-stubs/rdflib/parser.pyi index bc786b165..4c628bec9 100644 --- a/mypy-stubs/rdflib/parser.pyi +++ b/mypy-stubs/rdflib/parser.pyi @@ -1,27 +1,5 @@ from typing import Any -from xml.sax import xmlreader class Parser: def __init__(self) -> None: ... - def parse(self, source, sink) -> None: ... - -class InputSource(xmlreader.InputSource): - content_type: Any - auto_close: bool - def __init__(self, system_id: Any | None = ...) -> None: ... - def close(self) -> None: ... - -class StringInputSource(InputSource): - def __init__(self, value, system_id: Any | None = ...) -> None: ... - -class URLInputSource(InputSource): - url: Any - content_type: Any - response_info: Any - def __init__( - self, system_id: Any | None = ..., format: Any | None = ... - ) -> None: ... - -class FileInputSource(InputSource): - file: Any - def __init__(self, file) -> None: ... + def parse(self, source: Any, sink: Any) -> None: ... diff --git a/mypy-stubs/rdflib/paths.pyi b/mypy-stubs/rdflib/paths.pyi deleted file mode 100644 index 8858dcb3b..000000000 --- a/mypy-stubs/rdflib/paths.pyi +++ /dev/null @@ -1,67 +0,0 @@ -from typing import Any, Callable, Union - -from rdflib.term import Node as Node -from rdflib.term import URIRef as URIRef - -ZeroOrMore: str -OneOrMore: str -ZeroOrOne: str - -class Path: - __or__: Callable[[Path, Union[URIRef, Path]], AlternativePath] - __invert__: Callable[[Path], InvPath] - __neg__: Callable[[Path], NegatedPath] - __truediv__: Callable[[Path, Union[URIRef, Path]], SequencePath] - __mul__: Callable[[Path, str], MulPath] - def eval(self, graph, subj: Any | None = ..., obj: Any | None = ...) -> None: ... - def __hash__(self): ... - def __eq__(self, other): ... - def __lt__(self, other): ... - def __le__(self, other): ... - def __ne__(self, other): ... - def __gt__(self, other): ... - def __ge__(self, other): ... - -class InvPath(Path): - arg: Any - def __init__(self, arg) -> None: ... - def eval(self, graph, subj: Any | None = ..., obj: Any | None = ...) -> None: ... - def n3(self): ... - -class SequencePath(Path): - args: Any - def __init__(self, *args) -> None: ... - def eval(self, graph, subj: Any | None = ..., obj: Any | None = ...): ... - def n3(self): ... - -class AlternativePath(Path): - args: Any - def __init__(self, *args) -> None: ... - def eval(self, graph, subj: Any | None = ..., obj: Any | None = ...) -> None: ... - def n3(self): ... - -class MulPath(Path): - path: Any - mod: Any - zero: bool - more: bool - def __init__(self, path, mod) -> None: ... - def eval( - self, graph, subj: Any | None = ..., obj: Any | None = ..., first: bool = ... - ) -> None: ... - def n3(self): ... - -class NegatedPath(Path): - args: Any - def __init__(self, arg) -> None: ... - def eval(self, graph, subj: Any | None = ..., obj: Any | None = ...) -> None: ... - def n3(self): ... - -class PathList(list): ... - -def path_alternative(self, other): ... -def path_sequence(self, other): ... -def evalPath(graph, t): ... -def mul_path(p, mul): ... -def inv_path(p): ... -def neg_path(p): ... diff --git a/mypy-stubs/rdflib/plugin.pyi b/mypy-stubs/rdflib/plugin.pyi index fbd2810fb..9b94e99f3 100644 --- a/mypy-stubs/rdflib/plugin.pyi +++ b/mypy-stubs/rdflib/plugin.pyi @@ -2,24 +2,7 @@ from typing import Any, Type, TypeVar from rdflib.exceptions import Error -class PluginException(Error): ... - -class Plugin: - name: Any - kind: Any - module_path: Any - class_name: Any - def __init__(self, name, kind, module_path, class_name) -> None: ... - def getClass(self): ... - -class PKGPlugin(Plugin): - name: Any - kind: Any - ep: Any - def __init__(self, name, kind, ep) -> None: ... - def getClass(self): ... - -def register(name: str, kind, module_path, class_name): ... +def register(name: str, kind: Any, module_path: str, class_name: str) -> None: ... PluginT = TypeVar("PluginT") diff --git a/mypy-stubs/rdflib/plugins/parsers/notation3.pyi b/mypy-stubs/rdflib/plugins/parsers/notation3.pyi index 1413bf877..e022eda40 100644 --- a/mypy-stubs/rdflib/plugins/parsers/notation3.pyi +++ b/mypy-stubs/rdflib/plugins/parsers/notation3.pyi @@ -4,10 +4,8 @@ from typing import Any -from rdflib.parser import Parser - class BadSyntax(SyntaxError): lines = ... # type: Any - def __init__(self, uri, lines, argstr, i, why): ... + def __init__(self, uri: Any, lines: Any, argstr: Any, i: Any, why: Any): ... @property - def message(self): ... + def message(self) -> Any: ... diff --git a/mypy-stubs/rdflib/query.pyi b/mypy-stubs/rdflib/query.pyi index e9cd37a56..2b73dafe9 100644 --- a/mypy-stubs/rdflib/query.pyi +++ b/mypy-stubs/rdflib/query.pyi @@ -1,62 +1,24 @@ from io import BufferedIOBase -from typing import Any, Optional, Union - -class Processor: - def __init__(self, graph) -> None: ... - def query( - self, strOrQuery, initBindings=..., initNs=..., DEBUG: bool = ... - ) -> None: ... - -class UpdateProcessor: - def __init__(self, graph) -> None: ... - def update(self, strOrQuery, initBindings=..., initNs=...) -> None: ... - -class ResultException(Exception): ... - -class EncodeOnlyUnicode: - def __init__(self, stream) -> None: ... - def write(self, arg) -> None: ... - def __getattr__(self, name): ... - -class ResultRow(tuple): - def __new__(cls, values, labels): ... - def __getattr__(self, name): ... - def __getitem__(self, name): ... - def get(self, name, default: Any | None = ...): ... - def asdict(self): ... +from typing import Any, Dict, Optional, Union class Result: type: Any vars: Any askAnswer: Any graph: Any - def __init__(self, type_) -> None: ... + def __init__(self, type_: str) -> None: ... bindings: Any @staticmethod def parse( source: Any | None = ..., format: Any | None = ..., content_type: Any | None = ..., - **kwargs - ): ... + **kwargs: Any + ) -> Any: ... def serialize( self, destination: Optional[Union[str, BufferedIOBase]] = ..., encoding: str = ..., format: str = ..., - **args + **args: Any ) -> Optional[bytes]: ... - def __len__(self): ... - def __bool__(self): ... - def __iter__(self): ... - def __getattr__(self, name): ... - def __eq__(self, other): ... - -class ResultParser: - def __init__(self) -> None: ... - def parse(self, source, **kwargs) -> None: ... - -class ResultSerializer: - result: Any - def __init__(self, result) -> None: ... - def serialize(self, stream, encoding: str = ..., **kwargs) -> None: ... diff --git a/mypy-stubs/rdflib/resource.pyi b/mypy-stubs/rdflib/resource.pyi new file mode 100644 index 000000000..e520dbe66 --- /dev/null +++ b/mypy-stubs/rdflib/resource.pyi @@ -0,0 +1,33 @@ +from typing import Any, Iterable, Iterator, Tuple + +from _typeshed import Incomplete +from rdflib.graph import Graph, Seq +from rdflib.term import Node + +class Resource: + def __init__(self, graph: Graph, subject: Node) -> None: ... + graph: Incomplete + identifier: Incomplete + def add(self, p: Node, o: Node) -> None: ... + def remove(self, p: Node, o: Node | None = ...) -> None: ... + def set(self, p: Node, o: Node) -> None: ... + def subjects(self, predicate: Any | None = ...) -> Iterable[Node]: ... + def predicates(self, o: Incomplete | None = ...) -> Iterable[Node]: ... + def objects(self, predicate: Any | None = ...) -> Iterable[Node]: ... + def subject_predicates(self) -> Iterator[Tuple[Node, Node]]: ... + def subject_objects(self) -> Iterator[Tuple[Node, Node]]: ... + def predicate_objects(self) -> Iterator[Tuple[Node, Node]]: ... + def value( + self, p: Node, o: Node | None = ..., default: Any | None = ..., any: bool = ... + ) -> Any: ... + def label(self) -> Any: ... + def comment(self) -> Any: ... + def items(self) -> Iterator[Any]: ... + def transitive_objects( + self, predicate: Node, remember: Any | None = ... + ) -> Iterator[Any]: ... + def transitive_subjects( + self, predicate: Node, remember: Any | None = ... + ) -> Iterator[Any]: ... + def seq(self) -> Seq | None: ... + def qname(self) -> Any: ... diff --git a/mypy-stubs/rdflib/store.pyi b/mypy-stubs/rdflib/store.pyi index d60517327..fd6b3eda9 100644 --- a/mypy-stubs/rdflib/store.pyi +++ b/mypy-stubs/rdflib/store.pyi @@ -39,8 +39,10 @@ class Store: def triples(self, triple_pattern, context: Any | None = ...) -> None: ... def __len__(self, context: Any | None = ...) -> None: ... def contexts(self, triple: Any | None = ...) -> None: ... - def query(self, query, initNs, initBindings, queryGraph, **kwargs) -> None: ... - def update(self, update, initNs, initBindings, queryGraph, **kwargs) -> None: ... + def query(self, query, initNs, initBindings, queryGraph, **kwargs: Any) -> None: ... + def update( + self, update, initNs, initBindings, queryGraph, **kwargs: Any + ) -> None: ... def bind(self, prefix, namespace) -> None: ... def prefix(self, namespace) -> None: ... def namespace(self, prefix) -> None: ... diff --git a/mypy-stubs/rdflib/term.pyi b/mypy-stubs/rdflib/term.pyi index 2bc8e40ca..5b2fdd0ee 100644 --- a/mypy-stubs/rdflib/term.pyi +++ b/mypy-stubs/rdflib/term.pyi @@ -1,98 +1,49 @@ from typing import Any, Callable, Union -from .paths import AlternativePath, InvPath, NegatedPath, Path, SequencePath - class Node: ... class Identifier(Node, str): - def __new__(cls, value): ... - def eq(self, other): ... - def neq(self, other): ... - def __ne__(self, other): ... - def __eq__(self, other): ... - def __gt__(self, other): ... - def __lt__(self, other): ... - def __le__(self, other): ... - def __ge__(self, other): ... - def startswith(self, prefix, start=..., end=...) -> bool: ... - __hash__: Any + def __new__(cls, value: Union[Any, str, None]) -> "Identifier": ... + def eq(self, other: Any) -> bool: ... + def neq(self, other: Any) -> bool: ... class URIRef(Identifier): - __or__: Callable[[URIRef, Union[URIRef, Path]], AlternativePath] - __invert__: Callable[[URIRef], InvPath] - __neg__: Callable[[URIRef], NegatedPath] - __truediv__: Callable[[URIRef, Union[URIRef, Path]], SequencePath] - def __new__(cls, value, base: Any | None = ...): ... - def toPython(self): ... + def toPython(self) -> str: ... def n3(self, namespace_manager: Any | None = ...) -> str: ... - def defrag(self): ... - def __reduce__(self): ... - def __getnewargs__(self): ... - def __add__(self, other): ... - def __radd__(self, other): ... - def __mod__(self, other): ... - def de_skolemize(self): ... + def defrag(self) -> "URIRef": ... + def de_skolemize(self) -> "BNode": ... class Genid(URIRef): ... class RDFLibGenid(Genid): ... class BNode(Identifier): - def __new__(cls, value: Any | None = ..., _sn_gen=..., _prefix=...): ... - def toPython(self): ... - def n3(self, namespace_manager: Any | None = ...): ... - def __getnewargs__(self): ... - def __reduce__(self): ... - def skolemize(self, authority: Any | None = ..., basepath: Any | None = ...): ... + def toPython(self) -> str: ... + def n3(self, namespace_manager: Any | None = ...) -> str: ... + def skolemize( + self, authority: Any | None = ..., basepath: Any | None = ... + ) -> "RDFLibGenid": ... class Literal(Identifier): - __doc__: str - def __new__( - cls, - lexical_or_value, - lang: Any | None = ..., - datatype: Any | None = ..., - normalize: Any | None = ..., - ): ... - def normalize(self): ... + def normalize(self) -> "Literal": ... @property - def value(self): ... + def value(self) -> Any: ... @property - def language(self): ... + def language(self) -> str | None: ... @property - def datatype(self): ... - def __reduce__(self): ... - def __add__(self, val): ... - def __bool__(self): ... - def __neg__(self): ... - def __pos__(self): ... - def __abs__(self): ... - def __invert__(self): ... - def __gt__(self, other): ... - def __lt__(self, other): ... - def __le__(self, other): ... - def __ge__(self, other): ... - def __hash__(self): ... - def __eq__(self, other): ... - def eq(self, other): ... - def neq(self, other): ... - def n3(self, namespace_manager: Any | None = ...): ... - def toPython(self): ... + def datatype(self) -> Any: ... + def eq(self, other: Any) -> bool: ... + def neq(self, other: Any) -> bool: ... + def n3(self, namespace_manager: Any | None = ...) -> str: ... + def toPython(self) -> str: ... def bind( - datatype, - pythontype, - constructor: Any | None = ..., - lexicalizer: Any | None = ..., + datatype: str | None, + pythontype: type, + constructor: Callable[..., Any] | None = ..., + lexicalizer: Callable[..., Any] | None = ..., datatype_specific: bool = ..., ) -> None: ... class Variable(Identifier): - def __new__(cls, value): ... - def toPython(self): ... - def n3(self, namespace_manager: Any | None = ...): ... - def __reduce__(self): ... - -class Statement(Node, tuple): - def __new__(cls, triple, context): ... - def __reduce__(self): ... - def toPython(self): ... + def toPython(self) -> str: ... + def n3(self, namespace_manager: Any | None = ...) -> str: ... diff --git a/mypy-stubs/subprocess.pyi b/mypy-stubs/subprocess.pyi index f08a812d4..880ab4736 100644 --- a/mypy-stubs/subprocess.pyi +++ b/mypy-stubs/subprocess.pyi @@ -1,7 +1,22 @@ import sys -from _typeshed import Self, StrOrBytesPath from types import TracebackType -from typing import IO, Any, AnyStr, Callable, Generic, Iterable, Mapping, Sequence, Tuple, Type, TypeVar, Union, overload +from typing import ( + IO, + Any, + AnyStr, + Callable, + Generic, + Iterable, + Mapping, + Sequence, + Tuple, + Type, + TypeVar, + Union, + overload, +) + +from _typeshed import Self, StrOrBytesPath from typing_extensions import Literal if sys.version_info >= (3, 9): @@ -44,7 +59,13 @@ class CompletedProcess(Generic[_T]): # and writing all the overloads would be horrific. stdout: _T stderr: _T - def __init__(self, args: _CMD, returncode: int, stdout: _T | None = ..., stderr: _T | None = ...) -> None: ... + def __init__( + self, + args: _CMD, + returncode: int, + stdout: _T | None = ..., + stderr: _T | None = ..., + ) -> None: ... def check_returncode(self) -> None: ... if sys.version_info >= (3, 9): def __class_getitem__(cls, item: Any) -> GenericAlias: ... @@ -683,7 +704,13 @@ DEVNULL: int class SubprocessError(Exception): ... class TimeoutExpired(SubprocessError): - def __init__(self, cmd: _CMD, timeout: float, output: _TXT | None = ..., stderr: _TXT | None = ...) -> None: ... + def __init__( + self, + cmd: _CMD, + timeout: float, + output: _TXT | None = ..., + stderr: _TXT | None = ..., + ) -> None: ... # morally: _CMD cmd: Any timeout: float @@ -702,7 +729,13 @@ class CalledProcessError(SubprocessError): # morally: _TXT | None stdout: Any stderr: Any - def __init__(self, returncode: int, cmd: _CMD, output: _TXT | None = ..., stderr: _TXT | None = ...) -> None: ... + def __init__( + self, + returncode: int, + cmd: _CMD, + output: _TXT | None = ..., + stderr: _TXT | None = ..., + ) -> None: ... class Popen(Generic[AnyStr]): args: _CMD @@ -991,11 +1024,14 @@ class Popen(Generic[AnyStr]): encoding: str | None = ..., errors: str | None = ..., ) -> Popen[Any]: ... + def poll(self) -> int | None: ... if sys.version_info >= (3, 7): def wait(self, timeout: float | None = ...) -> int: ... else: - def wait(self, timeout: float | None = ..., endtime: float | None = ...) -> int: ... + def wait( + self, timeout: float | None = ..., endtime: float | None = ... + ) -> int: ... # Return str/bytes def communicate( self, @@ -1008,7 +1044,10 @@ class Popen(Generic[AnyStr]): def kill(self) -> None: ... def __enter__(self: Self) -> Self: ... def __exit__( - self, type: Type[BaseException] | None, value: BaseException | None, traceback: TracebackType | None + self, + type: Type[BaseException] | None, + value: BaseException | None, + traceback: TracebackType | None, ) -> None: ... if sys.version_info >= (3, 9): def __class_getitem__(cls, item: Any) -> GenericAlias: ... From d465406c8c76b27b29de7a08ca075e56fb0a5e46 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Mon, 1 Aug 2022 17:39:49 +0200 Subject: [PATCH 4/8] done fixing types? --- Makefile | 6 +- cwltool/cwlrdf.py | 77 ++- cwltool/cwlviewer.py | 41 +- cwltool/provenance_profile.py | 71 ++- cwltool/software_requirements.py | 6 +- mypy-stubs/arcp/parse.pyi | 4 +- mypy-stubs/coloredlogs/__init__.pyi | 110 +--- mypy-stubs/galaxy/__init__.pyi | 13 - mypy-stubs/galaxy/exceptions/__init__.pyi | 165 ------ mypy-stubs/galaxy/exceptions/error_codes.pyi | 17 - mypy-stubs/galaxy/jobs/__init__.pyi | 3 - mypy-stubs/galaxy/jobs/metrics/__init__.pyi | 41 -- .../galaxy/jobs/metrics/collectl/__init__.pyi | 3 - .../galaxy/jobs/metrics/collectl/cli.pyi | 12 - .../jobs/metrics/collectl/processes.pyi | 24 - .../galaxy/jobs/metrics/collectl/stats.pyi | 15 - .../jobs/metrics/collectl/subsystems.pyi | 35 -- mypy-stubs/galaxy/jobs/metrics/formatting.pyi | 8 - .../jobs/metrics/instrumenters/__init__.pyi | 17 - .../jobs/metrics/instrumenters/collectl.pyi | 24 - .../jobs/metrics/instrumenters/core.pyi | 20 - .../jobs/metrics/instrumenters/cpuinfo.pyi | 20 - .../galaxy/jobs/metrics/instrumenters/env.pyi | 20 - .../jobs/metrics/instrumenters/meminfo.pyi | 20 - .../jobs/metrics/instrumenters/uname.pyi | 20 - mypy-stubs/galaxy/objectstore/__init__.pyi | 180 ------- mypy-stubs/galaxy/objectstore/azure_blob.pyi | 33 -- mypy-stubs/galaxy/objectstore/pulsar.pyi | 31 -- mypy-stubs/galaxy/objectstore/rods.pyi | 38 -- mypy-stubs/galaxy/objectstore/s3.pyi | 38 -- .../objectstore/s3_multipart_upload.pyi | 13 - mypy-stubs/galaxy/tool_util/__init__.pyi | 3 - mypy-stubs/galaxy/tool_util/cwl/__init__.pyi | 11 - .../galaxy/tool_util/cwl/cwltool_deps.pyi | 27 - mypy-stubs/galaxy/tool_util/cwl/parser.pyi | 98 ---- .../galaxy/tool_util/cwl/representation.pyi | 12 - .../galaxy/tool_util/cwl/runtime_actions.pyi | 7 - mypy-stubs/galaxy/tool_util/cwl/schema.pyi | 35 -- mypy-stubs/galaxy/tool_util/deps/__init__.pyi | 20 - .../galaxy/tool_util/deps/brew_exts.pyi | 22 - .../galaxy/tool_util/deps/brew_util.pyi | 19 - mypy-stubs/galaxy/tool_util/deps/commands.pyi | 12 - .../galaxy/tool_util/deps/conda_compat.pyi | 22 - .../galaxy/tool_util/deps/conda_util.pyi | 87 ---- .../galaxy/tool_util/deps/containers.pyi | 53 -- .../galaxy/tool_util/deps/dependencies.pyi | 57 --- .../galaxy/tool_util/deps/dockerfiles.pyi | 19 - .../galaxy/tool_util/deps/installable.pyi | 15 - .../galaxy/tool_util/deps/mulled/__init__.pyi | 3 - .../galaxy/tool_util/deps/mulled/_cli.pyi | 5 - .../tool_util/deps/mulled/mulled_build.pyi | 30 -- .../deps/mulled/mulled_build_channel.pyi | 7 - .../deps/mulled/mulled_build_files.pyi | 10 - .../deps/mulled/mulled_build_tool.pyi | 8 - .../tool_util/deps/mulled/mulled_search.pyi | 23 - .../galaxy/tool_util/deps/mulled/util.pyi | 32 -- .../galaxy/tool_util/deps/requirements.pyi | 74 --- mypy-stubs/galaxy/tool_util/deps/views.pyi | 36 -- mypy-stubs/galaxy/tool_util/fetcher.pyi | 10 - mypy-stubs/galaxy/tool_util/lint.pyi | 46 -- mypy-stubs/galaxy/tool_util/lint_util.pyi | 5 - .../galaxy/tool_util/linters/__init__.pyi | 3 - .../galaxy/tool_util/linters/citations.pyi | 5 - .../galaxy/tool_util/linters/command.pyi | 6 - mypy-stubs/galaxy/tool_util/linters/cwl.pyi | 12 - .../galaxy/tool_util/linters/general.pyi | 19 - mypy-stubs/galaxy/tool_util/linters/help.pyi | 6 - .../galaxy/tool_util/linters/inputs.pyi | 8 - .../galaxy/tool_util/linters/outputs.pyi | 5 - mypy-stubs/galaxy/tool_util/linters/stdio.pyi | 7 - mypy-stubs/galaxy/tool_util/linters/tests.pyi | 7 - .../galaxy/tool_util/linters/xml_order.pyi | 10 - mypy-stubs/galaxy/tool_util/loader.pyi | 11 - .../galaxy/tool_util/loader_directory.pyi | 27 - .../galaxy/tool_util/locations/__init__.pyi | 7 - .../galaxy/tool_util/locations/dockstore.pyi | 22 - .../galaxy/tool_util/locations/file.pyi | 9 - .../galaxy/tool_util/locations/http.pyi | 13 - .../galaxy/tool_util/parser/__init__.pyi | 8 - mypy-stubs/galaxy/tool_util/parser/cwl.pyi | 42 -- .../galaxy/tool_util/parser/factory.pyi | 15 - .../galaxy/tool_util/parser/interface.pyi | 96 ---- .../tool_util/parser/output_actions.pyi | 217 -------- .../parser/output_collection_def.pyi | 29 -- mypy-stubs/galaxy/tool_util/parser/util.pyi | 9 - mypy-stubs/galaxy/tool_util/parser/xml.pyi | 104 ---- mypy-stubs/galaxy/tool_util/parser/yaml.pyi | 63 --- .../galaxy/tool_util/verify/__init__.pyi | 27 - .../tool_util/verify/asserts/__init__.pyi | 14 - .../tool_util/verify/asserts/tabular.pyi | 6 - .../galaxy/tool_util/verify/asserts/text.pyi | 9 - .../galaxy/tool_util/verify/asserts/xml.pyi | 15 - .../galaxy/tool_util/verify/test_data.pyi | 31 -- mypy-stubs/galaxy/util/__init__.pyi | 102 ---- mypy-stubs/galaxy/util/aliaspickler.pyi | 16 - mypy-stubs/galaxy/util/bunch.pyi | 14 - mypy-stubs/galaxy/util/bytesize.pyi | 10 - mypy-stubs/galaxy/util/checkers.pyi | 9 - mypy-stubs/galaxy/util/commands.pyi | 18 - mypy-stubs/galaxy/util/compression_utils.pyi | 46 -- mypy-stubs/galaxy/util/dbkeys.pyi | 23 - mypy-stubs/galaxy/util/expressions.pyi | 16 - mypy-stubs/galaxy/util/facts.pyi | 13 - mypy-stubs/galaxy/util/filelock.pyi | 17 - mypy-stubs/galaxy/util/form_builder.pyi | 110 ---- mypy-stubs/galaxy/util/getargspec.pyi | 1 - mypy-stubs/galaxy/util/hash_util.pyi | 11 - mypy-stubs/galaxy/util/heartbeat.pyi | 29 -- mypy-stubs/galaxy/util/image_util.pyi | 6 - mypy-stubs/galaxy/util/json.pyi | 23 - mypy-stubs/galaxy/util/jstree.pyi | 19 - mypy-stubs/galaxy/util/lazy_process.pyi | 18 - mypy-stubs/galaxy/util/monitors.pyi | 12 - mypy-stubs/galaxy/util/object_wrapper.pyi | 90 ---- mypy-stubs/galaxy/util/odict.pyi | 25 - .../galaxy/util/pastescript/__init__.pyi | 0 .../galaxy/util/pastescript/loadwsgi.pyi | 129 ----- mypy-stubs/galaxy/util/pastescript/serve.pyi | 94 ---- mypy-stubs/galaxy/util/path/__init__.pyi | 19 - mypy-stubs/galaxy/util/path/ntpath.pyi | 0 mypy-stubs/galaxy/util/path/posixpath.pyi | 0 mypy-stubs/galaxy/util/permutations.pyi | 9 - mypy-stubs/galaxy/util/plugin_config.pyi | 19 - mypy-stubs/galaxy/util/properties.pyi | 33 -- .../galaxy/util/renamed_temporary_file.pyi | 9 - mypy-stubs/galaxy/util/rules_dsl.pyi | 129 ----- mypy-stubs/galaxy/util/sanitize_html.pyi | 3 - mypy-stubs/galaxy/util/script.pyi | 29 -- mypy-stubs/galaxy/util/search.pyi | 1 - mypy-stubs/galaxy/util/simplegraph.pyi | 26 - mypy-stubs/galaxy/util/sleeper.pyi | 7 - mypy-stubs/galaxy/util/sockets.pyi | 5 - mypy-stubs/galaxy/util/specs.pyi | 7 - mypy-stubs/galaxy/util/sqlite.pyi | 2 - mypy-stubs/galaxy/util/submodules.pyi | 5 - mypy-stubs/galaxy/util/template.pyi | 22 - mypy-stubs/galaxy/util/tool_shed/__init__.pyi | 0 .../galaxy/util/tool_shed/common_util.pyi | 41 -- .../galaxy/util/tool_shed/encoding_util.pyi | 8 - mypy-stubs/galaxy/util/tool_shed/xml_util.pyi | 14 - mypy-stubs/galaxy/util/tool_version.pyi | 1 - mypy-stubs/galaxy/util/topsort.pyi | 15 - mypy-stubs/galaxy/util/ucsc.pyi | 12 - mypy-stubs/galaxy/util/validation.pyi | 6 - mypy-stubs/galaxy/util/watcher.pyi | 58 --- mypy-stubs/galaxy/util/web_compat.pyi | 1 - mypy-stubs/galaxy/util/xml_macros.pyi | 13 - mypy-stubs/galaxy/util/yaml_util.pyi | 11 - mypy-stubs/galaxy/util/zipstream.pyi | 20 - .../connectivity/edge_augmentation.pyi | 6 +- .../connectivity/edge_kcomponents.pyi | 3 - mypy-stubs/prov/constants.py | 217 ++++++++ mypy-stubs/prov/constants.pyi | 90 ---- mypy-stubs/prov/dot.pyi | 48 +- mypy-stubs/prov/model.pyi | 473 ++++++++++-------- mypy-stubs/pydot.pyi | 2 +- mypy-stubs/rdflib/graph.pyi | 87 +++- mypy-stubs/rdflib/namespace/__init__.pyi | 6 +- mypy-stubs/rdflib/query.pyi | 30 +- tests/test_provenance.py | 22 +- 160 files changed, 753 insertions(+), 4402 deletions(-) delete mode 100644 mypy-stubs/galaxy/__init__.pyi delete mode 100644 mypy-stubs/galaxy/exceptions/__init__.pyi delete mode 100644 mypy-stubs/galaxy/exceptions/error_codes.pyi delete mode 100644 mypy-stubs/galaxy/jobs/__init__.pyi delete mode 100644 mypy-stubs/galaxy/jobs/metrics/__init__.pyi delete mode 100644 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@@ -90,7 +90,7 @@ clean: check-python3 FORCE # Linting and code style related targets ## sorting imports using isort: https://github.com/timothycrosley/isort -sort_imports: $(PYSOURCES) +sort_imports: $(PYSOURCES) mypy-stubs isort $^ remove_unused_imports: $(PYSOURCES) @@ -114,10 +114,10 @@ codespell: ## format : check/fix all code indentation and formatting (runs black) format: - black --exclude cwltool/schemas setup.py cwltool.py cwltool tests + black --exclude cwltool/schemas setup.py cwltool.py cwltool tests mypy-stubs format-check: - black --diff --check --exclude cwltool/schemas setup.py cwltool.py cwltool tests + black --diff --check --exclude cwltool/schemas setup.py cwltool.py cwltool tests mypy-stubs ## pylint : run static code analysis on Python code pylint: $(PYSOURCES) diff --git a/cwltool/cwlrdf.py b/cwltool/cwlrdf.py index 529bc9777..1bfe8adcc 100644 --- a/cwltool/cwlrdf.py +++ b/cwltool/cwlrdf.py @@ -1,8 +1,9 @@ import urllib from codecs import StreamWriter -from typing import Any, Dict, Optional, TextIO, Union, cast +from typing import Any, Dict, Iterator, Optional, TextIO, Union, cast from rdflib import Graph +from rdflib.query import ResultRow from ruamel.yaml.comments import CommentedMap from schema_salad.jsonld_context import makerdf from schema_salad.utils import ContextType @@ -26,7 +27,7 @@ def printrdf(wflow: Process, ctx: ContextType, style: str) -> str: rdf = gather(wflow, ctx).serialize(format=style, encoding="utf-8") if not rdf: return "" - return cast(str, rdf.decode("utf-8")) + return rdf.decode("utf-8") def lastpart(uri: Any) -> str: @@ -37,13 +38,16 @@ def lastpart(uri: Any) -> str: def dot_with_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None: - qres = g.query( - """SELECT ?step ?run ?runtype + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT ?step ?run ?runtype WHERE { ?step cwl:run ?run . ?run rdf:type ?runtype . }""" - ) + ), + ) # ResultRow because the query is of type SELECT for step, run, _ in qres: stdout.write( @@ -51,14 +55,17 @@ def dot_with_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None: % (lastpart(step), f"{lastpart(step)} ({lastpart(run)})") ) - qres = g.query( - """SELECT ?step ?inp ?source + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT ?step ?inp ?source WHERE { ?wf Workflow:steps ?step . ?step cwl:inputs ?inp . ?inp cwl:source ?source . }""" - ) + ), + ) # ResultRow because the query is of type SELECT for step, inp, source in qres: stdout.write('"%s" [shape=box]\n' % (lastpart(inp))) @@ -69,13 +76,16 @@ def dot_with_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None: '"{}" -> "{}" [label="{}"]\n'.format(lastpart(inp), lastpart(step), "") ) - qres = g.query( - """SELECT ?step ?out + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT ?step ?out WHERE { ?wf Workflow:steps ?step . ?step cwl:outputs ?out . }""" - ) + ), + ) # ResultRow because the query is of type SELECT for step, out in qres: stdout.write('"%s" [shape=box]\n' % (lastpart(out))) @@ -83,13 +93,16 @@ def dot_with_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None: '"{}" -> "{}" [label="{}"]\n'.format(lastpart(step), lastpart(out), "") ) - qres = g.query( - """SELECT ?out ?source + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT ?out ?source WHERE { ?wf cwl:outputs ?out . ?out cwl:source ?source . }""" - ) + ), + ) # ResultRow because the query is of type SELECT for out, source in qres: stdout.write('"%s" [shape=octagon]\n' % (lastpart(out))) @@ -97,13 +110,16 @@ def dot_with_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> None: '"{}" -> "{}" [label="{}"]\n'.format(lastpart(source), lastpart(out), "") ) - qres = g.query( - """SELECT ?inp + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT ?inp WHERE { ?wf rdf:type cwl:Workflow . ?wf cwl:inputs ?inp . }""" - ) + ), + ) # ResultRow because the query is of type SELECT for (inp,) in qres: stdout.write('"%s" [shape=octagon]\n' % (lastpart(inp))) @@ -116,27 +132,33 @@ def dot_without_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> Non stdout.write("compound=true\n") subworkflows = set() - qres = g.query( - """SELECT ?run + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT ?run WHERE { ?wf rdf:type cwl:Workflow . ?wf Workflow:steps ?step . ?step cwl:run ?run . ?run rdf:type cwl:Workflow . } ORDER BY ?wf""" - ) + ), + ) # ResultRow because the query is of type SELECT for (run,) in qres: subworkflows.add(run) - qres = g.query( - """SELECT ?wf ?step ?run ?runtype + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT ?wf ?step ?run ?runtype WHERE { ?wf rdf:type cwl:Workflow . ?wf Workflow:steps ?step . ?step cwl:run ?run . ?run rdf:type ?runtype . } ORDER BY ?wf""" - ) + ), + ) # ResultRow because the query is of type SELECT currentwf = None # type: Optional[str] for wf, step, _run, runtype in qres: @@ -164,8 +186,10 @@ def dot_without_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> Non if currentwf is not None: stdout.write("}\n") - qres = g.query( - """SELECT DISTINCT ?src ?sink ?srcrun ?sinkrun + qres = cast( + Iterator[ResultRow], + g.query( + """SELECT DISTINCT ?src ?sink ?srcrun ?sinkrun WHERE { ?wf1 Workflow:steps ?src . ?wf2 Workflow:steps ?sink . @@ -175,7 +199,8 @@ def dot_without_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> Non ?src cwl:run ?srcrun . ?sink cwl:run ?sinkrun . }""" - ) + ), + ) # ResultRow because the query is of type SELECT for src, sink, srcrun, sinkrun in qres: attr = "" diff --git a/cwltool/cwlviewer.py b/cwltool/cwlviewer.py index 6ebe7e556..40527fa2a 100644 --- a/cwltool/cwlviewer.py +++ b/cwltool/cwlviewer.py @@ -1,5 +1,6 @@ """Visualize a CWL workflow.""" from pathlib import Path +from typing import Iterator, List, cast from urllib.parse import urlparse import pydot @@ -32,9 +33,12 @@ def _load_cwl_graph(self, rdf_description: str) -> rdflib.graph.Graph: def _set_inner_edges(self) -> None: with open(_get_inner_edges_query_path) as f: get_inner_edges_query = f.read() - inner_edges = self._rdf_graph.query( - get_inner_edges_query, initBindings={"root_graph": self._root_graph_uri} - ) + inner_edges = cast( + Iterator[rdflib.query.ResultRow], + self._rdf_graph.query( + get_inner_edges_query, initBindings={"root_graph": self._root_graph_uri} + ), + ) # ResultRow because the query is of type SELECT for inner_edge_row in inner_edges: source_label = ( inner_edge_row["source_label"] @@ -103,9 +107,12 @@ def _set_input_edges(self) -> None: inputs_subgraph.set("style", "dashed") inputs_subgraph.set("label", "Workflow Inputs") - input_edges = self._rdf_graph.query( - get_input_edges_query, initBindings={"root_graph": self._root_graph_uri} - ) + input_edges = cast( + Iterator[rdflib.query.ResultRow], + self._rdf_graph.query( + get_input_edges_query, initBindings={"root_graph": self._root_graph_uri} + ), + ) # ResultRow because the query is of type SELECT for input_row in input_edges: n = pydot.Node( "", @@ -130,9 +137,12 @@ def _set_output_edges(self) -> None: outputs_graph.set("style", "dashed") outputs_graph.set("label", "Workflow Outputs") outputs_graph.set("labelloc", "b") - output_edges = self._rdf_graph.query( - get_output_edges, initBindings={"root_graph": self._root_graph_uri} - ) + output_edges = cast( + Iterator[rdflib.query.ResultRow], + self._rdf_graph.query( + get_output_edges, initBindings={"root_graph": self._root_graph_uri} + ), + ) # ResultRow because the query is of type SELECT for output_edge_row in output_edges: n = pydot.Node( "", @@ -150,11 +160,14 @@ def _set_output_edges(self) -> None: def _get_root_graph_uri(self) -> rdflib.URIRef: with open(_get_root_query_path) as f: get_root_query = f.read() - root = list( - self._rdf_graph.query( - get_root_query, - ) - ) + root = cast( + List[rdflib.query.ResultRow], + list( + self._rdf_graph.query( + get_root_query, + ) + ), + ) # ResultRow because the query is of type SELECT if len(root) != 1: raise RuntimeError( "Cannot identify root workflow! Notice that only Workflows can be visualized" diff --git a/cwltool/provenance_profile.py b/cwltool/provenance_profile.py index 025f5581d..0252127bb 100644 --- a/cwltool/provenance_profile.py +++ b/cwltool/provenance_profile.py @@ -8,17 +8,27 @@ from socket import getfqdn from typing import ( Any, + Dict, List, MutableMapping, MutableSequence, Optional, + Sequence, Tuple, Union, cast, ) -from prov.identifier import Identifier -from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity +from prov.identifier import Identifier, QualifiedName +from prov.model import ( + PROV, + PROV_LABEL, + PROV_TYPE, + PROV_VALUE, + ProvDocument, + ProvEntity, + ProvRecord, +) from schema_salad.sourceline import SourceLine from typing_extensions import TYPE_CHECKING @@ -59,7 +69,7 @@ def copy_job_order( if not isinstance(job, WorkflowJob): # direct command line tool execution return job_order_object - customised_job = {} # type: CWLObjectType + customised_job: CWLObjectType = {} # new job object for RO debug = _logger.isEnabledFor(logging.DEBUG) for each, i in enumerate(job.tool["inputs"]): @@ -101,7 +111,7 @@ def __init__( self.document = ProvDocument() self.host_provenance = host_provenance self.user_provenance = user_provenance - self.engine_uuid = research_object.engine_uuid # type: str + self.engine_uuid = research_object.engine_uuid self.add_to_manifest = self.research_object.add_to_manifest if self.orcid: _logger.debug("[provenance] Creator ORCID: %s", self.orcid) @@ -109,7 +119,7 @@ def __init__( if self.full_name: _logger.debug("[provenance] Creator Full name: %s", self.full_name) self.workflow_run_uuid = run_uuid or uuid.uuid4() - self.workflow_run_uri = self.workflow_run_uuid.urn # type: str + self.workflow_run_uri = self.workflow_run_uuid.urn self.generate_prov_doc() def __str__(self) -> str: @@ -181,7 +191,10 @@ def host_provenance(document: ProvDocument) -> None: # by a user account, as cwltool is a command line tool account = self.document.agent(ACCOUNT_UUID) if self.orcid or self.full_name: - person = {PROV_TYPE: PROV["Person"], "prov:type": SCHEMA["Person"]} + person: Dict[Union[str, Identifier], Any] = { + PROV_TYPE: PROV["Person"], + "prov:type": SCHEMA["Person"], + } if self.full_name: person["prov:label"] = self.full_name person["foaf:name"] = self.full_name @@ -300,7 +313,7 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st if value["class"] != "File": raise ValueError("Must have class:File: %s" % value) # Need to determine file hash aka RO filename - entity = None # type: Optional[ProvEntity] + entity: Optional[ProvEntity] = None checksum = None if "checksum" in value: csum = cast(str, value["checksum"]) @@ -335,19 +348,25 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st # secondaryFiles. Note that multiple uses of a file might thus record # different names for the same entity, so we'll # make/track a specialized entity by UUID - file_id = value.setdefault("@id", uuid.uuid4().urn) + file_id = cast(str, value.setdefault("@id", uuid.uuid4().urn)) # A specialized entity that has just these names file_entity = self.document.entity( file_id, [(PROV_TYPE, WFPROV["Artifact"]), (PROV_TYPE, WF4EVER["File"])], - ) # type: ProvEntity + ) if "basename" in value: - file_entity.add_attributes({CWLPROV["basename"]: value["basename"]}) + file_entity.add_attributes( + {CWLPROV["basename"]: cast(str, value["basename"])} + ) if "nameroot" in value: - file_entity.add_attributes({CWLPROV["nameroot"]: value["nameroot"]}) + file_entity.add_attributes( + {CWLPROV["nameroot"]: cast(str, value["nameroot"])} + ) if "nameext" in value: - file_entity.add_attributes({CWLPROV["nameext"]: value["nameext"]}) + file_entity.add_attributes( + {CWLPROV["nameext"]: cast(str, value["nameext"])} + ) self.document.specializationOf(file_entity, entity) # Check for secondaries @@ -406,8 +425,10 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: # dir_bundle.identifier, {PROV["type"]: ORE["ResourceMap"], # ORE["describes"]: coll_b.identifier}) - coll_attribs = [(ORE["isDescribedBy"], dir_bundle.identifier)] - coll_b_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] + coll_attribs: List[Tuple[Union[str, Identifier], Any]] = [ + (ORE["isDescribedBy"], dir_bundle.identifier) + ] + coll_b_attribs: List[Tuple[Union[str, Identifier], Any]] = [] # FIXME: .listing might not be populated yet - hopefully # a later call to this method will sort that @@ -433,7 +454,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: m_entity.add_attributes( { - PROV["pairKey"]: entry["basename"], + PROV["pairKey"]: cast(str, entry["basename"]), PROV["pairEntity"]: entity, } ) @@ -444,7 +465,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: m_b.add_asserted_type(ORE["Proxy"]) m_b.add_attributes( { - RO["entryName"]: entry["basename"], + RO["entryName"]: cast(str, entry["basename"]), ORE["proxyIn"]: coll, ORE["proxyFor"]: entity, } @@ -485,7 +506,7 @@ def declare_string(self, value: str) -> Tuple[ProvEntity, str]: data_id = "data:%s" % PurePosixPath(data_file).stem entity = self.document.entity( data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)} - ) # type: ProvEntity + ) return entity, checksum def declare_artefact(self, value: Any) -> ProvEntity: @@ -525,7 +546,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: # Already processed this value, but it might not be in this PROV entities = self.document.get_record(value["@id"]) if entities: - return entities[0] + return cast(List[ProvEntity], entities)[0] # else, unknown in PROV, re-add below as if it's fresh # Base case - we found a File we need to update @@ -556,7 +577,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: coll.add_asserted_type(CWLPROV[value["class"]]) # Let's iterate and recurse - coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] + coll_attribs: List[Tuple[Union[str, Identifier], Any]] = [] for (key, val) in value.items(): v_ent = self.declare_artefact(val) self.document.membership(coll, v_ent) @@ -709,20 +730,22 @@ def prospective_prov(self, job: JobsType) -> None: ) # TODO: Declare roles/parameters as well - def activity_has_provenance(self, activity, prov_ids): - # type: (str, List[Identifier]) -> None + def activity_has_provenance( + self, activity: str, prov_ids: Sequence[Identifier] + ) -> None: """Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files.""" # NOTE: The below will only work if the corresponding metadata/provenance arcp URI # is a pre-registered namespace in the PROV Document - attribs = [(PROV["has_provenance"], prov_id) for prov_id in prov_ids] + attribs: List[Tuple[Union[str, Identifier], Any]] = [ + (PROV["has_provenance"], prov_id) for prov_id in prov_ids + ] self.document.activity(activity, other_attributes=attribs) # Tip: we can't use https://www.w3.org/TR/prov-links/#term-mention # as prov:mentionOf() is only for entities, not activities uris = [i.uri for i in prov_ids] self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) - def finalize_prov_profile(self, name): - # type: (Optional[str]) -> List[Identifier] + def finalize_prov_profile(self, name: Optional[str]) -> List[QualifiedName]: """Transfer the provenance related files to the RO.""" # NOTE: Relative posix path if name is None: diff --git a/cwltool/software_requirements.py b/cwltool/software_requirements.py index b91946160..d80eb66ba 100644 --- a/cwltool/software_requirements.py +++ b/cwltool/software_requirements.py @@ -135,10 +135,8 @@ def get_container_from_software_requirements( ) -> Optional[str]: if use_biocontainers: ensure_galaxy_lib_available() - from galaxy.tool_util.deps.containers import ( - DOCKER_CONTAINER_TYPE, - ContainerRegistry, - ) + from galaxy.tool_util.deps.container_classes import DOCKER_CONTAINER_TYPE + from galaxy.tool_util.deps.containers import ContainerRegistry from galaxy.tool_util.deps.dependencies import AppInfo, ToolInfo app_info = AppInfo( diff --git a/mypy-stubs/arcp/parse.pyi b/mypy-stubs/arcp/parse.pyi index 207328f7d..560671663 100644 --- a/mypy-stubs/arcp/parse.pyi +++ b/mypy-stubs/arcp/parse.pyi @@ -1,6 +1,6 @@ from typing import Any, Tuple, Union from urllib.parse import ParseResult -from uuid import NAMESPACE_URL as NAMESPACE_URL +from uuid import NAMESPACE_URL, UUID SCHEME: str @@ -15,7 +15,7 @@ class ARCPParseResult(ParseResult): @property def name(self) -> str: ... @property - def uuid(self) -> str: ... + def uuid(self) -> UUID: ... @property def ni(self) -> str | None: ... def ni_uri(self, authority: str = ...) -> str | None: ... diff --git a/mypy-stubs/coloredlogs/__init__.pyi b/mypy-stubs/coloredlogs/__init__.pyi index c6842e0d8..7a698c508 100644 --- a/mypy-stubs/coloredlogs/__init__.pyi +++ b/mypy-stubs/coloredlogs/__init__.pyi @@ -1,109 +1,7 @@ -# Stubs for coloredlogs (Python 3.7) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - import logging -from typing import Any, Optional - -WINDOWS: Any -NEED_COLORAMA = WINDOWS -DEFAULT_LOG_LEVEL: Any -DEFAULT_LOG_FORMAT: str -DEFAULT_DATE_FORMAT: str -CHROOT_FILES: Any -CAN_USE_BOLD_FONT: Any -DEFAULT_FIELD_STYLES: Any -DEFAULT_LEVEL_STYLES: Any -DEFAULT_FORMAT_STYLE: str -FORMAT_STYLE_PATTERNS: Any - -def auto_install() -> None: ... -def install(level: Optional[Any] = ..., **kw: Any): ... -def check_style(value: Any): ... -def increase_verbosity() -> None: ... -def decrease_verbosity() -> None: ... -def is_verbose(): ... -def get_level(): ... -def set_level(level: Any) -> None: ... -def adjust_level(logger: Any, level: Any) -> None: ... -def find_defined_levels(): ... -def level_to_number(value: Any): ... -def find_level_aliases(): ... -def parse_encoded_styles(text: Any, normalize_key: Optional[Any] = ...): ... -def find_hostname(use_chroot: bool = ...): ... -def find_program_name(): ... -def replace_handler(logger: Any, match_handler: Any, reconfigure: Any): ... -def find_handler(logger: Any, match_handler: Any): ... -def match_stream_handler(handler: Any, streams: Any = ...): ... -def walk_propagation_tree(logger: Any) -> None: ... - -class BasicFormatter(logging.Formatter): - def formatTime(self, record: Any, datefmt: Optional[Any] = ...): ... - -class ColoredFormatter(BasicFormatter): - nn: Any = ... - log_record_factory: Any = ... - level_styles: Any = ... - field_styles: Any = ... - def __init__( - self, - fmt: Optional[Any] = ..., - datefmt: Optional[Any] = ..., - level_styles: Optional[Any] = ..., - field_styles: Optional[Any] = ..., - style: Any = ..., - ) -> None: ... - def colorize_format(self, fmt: Any, style: Any = ...): ... - def format(self, record: Any): ... - -class Empty: ... - -class HostNameFilter(logging.Filter): - @classmethod - def install( - cls, - handler: Any, - fmt: Optional[Any] = ..., - use_chroot: bool = ..., - style: Any = ..., - ): ... - hostname: Any = ... - def __init__(self, use_chroot: bool = ...) -> None: ... - def filter(self, record: Any): ... - -class ProgramNameFilter(logging.Filter): - @classmethod - def install( - cls, handler: Any, fmt: Any, programname: Optional[Any] = ..., style: Any = ... - ): ... - programname: Any = ... - def __init__(self, programname: Optional[Any] = ...) -> None: ... - def filter(self, record: Any): ... - -class StandardErrorHandler(logging.StreamHandler): - def __init__(self, level: Any = ...) -> None: ... - @property - def stream(self): ... - -class FormatStringParser: - style: Any = ... - capturing_pattern: Any = ... - raw_pattern: Any = ... - tokenize_pattern: Any = ... - name_pattern: Any = ... - def __init__(self, style: Any = ...) -> None: ... - def contains_field(self, format_string: Any, field_name: Any): ... - def get_field_names(self, format_string: Any): ... - def get_grouped_pairs(self, format_string: Any): ... - def get_pairs(self, format_string: Any) -> None: ... - def get_pattern(self, field_name: Any): ... - def get_tokens(self, format_string: Any): ... +from typing import Any -class FormatStringToken: ... +def install(level: int | str | None = ..., **kw: Any) -> None: ... -class NameNormalizer: - aliases: Any = ... - def __init__(self) -> None: ... - def normalize_name(self, name: Any): ... - def normalize_keys(self, value: Any): ... - def get(self, normalized_dict: Any, name: Any): ... +class BasicFormatter(logging.Formatter): ... +class ColoredFormatter(BasicFormatter): ... diff --git a/mypy-stubs/galaxy/__init__.pyi b/mypy-stubs/galaxy/__init__.pyi deleted file mode 100644 index aa2f6e6ef..000000000 --- a/mypy-stubs/galaxy/__init__.pyi +++ /dev/null @@ -1,13 +0,0 @@ -# Stubs for galaxy (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -PROJECT_NAME = ... # type: str -PROJECT_OWNER = ... # type: str -PROJECT_USERAME = ... # type: str -PROJECT_URL = ... # type: str -PROJECT_AUTHOR = ... # type: str -PROJECT_EMAIL = ... # type: str -RAW_CONTENT_URL = ... # type: Any diff --git a/mypy-stubs/galaxy/exceptions/__init__.pyi b/mypy-stubs/galaxy/exceptions/__init__.pyi deleted file mode 100644 index 21c935bf8..000000000 --- a/mypy-stubs/galaxy/exceptions/__init__.pyi +++ /dev/null @@ -1,165 +0,0 @@ -# Stubs for galaxy.exceptions (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from ..exceptions import error_codes as error_codes - -class MessageException(Exception): - status_code = ... # type: int - err_code = ... # type: Any - err_msg = ... # type: Any - type = ... # type: Any - extra_error_info = ... # type: Any - def __init__( - self, err_msg: Optional[Any] = ..., type: str = ..., **extra_error_info - ) -> None: ... - -class ItemDeletionException(MessageException): ... -class ObjectInvalid(Exception): ... - -class ActionInputError(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - def __init__(self, err_msg, type: str = ...) -> None: ... - -class DuplicatedSlugException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class DuplicatedIdentifierException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ObjectAttributeInvalidException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ObjectAttributeMissingException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class MalformedId(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class MalformedContents(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class UnknownContentsType(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class RequestParameterMissingException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ToolMetaParameterException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ToolMissingException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class RequestParameterInvalidException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class AuthenticationFailed(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class AuthenticationRequired(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ItemAccessibilityException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ItemOwnershipException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ConfigDoesNotAllowException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class InsufficientPermissionsException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class AdminRequiredException(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ObjectNotFound(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class DeprecatedMethod(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class Conflict(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ConfigurationError(Exception): - status_code = ... # type: int - err_code = ... # type: Any - -class InconsistentDatabase(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class InternalServerError(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class NotImplemented(MessageException): - status_code = ... # type: int - err_code = ... # type: Any - -class ContainerCLIError(Exception): - stdout = ... # type: Any - stderr = ... # type: Any - returncode = ... # type: Any - command = ... # type: Any - subprocess_command = ... # type: Any - def __init__( - self, - msg: Optional[Any] = ..., - stdout: Optional[Any] = ..., - stderr: Optional[Any] = ..., - returncode: Optional[Any] = ..., - command: Optional[Any] = ..., - subprocess_command: Optional[Any] = ..., - **kwargs - ) -> None: ... - -class ContainerNotFound(Exception): - container_id = ... # type: Any - def __init__( - self, msg: Optional[Any] = ..., container_id: Optional[Any] = ..., **kwargs - ) -> None: ... - -class ContainerImageNotFound(Exception): - image = ... # type: Any - def __init__( - self, msg: Optional[Any] = ..., image: Optional[Any] = ..., **kwargs - ) -> None: ... - -class ContainerRunError(Exception): - image = ... # type: Any - command = ... # type: Any - def __init__( - self, - msg: Optional[Any] = ..., - image: Optional[Any] = ..., - command: Optional[Any] = ..., - **kwargs - ) -> None: ... diff --git a/mypy-stubs/galaxy/exceptions/error_codes.pyi b/mypy-stubs/galaxy/exceptions/error_codes.pyi deleted file mode 100644 index b25ca3e99..000000000 --- a/mypy-stubs/galaxy/exceptions/error_codes.pyi +++ /dev/null @@ -1,17 +0,0 @@ -# Stubs for galaxy.exceptions.error_codes (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -UNKNOWN_ERROR_MESSAGE = ... # type: str - -class ErrorCode: - code = ... # type: Any - default_error_message = ... # type: Any - def __init__(self, code, default_error_message) -> None: ... - def __int__(self): ... - -error_codes_json = ... # type: Any -name = ... # type: Any -error_code_obj = ... # type: Any diff --git a/mypy-stubs/galaxy/jobs/__init__.pyi b/mypy-stubs/galaxy/jobs/__init__.pyi deleted file mode 100644 index e3b11dc28..000000000 --- a/mypy-stubs/galaxy/jobs/__init__.pyi +++ /dev/null @@ -1,3 +0,0 @@ -# Stubs for galaxy.jobs (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. diff --git a/mypy-stubs/galaxy/jobs/metrics/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/__init__.pyi deleted file mode 100644 index 7f494712b..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/__init__.pyi +++ /dev/null @@ -1,41 +0,0 @@ -# Stubs for galaxy.jobs.metrics (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from ..metrics import formatting as formatting - -log = ... # type: Any -DEFAULT_FORMATTER = ... # type: Any - -class JobMetrics: - plugin_classes = ... # type: Any - default_job_instrumenter = ... # type: Any - job_instrumenters = ... # type: Any - def __init__(self, conf_file: Optional[Any] = ..., **kwargs) -> None: ... - def format(self, plugin, key, value): ... - def set_destination_conf_file(self, destination_id, conf_file): ... - def set_destination_conf_element(self, destination_id, element): ... - def set_destination_instrumenter( - self, destination_id, job_instrumenter: Optional[Any] = ... - ): ... - def collect_properties(self, destination_id, job_id, job_directory): ... - -class NullJobInstrumenter: - def pre_execute_commands(self, job_directory): ... - def post_execute_commands(self, job_directory): ... - def collect_properties(self, job_id, job_directory): ... - -NULL_JOB_INSTRUMENTER = ... # type: Any - -class JobInstrumenter: - extra_kwargs = ... # type: Any - plugin_classes = ... # type: Any - plugins = ... # type: Any - def __init__(self, plugin_classes, plugins_source, **kwargs) -> None: ... - def pre_execute_commands(self, job_directory): ... - def post_execute_commands(self, job_directory): ... - def collect_properties(self, job_id, job_directory): ... - @staticmethod - def from_file(plugin_classes, conf_file, **kwargs): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi deleted file mode 100644 index ee480022b..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/collectl/__init__.pyi +++ /dev/null @@ -1,3 +0,0 @@ -# Stubs for galaxy.jobs.metrics.collectl (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. diff --git a/mypy-stubs/galaxy/jobs/metrics/collectl/cli.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/cli.pyi deleted file mode 100644 index 88e3120dd..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/collectl/cli.pyi +++ /dev/null @@ -1,12 +0,0 @@ -# Stubs for galaxy.jobs.metrics.collectl.cli (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -class CollectlCli: - mode = ... # type: Any - command_args = ... # type: Any - def __init__(self, **kwargs) -> None: ... - def build_command_line(self): ... - def run(self, stdout: Any = ..., stderr: Any = ...): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/collectl/processes.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/processes.pyi deleted file mode 100644 index ad6fbd88a..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/collectl/processes.pyi +++ /dev/null @@ -1,24 +0,0 @@ -# Stubs for galaxy.jobs.metrics.collectl.processes (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -def generate_process_statistics(collectl_playback_cli, pid, statistics: Any = ...): ... - -class CollectlProcessSummarizer: - pid = ... # type: Any - statistics = ... # type: Any - columns_of_interest = ... # type: Any - tree_statistics = ... # type: Any - process_accum_statistics = ... # type: Any - interval_count = ... # type: int - def __init__(self, pid, statistics) -> None: ... - def handle_interval(self, interval): ... - def get_statistics(self): ... - -class CollectlProcessInterval: - rows = ... # type: Any - def __init__(self) -> None: ... - def row_is_in(self, row): ... - def add_row(self, row): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/collectl/stats.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/stats.pyi deleted file mode 100644 index 39f0c8d0d..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/collectl/stats.pyi +++ /dev/null @@ -1,15 +0,0 @@ -# Stubs for galaxy.jobs.metrics.collectl.stats (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -class StatisticsTracker: - min = ... # type: Any - max = ... # type: Any - count = ... # type: int - sum = ... # type: int - def __init__(self) -> None: ... - def track(self, value): ... - @property - def avg(self): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/collectl/subsystems.pyi b/mypy-stubs/galaxy/jobs/metrics/collectl/subsystems.pyi deleted file mode 100644 index 1da48e66d..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/collectl/subsystems.pyi +++ /dev/null @@ -1,35 +0,0 @@ -# Stubs for galaxy.jobs.metrics.collectl.subsystems (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -class CollectlSubsystem: - @property - def command_line_arg(self): ... - @property - def name(self, job_directory): ... - -class ProcessesSubsystem(CollectlSubsystem): - command_line_arg = ... # type: str - name = ... # type: str - -class CpuSubsystem(CollectlSubsystem): - command_line_arg = ... # type: str - name = ... # type: str - -class DiskSubsystem(CollectlSubsystem): - command_line_arg = ... # type: str - name = ... # type: str - -class NetworkSubsystem(CollectlSubsystem): - command_line_arg = ... # type: str - name = ... # type: str - -class EnvironmentSubsystem(CollectlSubsystem): - command_line_arg = ... # type: str - name = ... # type: str - -class MemorySubsystem(CollectlSubsystem): - command_line_arg = ... # type: str - name = ... # type: str - -def get_subsystem(name): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/formatting.pyi b/mypy-stubs/galaxy/jobs/metrics/formatting.pyi deleted file mode 100644 index ebc91b1ff..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/formatting.pyi +++ /dev/null @@ -1,8 +0,0 @@ -# Stubs for galaxy.jobs.metrics.formatting (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -class JobMetricFormatter: - def format(self, key, value): ... - -def seconds_to_str(value): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi deleted file mode 100644 index 1a9650669..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/__init__.pyi +++ /dev/null @@ -1,17 +0,0 @@ -# Stubs for galaxy.jobs.metrics.instrumenters (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -from ...metrics import formatting as formatting - -INSTRUMENT_FILE_PREFIX = ... # type: str - -class InstrumentPlugin: - formatter = ... # type: Any - @property - def plugin_type(self): ... - def pre_execute_instrument(self, job_directory): ... - def post_execute_instrument(self, job_directory): ... - def job_properties(self, job_id, job_directory): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi deleted file mode 100644 index 3ddaaa9e3..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/collectl.pyi +++ /dev/null @@ -1,24 +0,0 @@ -# Stubs for galaxy.jobs.metrics.instrumenters.collectl (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -import formatting - -from ..instrumenters import InstrumentPlugin - -class CollectlFormatter(formatting.JobMetricFormatter): - def format(self, key, value): ... - -class CollectlPlugin(InstrumentPlugin): - plugin_type = ... # type: str - formatter = ... # type: Any - saved_logs_path = ... # type: Any - summarize_process_data = ... # type: Any - log_collectl_program_output = ... # type: Any - process_statistics = ... # type: Any - def __init__(self, **kwargs) -> None: ... - def pre_execute_instrument(self, job_directory): ... - def post_execute_instrument(self, job_directory): ... - def job_properties(self, job_id, job_directory): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi deleted file mode 100644 index 48d76eedd..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/core.pyi +++ /dev/null @@ -1,20 +0,0 @@ -# Stubs for galaxy.jobs.metrics.instrumenters.core (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -import formatting - -from ..instrumenters import InstrumentPlugin - -class CorePluginFormatter(formatting.JobMetricFormatter): - def format(self, key, value): ... - -class CorePlugin(InstrumentPlugin): - plugin_type = ... # type: str - formatter = ... # type: Any - def __init__(self, **kwargs) -> None: ... - def pre_execute_instrument(self, job_directory): ... - def post_execute_instrument(self, job_directory): ... - def job_properties(self, job_id, job_directory): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi deleted file mode 100644 index e17cd1f75..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi +++ /dev/null @@ -1,20 +0,0 @@ -# Stubs for galaxy.jobs.metrics.instrumenters.cpuinfo (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -import formatting - -from ..instrumenters import InstrumentPlugin - -class CpuInfoFormatter(formatting.JobMetricFormatter): - def format(self, key, value): ... - -class CpuInfoPlugin(InstrumentPlugin): - plugin_type = ... # type: str - formatter = ... # type: Any - verbose = ... # type: Any - def __init__(self, **kwargs) -> None: ... - def pre_execute_instrument(self, job_directory): ... - def job_properties(self, job_id, job_directory): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi deleted file mode 100644 index afbd1a16e..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/env.pyi +++ /dev/null @@ -1,20 +0,0 @@ -# Stubs for galaxy.jobs.metrics.instrumenters.env (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -import formatting - -from ..instrumenters import InstrumentPlugin - -class EnvFormatter(formatting.JobMetricFormatter): ... - -class EnvPlugin(InstrumentPlugin): - plugin_type = ... # type: str - formatter = ... # type: Any - variables = ... # type: Any - def __init__(self, **kwargs) -> None: ... - def pre_execute_instrument(self, job_directory): ... - def post_execute_instrument(self, job_directory): ... - def job_properties(self, job_id, job_directory): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi deleted file mode 100644 index 252012d92..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/meminfo.pyi +++ /dev/null @@ -1,20 +0,0 @@ -# Stubs for galaxy.jobs.metrics.instrumenters.meminfo (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -import formatting - -from ..instrumenters import InstrumentPlugin - -class MemInfoFormatter(formatting.JobMetricFormatter): - def format(self, key, value): ... - -class MemInfoPlugin(InstrumentPlugin): - plugin_type = ... # type: str - formatter = ... # type: Any - verbose = ... # type: Any - def __init__(self, **kwargs) -> None: ... - def pre_execute_instrument(self, job_directory): ... - def job_properties(self, job_id, job_directory): ... diff --git a/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi b/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi deleted file mode 100644 index d0c6cff2a..000000000 --- a/mypy-stubs/galaxy/jobs/metrics/instrumenters/uname.pyi +++ /dev/null @@ -1,20 +0,0 @@ -# Stubs for galaxy.jobs.metrics.instrumenters.uname (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -import formatting - -from ..instrumenters import InstrumentPlugin - -class UnameFormatter(formatting.JobMetricFormatter): - def format(self, key, value): ... - -class UnamePlugin(InstrumentPlugin): - plugin_type = ... # type: str - formatter = ... # type: Any - uname_args = ... # type: Any - def __init__(self, **kwargs) -> None: ... - def pre_execute_instrument(self, job_directory): ... - def job_properties(self, job_id, job_directory): ... diff --git a/mypy-stubs/galaxy/objectstore/__init__.pyi b/mypy-stubs/galaxy/objectstore/__init__.pyi deleted file mode 100644 index 8af0e6095..000000000 --- a/mypy-stubs/galaxy/objectstore/__init__.pyi +++ /dev/null @@ -1,180 +0,0 @@ -# Stubs for galaxy.objectstore (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -object_session = ... # type: Any -NO_SESSION_ERROR_MESSAGE = ... # type: str -log = ... # type: Any - -class ObjectStore: - running = ... # type: bool - extra_dirs = ... # type: Any - config = ... # type: Any - check_old_style = ... # type: Any - def __init__(self, config, **kwargs) -> None: ... - def shutdown(self): ... - def exists( - self, - obj, - base_dir: Optional[Any] = ..., - dir_only: bool = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - ): ... - def file_ready( - self, - obj, - base_dir: Optional[Any] = ..., - dir_only: bool = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def create( - self, - obj, - base_dir: Optional[Any] = ..., - dir_only: bool = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def empty( - self, - obj, - base_dir: Optional[Any] = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def size( - self, - obj, - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def delete( - self, - obj, - entire_dir: bool = ..., - base_dir: Optional[Any] = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def get_data( - self, - obj, - start: int = ..., - count: int = ..., - base_dir: Optional[Any] = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def get_filename( - self, - obj, - base_dir: Optional[Any] = ..., - dir_only: bool = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def update_from_file( - self, - obj, - base_dir: Optional[Any] = ..., - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - file_name: Optional[Any] = ..., - create: bool = ..., - ): ... - def get_object_url( - self, - obj, - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - obj_dir: bool = ..., - ): ... - def get_store_usage_percent(self): ... - -class DiskObjectStore(ObjectStore): - file_path = ... # type: Any - def __init__( - self, - config, - config_xml: Optional[Any] = ..., - file_path: Optional[Any] = ..., - extra_dirs: Optional[Any] = ..., - ) -> None: ... - def exists(self, obj, **kwargs): ... - def create(self, obj, **kwargs): ... - def empty(self, obj, **kwargs): ... - def size(self, obj, **kwargs): ... - def delete(self, obj, entire_dir: bool = ..., **kwargs): ... - def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... - def get_filename(self, obj, **kwargs): ... - def update_from_file( - self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs - ): ... - def get_object_url(self, obj, **kwargs): ... - def get_store_usage_percent(self): ... - -class NestedObjectStore(ObjectStore): - backends = ... # type: Any - def __init__(self, config, config_xml: Optional[Any] = ...) -> None: ... - def shutdown(self): ... - def exists(self, obj, **kwargs): ... - def file_ready(self, obj, **kwargs): ... - def create(self, obj, **kwargs): ... - def empty(self, obj, **kwargs): ... - def size(self, obj, **kwargs): ... - def delete(self, obj, **kwargs): ... - def get_data(self, obj, **kwargs): ... - def get_filename(self, obj, **kwargs): ... - def update_from_file(self, obj, **kwargs): ... - def get_object_url(self, obj, **kwargs): ... - -class DistributedObjectStore(NestedObjectStore): - distributed_config = ... # type: Any - backends = ... # type: Any - weighted_backend_ids = ... # type: Any - original_weighted_backend_ids = ... # type: Any - max_percent_full = ... # type: Any - global_max_percent_full = ... # type: float - sleeper = ... # type: Any - filesystem_monitor_thread = ... # type: Any - def __init__( - self, config, config_xml: Optional[Any] = ..., fsmon: bool = ... - ) -> None: ... - def shutdown(self): ... - def create(self, obj, **kwargs): ... - -class HierarchicalObjectStore(NestedObjectStore): - backends = ... # type: Any - def __init__( - self, config, config_xml: Optional[Any] = ..., fsmon: bool = ... - ) -> None: ... - def exists(self, obj, **kwargs): ... - def create(self, obj, **kwargs): ... - -def build_object_store_from_config( - config, fsmon: bool = ..., config_xml: Optional[Any] = ... -): ... -def local_extra_dirs(func): ... -def convert_bytes(bytes): ... diff --git a/mypy-stubs/galaxy/objectstore/azure_blob.pyi b/mypy-stubs/galaxy/objectstore/azure_blob.pyi deleted file mode 100644 index 3ab6e9240..000000000 --- a/mypy-stubs/galaxy/objectstore/azure_blob.pyi +++ /dev/null @@ -1,33 +0,0 @@ -# Stubs for galaxy.objectstore.azure_blob (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from ..objectstore import ObjectStore as ObjectStore -from ..objectstore import convert_bytes as convert_bytes - -BlockBlobService = ... # type: Any -NO_BLOBSERVICE_ERROR_MESSAGE = ... # type: str -log = ... # type: Any - -class AzureBlobObjectStore(ObjectStore): - staging_path = ... # type: Any - transfer_progress = ... # type: int - cache_size = ... # type: Any - sleeper = ... # type: Any - cache_monitor_thread = ... # type: Any - def __init__(self, config, config_xml) -> None: ... - def exists(self, obj, **kwargs): ... - def file_ready(self, obj, **kwargs): ... - def create(self, obj, **kwargs): ... - def empty(self, obj, **kwargs): ... - def size(self, obj, **kwargs): ... - def delete(self, obj, entire_dir: bool = ..., **kwargs): ... - def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... - def get_filename(self, obj, **kwargs): ... - def update_from_file( - self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs - ): ... - def get_object_url(self, obj, **kwargs): ... - def get_store_usage_percent(self): ... diff --git a/mypy-stubs/galaxy/objectstore/pulsar.pyi b/mypy-stubs/galaxy/objectstore/pulsar.pyi deleted file mode 100644 index 858800ed2..000000000 --- a/mypy-stubs/galaxy/objectstore/pulsar.pyi +++ /dev/null @@ -1,31 +0,0 @@ -# Stubs for galaxy.objectstore.pulsar (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from ..objectstore import ObjectStore as ObjectStore - -ObjectStoreClientManager = ... # type: Any - -class PulsarObjectStore(ObjectStore): - pulsar_client = ... # type: Any - def __init__(self, config, config_xml) -> None: ... - def exists(self, obj, **kwds): ... - def file_ready(self, obj, **kwds): ... - def create(self, obj, **kwds): ... - def empty(self, obj, **kwds): ... - def size(self, obj, **kwds): ... - def delete(self, obj, **kwds): ... - def get_data(self, obj, **kwds): ... - def get_filename(self, obj, **kwds): ... - def update_from_file(self, obj, **kwds): ... - def get_store_usage_percent(self): ... - def get_object_url( - self, - obj, - extra_dir: Optional[Any] = ..., - extra_dir_at_root: bool = ..., - alt_name: Optional[Any] = ..., - ): ... - def shutdown(self): ... diff --git a/mypy-stubs/galaxy/objectstore/rods.pyi b/mypy-stubs/galaxy/objectstore/rods.pyi deleted file mode 100644 index 6e25e17ab..000000000 --- a/mypy-stubs/galaxy/objectstore/rods.pyi +++ /dev/null @@ -1,38 +0,0 @@ -# Stubs for galaxy.objectstore.rods (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from posixpath import basename as path_basename -from posixpath import dirname as path_dirname -from posixpath import join as path_join -from typing import Any, Optional - -from ..objectstore import DiskObjectStore as DiskObjectStore -from ..objectstore import local_extra_dirs as local_extra_dirs - -irods = ... # type: Any -IRODS_IMPORT_MESSAGE = ... # type: str -log = ... # type: Any - -class IRODSObjectStore(DiskObjectStore): - cache_path = ... # type: Any - default_resource = ... # type: Any - root_collection_path = ... # type: Any - root_collection = ... # type: Any - def __init__( - self, config, file_path: Optional[Any] = ..., extra_dirs: Optional[Any] = ... - ) -> None: ... - def exists(self, obj, **kwargs): ... - def create(self, obj, **kwargs): ... - def empty(self, obj, **kwargs): ... - def size(self, obj, **kwargs): ... - def delete(self, obj, entire_dir: bool = ..., **kwargs): ... - def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... - def get_filename(self, obj, **kwargs): ... - def update_from_file( - self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs - ): ... - def get_object_url(self, obj, **kwargs): ... - def get_store_usage_percent(self): ... - -def rods_connect(): ... diff --git a/mypy-stubs/galaxy/objectstore/s3.pyi b/mypy-stubs/galaxy/objectstore/s3.pyi deleted file mode 100644 index 34b7c1f88..000000000 --- a/mypy-stubs/galaxy/objectstore/s3.pyi +++ /dev/null @@ -1,38 +0,0 @@ -# Stubs for galaxy.objectstore.s3 (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from ..objectstore import ObjectStore as ObjectStore -from ..objectstore import convert_bytes as convert_bytes -from .s3_multipart_upload import multipart_upload as multipart_upload - -boto = ... # type: Any -NO_BOTO_ERROR_MESSAGE = ... # type: str -log = ... # type: Any - -class S3ObjectStore(ObjectStore): - staging_path = ... # type: Any - transfer_progress = ... # type: int - bucket = ... # type: Any - cache_size = ... # type: Any - sleeper = ... # type: Any - cache_monitor_thread = ... # type: Any - use_axel = ... # type: bool - def __init__(self, config, config_xml) -> None: ... - def file_ready(self, obj, **kwargs): ... - def exists(self, obj, **kwargs): ... - def create(self, obj, **kwargs): ... - def empty(self, obj, **kwargs): ... - def size(self, obj, **kwargs): ... - def delete(self, obj, entire_dir: bool = ..., **kwargs): ... - def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ... - def get_filename(self, obj, **kwargs): ... - def update_from_file( - self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs - ): ... - def get_object_url(self, obj, **kwargs): ... - def get_store_usage_percent(self): ... - -class SwiftObjectStore(S3ObjectStore): ... diff --git a/mypy-stubs/galaxy/objectstore/s3_multipart_upload.pyi b/mypy-stubs/galaxy/objectstore/s3_multipart_upload.pyi deleted file mode 100644 index 9bf1d8726..000000000 --- a/mypy-stubs/galaxy/objectstore/s3_multipart_upload.pyi +++ /dev/null @@ -1,13 +0,0 @@ -# Stubs for galaxy.objectstore.s3_multipart_upload (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -boto = ... # type: Any - -def map_wrap(f): ... -def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname): ... -def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part): ... -def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size): ... -def multimap(cores: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/__init__.pyi b/mypy-stubs/galaxy/tool_util/__init__.pyi deleted file mode 100644 index ff77e3d7d..000000000 --- a/mypy-stubs/galaxy/tool_util/__init__.pyi +++ /dev/null @@ -1,3 +0,0 @@ -# Stubs for galaxy.tools (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. diff --git a/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi b/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi deleted file mode 100644 index 9d1473947..000000000 --- a/mypy-stubs/galaxy/tool_util/cwl/__init__.pyi +++ /dev/null @@ -1,11 +0,0 @@ -# Stubs for galaxy.tools.cwl (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from .cwltool_deps import needs_shell_quoting as needs_shell_quoting -from .cwltool_deps import shellescape as shellescape -from .parser import tool_proxy as tool_proxy -from .parser import workflow_proxy as workflow_proxy -from .representation import to_cwl_job as to_cwl_job -from .representation import to_galaxy_parameters as to_galaxy_parameters -from .runtime_actions import handle_outputs as handle_outputs diff --git a/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi b/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi deleted file mode 100644 index 767b9a07c..000000000 --- a/mypy-stubs/galaxy/tool_util/cwl/cwltool_deps.pyi +++ /dev/null @@ -1,27 +0,0 @@ -# Stubs for galaxy.tools.cwl.cwltool_deps (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -import schema_salad as schema_salad -import shellescape as shellescape -from schema_salad import ref_resolver as ref_resolver - -from cwltool import load_tool as load_tool -from cwltool import main as main -from cwltool import pathmapper as pathmapper -from cwltool import process as process -from cwltool import workflow as workflow - -main = ... # type: Any -workflow = ... # type: Any -process = ... # type: Any -pathmapper = ... # type: Any -load_tool = ... # type: Any -shellescape = ... # type: Any -schema_salad = ... # type: Any -ref_resolver = ... # type: Any -needs_shell_quoting = ... # type: Any - -def ensure_cwltool_available(): ... diff --git a/mypy-stubs/galaxy/tool_util/cwl/parser.pyi b/mypy-stubs/galaxy/tool_util/cwl/parser.pyi deleted file mode 100644 index 02c0459af..000000000 --- a/mypy-stubs/galaxy/tool_util/cwl/parser.pyi +++ /dev/null @@ -1,98 +0,0 @@ -# Stubs for galaxy.tools.cwl.parser (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -def tool_proxy(tool_path, strict_cwl_validation: bool = ...): ... -def load_job_proxy(job_directory, strict_cwl_validation: bool = ...): ... - -class ToolProxy: - def __init__(self, tool, tool_path) -> None: ... - def job_proxy(self, input_dict, output_dict, job_directory: str = ...): ... - def input_instances(self): ... - def output_instances(self): ... - def docker_identifier(self): ... - def description(self): ... - def label(self): ... - -class CommandLineToolProxy(ToolProxy): - def description(self): ... - def label(self): ... - def input_instances(self): ... - def output_instances(self): ... - def docker_identifier(self): ... - -class ExpressionToolProxy(CommandLineToolProxy): ... - -class JobProxy: - def __init__(self, tool_proxy, input_dict, output_dict, job_directory) -> None: ... - def cwl_job(self): ... - @property - def is_command_line_job(self): ... - @property - def command_line(self): ... - @property - def stdin(self): ... - @property - def stdout(self): ... - @property - def environment(self): ... - @property - def generate_files(self): ... - def collect_outputs(self, tool_working_directory): ... - def save_job(self): ... - def output_id(self, output_name): ... - def output_path(self, output_name): ... - def output_secondary_files_dir(self, output_name, create: bool = ...): ... - def stage_files(self): ... - -class WorkflowProxy: - def __init__(self, workflow, workflow_path) -> None: ... - def step_proxies(self): ... - @property - def runnables(self): ... - def to_dict(self): ... - -class StepProxy: - def __init__(self, workflow_proxy, step) -> None: ... - def to_dict(self): ... - -class ConditionalInstance: - input_type = ... # type: Any - name = ... # type: Any - case = ... # type: Any - whens = ... # type: Any - def __init__(self, name, case, whens) -> None: ... - def to_dict(self): ... - -class SelectInputInstance: - input_type = ... # type: Any - name = ... # type: Any - label = ... # type: Any - description = ... # type: Any - options = ... # type: Any - def __init__(self, name, label, description, options) -> None: ... - def to_dict(self): ... - -class InputInstance: - input_type = ... # type: Any - name = ... # type: Any - label = ... # type: Any - description = ... # type: Any - required = ... # type: bool - array = ... # type: Any - area = ... # type: Any - def __init__( - self, name, label, description, input_type, array: bool = ..., area: bool = ... - ) -> None: ... - def to_dict(self, itemwise: bool = ...): ... - -class OutputInstance: - name = ... # type: Any - output_data_type = ... # type: Any - output_type = ... # type: Any - path = ... # type: Any - def __init__( - self, name, output_data_type, output_type, path: Optional[Any] = ... - ) -> None: ... diff --git a/mypy-stubs/galaxy/tool_util/cwl/representation.pyi b/mypy-stubs/galaxy/tool_util/cwl/representation.pyi deleted file mode 100644 index ef2cc45fe..000000000 --- a/mypy-stubs/galaxy/tool_util/cwl/representation.pyi +++ /dev/null @@ -1,12 +0,0 @@ -# Stubs for galaxy.tools.cwl.representation (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -log = ... # type: Any -NOT_PRESENT = ... # type: Any -GALAXY_TO_CWL_TYPES = ... # type: Any - -def to_cwl_job(tool, param_dict, local_working_directory): ... -def to_galaxy_parameters(tool, as_dict): ... diff --git a/mypy-stubs/galaxy/tool_util/cwl/runtime_actions.pyi b/mypy-stubs/galaxy/tool_util/cwl/runtime_actions.pyi deleted file mode 100644 index 4f1558d99..000000000 --- a/mypy-stubs/galaxy/tool_util/cwl/runtime_actions.pyi +++ /dev/null @@ -1,7 +0,0 @@ -# Stubs for galaxy.tools.cwl.runtime_actions (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -def handle_outputs(job_directory: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/cwl/schema.pyi b/mypy-stubs/galaxy/tool_util/cwl/schema.pyi deleted file mode 100644 index e801827d3..000000000 --- a/mypy-stubs/galaxy/tool_util/cwl/schema.pyi +++ /dev/null @@ -1,35 +0,0 @@ -# Stubs for galaxy.tools.cwl.schema (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from collections import namedtuple -from typing import Any - -from .cwltool_deps import ensure_cwltool_available as ensure_cwltool_available -from .cwltool_deps import load_tool as load_tool -from .cwltool_deps import schema_salad as schema_salad -from .cwltool_deps import workflow as workflow - -RawProcessReference = namedtuple("RawProcessReference", ["process_object", "uri"]) - -ProcessDefinition = namedtuple( - "ProcessDefinition", - [ - "process_object", - "metadata", - "document_loader", - "avsc_names", - "raw_process_reference", - ], -) - -class SchemaLoader: - def __init__(self, strict: bool = ...) -> None: ... - @property - def raw_document_loader(self): ... - def raw_process_reference(self, path): ... - def process_definition(self, raw_reference): ... - def tool(self, **kwds): ... - -schema_loader = ... # type: Any -non_strict_schema_loader = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/deps/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/__init__.pyi deleted file mode 100644 index d6cbbd5d8..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/__init__.pyi +++ /dev/null @@ -1,20 +0,0 @@ -from typing import Any, Dict, List, Optional - -from .requirements import ToolRequirement as ToolRequirement -from .requirements import ToolRequirements as ToolRequirements - -def build_dependency_manager( - app_config_dict: Any, resolution_config_dict: Any, conf_file: Any -) -> DependencyManager: ... - -class DependencyManager: - default_base_path: str - def __init__( - self, - default_base_path: str, - conf_file: Optional[Any] = ..., - app_config: Any = ..., - ) -> None: ... - def dependency_shell_commands( - self, requirements: ToolRequirements, **kwds: Dict[str, str] - ) -> List[str]: ... diff --git a/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi b/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi deleted file mode 100644 index b2811528a..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/brew_exts.pyi +++ /dev/null @@ -1,22 +0,0 @@ -from collections.abc import Generator - -from _typeshed import Incomplete - -WHITESPACE_PATTERN: Incomplete -DESCRIPTION: str -DEFAULT_HOMEBREW_ROOT: Incomplete -NO_BREW_ERROR_MESSAGE: str -CANNOT_DETERMINE_TAP_ERROR_MESSAGE: str -VERBOSE: bool -RELAXED: bool -BREW_ARGS: Incomplete - -class BrewContext: - homebrew_prefix: Incomplete - homebrew_cellar: Incomplete - def __init__(self, args: Incomplete | None = ...) -> None: ... - -def main() -> None: ... - -# def execute(cmds, env: Incomplete | None = ...): ... -# def which(file): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi b/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi deleted file mode 100644 index b0d1e4b69..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/brew_util.pyi +++ /dev/null @@ -1,19 +0,0 @@ -# Stubs for galaxy.tools.deps.brew_util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -from ..deps import brew_exts as brew_exts - -DEFAULT_TAP = ... # type: str - -class HomebrewRecipe: - recipe = ... # type: Any - version = ... # type: Any - tap = ... # type: Any - def __init__(self, recipe, version, tap) -> None: ... - -def requirements_to_recipes(requirements): ... -def requirement_to_recipe(requirement): ... -def requirements_to_recipe_contexts(requirements, brew_context): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/commands.pyi b/mypy-stubs/galaxy/tool_util/deps/commands.pyi deleted file mode 100644 index 1d3c89bcc..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/commands.pyi +++ /dev/null @@ -1,12 +0,0 @@ -# Stubs for galaxy.tools.deps.commands (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -# def redirecting_io(sys: Any = ...): ... -# def redirect_aware_commmunicate(p, sys: Any = ...): ... -# def shell(cmds, env: Optional[Any] = ..., **kwds): ... -# def shell_process(cmds, env: Optional[Any] = ..., **kwds): ... -# def execute(cmds): ... -# def download_command(url, to: Any = ..., quote_url: bool = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi b/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi deleted file mode 100644 index a61350472..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/conda_compat.pyi +++ /dev/null @@ -1,22 +0,0 @@ -# Stubs for galaxy.tools.deps.conda_compat (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from conda_build.metadata import MetaData as MetaData - -MetaData = ... # type: Any - -class _Memoized: - func = ... # type: Any - cache = ... # type: Any - def __init__(self, func) -> None: ... - def __call__(self, *args): ... - -def raw_metadata(recipe_dir): ... - -class _MetaData: - meta = ... # type: Any - def __init__(self, input_dir) -> None: ... - def get_value(self, field, default: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi b/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi deleted file mode 100644 index ee9102c0a..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/conda_util.pyi +++ /dev/null @@ -1,87 +0,0 @@ -# Stubs for galaxy.tools.deps.conda_util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from sys import platform as _platform -from typing import Any, Optional - -import installable - -class CondaContext(installable.InstallableContext): - installable_description = ... # type: str - condarc_override = ... # type: Any - conda_exec = ... # type: Any - debug = ... # type: Any - shell_exec = ... # type: Any - copy_dependencies = ... # type: Any - conda_prefix = ... # type: Any - ensure_channels = ... # type: Any - ensured_channels = ... # type: bool - use_local = ... # type: Any - def __init__( - self, - conda_prefix: Optional[Any] = ..., - conda_exec: Optional[Any] = ..., - shell_exec: Optional[Any] = ..., - debug: bool = ..., - ensure_channels: str = ..., - condarc_override: Optional[Any] = ..., - use_path_exec: Any = ..., - copy_dependencies: bool = ..., - use_local: Any = ..., - ) -> None: ... - @property - def conda_version(self): ... - @property - def conda_build_available(self): ... - def ensure_channels_configured(self): ... - def ensure_conda_build_installed_if_needed(self): ... - def conda_info(self): ... - def is_conda_installed(self): ... - def can_install_conda(self): ... - def load_condarc(self): ... - def save_condarc(self, conf): ... - @property - def condarc(self): ... - def command(self, operation, args): ... - def exec_command(self, operation, args): ... - def exec_create(self, args, allow_local: bool = ...): ... - def exec_remove(self, args): ... - def exec_install(self, args, allow_local: bool = ...): ... - def exec_clean(self, args: Any = ..., quiet: bool = ...): ... - def export_list(self, name, path): ... - def env_path(self, env_name): ... - @property - def envs_path(self): ... - def has_env(self, env_name): ... - @property - def deactivate(self): ... - @property - def activate(self): ... - def is_installed(self): ... - def can_install(self): ... - @property - def parent_path(self): ... - -class CondaTarget: - package = ... # type: Any - version = ... # type: Any - channel = ... # type: Any - def __init__( - self, package, version: Optional[Any] = ..., channel: Optional[Any] = ... - ) -> None: ... - @property - def package_specifier(self): ... - @property - def install_environment(self): ... - def __hash__(self): ... - def __eq__(self, other): ... - def __ne__(self, other): ... - -def install_conda( - conda_context: Optional[Any] = ..., force_conda_build: bool = ... -): ... -def install_conda_target( - conda_target, conda_context: Optional[Any] = ..., skip_environment: bool = ... -): ... -def requirements_to_conda_targets(requirements, conda_context: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/containers.pyi b/mypy-stubs/galaxy/tool_util/deps/containers.pyi deleted file mode 100644 index 3827a0be6..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/containers.pyi +++ /dev/null @@ -1,53 +0,0 @@ -# Stubs for galaxy.tools.deps.containers (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Dict, Optional, Sequence - -from .dependencies import AppInfo, JobInfo, ToolInfo -from .requirements import ( - DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES as DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, -) -from .requirements import DEFAULT_CONTAINER_SHELL as DEFAULT_CONTAINER_SHELL -from .requirements import ContainerDescription - -log = ... # type: Any -DOCKER_CONTAINER_TYPE = ... # type: str -SINGULARITY_CONTAINER_TYPE = ... # type: str -DEFAULT_CONTAINER_TYPE = ... # type: Any -ALL_CONTAINER_TYPES = ... # type: Any -LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = ... # type: str - -class ContainerRegistry: - resolver_classes = ... # type: Any - enable_beta_mulled_containers = ... # type: Any - app_info: AppInfo - container_resolvers = ... # type: Any - def __init__(self, app_info: AppInfo) -> None: ... - def find_best_container_description( - self, enabled_container_types: Sequence[str], tool_info: ToolInfo - ) -> ContainerDescription | None: ... - -class Container: - container_id = ... # type: Any - app_info = ... # type: Any - tool_info = ... # type: Any - destination_info = ... # type: Any - job_info = ... # type: Any - container_description = ... # type: Any - def __init__( - self, - container_id: str, - app_info: AppInfo, - tool_info: ToolInfo, - destination_info: Dict[str, str], - job_info: JobInfo, - container_description: ContainerDescription, - ) -> None: ... - @property - def resolve_dependencies(self) -> bool: ... - @property - def shell(self) -> str: ... - def containerize_command(self, command: str) -> str: ... - -# def docker_cache_path(cache_directory, container_id): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi b/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi deleted file mode 100644 index 0ae396c27..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/dependencies.pyi +++ /dev/null @@ -1,57 +0,0 @@ -# Stubs for galaxy.tools.deps.dependencies (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -class AppInfo: - galaxy_root_dir = ... # type: Any - default_file_path = ... # type: Any - outputs_to_working_directory = ... # type: Any - container_image_cache_path = ... # type: Any - library_import_dir = ... # type: Any - enable_mulled_containers = ... # type: Any - containers_resolvers_config_file = ... # type: Any - involucro_path = ... # type: Any - involucro_auto_init = ... # type: Any - def __init__( - self, - galaxy_root_dir: Optional[Any] = ..., - default_file_path: Optional[Any] = ..., - outputs_to_working_directory: bool = ..., - container_image_cache_path: Optional[Any] = ..., - library_import_dir: Optional[Any] = ..., - enable_mulled_containers: bool = ..., - containers_resolvers_config_file: Optional[Any] = ..., - involucro_path: Optional[Any] = ..., - involucro_auto_init: bool = ..., - ) -> None: ... - -class ToolInfo: - container_descriptions = ... # type: Any - requirements = ... # type: Any - requires_galaxy_python_environment = ... # type: Any - env_pass_through = ... # type: Any - def __init__( - self, - container_descriptions: Any = ..., - requirements: Any = ..., - requires_galaxy_python_environment: bool = ..., - ) -> None: ... - -class JobInfo: - working_directory: str - tool_directory: str - job_directory: str - tmp_directory: str - home_directory: str - job_directory_type: str - def __init__( - self, - working_directory: str, - tool_directory: str, - job_directory: str, - tmp_directory: str, - home_directory: str, - job_directory_type: str, - ): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi b/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi deleted file mode 100644 index 880ddab2d..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/dockerfiles.pyi +++ /dev/null @@ -1,19 +0,0 @@ -# Stubs for galaxy.tools.deps.dockerfiles (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from ...tools import loader_directory as loader_directory -from ..deps import commands as commands -from ..deps.containers import docker_cache_path as docker_cache_path -from ..deps.requirements import ( - parse_requirements_from_xml as parse_requirements_from_xml, -) - -log = ... # type: Any - -def docker_host_args(**kwds): ... -def dockerfile_build( - path, dockerfile: Optional[Any] = ..., error: Any = ..., **kwds -): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/installable.pyi b/mypy-stubs/galaxy/tool_util/deps/installable.pyi deleted file mode 100644 index 818eaa26e..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/installable.pyi +++ /dev/null @@ -1,15 +0,0 @@ -# Stubs for galaxy.tools.deps.installable (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -log = ... # type: Any - -class InstallableContext: - def is_installed(self): ... - def can_install(self): ... - def installable_description(self): ... - def parent_path(self): ... - -def ensure_installed(installable_context, install_func, auto_init): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi deleted file mode 100644 index 2c36270f6..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/__init__.pyi +++ /dev/null @@ -1,3 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/_cli.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/_cli.pyi deleted file mode 100644 index db35991cc..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/_cli.pyi +++ /dev/null @@ -1,5 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled._cli (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def arg_parser(argv, globals): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi deleted file mode 100644 index c4c881a5c..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build.pyi +++ /dev/null @@ -1,30 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled.mulled_build (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from sys import platform as _platform -from typing import Any, Optional - -import installable - -class BuildExistsException(Exception): ... - -class InvolucroContext(installable.InstallableContext): - installable_description = ... # type: str - involucro_bin = ... # type: str - shell_exec = ... # type: Any - verbose = ... # type: Any - def __init__( - self, - involucro_bin: Optional[Any] = ..., - shell_exec: Optional[Any] = ..., - verbose: str = ..., - ) -> None: ... - def build_command(self, involucro_args): ... - def exec_command(self, involucro_args): ... - def is_installed(self): ... - def can_install(self): ... - @property - def parent_path(self): ... - -def main(argv: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_channel.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_channel.pyi deleted file mode 100644 index c0039bf4d..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_channel.pyi +++ /dev/null @@ -1,7 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled.mulled_build_channel (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -def main(argv: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi deleted file mode 100644 index 5e725df4f..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_files.pyi +++ /dev/null @@ -1,10 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled.mulled_build_files (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from collections import namedtuple -from typing import Any, Optional - -def main(argv: Optional[Any] = ...): ... - -_Line = namedtuple("_Line", ["targets", "image_build", "name_override"]) diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_tool.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_tool.pyi deleted file mode 100644 index e4af0daca..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_build_tool.pyi +++ /dev/null @@ -1,8 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled.mulled_build_tool (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -def main(argv: Optional[Any] = ...): ... -def requirements_to_mulled_targets(requirements): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_search.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_search.pyi deleted file mode 100644 index 9c8e9c23e..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/mulled_search.pyi +++ /dev/null @@ -1,23 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled.mulled_search (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -requests = ... # type: Any -Schema = ... # type: Any -TEXT = ... # type: Any -STORED = ... # type: Any -create_in = ... # type: Any -QueryParser = ... # type: Any -QUAY_API_URL = ... # type: str - -class QuaySearch: - index = ... # type: Any - organization = ... # type: Any - def __init__(self, organization) -> None: ... - def build_index(self): ... - def search_repository(self, search_string, non_strict): ... - def get_additional_repository_information(self, repository_string): ... - -def main(argv: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi b/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi deleted file mode 100644 index 0c7948b60..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/mulled/util.pyi +++ /dev/null @@ -1,32 +0,0 @@ -# Stubs for galaxy.tools.deps.mulled.util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from collections import namedtuple -from typing import Any, Optional - -def quay_versions(namespace, pkg_name): ... -def mulled_tags_for(namespace, image, tag_prefix: Optional[Any] = ...): ... -def split_tag(tag): ... -def version_sorted(elements): ... - -Target = namedtuple("Target", ["package_name", "version", "build"]) - -def build_target( - package_name, - version: Optional[Any] = ..., - build: Optional[Any] = ..., - tag: Optional[Any] = ..., -): ... -def conda_build_target_str(target): ... -def v1_image_name( - targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ... -): ... -def v2_image_name( - targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ... -): ... - -image_name = ... # type: Any - -# Names in __all__ with no definition: -# Target diff --git a/mypy-stubs/galaxy/tool_util/deps/requirements.pyi b/mypy-stubs/galaxy/tool_util/deps/requirements.pyi deleted file mode 100644 index 3307bb3fb..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/requirements.pyi +++ /dev/null @@ -1,74 +0,0 @@ -from typing import Any, Dict, Iterable, List, Union - -from _typeshed import Incomplete - -DEFAULT_REQUIREMENT_TYPE: str -DEFAULT_REQUIREMENT_VERSION: Incomplete - -class ToolRequirement: - name: Incomplete - type: Incomplete - version: Incomplete - specs: Incomplete - def __init__( - self, - name: Incomplete | None = ..., - type: Incomplete | None = ..., - version: Incomplete | None = ..., - specs: Incomplete | None = ..., - ) -> None: ... - def to_dict(self) -> Dict[str, str]: ... - def copy(self) -> ToolRequirement: ... - @staticmethod - def from_dict(d: Dict[str, str]) -> "ToolRequirement": ... - def __eq__(self, other: Any) -> bool: ... - def __ne__(self, other: Any) -> bool: ... - def __hash__(self) -> int: ... - -class ToolRequirements: - tool_requirements: Incomplete - def __init__( - self, - tool_requirements: List[Union[ToolRequirement, Dict[str, str]]] | None = ..., - ) -> None: ... - @staticmethod - def from_list( - requirements: List[Union[ToolRequirement, Dict[str, str]]] - ) -> "ToolRequirements": ... - @property - def resolvable(self) -> "ToolRequirements": ... - @property - def packages(self) -> "ToolRequirements": ... - def to_list(self) -> List[Dict[str, str]]: ... - def append(self, requirement: Union[ToolRequirement, Dict[str, str]]) -> None: ... - def __eq__(self, other: Any) -> bool: ... - def __ne__(self, other: Any) -> bool: ... - def __iter__(self) -> Iterable[ToolRequirement]: ... - def __getitem__(self, ii: int) -> ToolRequirement: ... - def __len__(self) -> int: ... - def __hash__(self) -> int: ... - def to_dict(self) -> List[Dict[str, str]]: ... - -DEFAULT_CONTAINER_TYPE: str -DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES: bool -DEFAULT_CONTAINER_SHELL: str - -class ContainerDescription: - identifier: str | None - type: str - resolve_dependencies: bool - shell: str - explicit: bool - def __init__( - self, - identifier: str | None = ..., - type: str = ..., - resolve_dependencies: bool = ..., - shell: str = ..., - ) -> None: ... - def to_dict(self, *args: Any, **kwds: Any) -> Dict[str, str]: ... - @staticmethod - def from_dict(dict: Dict[str, str]) -> "ContainerDescription": ... - -# def parse_requirements_from_dict(root_dict): ... -# def parse_requirements_from_xml(xml_root): ... diff --git a/mypy-stubs/galaxy/tool_util/deps/views.pyi b/mypy-stubs/galaxy/tool_util/deps/views.pyi deleted file mode 100644 index 271f2b57a..000000000 --- a/mypy-stubs/galaxy/tool_util/deps/views.pyi +++ /dev/null @@ -1,36 +0,0 @@ -# Stubs for galaxy.tools.deps.views (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -class DependencyResolversView: - def __init__(self, app) -> None: ... - def index(self): ... - def show(self, index): ... - def reload(self): ... - def manager_requirements(self): ... - def resolver_requirements(self, index): ... - def manager_dependency(self, **kwds): ... - def resolver_dependency(self, index, **kwds): ... - def show_dependencies( - self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ... - ): ... - def uninstall_dependencies(self, index: Optional[Any] = ..., **payload): ... - @property - def unused_dependency_paths(self): ... - def remove_unused_dependency_paths(self, envs): ... - def install_dependencies(self, requirements): ... - def install_dependency(self, index: Optional[Any] = ..., **payload): ... - @property - def installable_resolvers(self): ... - @property - def uninstallable_resolvers(self): ... - @property - def tool_ids_by_requirements(self): ... - @property - def toolbox_requirements_status(self): ... - def get_requirements_status( - self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ... - ): ... - def clean(self, index: Optional[Any] = ..., **kwds): ... diff --git a/mypy-stubs/galaxy/tool_util/fetcher.pyi b/mypy-stubs/galaxy/tool_util/fetcher.pyi deleted file mode 100644 index 221bc58a8..000000000 --- a/mypy-stubs/galaxy/tool_util/fetcher.pyi +++ /dev/null @@ -1,10 +0,0 @@ -# Stubs for galaxy.tools.fetcher (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -class ToolLocationFetcher: - resolver_classes = ... # type: Any - def __init__(self) -> None: ... - def to_tool_path(self, path_or_uri_like, **kwds): ... diff --git a/mypy-stubs/galaxy/tool_util/lint.pyi b/mypy-stubs/galaxy/tool_util/lint.pyi deleted file mode 100644 index ddf1a78e5..000000000 --- a/mypy-stubs/galaxy/tool_util/lint.pyi +++ /dev/null @@ -1,46 +0,0 @@ -# Stubs for galaxy.tools.lint (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -from .parser import get_tool_source as get_tool_source - -LEVEL_ALL = ... # type: str -LEVEL_WARN = ... # type: str -LEVEL_ERROR = ... # type: str - -def lint_tool_source( - tool_source, - level: Any = ..., - fail_level: Any = ..., - extra_modules: Any = ..., - skip_types: Any = ..., -): ... -def lint_xml( - tool_xml, - level: Any = ..., - fail_level: Any = ..., - extra_modules: Any = ..., - skip_types: Any = ..., -): ... -def lint_tool_source_with(lint_context, tool_source, extra_modules: Any = ...): ... -def lint_xml_with(lint_context, tool_xml, extra_modules: Any = ...): ... - -class LintContext: - skip_types = ... # type: Any - level = ... # type: Any - found_errors = ... # type: bool - found_warns = ... # type: bool - def __init__(self, level, skip_types: Any = ...) -> None: ... - printed_linter_info = ... # type: bool - valid_messages = ... # type: Any - info_messages = ... # type: Any - warn_messages = ... # type: Any - error_messages = ... # type: Any - def lint(self, name, lint_func, lint_target): ... - def valid(self, message, *args): ... - def info(self, message, *args): ... - def error(self, message, *args): ... - def warn(self, message, *args): ... - def failed(self, fail_level): ... diff --git a/mypy-stubs/galaxy/tool_util/lint_util.pyi b/mypy-stubs/galaxy/tool_util/lint_util.pyi deleted file mode 100644 index e1e1ac02b..000000000 --- a/mypy-stubs/galaxy/tool_util/lint_util.pyi +++ /dev/null @@ -1,5 +0,0 @@ -# Stubs for galaxy.tools.lint_util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def is_datasource(tool_xml): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/__init__.pyi b/mypy-stubs/galaxy/tool_util/linters/__init__.pyi deleted file mode 100644 index 725c48e0d..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/__init__.pyi +++ /dev/null @@ -1,3 +0,0 @@ -# Stubs for galaxy.tools.linters (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. diff --git a/mypy-stubs/galaxy/tool_util/linters/citations.pyi b/mypy-stubs/galaxy/tool_util/linters/citations.pyi deleted file mode 100644 index 5378b8ded..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/citations.pyi +++ /dev/null @@ -1,5 +0,0 @@ -# Stubs for galaxy.tools.linters.citations (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def lint_citations(tool_xml, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/command.pyi b/mypy-stubs/galaxy/tool_util/linters/command.pyi deleted file mode 100644 index 2e6863537..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/command.pyi +++ /dev/null @@ -1,6 +0,0 @@ -# Stubs for galaxy.tools.linters.command (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def lint_command(tool_xml, lint_ctx): ... -def get_command(tool_xml): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/cwl.pyi b/mypy-stubs/galaxy/tool_util/linters/cwl.pyi deleted file mode 100644 index a94292e46..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/cwl.pyi +++ /dev/null @@ -1,12 +0,0 @@ -# Stubs for galaxy.tools.linters.cwl (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -lint_tool_types = ... # type: Any - -def lint_cwl_validation(tool_source, lint_ctx): ... -def lint_new_draft(tool_source, lint_ctx): ... -def lint_docker_image(tool_source, lint_ctx): ... -def lint_description(tool_source, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/general.pyi b/mypy-stubs/galaxy/tool_util/linters/general.pyi deleted file mode 100644 index 812e6e9f7..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/general.pyi +++ /dev/null @@ -1,19 +0,0 @@ -# Stubs for galaxy.tools.linters.general (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -ERROR_VERSION_MSG = ... # type: str -VALID_VERSION_MSG = ... # type: str -ERROR_NAME_MSG = ... # type: str -VALID_NAME_MSG = ... # type: str -ERROR_ID_MSG = ... # type: str -VALID_ID_MSG = ... # type: str -PROFILE_PATTERN = ... # type: Any -PROFILE_INFO_DEFAULT_MSG = ... # type: str -PROFILE_INFO_SPECIFIED_MSG = ... # type: str -PROFILE_INVALID_MSG = ... # type: str -lint_tool_types = ... # type: Any - -def lint_general(tool_source, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/help.pyi b/mypy-stubs/galaxy/tool_util/linters/help.pyi deleted file mode 100644 index 306fa3bda..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/help.pyi +++ /dev/null @@ -1,6 +0,0 @@ -# Stubs for galaxy.tools.linters.help (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def lint_help(tool_xml, lint_ctx): ... -def rst_invalid(text): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/inputs.pyi b/mypy-stubs/galaxy/tool_util/linters/inputs.pyi deleted file mode 100644 index c06f46c9e..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/inputs.pyi +++ /dev/null @@ -1,8 +0,0 @@ -# Stubs for galaxy.tools.linters.inputs (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from ..lint_util import is_datasource as is_datasource - -def lint_inputs(tool_xml, lint_ctx): ... -def lint_repeats(tool_xml, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/outputs.pyi b/mypy-stubs/galaxy/tool_util/linters/outputs.pyi deleted file mode 100644 index ecb922098..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/outputs.pyi +++ /dev/null @@ -1,5 +0,0 @@ -# Stubs for galaxy.tools.linters.outputs (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def lint_output(tool_xml, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/stdio.pyi b/mypy-stubs/galaxy/tool_util/linters/stdio.pyi deleted file mode 100644 index d7c2927c9..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/stdio.pyi +++ /dev/null @@ -1,7 +0,0 @@ -# Stubs for galaxy.tools.linters.stdio (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from .command import get_command as get_command - -def lint_stdio(tool_source, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/tests.pyi b/mypy-stubs/galaxy/tool_util/linters/tests.pyi deleted file mode 100644 index d9c7cf0f9..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/tests.pyi +++ /dev/null @@ -1,7 +0,0 @@ -# Stubs for galaxy.tools.linters.tests (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from ..lint_util import is_datasource as is_datasource - -def lint_tsts(tool_xml, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/linters/xml_order.pyi b/mypy-stubs/galaxy/tool_util/linters/xml_order.pyi deleted file mode 100644 index a3904f6c2..000000000 --- a/mypy-stubs/galaxy/tool_util/linters/xml_order.pyi +++ /dev/null @@ -1,10 +0,0 @@ -# Stubs for galaxy.tools.linters.xml_order (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -TAG_ORDER = ... # type: Any -DATASOURCE_TAG_ORDER = ... # type: Any - -def lint_xml_order(tool_xml, lint_ctx): ... diff --git a/mypy-stubs/galaxy/tool_util/loader.pyi b/mypy-stubs/galaxy/tool_util/loader.pyi deleted file mode 100644 index d7ee04a05..000000000 --- a/mypy-stubs/galaxy/tool_util/loader.pyi +++ /dev/null @@ -1,11 +0,0 @@ -# Stubs for galaxy.tools.loader (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -from galaxy.util.xml_macros import imported_macro_paths as imported_macro_paths -from galaxy.util.xml_macros import raw_tool_xml_tree as raw_tool_xml_tree -from galaxy.util.xml_macros import template_macro_params as template_macro_params - -load_tool = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/loader_directory.pyi b/mypy-stubs/galaxy/tool_util/loader_directory.pyi deleted file mode 100644 index b52abdc55..000000000 --- a/mypy-stubs/galaxy/tool_util/loader_directory.pyi +++ /dev/null @@ -1,27 +0,0 @@ -# Stubs for galaxy.tools.loader_directory (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -def find_possible_tools_from_path( - path, recursive: bool = ..., enable_beta_formats: bool = ... -): ... -def load_tool_sources_from_path( - path, - load_exception_handler: Any = ..., - recursive: bool = ..., - register_load_errors: bool = ..., -): ... -def load_tool_elements_from_path( - path, - load_exception_handler: Any = ..., - recursive: bool = ..., - register_load_errors: bool = ..., -): ... -def is_tool_load_error(obj): ... -def looks_like_a_tool_xml(path): ... -def is_a_yaml_with_class(path, classes): ... -def looks_like_a_tool_yaml(path): ... -def looks_like_a_cwl_artifact(path, classes: Optional[Any] = ...): ... -def looks_like_a_tool_cwl(path): ... diff --git a/mypy-stubs/galaxy/tool_util/locations/__init__.pyi b/mypy-stubs/galaxy/tool_util/locations/__init__.pyi deleted file mode 100644 index af99abd8b..000000000 --- a/mypy-stubs/galaxy/tool_util/locations/__init__.pyi +++ /dev/null @@ -1,7 +0,0 @@ -# Stubs for galaxy.tools.locations (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -class ToolLocationResolver: - def scheme(self): ... - def get_tool_source_path(self, uri_like): ... diff --git a/mypy-stubs/galaxy/tool_util/locations/dockstore.pyi b/mypy-stubs/galaxy/tool_util/locations/dockstore.pyi deleted file mode 100644 index 0ef01352e..000000000 --- a/mypy-stubs/galaxy/tool_util/locations/dockstore.pyi +++ /dev/null @@ -1,22 +0,0 @@ -# Stubs for galaxy.tools.locations.dockstore (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -from ..locations import ToolLocationResolver - -class DockStoreResolver(ToolLocationResolver): - scheme = ... # type: str - def get_tool_source_path(self, uri_like): ... - -class _Ga4ghToolClient: - base_url = ... # type: Any - def __init__(self, base_url: str = ...) -> None: ... - def get_tools(self): ... - def get_tool(self, tool_id): ... - def get_tool_version(self, tool_id, version: str = ...): ... - def get_tool_descriptor( - self, tool_id, version: str = ..., tool_type: str = ... - ): ... - def get_tool_cwl(self, tool_id, version: str = ..., as_string: bool = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/locations/file.pyi b/mypy-stubs/galaxy/tool_util/locations/file.pyi deleted file mode 100644 index 8268d650f..000000000 --- a/mypy-stubs/galaxy/tool_util/locations/file.pyi +++ /dev/null @@ -1,9 +0,0 @@ -# Stubs for galaxy.tools.locations.file (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from ..locations import ToolLocationResolver as ToolLocationResolver - -class HttpToolResolver(ToolLocationResolver): - scheme = ... # type: str - def get_tool_source_path(self, uri_like): ... diff --git a/mypy-stubs/galaxy/tool_util/locations/http.pyi b/mypy-stubs/galaxy/tool_util/locations/http.pyi deleted file mode 100644 index 2687afcef..000000000 --- a/mypy-stubs/galaxy/tool_util/locations/http.pyi +++ /dev/null @@ -1,13 +0,0 @@ -# Stubs for galaxy.tools.locations.http (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from ..locations import ToolLocationResolver - -class HttpToolResolver(ToolLocationResolver): - scheme = ... # type: str - def __init__(self, **kwds) -> None: ... - def get_tool_source_path(self, uri_like): ... - -class HttpsToolResolver(HttpToolResolver): - scheme = ... # type: str diff --git a/mypy-stubs/galaxy/tool_util/parser/__init__.pyi b/mypy-stubs/galaxy/tool_util/parser/__init__.pyi deleted file mode 100644 index a2e601725..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/__init__.pyi +++ /dev/null @@ -1,8 +0,0 @@ -# Stubs for galaxy.tools.parser (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from .factory import get_input_source as get_input_source -from .factory import get_tool_source as get_tool_source -from .interface import ToolSource as ToolSource -from .output_objects import ToolOutputCollectionPart as ToolOutputCollectionPart diff --git a/mypy-stubs/galaxy/tool_util/parser/cwl.pyi b/mypy-stubs/galaxy/tool_util/parser/cwl.pyi deleted file mode 100644 index c9fb631fb..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/cwl.pyi +++ /dev/null @@ -1,42 +0,0 @@ -# Stubs for galaxy.tools.parser.cwl (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -from .interface import PageSource as PageSource -from .interface import PagesSource as PagesSource -from .interface import ToolSource as ToolSource -from .interface import ToolStdioExitCode as ToolStdioExitCode -from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup -from .output_objects import ToolOutput as ToolOutput -from .yaml import YamlInputSource as YamlInputSource - -log = ... # type: Any - -class CwlToolSource(ToolSource): - def __init__(self, tool_file, strict_cwl_validation: bool = ...) -> None: ... - @property - def tool_proxy(self): ... - def parse_tool_type(self): ... - def parse_id(self): ... - def parse_name(self): ... - def parse_command(self): ... - def parse_environment_variables(self): ... - def parse_edam_operations(self): ... - def parse_edam_topics(self): ... - def parse_help(self): ... - def parse_sanitize(self): ... - def parse_strict_shell(self): ... - def parse_stdio(self): ... - def parse_interpreter(self): ... - def parse_version(self): ... - def parse_description(self): ... - def parse_input_pages(self): ... - def parse_outputs(self, tool): ... - def parse_requirements_and_containers(self): ... - def parse_profile(self): ... - -class CwlPageSource(PageSource): - def __init__(self, tool_proxy) -> None: ... - def parse_input_sources(self): ... diff --git a/mypy-stubs/galaxy/tool_util/parser/factory.pyi b/mypy-stubs/galaxy/tool_util/parser/factory.pyi deleted file mode 100644 index d3b4244b0..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/factory.pyi +++ /dev/null @@ -1,15 +0,0 @@ -# Stubs for galaxy.tools.parser.factory (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from galaxy.tools.loader import load_tool as load_tool_xml - -def get_tool_source( - config_file: Optional[Any] = ..., - xml_tree: Optional[Any] = ..., - enable_beta_formats: bool = ..., - tool_location_fetcher: Optional[Any] = ..., -): ... -def get_input_source(content): ... diff --git a/mypy-stubs/galaxy/tool_util/parser/interface.pyi b/mypy-stubs/galaxy/tool_util/parser/interface.pyi deleted file mode 100644 index e219c74a3..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/interface.pyi +++ /dev/null @@ -1,96 +0,0 @@ -# Stubs for galaxy.tools.parser.interface (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -NOT_IMPLEMENTED_MESSAGE = ... # type: str - -class ToolSource: - default_is_multi_byte = ... # type: bool - def parse_id(self): ... - def parse_version(self): ... - def parse_tool_module(self): ... - def parse_action_module(self): ... - def parse_tool_type(self): ... - def parse_name(self): ... - def parse_description(self): ... - def parse_is_multi_byte(self): ... - def parse_display_interface(self, default): ... - def parse_require_login(self, default): ... - def parse_request_param_translation_elem(self): ... - def parse_command(self): ... - def parse_environment_variables(self): ... - def parse_interpreter(self): ... - def parse_redirect_url_params_elem(self): ... - def parse_version_command(self): ... - def parse_version_command_interpreter(self): ... - def parse_parallelism(self): ... - def parse_hidden(self): ... - def parse_sanitize(self): ... - def parse_refresh(self): ... - def parse_requirements_and_containers(self): ... - def parse_input_pages(self): ... - def parse_outputs(self, tool): ... - def parse_strict_shell(self): ... - def parse_stdio(self): ... - def parse_help(self): ... - def parse_profile(self): ... - def parse_tests_to_dict(self): ... - -class PagesSource: - page_sources = ... # type: Any - def __init__(self, page_sources) -> None: ... - @property - def inputs_defined(self): ... - -class PageSource: - def parse_display(self): ... - def parse_input_sources(self): ... - -class InputSource: - default_optional = ... # type: bool - def elem(self): ... - def get(self, key, value: Optional[Any] = ...): ... - def get_bool(self, key, default): ... - def parse_label(self): ... - def parse_help(self): ... - def parse_sanitizer_elem(self): ... - def parse_validator_elems(self): ... - def parse_optional(self, default: Optional[Any] = ...): ... - def parse_dynamic_options_elem(self): ... - def parse_static_options(self): ... - def parse_conversion_tuples(self): ... - def parse_nested_inputs_source(self): ... - def parse_test_input_source(self): ... - def parse_when_input_sources(self): ... - -class ToolStdioRegex: - match = ... # type: str - stdout_match = ... # type: bool - stderr_match = ... # type: bool - error_level = ... # type: str - desc = ... # type: str - def __init__(self) -> None: ... - -class ToolStdioExitCode: - range_start = ... # type: Any - range_end = ... # type: Any - error_level = ... # type: str - desc = ... # type: str - def __init__(self) -> None: ... - -class TestCollectionDef: - elements = ... # type: Any - collection_type = ... # type: Any - name = ... # type: Any - def __init__(self, elem, parse_param_elem) -> None: ... - def collect_inputs(self): ... - -class TestCollectionOutputDef: - name = ... # type: Any - collection_type = ... # type: Any - count = ... # type: Any - attrib = ... # type: Any - element_tests = ... # type: Any - def __init__(self, name, attrib, element_tests) -> None: ... diff --git a/mypy-stubs/galaxy/tool_util/parser/output_actions.pyi b/mypy-stubs/galaxy/tool_util/parser/output_actions.pyi deleted file mode 100644 index a045a4f08..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/output_actions.pyi +++ /dev/null @@ -1,217 +0,0 @@ -# Stubs for galaxy.tools.parser.output_actions (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -log = ... # type: Any -COLLECTION_ATTRIBUTES = ... # type: Any - -class ToolOutputActionGroup: - tag = ... # type: str - parent = ... # type: Any - actions = ... # type: Any - def __init__(self, parent, config_elem) -> None: ... - def apply_action(self, output_dataset, other_values): ... - @property - def tool(self): ... - def __len__(self): ... - -class ToolOutputActionConditionalWhen(ToolOutputActionGroup): - tag = ... # type: str - @classmethod - def from_elem(cls, parent, when_elem): ... - value = ... # type: Any - def __init__(self, parent, config_elem, value) -> None: ... - def is_case(self, output_dataset, other_values): ... - def get_ref(self, output_dataset, other_values): ... - def apply_action(self, output_dataset, other_values): ... - -class ValueToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen): - tag = ... # type: str - def is_case(self, output_dataset, other_values): ... - -class DatatypeIsInstanceToolOutputActionConditionalWhen( - ToolOutputActionConditionalWhen -): - tag = ... # type: str - value = ... # type: Any - def __init__(self, parent, config_elem, value) -> None: ... - def is_case(self, output_dataset, other_values): ... - -class ToolOutputActionConditional: - tag = ... # type: str - parent = ... # type: Any - name = ... # type: Any - cases = ... # type: Any - def __init__(self, parent, config_elem) -> None: ... - def apply_action(self, output_dataset, other_values): ... - @property - def tool(self): ... - -class ToolOutputAction: - tag = ... # type: str - @classmethod - def from_elem(cls, parent, elem): ... - parent = ... # type: Any - default = ... # type: Any - option = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def apply_action(self, output_dataset, other_values): ... - @property - def tool(self): ... - -class ToolOutputActionOption: - tag = ... # type: str - @classmethod - def from_elem(cls, parent, elem): ... - parent = ... # type: Any - filters = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def get_value(self, other_values): ... - @property - def tool(self): ... - -class NullToolOutputActionOption(ToolOutputActionOption): - tag = ... # type: str - def get_value(self, other_values): ... - -class FromFileToolOutputActionOption(ToolOutputActionOption): - tag = ... # type: str - name = ... # type: Any - column = ... # type: Any - offset = ... # type: Any - separator = ... # type: Any - options = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def get_value(self, other_values): ... - -class FromParamToolOutputActionOption(ToolOutputActionOption): - tag = ... # type: str - name = ... # type: Any - column = ... # type: Any - offset = ... # type: Any - param_attribute = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def get_value(self, other_values): ... - -class FromDataTableOutputActionOption(ToolOutputActionOption): - tag = ... # type: str - name = ... # type: Any - missing_tool_data_table_name = ... # type: Any - options = ... # type: Any - column = ... # type: Any - offset = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def get_value(self, other_values): ... - -class MetadataToolOutputAction(ToolOutputAction): - tag = ... # type: str - name = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def apply_action(self, output_dataset, other_values): ... - -class FormatToolOutputAction(ToolOutputAction): - tag = ... # type: str - default = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def apply_action(self, output_dataset, other_values): ... - -class ToolOutputActionOptionFilter: - tag = ... # type: str - @classmethod - def from_elem(cls, parent, elem): ... - parent = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - @property - def tool(self): ... - -class ParamValueToolOutputActionOptionFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - ref = ... # type: Any - value = ... # type: Any - column = ... # type: Any - keep = ... # type: Any - compare = ... # type: Any - cast = ... # type: Any - param_attribute = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -class InsertColumnToolOutputActionOptionFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - ref = ... # type: Any - value = ... # type: Any - column = ... # type: Any - iterate = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -class MultipleSplitterFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - column = ... # type: Any - separator = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -class ColumnStripFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - column = ... # type: Any - strip = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -class ColumnReplaceFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - old_column = ... # type: Any - old_value = ... # type: Any - new_value = ... # type: Any - new_column = ... # type: Any - column = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -class MetadataValueFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - ref = ... # type: Any - name = ... # type: Any - column = ... # type: Any - keep = ... # type: Any - compare = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -class BooleanFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - column = ... # type: Any - keep = ... # type: Any - cast = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -class StringFunctionFilter(ToolOutputActionOptionFilter): - tag = ... # type: str - column = ... # type: Any - function = ... # type: Any - def __init__(self, parent, elem) -> None: ... - def filter_options(self, options, other_values): ... - -action_types = ... # type: Any -option_types = ... # type: Any -filter_types = ... # type: Any - -def parse_cast_attribute(cast): ... -def parse_compare_type(compare): ... -def compare_eq(value1, value2): ... -def compare_neq(value1, value2): ... -def compare_gt(value1, value2): ... -def compare_gte(value1, value2): ... -def compare_lt(value1, value2): ... -def compare_lte(value1, value2): ... -def compare_in(value1, value2): ... -def compare_startswith(value1, value2): ... -def compare_endswith(value1, value2): ... -def compare_re_search(value1, value2): ... - -compare_types = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/parser/output_collection_def.pyi b/mypy-stubs/galaxy/tool_util/parser/output_collection_def.pyi deleted file mode 100644 index 2cc4b1bd7..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/output_collection_def.pyi +++ /dev/null @@ -1,29 +0,0 @@ -# Stubs for galaxy.tools.parser.output_collection_def (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -DEFAULT_EXTRA_FILENAME_PATTERN = ... # type: str -DEFAULT_SORT_BY = ... # type: str -DEFAULT_SORT_COMP = ... # type: str -NAMED_PATTERNS = ... # type: Any -INPUT_DBKEY_TOKEN = ... # type: str -LEGACY_DEFAULT_DBKEY = ... # type: Any - -def dataset_collector_descriptions_from_elem(elem, legacy: bool = ...): ... -def dataset_collector_descriptions_from_list(discover_datasets_dicts): ... - -class DatasetCollectionDescription: - pattern = ... # type: Any - default_dbkey = ... # type: Any - default_ext = ... # type: Any - default_visible = ... # type: Any - directory = ... # type: Any - assign_primary_output = ... # type: Any - sort_reverse = ... # type: bool - sort_key = ... # type: Any - sort_comp = ... # type: Any - def __init__(self, **kwargs) -> None: ... - -DEFAULT_DATASET_COLLECTOR_DESCRIPTION = ... # type: Any diff --git a/mypy-stubs/galaxy/tool_util/parser/util.pyi b/mypy-stubs/galaxy/tool_util/parser/util.pyi deleted file mode 100644 index 97b33962c..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/util.pyi +++ /dev/null @@ -1,9 +0,0 @@ -# Stubs for galaxy.tools.parser.util (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from .interface import ToolStdioExitCode as ToolStdioExitCode -from .interface import ToolStdioRegex as ToolStdioRegex - -def error_on_exit_code(): ... -def aggressive_error_checks(): ... diff --git a/mypy-stubs/galaxy/tool_util/parser/xml.pyi b/mypy-stubs/galaxy/tool_util/parser/xml.pyi deleted file mode 100644 index 439919eb8..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/xml.pyi +++ /dev/null @@ -1,104 +0,0 @@ -# Stubs for galaxy.tools.parser.xml (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from .interface import InputSource as InputSource -from .interface import PageSource as PageSource -from .interface import PagesSource as PagesSource -from .interface import TestCollectionDef as TestCollectionDef -from .interface import TestCollectionOutputDef as TestCollectionOutputDef -from .interface import ToolSource as ToolSource -from .interface import ToolStdioExitCode as ToolStdioExitCode -from .interface import ToolStdioRegex as ToolStdioRegex -from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup -from .output_collection_def import ( - dataset_collector_descriptions_from_elem as dataset_collector_descriptions_from_elem, -) -from .output_objects import ToolOutput as ToolOutput -from .output_objects import ToolOutputCollection as ToolOutputCollection -from .output_objects import ( - ToolOutputCollectionStructure as ToolOutputCollectionStructure, -) -from .util import aggressive_error_checks as aggressive_error_checks -from .util import error_on_exit_code as error_on_exit_code - -log = ... # type: Any - -class XmlToolSource(ToolSource): - xml_tree = ... # type: Any - root = ... # type: Any - legacy_defaults = ... # type: Any - def __init__(self, xml_tree, source_path: Optional[Any] = ...) -> None: ... - def parse_version(self): ... - def parse_id(self): ... - def parse_tool_module(self): ... - def parse_action_module(self): ... - def parse_tool_type(self): ... - def parse_name(self): ... - def parse_edam_operations(self): ... - def parse_edam_topics(self): ... - def parse_description(self): ... - def parse_is_multi_byte(self): ... - def parse_display_interface(self, default): ... - def parse_require_login(self, default): ... - def parse_request_param_translation_elem(self): ... - def parse_command(self): ... - def parse_environment_variables(self): ... - def parse_interpreter(self): ... - def parse_version_command(self): ... - def parse_version_command_interpreter(self): ... - def parse_parallelism(self): ... - def parse_hidden(self): ... - def parse_redirect_url_params_elem(self): ... - def parse_sanitize(self): ... - def parse_refresh(self): ... - def parse_requirements_and_containers(self): ... - def parse_input_pages(self): ... - def parse_outputs(self, tool): ... - def parse_stdio(self): ... - def parse_strict_shell(self): ... - def parse_help(self): ... - def parse_tests_to_dict(self): ... - def parse_profile(self): ... - -class StdioParser: - stdio_exit_codes = ... # type: Any - stdio_regexes = ... # type: Any - def __init__(self, root) -> None: ... - def parse_stdio_exit_codes(self, stdio_elem): ... - def parse_stdio_regexes(self, stdio_elem): ... - def parse_error_level(self, err_level): ... - -class XmlPagesSource(PagesSource): - input_elem = ... # type: Any - def __init__(self, root) -> None: ... - @property - def inputs_defined(self): ... - -class XmlPageSource(PageSource): - parent_elem = ... # type: Any - def __init__(self, parent_elem) -> None: ... - def parse_display(self): ... - def parse_input_sources(self): ... - -class XmlInputSource(InputSource): - input_elem = ... # type: Any - input_type = ... # type: Any - def __init__(self, input_elem) -> None: ... - def parse_input_type(self): ... - def elem(self): ... - def get(self, key, value: Optional[Any] = ...): ... - def get_bool(self, key, default): ... - def parse_label(self): ... - def parse_help(self): ... - def parse_sanitizer_elem(self): ... - def parse_validator_elems(self): ... - def parse_dynamic_options_elem(self): ... - def parse_static_options(self): ... - def parse_optional(self, default: Optional[Any] = ...): ... - def parse_conversion_tuples(self): ... - def parse_nested_inputs_source(self): ... - def parse_test_input_source(self): ... - def parse_when_input_sources(self): ... diff --git a/mypy-stubs/galaxy/tool_util/parser/yaml.pyi b/mypy-stubs/galaxy/tool_util/parser/yaml.pyi deleted file mode 100644 index 834451be7..000000000 --- a/mypy-stubs/galaxy/tool_util/parser/yaml.pyi +++ /dev/null @@ -1,63 +0,0 @@ -# Stubs for galaxy.tools.parser.yaml (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from .interface import InputSource as InputSource -from .interface import PageSource as PageSource -from .interface import PagesSource as PagesSource -from .interface import ToolSource as ToolSource -from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup -from .output_collection_def import ( - dataset_collector_descriptions_from_list as dataset_collector_descriptions_from_list, -) -from .output_objects import ToolOutput as ToolOutput -from .output_objects import ToolOutputCollection as ToolOutputCollection -from .output_objects import ( - ToolOutputCollectionStructure as ToolOutputCollectionStructure, -) -from .util import error_on_exit_code as error_on_exit_code - -class YamlToolSource(ToolSource): - root_dict = ... # type: Any - def __init__(self, root_dict, source_path: Optional[Any] = ...) -> None: ... - def parse_id(self): ... - def parse_version(self): ... - def parse_name(self): ... - def parse_description(self): ... - def parse_edam_operations(self): ... - def parse_edam_topics(self): ... - def parse_is_multi_byte(self): ... - def parse_sanitize(self): ... - def parse_display_interface(self, default): ... - def parse_require_login(self, default): ... - def parse_command(self): ... - def parse_environment_variables(self): ... - def parse_interpreter(self): ... - def parse_version_command(self): ... - def parse_version_command_interpreter(self): ... - def parse_requirements_and_containers(self): ... - def parse_input_pages(self): ... - def parse_strict_shell(self): ... - def parse_stdio(self): ... - def parse_help(self): ... - def parse_outputs(self, tool): ... - def parse_tests_to_dict(self): ... - def parse_profile(self): ... - -class YamlPageSource(PageSource): - inputs_list = ... # type: Any - def __init__(self, inputs_list) -> None: ... - def parse_input_sources(self): ... - -class YamlInputSource(InputSource): - input_dict = ... # type: Any - def __init__(self, input_dict) -> None: ... - def get(self, key, default: Optional[Any] = ...): ... - def get_bool(self, key, default): ... - def parse_input_type(self): ... - def parse_nested_inputs_source(self): ... - def parse_test_input_source(self): ... - def parse_when_input_sources(self): ... - def parse_static_options(self): ... diff --git a/mypy-stubs/galaxy/tool_util/verify/__init__.pyi b/mypy-stubs/galaxy/tool_util/verify/__init__.pyi deleted file mode 100644 index 5271b6308..000000000 --- a/mypy-stubs/galaxy/tool_util/verify/__init__.pyi +++ /dev/null @@ -1,27 +0,0 @@ -# Stubs for galaxy.tools.verify (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any, Optional - -from .asserts import verify_assertions as verify_assertions -from .test_data import TestDataResolver as TestDataResolver - -log = ... # type: Any -DEFAULT_TEST_DATA_RESOLVER = ... # type: Any - -def verify( - item_label, - output_content, - attributes, - filename: Optional[Any] = ..., - get_filename: Optional[Any] = ..., - keep_outputs_dir: Optional[Any] = ..., - verify_extra_files: Optional[Any] = ..., -): ... -def make_temp_fname(fname: Optional[Any] = ...): ... -def check_command(command, description): ... -def files_diff(file1, file2, attributes: Optional[Any] = ...): ... -def files_re_match(file1, file2, attributes: Optional[Any] = ...): ... -def files_re_match_multiline(file1, file2, attributes: Optional[Any] = ...): ... -def files_contains(file1, file2, attributes: Optional[Any] = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/verify/asserts/__init__.pyi b/mypy-stubs/galaxy/tool_util/verify/asserts/__init__.pyi deleted file mode 100644 index 3ba17d3da..000000000 --- a/mypy-stubs/galaxy/tool_util/verify/asserts/__init__.pyi +++ /dev/null @@ -1,14 +0,0 @@ -# Stubs for galaxy.tools.verify.asserts (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -log = ... # type: Any -assertion_module_names = ... # type: Any -assertion_modules = ... # type: Any -full_assertion_module_name = ... # type: Any -assertion_module = ... # type: Any - -def verify_assertions(data, assertion_description_list): ... -def verify_assertion(data, assertion_description): ... diff --git a/mypy-stubs/galaxy/tool_util/verify/asserts/tabular.pyi b/mypy-stubs/galaxy/tool_util/verify/asserts/tabular.pyi deleted file mode 100644 index 4515eab5f..000000000 --- a/mypy-stubs/galaxy/tool_util/verify/asserts/tabular.pyi +++ /dev/null @@ -1,6 +0,0 @@ -# Stubs for galaxy.tools.verify.asserts.tabular (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def get_first_line(output): ... -def assert_has_n_columns(output, n, sep: str = ...): ... diff --git a/mypy-stubs/galaxy/tool_util/verify/asserts/text.pyi b/mypy-stubs/galaxy/tool_util/verify/asserts/text.pyi deleted file mode 100644 index 549d53481..000000000 --- a/mypy-stubs/galaxy/tool_util/verify/asserts/text.pyi +++ /dev/null @@ -1,9 +0,0 @@ -# Stubs for galaxy.tools.verify.asserts.text (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def assert_has_text(output, text): ... -def assert_not_has_text(output, text): ... -def assert_has_line(output, line): ... -def assert_has_text_matching(output, expression): ... -def assert_has_line_matching(output, expression): ... diff --git a/mypy-stubs/galaxy/tool_util/verify/asserts/xml.pyi b/mypy-stubs/galaxy/tool_util/verify/asserts/xml.pyi deleted file mode 100644 index 57af9c728..000000000 --- a/mypy-stubs/galaxy/tool_util/verify/asserts/xml.pyi +++ /dev/null @@ -1,15 +0,0 @@ -# Stubs for galaxy.tools.verify.asserts.xml (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -def to_xml(output): ... -def xml_find_text(output, path): ... -def xml_find(output, path): ... -def assert_is_valid_xml(output): ... -def assert_has_element_with_path(output, path): ... -def assert_has_n_elements_with_path(output, path, n): ... -def assert_element_text_matches(output, path, expression): ... -def assert_element_text_is(output, path, text): ... -def assert_attribute_matches(output, path, attribute, expression): ... -def assert_attribute_is(output, path, attribute, text): ... -def assert_element_text(output, path, verify_assertions_function, children): ... diff --git a/mypy-stubs/galaxy/tool_util/verify/test_data.pyi b/mypy-stubs/galaxy/tool_util/verify/test_data.pyi deleted file mode 100644 index 1fe6f0d38..000000000 --- a/mypy-stubs/galaxy/tool_util/verify/test_data.pyi +++ /dev/null @@ -1,31 +0,0 @@ -# Stubs for galaxy.tools.verify.test_data (Python 3.4) -# -# NOTE: This dynamically typed stub was automatically generated by stubgen. - -from typing import Any - -UPDATE_TEMPLATE = ... # type: Any -UPDATE_FAILED_TEMPLATE = ... # type: Any -LIST_SEP = ... # type: Any - -class TestDataResolver: - resolvers = ... # type: Any - def __init__(self, env_var: str = ..., environ: Any = ...) -> None: ... - def get_filename(self, name): ... - -def build_resolver(uri, environ): ... - -class FileDataResolver: - file_dir = ... # type: Any - def __init__(self, file_dir) -> None: ... - def exists(self, filename): ... - def path(self, filename): ... - -class GitDataResolver(FileDataResolver): - repository = ... # type: Any - updated = ... # type: bool - fetch_data = ... # type: Any - def __init__(self, repository, environ) -> None: ... - def exists(self, filename): ... - def update_repository(self): ... - def execute(self, cmd): ... diff --git a/mypy-stubs/galaxy/util/__init__.pyi b/mypy-stubs/galaxy/util/__init__.pyi deleted file mode 100644 index d97198b21..000000000 --- a/mypy-stubs/galaxy/util/__init__.pyi +++ /dev/null @@ -1,102 +0,0 @@ -import collections -from collections.abc import Generator - -from _typeshed import Incomplete - -LXML_AVAILABLE: bool -inflector: Incomplete -log: Incomplete -namedtuple = collections.namedtuple -CHUNK_SIZE: int -DATABASE_MAX_STRING_SIZE: int -DATABASE_MAX_STRING_SIZE_PRETTY: str -gzip_magic: bytes -bz2_magic: bytes -DEFAULT_ENCODING: Incomplete -NULL_CHAR: bytes -BINARY_CHARS: Incomplete -FILENAME_VALID_CHARS: str -RW_R__R__: Incomplete -RWXR_XR_X: Incomplete -RWXRWXRWX: Incomplete -XML: Incomplete -defaultdict = collections.defaultdict - -# def xml_to_string(elem, pretty: bool = ...): ... -# def xml_element_compare(elem1, elem2): ... -# def xml_element_list_compare(elem_list1, elem_list2): ... -# def xml_element_to_dict(elem): ... -# def pretty_print_xml(elem, level: int = ...): ... -# def get_file_size(value, default: Incomplete | None = ...): ... -# def shrink_stream_by_size(value, size, join_by: bytes = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ... -# def shrink_and_unicodify(stream): ... -# def shrink_string_by_size(value, size, join_by: str = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ... -# def pretty_print_time_interval(time: bool = ..., precise: bool = ..., utc: bool = ...): ... -# def pretty_print_json(json_data, is_json_string: bool = ...): ... - -valid_chars: Incomplete -mapped_chars: Incomplete - -# def restore_text(text, character_map=...): ... -# def sanitize_text(text, valid_characters=..., character_map=..., invalid_character: str = ...): ... -# def sanitize_lists_to_string(values, valid_characters=..., character_map=..., invalid_character: str = ...): ... -# def sanitize_param(value, valid_characters=..., character_map=..., invalid_character: str = ...): ... - -valid_filename_chars: Incomplete -invalid_filenames: Incomplete - -# def sanitize_for_filename(text, default: Incomplete | None = ...): ... -# def find_instance_nested(item, instances, match_key: Incomplete | None = ...): ... -# def mask_password_from_url(url): ... -# def ready_name_for_url(raw_name): ... -# def which(file): ... -# def in_directory(file, directory, local_path_module=...): ... -# def merge_sorted_iterables(operator, *iterables) -> None: ... - -# def rst_to_html(s, error: bool = ...): ... -# def xml_text(root, name: Incomplete | None = ...): ... -# def parse_resource_parameters(resource_param_file): ... - -truthy: Incomplete -falsy: Incomplete - -# def asbool(obj): ... -# def string_as_bool(string): ... -# def string_as_bool_or_none(string): ... -# def listify(item, do_strip: bool = ...): ... -# def commaify(amount): ... -# def roundify(amount, sfs: int = ...): ... -# def unicodify(value, encoding=..., error: str = ..., strip_null: bool = ..., log_exception: bool = ...): ... -# def smart_str(s, encoding=..., strings_only: bool = ..., errors: str = ...): ... -# def strip_control_characters(s): ... -# def object_to_string(obj): ... -# def string_to_object(s): ... -# def clean_multiline_string(multiline_string, sep: str = ...): ... - -# def compare_urls(url1, url2, compare_scheme: bool = ..., compare_hostname: bool = ..., compare_path: bool = ...): ... -# def read_build_sites(filename, check_builds: bool = ...): ... -# def relativize_symlinks(path, start: Incomplete | None = ..., followlinks: bool = ...) -> None: ... -# def stringify_dictionary_keys(in_dict): ... -# def mkstemp_ln(src, prefix: str = ...): ... -# def umask_fix_perms(path, umask, unmasked_perms, gid: Incomplete | None = ...) -> None: ... -# def docstring_trim(docstring): ... -# def nice_size(size): ... -# def size_to_bytes(size): ... -# def send_mail(frm, to, subject, body, config, html: Incomplete | None = ...) -> None: ... -# def force_symlink(source, link_name) -> None: ... -# def move_merge(source, target): ... -# def safe_str_cmp(a, b): ... - -galaxy_root_path: Incomplete -galaxy_samples_path: Incomplete - -# def galaxy_directory(): ... -# def galaxy_samples_directory(): ... -# def config_directories_from_setting(directories_setting, galaxy_root=...): ... -# def parse_int(value, min_val: Incomplete | None = ..., max_val: Incomplete | None = ..., default: Incomplete | None = ..., allow_none: bool = ...): ... -# def parse_non_hex_float(s): ... -# def build_url(base_url, port: int = ..., scheme: str = ..., pathspec: Incomplete | None = ..., params: Incomplete | None = ..., doseq: bool = ...): ... -# def url_get(base_url, auth: Incomplete | None = ..., pathspec: Incomplete | None = ..., params: Incomplete | None = ..., max_retries: int = ..., backoff_factor: int = ...): ... -# def download_to_file(url, dest_file_path, timeout: int = ..., chunk_size=...) -> None: ... - -# def get_executable(): ... diff --git a/mypy-stubs/galaxy/util/aliaspickler.pyi b/mypy-stubs/galaxy/util/aliaspickler.pyi deleted file mode 100644 index 245177634..000000000 --- a/mypy-stubs/galaxy/util/aliaspickler.pyi +++ /dev/null @@ -1,16 +0,0 @@ -import pickle - -from _typeshed import Incomplete - -class AliasUnpickler(pickle.Unpickler): - aliases: Incomplete - def __init__(self, aliases, *args, **kw) -> None: ... - def find_class(self, module, name): ... - -class AliasPickleModule: - aliases: Incomplete - def __init__(self, aliases) -> None: ... - def dump(self, obj, fileobj, protocol: int = ...): ... - def dumps(self, obj, protocol: int = ...): ... - def load(self, fileobj): ... - def loads(self, string): ... diff --git a/mypy-stubs/galaxy/util/bunch.pyi b/mypy-stubs/galaxy/util/bunch.pyi deleted file mode 100644 index 424097035..000000000 --- a/mypy-stubs/galaxy/util/bunch.pyi +++ /dev/null @@ -1,14 +0,0 @@ -from _typeshed import Incomplete - -class Bunch: - def __init__(self, **kwds) -> None: ... - def dict(self): ... - def get(self, key, default: Incomplete | None = ...): ... - def __iter__(self): ... - def items(self): ... - def keys(self): ... - def values(self): ... - def __bool__(self): ... - __nonzero__: Incomplete - def __setitem__(self, k, v) -> None: ... - def __contains__(self, item): ... diff --git a/mypy-stubs/galaxy/util/bytesize.pyi b/mypy-stubs/galaxy/util/bytesize.pyi deleted file mode 100644 index d6b923350..000000000 --- a/mypy-stubs/galaxy/util/bytesize.pyi +++ /dev/null @@ -1,10 +0,0 @@ -from _typeshed import Incomplete - -SUFFIX_TO_BYTES: Incomplete - -class ByteSize: - value: Incomplete - def __init__(self, value) -> None: ... - def to_unit(self, unit: Incomplete | None = ..., as_string: bool = ...): ... - -def parse_bytesize(value): ... diff --git a/mypy-stubs/galaxy/util/checkers.pyi b/mypy-stubs/galaxy/util/checkers.pyi deleted file mode 100644 index eedae9b05..000000000 --- a/mypy-stubs/galaxy/util/checkers.pyi +++ /dev/null @@ -1,9 +0,0 @@ -def check_html(name, file_path: bool = ...): ... -def check_binary(name, file_path: bool = ...): ... -def check_gzip(file_path, check_content: bool = ...): ... -def check_bz2(file_path, check_content: bool = ...): ... -def check_zip(file_path, check_content: bool = ..., files: int = ...): ... -def is_bz2(file_path): ... -def is_gzip(file_path): ... -def is_zip(file_path): ... -def check_image(file_path): ... diff --git a/mypy-stubs/galaxy/util/commands.pyi b/mypy-stubs/galaxy/util/commands.pyi deleted file mode 100644 index 0210333bd..000000000 --- a/mypy-stubs/galaxy/util/commands.pyi +++ /dev/null @@ -1,18 +0,0 @@ -from _typeshed import Incomplete -from galaxy.util import which as which - -def redirecting_io(sys=...): ... -def redirect_aware_commmunicate(p, sys=...): ... -def shell(cmds, env: Incomplete | None = ..., **kwds): ... -def shell_process(cmds, env: Incomplete | None = ..., **kwds): ... -def execute(cmds, input: Incomplete | None = ...): ... -def argv_to_str(command_argv, quote: bool = ...): ... -def download_command(url, to=...): ... - -class CommandLineException(Exception): - command: Incomplete - stdout: Incomplete - stderr: Incomplete - returncode: Incomplete - message: Incomplete - def __init__(self, command, stdout, stderr, returncode) -> None: ... diff --git a/mypy-stubs/galaxy/util/compression_utils.pyi b/mypy-stubs/galaxy/util/compression_utils.pyi deleted file mode 100644 index d2b9d4ccb..000000000 --- a/mypy-stubs/galaxy/util/compression_utils.pyi +++ /dev/null @@ -1,46 +0,0 @@ -from collections.abc import Generator - -from _typeshed import Incomplete - -from .checkers import bz2 as bz2 -from .checkers import is_bz2 as is_bz2 -from .checkers import is_gzip as is_gzip - -log: Incomplete - -def get_fileobj( - filename, mode: str = ..., compressed_formats: Incomplete | None = ... -): ... -def get_fileobj_raw( - filename, mode: str = ..., compressed_formats: Incomplete | None = ... -): ... -def file_iter( - fname, sep: Incomplete | None = ... -) -> Generator[Incomplete, None, None]: ... - -class CompressedFile: - @staticmethod - def can_decompress(file_path): ... - file_type: str - file_name: Incomplete - type: Incomplete - archive: Incomplete - def __init__(self, file_path, mode: str = ...) -> None: ... - @property - def common_prefix_dir(self): ... - def extract(self, path): ... - def safemembers(self) -> Generator[Incomplete, None, None]: ... - def getmembers_tar(self): ... - def getmembers_zip(self): ... - def getname_tar(self, item): ... - def getname_zip(self, item): ... - def getmember(self, name): ... - def getmembers(self): ... - def getname(self, member): ... - def isdir(self, member): ... - def isdir_tar(self, member): ... - def isdir_zip(self, member): ... - def isfile(self, member): ... - def open_tar(self, filepath, mode): ... - def open_zip(self, filepath, mode): ... - def zipfile_ok(self, path_to_archive): ... diff --git a/mypy-stubs/galaxy/util/dbkeys.pyi b/mypy-stubs/galaxy/util/dbkeys.pyi deleted file mode 100644 index f5337dd61..000000000 --- a/mypy-stubs/galaxy/util/dbkeys.pyi +++ /dev/null @@ -1,23 +0,0 @@ -from _typeshed import Incomplete -from galaxy.util import galaxy_directory as galaxy_directory, unicodify as unicodify -from galaxy.util.object_wrapper import ( - sanitize_lists_to_string as sanitize_lists_to_string, -) - -log: Incomplete - -def read_dbnames(filename): ... - -class GenomeBuilds: - default_value: str - default_name: str - def __init__( - self, app, data_table_name: str = ..., load_old_style: bool = ... - ) -> None: ... - def get_genome_build_names(self, trans: Incomplete | None = ...): ... - def get_chrom_info( - self, - dbkey, - trans: Incomplete | None = ..., - custom_build_hack_get_len_from_fasta_conversion: bool = ..., - ): ... diff --git a/mypy-stubs/galaxy/util/expressions.pyi b/mypy-stubs/galaxy/util/expressions.pyi deleted file mode 100644 index 1dcde253d..000000000 --- a/mypy-stubs/galaxy/util/expressions.pyi +++ /dev/null @@ -1,16 +0,0 @@ -from collections.abc import MutableMapping - -from _typeshed import Incomplete - -class ExpressionContext(MutableMapping): - dict: Incomplete - parent: Incomplete - def __init__(self, dict, parent: Incomplete | None = ...) -> None: ... - def __delitem__(self, key) -> None: ... - def __iter__(self): ... - def __len__(self): ... - def __getitem__(self, key): ... - def __setitem__(self, key, value) -> None: ... - def __contains__(self, key): ... - def __bool__(self): ... - __nonzero__: Incomplete diff --git a/mypy-stubs/galaxy/util/facts.pyi b/mypy-stubs/galaxy/util/facts.pyi deleted file mode 100644 index 497dadf6b..000000000 --- a/mypy-stubs/galaxy/util/facts.pyi +++ /dev/null @@ -1,13 +0,0 @@ -from _typeshed import Incomplete -from collections.abc import MutableMapping - -class Facts(MutableMapping): - __dict__: Incomplete - def __init__(self, config: Incomplete | None = ..., **kwargs) -> None: ... - def __getitem__(self, key): ... - def __setitem__(self, key, value): ... - def __delitem__(self, key): ... - def __iter__(self): ... - def __len__(self): ... - -def get_facts(config: Incomplete | None = ..., **kwargs): ... diff --git a/mypy-stubs/galaxy/util/filelock.pyi b/mypy-stubs/galaxy/util/filelock.pyi deleted file mode 100644 index 55a3ecaab..000000000 --- a/mypy-stubs/galaxy/util/filelock.pyi +++ /dev/null @@ -1,17 +0,0 @@ -from _typeshed import Incomplete - -class FileLockException(Exception): ... - -class FileLock: - is_locked: bool - lockfile: Incomplete - file_name: Incomplete - timeout: Incomplete - delay: Incomplete - def __init__(self, file_name, timeout: int = ..., delay: float = ...) -> None: ... - fd: Incomplete - def acquire(self) -> None: ... - def release(self) -> None: ... - def __enter__(self): ... - def __exit__(self, type, value, traceback) -> None: ... - def __del__(self) -> None: ... diff --git a/mypy-stubs/galaxy/util/form_builder.pyi b/mypy-stubs/galaxy/util/form_builder.pyi deleted file mode 100644 index dbd6ea2ed..000000000 --- a/mypy-stubs/galaxy/util/form_builder.pyi +++ /dev/null @@ -1,110 +0,0 @@ -from _typeshed import Incomplete -from galaxy.util import asbool as asbool - -log: Incomplete - -class BaseField: - name: Incomplete - label: Incomplete - value: Incomplete - disabled: Incomplete - optional: Incomplete - help: Incomplete - def __init__( - self, - name, - value: Incomplete | None = ..., - label: Incomplete | None = ..., - **kwds - ) -> None: ... - def to_dict(self): ... - -class TextField(BaseField): - def to_dict(self): ... - -class PasswordField(BaseField): - def to_dict(self): ... - -class TextArea(BaseField): - def to_dict(self): ... - -class CheckboxField(BaseField): - @staticmethod - def is_checked(value): ... - def to_dict(self): ... - -class SelectField(BaseField): - field_id: Incomplete - multiple: Incomplete - refresh_on_change: Incomplete - selectlist: Incomplete - options: Incomplete - display: Incomplete - def __init__( - self, - name, - multiple: Incomplete | None = ..., - display: Incomplete | None = ..., - field_id: Incomplete | None = ..., - value: Incomplete | None = ..., - selectlist: Incomplete | None = ..., - refresh_on_change: bool = ..., - **kwds - ) -> None: ... - def add_option(self, text, value, selected: bool = ...) -> None: ... - def to_dict(self): ... - -class AddressField(BaseField): - @staticmethod - def fields(): ... - user: Incomplete - security: Incomplete - def __init__( - self, - name, - user: Incomplete | None = ..., - value: Incomplete | None = ..., - security: Incomplete | None = ..., - **kwds - ) -> None: ... - def to_dict(self): ... - -class WorkflowField(BaseField): - user: Incomplete - value: Incomplete - security: Incomplete - def __init__( - self, - name, - user: Incomplete | None = ..., - value: Incomplete | None = ..., - security: Incomplete | None = ..., - **kwds - ) -> None: ... - def to_dict(self): ... - -class WorkflowMappingField(BaseField): - user: Incomplete - def __init__( - self, - name, - user: Incomplete | None = ..., - value: Incomplete | None = ..., - **kwds - ) -> None: ... - -class HistoryField(BaseField): - user: Incomplete - value: Incomplete - security: Incomplete - def __init__( - self, - name, - user: Incomplete | None = ..., - value: Incomplete | None = ..., - security: Incomplete | None = ..., - **kwds - ) -> None: ... - def to_dict(self): ... - -def get_suite(): ... diff --git a/mypy-stubs/galaxy/util/getargspec.pyi b/mypy-stubs/galaxy/util/getargspec.pyi deleted file mode 100644 index d0c74c235..000000000 --- a/mypy-stubs/galaxy/util/getargspec.pyi +++ /dev/null @@ -1 +0,0 @@ -def getfullargspec(func): ... diff --git a/mypy-stubs/galaxy/util/hash_util.pyi b/mypy-stubs/galaxy/util/hash_util.pyi deleted file mode 100644 index b9e737db4..000000000 --- a/mypy-stubs/galaxy/util/hash_util.pyi +++ /dev/null @@ -1,11 +0,0 @@ -import hashlib as hashlib - -sha1 = hashlib.sha1 -sha256 = hashlib.sha256 -sha512 = hashlib.sha512 -sha = sha1 -md5 = hashlib.md5 - -def new_secure_hash(text_type): ... -def hmac_new(key, value): ... -def is_hashable(value): ... diff --git a/mypy-stubs/galaxy/util/heartbeat.pyi b/mypy-stubs/galaxy/util/heartbeat.pyi deleted file mode 100644 index fea3aa044..000000000 --- a/mypy-stubs/galaxy/util/heartbeat.pyi +++ /dev/null @@ -1,29 +0,0 @@ -import threading - -from _typeshed import Incomplete - -def get_current_thread_object_dict(): ... - -class Heartbeat(threading.Thread): - config: Incomplete - should_stop: bool - period: Incomplete - fname: Incomplete - file: Incomplete - fname_nonsleeping: Incomplete - file_nonsleeping: Incomplete - pid: Incomplete - nonsleeping_heartbeats: Incomplete - wait_event: Incomplete - def __init__( - self, config, name: str = ..., period: int = ..., fname: str = ... - ) -> None: ... - def run(self) -> None: ... - def open_logs(self) -> None: ... - def close_logs(self) -> None: ... - def dump(self) -> None: ... - def shutdown(self) -> None: ... - def thread_is_sleeping(self, last_stack_frame): ... - def get_interesting_stack_frame(self, stack_frames): ... - def print_nonsleeping(self, threads_object_dict) -> None: ... - def dump_signal_handler(self, signum, frame) -> None: ... diff --git a/mypy-stubs/galaxy/util/image_util.pyi b/mypy-stubs/galaxy/util/image_util.pyi deleted file mode 100644 index 59a3e3a6c..000000000 --- a/mypy-stubs/galaxy/util/image_util.pyi +++ /dev/null @@ -1,6 +0,0 @@ -from _typeshed import Incomplete - -log: Incomplete - -def image_type(filename): ... -def check_image_type(filename, types): ... diff --git a/mypy-stubs/galaxy/util/json.pyi b/mypy-stubs/galaxy/util/json.pyi deleted file mode 100644 index be04dffe3..000000000 --- a/mypy-stubs/galaxy/util/json.pyi +++ /dev/null @@ -1,23 +0,0 @@ -import json - -from _typeshed import Incomplete - -to_json_string = json.dumps -from_json_string = json.loads - -def safe_dumps(*args, **kwargs): ... -def validate_jsonrpc_request(request, regular_methods, notification_methods): ... -def validate_jsonrpc_response(response, id: Incomplete | None = ...): ... -def jsonrpc_request( - method, - params: Incomplete | None = ..., - id: Incomplete | None = ..., - jsonrpc: str = ..., -): ... -def jsonrpc_response( - request: Incomplete | None = ..., - id: Incomplete | None = ..., - result: Incomplete | None = ..., - error: Incomplete | None = ..., - jsonrpc: str = ..., -): ... diff --git a/mypy-stubs/galaxy/util/jstree.pyi b/mypy-stubs/galaxy/util/jstree.pyi deleted file mode 100644 index 3106df4d8..000000000 --- a/mypy-stubs/galaxy/util/jstree.pyi +++ /dev/null @@ -1,19 +0,0 @@ -import dictobj -from _typeshed import Incomplete -from typing import NamedTuple - -class Path(NamedTuple): - path: Incomplete - id: Incomplete - options: Incomplete - -class Node(dictobj.DictionaryObject): - def __init__(self, path, oid, **kwargs) -> None: ... - def jsonData(self): ... - -class JSTree(dictobj.DictionaryObject): - def __init__(self, paths, **kwargs) -> None: ... - def pretty( - self, root: Incomplete | None = ..., depth: int = ..., spacing: int = ... - ): ... - def jsonData(self): ... diff --git a/mypy-stubs/galaxy/util/lazy_process.pyi b/mypy-stubs/galaxy/util/lazy_process.pyi deleted file mode 100644 index 6831c8375..000000000 --- a/mypy-stubs/galaxy/util/lazy_process.pyi +++ /dev/null @@ -1,18 +0,0 @@ -from _typeshed import Incomplete - -class LazyProcess: - command_and_args: Incomplete - thread_lock: Incomplete - allow_process_request: bool - process: Incomplete - def __init__(self, command_and_args) -> None: ... - def start_process(self) -> None: ... - def shutdown(self) -> None: ... - @property - def running(self): ... - -class NoOpLazyProcess: - def start_process(self) -> None: ... - def shutdown(self) -> None: ... - @property - def running(self): ... diff --git a/mypy-stubs/galaxy/util/monitors.pyi b/mypy-stubs/galaxy/util/monitors.pyi deleted file mode 100644 index 1e1128e76..000000000 --- a/mypy-stubs/galaxy/util/monitors.pyi +++ /dev/null @@ -1,12 +0,0 @@ -from .sleeper import Sleeper as Sleeper -from .web_compat import register_postfork_function as register_postfork_function -from _typeshed import Incomplete - -log: Incomplete -DEFAULT_MONITOR_THREAD_JOIN_TIMEOUT: int - -class Monitors: - def start_monitoring(self) -> None: ... - monitor_running: bool - def stop_monitoring(self) -> None: ... - def shutdown_monitor(self) -> None: ... diff --git a/mypy-stubs/galaxy/util/object_wrapper.pyi b/mypy-stubs/galaxy/util/object_wrapper.pyi deleted file mode 100644 index 8d320674b..000000000 --- a/mypy-stubs/galaxy/util/object_wrapper.pyi +++ /dev/null @@ -1,90 +0,0 @@ -from _typeshed import Incomplete - -NoneType: Incomplete -NotImplementedType: Incomplete -EllipsisType: Incomplete -XRangeType = range -SliceType = slice -BufferType = SliceType -DictProxyType = SliceType -log: Incomplete -__CALLABLE_TYPES__: Incomplete -__WRAP_NO_SUBCLASS__: Incomplete -__DONT_SANITIZE_TYPES__: Incomplete -__WRAP_SEQUENCES__: Incomplete -__WRAP_SETS__: Incomplete -__WRAP_MAPPINGS__: Incomplete -VALID_CHARACTERS: Incomplete -CHARACTER_MAP: Incomplete -INVALID_CHARACTER: str - -def coerce(x, y): ... -def cmp(x, y): ... -def sanitize_lists_to_string( - values, valid_characters=..., character_map=..., invalid_character=... -): ... -def wrap_with_safe_string(value, no_wrap_classes: Incomplete | None = ...): ... - -class SafeStringWrapper: - __UNSANITIZED_ATTRIBUTE_NAME__: str - __NO_WRAP_NAMES__: Incomplete - def __new__(cls, *arg, **kwd): ... - unsanitized: Incomplete - __safe_string_wrapper_function__: Incomplete - def __init__(self, value, safe_string_wrapper_function=...) -> None: ... - def __lt__(self, other): ... - def __le__(self, other): ... - def __eq__(self, other): ... - def __ne__(self, other): ... - def __gt__(self, other): ... - def __ge__(self, other): ... - def __cmp__(self, other): ... - def __hash__(self): ... - def __bool__(self): ... - __nonzero__: Incomplete - def __getattr__(self, name): ... - def __setattr__(self, name, value): ... - def __delattr__(self, name): ... - def __getattribute__(self, name): ... - def __len__(self): ... - def __getitem__(self, key): ... - def __setitem__(self, key, value) -> None: ... - def __delitem__(self, key) -> None: ... - def __iter__(self): ... - def __contains__(self, item): ... - def __getslice__(self, i, j): ... - def __setslice__(self, i, j, value) -> None: ... - def __delslice__(self, i, j) -> None: ... - def __add__(self, other): ... - def __sub__(self, other): ... - def __mul__(self, other): ... - def __floordiv__(self, other): ... - def __mod__(self, other): ... - def __divmod__(self, other): ... - def __pow__(self, *other): ... - def __lshift__(self, other): ... - def __rshift__(self, other): ... - def __and__(self, other): ... - def __xor__(self, other): ... - def __or__(self, other): ... - def __div__(self, other): ... - def __truediv__(self, other): ... - def __rpow__(self, other): ... - def __neg__(self): ... - def __pos__(self): ... - def __abs__(self): ... - def __invert__(self): ... - def __complex__(self): ... - def __int__(self): ... - def __float__(self): ... - def __oct__(self): ... - def __hex__(self): ... - def __index__(self): ... - def __coerce__(self, other): ... - def __enter__(self): ... - def __exit__(self, *args): ... - -class CallableSafeStringWrapper(SafeStringWrapper): - def __call__(self, *args, **kwds): ... - -def pickle_SafeStringWrapper(safe_object): ... diff --git a/mypy-stubs/galaxy/util/odict.pyi b/mypy-stubs/galaxy/util/odict.pyi deleted file mode 100644 index ecbd4969f..000000000 --- a/mypy-stubs/galaxy/util/odict.pyi +++ /dev/null @@ -1,25 +0,0 @@ -from collections import UserDict -from collections.abc import Generator - -from _typeshed import Incomplete - -dict_alias = dict - -class odict(UserDict): - def __init__(self, dict: Incomplete | None = ...) -> None: ... - def __delitem__(self, key) -> None: ... - def __setitem__(self, key, item) -> None: ... - def clear(self) -> None: ... - def copy(self): ... - def items(self): ... - def keys(self): ... - def popitem(self): ... - def setdefault(self, key, failobj: Incomplete | None = ...): ... - def update(self, dict) -> None: ... - def values(self): ... - def iterkeys(self): ... - def itervalues(self) -> Generator[Incomplete, None, None]: ... - def iteritems(self) -> Generator[Incomplete, None, None]: ... - def __iter__(self): ... - def reverse(self) -> None: ... - def insert(self, index, key, item) -> None: ... diff --git a/mypy-stubs/galaxy/util/pastescript/__init__.pyi b/mypy-stubs/galaxy/util/pastescript/__init__.pyi deleted file mode 100644 index e69de29bb..000000000 diff --git a/mypy-stubs/galaxy/util/pastescript/loadwsgi.pyi b/mypy-stubs/galaxy/util/pastescript/loadwsgi.pyi deleted file mode 100644 index 4037dceea..000000000 --- a/mypy-stubs/galaxy/util/pastescript/loadwsgi.pyi +++ /dev/null @@ -1,129 +0,0 @@ -from _typeshed import Incomplete -from typing import List, Optional, Union - -class _ObjectType: - name: Optional[str] - egg_protocols: Optional[List[Union[str, List[str]]]] - config_prefixes: Optional[List[Union[List[str], str]]] - def __init__(self) -> None: ... - def invoke(self, context): ... - -class _App(_ObjectType): - name: str - egg_protocols: Incomplete - config_prefixes: Incomplete - def invoke(self, context): ... - -class _Filter(_ObjectType): - name: str - egg_protocols: Incomplete - config_prefixes: Incomplete - def invoke(self, context): ... - -class _Server(_ObjectType): - name: str - egg_protocols: Incomplete - config_prefixes: Incomplete - def invoke(self, context): ... - -class _PipeLine(_ObjectType): - name: str - def invoke(self, context): ... - -class _FilterApp(_ObjectType): - name: str - def invoke(self, context): ... - -class _FilterWith(_App): - name: str - def invoke(self, context): ... - -def loadapp(uri, name: Incomplete | None = ..., **kw): ... -def loadfilter(uri, name: Incomplete | None = ..., **kw): ... -def loadserver(uri, name: Incomplete | None = ..., **kw): ... -def appconfig( - uri, - name: Incomplete | None = ..., - relative_to: Incomplete | None = ..., - global_conf: Incomplete | None = ..., -): ... - -class _Loader: - def get_app( - self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... - ): ... - def get_filter( - self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... - ): ... - def get_server( - self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... - ): ... - def app_context( - self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... - ): ... - def filter_context( - self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... - ): ... - def server_context( - self, name: Incomplete | None = ..., global_conf: Incomplete | None = ... - ): ... - def absolute_name(self, name): ... - -class ConfigLoader(_Loader): - filename: Incomplete - parser: Incomplete - def __init__(self, filename) -> None: ... - def update_defaults(self, new_defaults, overwrite: bool = ...) -> None: ... - def get_context( - self, - object_type, - name: Incomplete | None = ..., - global_conf: Incomplete | None = ..., - ): ... - def find_config_section(self, object_type, name: Incomplete | None = ...): ... - -class EggLoader(_Loader): - spec: Incomplete - def __init__(self, spec) -> None: ... - def get_context( - self, - object_type, - name: Incomplete | None = ..., - global_conf: Incomplete | None = ..., - ): ... - def find_egg_entry_point(self, object_type, name: Incomplete | None = ...): ... - -class FuncLoader(_Loader): - spec: Incomplete - def __init__(self, spec) -> None: ... - def get_context( - self, - object_type, - name: Incomplete | None = ..., - global_conf: Incomplete | None = ..., - ): ... - -class LoaderContext: - object: Incomplete - object_type: Incomplete - protocol: Incomplete - global_conf: Incomplete - local_conf: Incomplete - loader: Incomplete - distribution: Incomplete - entry_point_name: Incomplete - def __init__( - self, - obj, - object_type, - protocol, - global_conf, - local_conf, - loader, - distribution: Incomplete | None = ..., - entry_point_name: Incomplete | None = ..., - ) -> None: ... - def create(self): ... - def config(self): ... - -class AttrDict(dict): ... diff --git a/mypy-stubs/galaxy/util/pastescript/serve.pyi b/mypy-stubs/galaxy/util/pastescript/serve.pyi deleted file mode 100644 index ea9d9f3b9..000000000 --- a/mypy-stubs/galaxy/util/pastescript/serve.pyi +++ /dev/null @@ -1,94 +0,0 @@ -import optparse -from .loadwsgi import loadapp as loadapp, loadserver as loadserver -from _typeshed import Incomplete -from typing import Optional - -difflib: Incomplete - -class BoolOptionParser(optparse.OptionParser): ... - -class BadCommand(Exception): - message: Incomplete - exit_code: Incomplete - def __init__(self, message, exit_code: int = ...) -> None: ... - -class NoDefault: ... - -class Command: - command_name: Incomplete - def __init__(self, name) -> None: ... - max_args: Incomplete - max_args_error: str - min_args: Optional[int] - min_args_error: str - required_args: Incomplete - takes_config_file: Optional[int] - group_name: str - description: Optional[str] - usage: str - hidden: bool - default_verbosity: int - default_interactive: int - return_code: int - BadCommand: Incomplete - interactive: Incomplete - verbose: Incomplete - simulate: Incomplete - def run(self, args): ... - def parse_args(self, args) -> None: ... - def pad(self, s, length, dir: str = ...): ... - standard_parser: Incomplete - def quote_first_command_arg(self, arg): ... - def parse_vars(self, args): ... - def logging_file_config(self, config_file) -> None: ... - -class NotFoundCommand(Command): - def run(self, args): ... - -MAXFD: int -jython: Incomplete - -class DaemonizeException(Exception): ... - -class ServeCommand(Command): - min_args: int - usage: str - takes_config_file: int - summary: str - description: Optional[str] - requires_config_file: bool - parser: Incomplete - default_verbosity: int - possible_subcommands: Incomplete - def command(self): ... - def daemonize(self) -> None: ... - def record_pid(self, pid_file) -> None: ... - def stop_daemon(self): ... - def show_status(self): ... - def restart_with_reloader(self) -> None: ... - def restart_with_monitor(self, reloader: bool = ...): ... - def change_user_group(self, user, group) -> None: ... - -class LazyWriter: - filename: Incomplete - fileobj: Incomplete - lock: Incomplete - mode: Incomplete - def __init__(self, filename, mode: str = ...) -> None: ... - def open(self): ... - def write(self, text) -> None: ... - def writelines(self, text) -> None: ... - def flush(self) -> None: ... - -def live_pidfile(pidfile): ... -def read_pidfile(filename): ... -def ensure_port_cleanup( - bound_addresses, maxtries: int = ..., sleeptime: int = ... -) -> None: ... - -python_version: Incomplete -parser: Incomplete -commands: Incomplete - -def run(args: Incomplete | None = ...) -> None: ... -def invoke(command, command_name, options, args) -> None: ... diff --git a/mypy-stubs/galaxy/util/path/__init__.pyi b/mypy-stubs/galaxy/util/path/__init__.pyi deleted file mode 100644 index 5f49b9785..000000000 --- a/mypy-stubs/galaxy/util/path/__init__.pyi +++ /dev/null @@ -1,19 +0,0 @@ -from collections.abc import Generator - -from _typeshed import Incomplete - -def safe_walk( - path, allowlist: Incomplete | None = ... -) -> Generator[Incomplete, None, None]: ... -def unsafe_walk( - path, allowlist: Incomplete | None = ..., username: Incomplete | None = ... -): ... -def joinext(root, ext): ... -def has_ext(path, ext, aliases: bool = ..., ignore: Incomplete | None = ...): ... -def get_ext(path, ignore: Incomplete | None = ..., canonicalize: bool = ...): ... - -class Extensions(dict): - def __missing__(self, key): ... - def canonicalize(self, ext): ... - -extensions: Incomplete diff --git a/mypy-stubs/galaxy/util/path/ntpath.pyi b/mypy-stubs/galaxy/util/path/ntpath.pyi deleted file mode 100644 index e69de29bb..000000000 diff --git a/mypy-stubs/galaxy/util/path/posixpath.pyi b/mypy-stubs/galaxy/util/path/posixpath.pyi deleted file mode 100644 index e69de29bb..000000000 diff --git a/mypy-stubs/galaxy/util/permutations.pyi b/mypy-stubs/galaxy/util/permutations.pyi deleted file mode 100644 index d3f6e3139..000000000 --- a/mypy-stubs/galaxy/util/permutations.pyi +++ /dev/null @@ -1,9 +0,0 @@ -from _typeshed import Incomplete -from galaxy.exceptions import MessageException as MessageException -from galaxy.util.bunch import Bunch as Bunch - -input_classification: Incomplete - -class InputMatchedException(MessageException): ... - -def expand_multi_inputs(inputs, classifier, key_filter: Incomplete | None = ...): ... diff --git a/mypy-stubs/galaxy/util/plugin_config.pyi b/mypy-stubs/galaxy/util/plugin_config.pyi deleted file mode 100644 index 4c9a5e123..000000000 --- a/mypy-stubs/galaxy/util/plugin_config.pyi +++ /dev/null @@ -1,19 +0,0 @@ -from typing import NamedTuple - -from _typeshed import Incomplete -from galaxy.util.submodules import import_submodules as import_submodules - -class PluginConfigSource(NamedTuple): - type: Incomplete - source: Incomplete - -def plugins_dict(module, plugin_type_identifier): ... -def load_plugins( - plugins_dict, - plugin_source, - extra_kwds: Incomplete | None = ..., - plugin_type_keys=..., - dict_to_list_key: Incomplete | None = ..., -): ... -def plugin_source_from_path(path): ... -def plugin_source_from_dict(as_dict): ... diff --git a/mypy-stubs/galaxy/util/properties.pyi b/mypy-stubs/galaxy/util/properties.pyi deleted file mode 100644 index 0b66754ed..000000000 --- a/mypy-stubs/galaxy/util/properties.pyi +++ /dev/null @@ -1,33 +0,0 @@ -from configparser import ConfigParser - -from _typeshed import Incomplete - -def find_config_file( - names, - exts: Incomplete | None = ..., - dirs: Incomplete | None = ..., - include_samples: bool = ..., -): ... -def load_app_properties( - kwds: Incomplete | None = ..., - ini_file: Incomplete | None = ..., - ini_section: Incomplete | None = ..., - config_file: Incomplete | None = ..., - config_section: Incomplete | None = ..., - config_prefix: str = ..., -): ... - -class NicerConfigParser(ConfigParser): - filename: Incomplete - def __init__(self, filename, *args, **kw) -> None: ... - read_file: Incomplete - def defaults(self): ... - - class InterpolateWrapper: - def __init__(self, original) -> None: ... - def __getattr__(self, name): ... - def before_get(self, parser, section, option, value, defaults): ... - -running_from_source: Incomplete - -def get_data_dir(properties): ... diff --git a/mypy-stubs/galaxy/util/renamed_temporary_file.pyi b/mypy-stubs/galaxy/util/renamed_temporary_file.pyi deleted file mode 100644 index afdf5701d..000000000 --- a/mypy-stubs/galaxy/util/renamed_temporary_file.pyi +++ /dev/null @@ -1,9 +0,0 @@ -from _typeshed import Incomplete - -class RenamedTemporaryFile: - tmpfile: Incomplete - final_path: Incomplete - def __init__(self, final_path, **kwargs) -> None: ... - def __getattr__(self, attr): ... - def __enter__(self): ... - def __exit__(self, exc_type, exc_val, exc_tb): ... diff --git a/mypy-stubs/galaxy/util/rules_dsl.pyi b/mypy-stubs/galaxy/util/rules_dsl.pyi deleted file mode 100644 index d9f0fa1ec..000000000 --- a/mypy-stubs/galaxy/util/rules_dsl.pyi +++ /dev/null @@ -1,129 +0,0 @@ -import abc -from _typeshed import Incomplete -from typing import List, Type - -def get_rules_specification(): ... -def apply_regex( - regex, - target, - data, - replacement: Incomplete | None = ..., - group_count: Incomplete | None = ..., -): ... - -class BaseRuleDefinition(metaclass=abc.ABCMeta): - @property - @abc.abstractmethod - def rule_type(self): ... - @abc.abstractmethod - def validate_rule(self, rule): ... - @abc.abstractmethod - def apply(self, rule, data, sources): ... - -class AddColumnMetadataRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddColumnGroupTagValueRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddColumnConcatenateRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddColumnBasenameRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddColumnRegexRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddColumnRownumRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddColumnValueRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddColumnSubstrRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class RemoveColumnsRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddFilterRegexRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddFilterCountRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddFilterEmptyRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddFilterMatchesRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class AddFilterCompareRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class SortRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class SwapColumnsRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -class SplitColumnsRuleDefinition(BaseRuleDefinition): - rule_type: str - def validate_rule(self, rule) -> None: ... - def apply(self, rule, data, sources): ... - -def flat_map(f, items): ... - -class RuleSet: - raw_rules: Incomplete - raw_mapping: Incomplete - def __init__(self, rule_set_as_dict) -> None: ... - @property - def rules(self): ... - def apply(self, data, sources): ... - @property - def has_errors(self): ... - @property - def mapping_as_dict(self): ... - @property - def identifier_columns(self): ... - @property - def collection_type(self): ... - @property - def display(self): ... - -RULES_DEFINITION_CLASSES: List[Type[BaseRuleDefinition]] -RULES_DEFINITIONS: Incomplete diff --git a/mypy-stubs/galaxy/util/sanitize_html.pyi b/mypy-stubs/galaxy/util/sanitize_html.pyi deleted file mode 100644 index a68479c22..000000000 --- a/mypy-stubs/galaxy/util/sanitize_html.pyi +++ /dev/null @@ -1,3 +0,0 @@ -from galaxy.util import unicodify as unicodify - -def sanitize_html(htmlSource, allow_data_urls: bool = ...): ... diff --git a/mypy-stubs/galaxy/util/script.pyi b/mypy-stubs/galaxy/util/script.pyi deleted file mode 100644 index 7461cd81a..000000000 --- a/mypy-stubs/galaxy/util/script.pyi +++ /dev/null @@ -1,29 +0,0 @@ -from _typeshed import Incomplete -from galaxy.util.properties import ( - find_config_file as find_config_file, - load_app_properties as load_app_properties, -) - -DESCRIPTION: Incomplete -ACTIONS: Incomplete -ARGUMENTS: Incomplete -DEFAULT_ACTION: Incomplete -ARG_HELP_CONFIG_FILE: str - -def main_factory( - description: Incomplete | None = ..., - actions: Incomplete | None = ..., - arguments: Incomplete | None = ..., - default_action: Incomplete | None = ..., -): ... -def main(argv: Incomplete | None = ...) -> None: ... -def app_properties_from_args( - args, legacy_config_override: Incomplete | None = ..., app: Incomplete | None = ... -): ... -def config_file_from_args( - args, legacy_config_override: Incomplete | None = ..., app: Incomplete | None = ... -): ... -def populate_config_args(parser) -> None: ... -def set_log_handler( - filename: Incomplete | None = ..., stream: Incomplete | None = ... -): ... diff --git a/mypy-stubs/galaxy/util/search.pyi b/mypy-stubs/galaxy/util/search.pyi deleted file mode 100644 index 5c3c4a7a0..000000000 --- a/mypy-stubs/galaxy/util/search.pyi +++ /dev/null @@ -1 +0,0 @@ -def parse_filters(search_term, filters): ... diff --git a/mypy-stubs/galaxy/util/simplegraph.pyi b/mypy-stubs/galaxy/util/simplegraph.pyi deleted file mode 100644 index e057eb455..000000000 --- a/mypy-stubs/galaxy/util/simplegraph.pyi +++ /dev/null @@ -1,26 +0,0 @@ -from collections.abc import Generator - -from _typeshed import Incomplete - -class SimpleGraphNode: - index: Incomplete - data: Incomplete - def __init__(self, index, **data) -> None: ... - -class SimpleGraphEdge: - source_index: Incomplete - target_index: Incomplete - data: Incomplete - def __init__(self, source_index, target_index, **data) -> None: ... - -class SimpleGraph: - nodes: Incomplete - edges: Incomplete - def __init__( - self, nodes: Incomplete | None = ..., edges: Incomplete | None = ... - ) -> None: ... - def add_node(self, node_id, **data): ... - def add_edge(self, source_id, target_id, **data): ... - def gen_node_dicts(self) -> Generator[Incomplete, None, None]: ... - def gen_edge_dicts(self) -> Generator[Incomplete, None, None]: ... - def as_dict(self): ... diff --git a/mypy-stubs/galaxy/util/sleeper.pyi b/mypy-stubs/galaxy/util/sleeper.pyi deleted file mode 100644 index 47b04fe80..000000000 --- a/mypy-stubs/galaxy/util/sleeper.pyi +++ /dev/null @@ -1,7 +0,0 @@ -from _typeshed import Incomplete - -class Sleeper: - condition: Incomplete - def __init__(self) -> None: ... - def sleep(self, seconds) -> None: ... - def wake(self) -> None: ... diff --git a/mypy-stubs/galaxy/util/sockets.pyi b/mypy-stubs/galaxy/util/sockets.pyi deleted file mode 100644 index 401c1d60a..000000000 --- a/mypy-stubs/galaxy/util/sockets.pyi +++ /dev/null @@ -1,5 +0,0 @@ -from _typeshed import Incomplete -from galaxy.util import commands as commands - -def get_ip(): ... -def unused_port(range: Incomplete | None = ...): ... diff --git a/mypy-stubs/galaxy/util/specs.pyi b/mypy-stubs/galaxy/util/specs.pyi deleted file mode 100644 index 3727d149c..000000000 --- a/mypy-stubs/galaxy/util/specs.pyi +++ /dev/null @@ -1,7 +0,0 @@ -from galaxy import util as util - -def to_str_or_none(value): ... -def to_bool_or_none(value): ... -def to_bool(value): ... -def to_float_or_none(value): ... -def is_in(*args): ... diff --git a/mypy-stubs/galaxy/util/sqlite.pyi b/mypy-stubs/galaxy/util/sqlite.pyi deleted file mode 100644 index d190ccb49..000000000 --- a/mypy-stubs/galaxy/util/sqlite.pyi +++ /dev/null @@ -1,2 +0,0 @@ -def is_read_only_query(query): ... -def connect(path): ... diff --git a/mypy-stubs/galaxy/util/submodules.pyi b/mypy-stubs/galaxy/util/submodules.pyi deleted file mode 100644 index 370654d1a..000000000 --- a/mypy-stubs/galaxy/util/submodules.pyi +++ /dev/null @@ -1,5 +0,0 @@ -from _typeshed import Incomplete - -log: Incomplete - -def import_submodules(module, ordered: bool = ..., recursive: bool = ...): ... diff --git a/mypy-stubs/galaxy/util/template.pyi b/mypy-stubs/galaxy/util/template.pyi deleted file mode 100644 index 89012e9ac..000000000 --- a/mypy-stubs/galaxy/util/template.pyi +++ /dev/null @@ -1,22 +0,0 @@ -from . import unicodify as unicodify -from Cheetah.Compiler import Compiler -from _typeshed import Incomplete - -refactoring_tool: Incomplete - -class FixedModuleCodeCompiler(Compiler): - module_code: Incomplete - def getModuleCode(self): ... - -def create_compiler_class(module_code): ... -def fill_template( - template_text, - context: Incomplete | None = ..., - retry: int = ..., - compiler_class=..., - first_exception: Incomplete | None = ..., - futurized: bool = ..., - python_template_version: str = ..., - **kwargs -): ... -def futurize_preprocessor(source): ... diff --git a/mypy-stubs/galaxy/util/tool_shed/__init__.pyi b/mypy-stubs/galaxy/util/tool_shed/__init__.pyi deleted file mode 100644 index e69de29bb..000000000 diff --git a/mypy-stubs/galaxy/util/tool_shed/common_util.pyi b/mypy-stubs/galaxy/util/tool_shed/common_util.pyi deleted file mode 100644 index c972c1593..000000000 --- a/mypy-stubs/galaxy/util/tool_shed/common_util.pyi +++ /dev/null @@ -1,41 +0,0 @@ -from _typeshed import Incomplete -from galaxy import util as util -from galaxy.util.tool_shed import encoding_util as encoding_util, xml_util as xml_util - -log: Incomplete -REPOSITORY_OWNER: str -MIGRATE_DIR: Incomplete -TOOL_MIGRATION_SCRIPTS_DIR: Incomplete -TOOL_MIGRATION_VERSIONS_DIR: Incomplete - -def accumulate_tool_dependencies( - tool_shed_accessible, tool_dependencies, all_tool_dependencies -): ... -def check_for_missing_tools( - app, tool_panel_configs, latest_tool_migration_script_number -): ... -def check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict): ... -def generate_clone_url_for_installed_repository(app, repository): ... -def generate_clone_url_for_repository_in_tool_shed(user, repository): ... -def generate_clone_url_from_repo_info_tup(app, repo_info_tup): ... -def get_non_shed_tool_panel_configs(app): ... -def get_repository_dependencies( - app, tool_shed_url, repository_name, repository_owner, changeset_revision -): ... -def get_protocol_from_tool_shed_url(tool_shed_url): ... -def get_tool_dependencies( - app, tool_shed_url, repository_name, repository_owner, changeset_revision -): ... -def get_tool_shed_repository_ids(as_string: bool = ..., **kwd): ... -def get_tool_shed_url_from_tool_shed_registry(app, tool_shed): ... -def get_tool_shed_repository_url(app, tool_shed, owner, name): ... -def get_user_by_username(app, username): ... -def handle_galaxy_url(trans, **kwd): ... -def handle_tool_shed_url_protocol(app, shed_url): ... -def parse_repository_dependency_tuple( - repository_dependency_tuple, contains_error: bool = ... -): ... -def remove_port_from_tool_shed_url(tool_shed_url): ... -def remove_protocol_and_port_from_tool_shed_url(tool_shed_url): ... -def remove_protocol_and_user_from_clone_url(repository_clone_url): ... -def remove_protocol_from_tool_shed_url(tool_shed_url): ... diff --git a/mypy-stubs/galaxy/util/tool_shed/encoding_util.pyi b/mypy-stubs/galaxy/util/tool_shed/encoding_util.pyi deleted file mode 100644 index 9dfeeb282..000000000 --- a/mypy-stubs/galaxy/util/tool_shed/encoding_util.pyi +++ /dev/null @@ -1,8 +0,0 @@ -from galaxy.util import smart_str as smart_str, unicodify as unicodify -from galaxy.util.hash_util import hmac_new as hmac_new - -encoding_sep: str -encoding_sep2: str - -def tool_shed_decode(value): ... -def tool_shed_encode(val): ... diff --git a/mypy-stubs/galaxy/util/tool_shed/xml_util.pyi b/mypy-stubs/galaxy/util/tool_shed/xml_util.pyi deleted file mode 100644 index e0958b4e3..000000000 --- a/mypy-stubs/galaxy/util/tool_shed/xml_util.pyi +++ /dev/null @@ -1,14 +0,0 @@ -from _typeshed import Incomplete -from galaxy.util import ( - etree as etree, - unicodify as unicodify, - xml_to_string as xml_to_string, -) - -log: Incomplete - -def create_and_write_tmp_file(elem): ... -def create_element( - tag, attributes: Incomplete | None = ..., sub_elements: Incomplete | None = ... -): ... -def parse_xml(file_name, check_exists: bool = ...): ... diff --git a/mypy-stubs/galaxy/util/tool_version.pyi b/mypy-stubs/galaxy/util/tool_version.pyi deleted file mode 100644 index 4c6e6b690..000000000 --- a/mypy-stubs/galaxy/util/tool_version.pyi +++ /dev/null @@ -1 +0,0 @@ -def remove_version_from_guid(guid): ... diff --git a/mypy-stubs/galaxy/util/topsort.pyi b/mypy-stubs/galaxy/util/topsort.pyi deleted file mode 100644 index b6a74be87..000000000 --- a/mypy-stubs/galaxy/util/topsort.pyi +++ /dev/null @@ -1,15 +0,0 @@ -from _typeshed import Incomplete - -class CycleError(Exception): - preds: Incomplete - def __init__(self, sofar, numpreds, succs) -> None: ... - def get_partial(self): ... - def get_pred_counts(self): ... - def get_succs(self): ... - def get_elements(self): ... - def get_pairlist(self): ... - def get_preds(self): ... - def pick_a_cycle(self): ... - -def topsort(pairlist): ... -def topsort_levels(pairlist): ... diff --git a/mypy-stubs/galaxy/util/ucsc.pyi b/mypy-stubs/galaxy/util/ucsc.pyi deleted file mode 100644 index b291ef8c6..000000000 --- a/mypy-stubs/galaxy/util/ucsc.pyi +++ /dev/null @@ -1,12 +0,0 @@ -from _typeshed import Incomplete - -class UCSCLimitException(Exception): ... - -class UCSCOutWrapper: - other: Incomplete - lookahead: Incomplete - def __init__(self, other) -> None: ... - def __iter__(self): ... - def __next__(self): ... - def next(self): ... - def readline(self): ... diff --git a/mypy-stubs/galaxy/util/validation.pyi b/mypy-stubs/galaxy/util/validation.pyi deleted file mode 100644 index 6bb0b7c35..000000000 --- a/mypy-stubs/galaxy/util/validation.pyi +++ /dev/null @@ -1,6 +0,0 @@ -from galaxy import exceptions as exceptions -from galaxy.util.sanitize_html import sanitize_html as sanitize_html - -def validate_and_sanitize_basestring(key, val): ... -def validate_and_sanitize_basestring_list(key, val): ... -def validate_boolean(key, val): ... diff --git a/mypy-stubs/galaxy/util/watcher.pyi b/mypy-stubs/galaxy/util/watcher.pyi deleted file mode 100644 index b9d03f338..000000000 --- a/mypy-stubs/galaxy/util/watcher.pyi +++ /dev/null @@ -1,58 +0,0 @@ -from _typeshed import Incomplete -from galaxy.util.hash_util import md5_hash_file as md5_hash_file -from watchdog.events import FileSystemEventHandler - -can_watch: bool -FileSystemEventHandler = object -log: Incomplete - -def get_observer_class(config_name, config_value, default, monitor_what_str): ... -def get_watcher( - config, - config_name, - default: str = ..., - monitor_what_str: Incomplete | None = ..., - watcher_class: Incomplete | None = ..., - event_handler_class: Incomplete | None = ..., - **kwargs -): ... - -class BaseWatcher: - observer: Incomplete - observer_class: Incomplete - event_handler: Incomplete - monitored_dirs: Incomplete - def __init__(self, observer_class, even_handler_class, **kwargs) -> None: ... - def start(self) -> None: ... - def monitor(self, dir_path, recursive: bool = ...) -> None: ... - def resume_watching(self) -> None: ... - def shutdown(self) -> None: ... - -class Watcher(BaseWatcher): - path_hash: Incomplete - file_callbacks: Incomplete - dir_callbacks: Incomplete - ignore_extensions: Incomplete - require_extensions: Incomplete - event_handler: Incomplete - def __init__(self, observer_class, event_handler_class, **kwargs) -> None: ... - def watch_file(self, file_path, callback: Incomplete | None = ...) -> None: ... - def watch_directory( - self, - dir_path, - callback: Incomplete | None = ..., - recursive: bool = ..., - ignore_extensions: Incomplete | None = ..., - require_extensions: Incomplete | None = ..., - ) -> None: ... - -class EventHandler(FileSystemEventHandler): - watcher: Incomplete - def __init__(self, watcher) -> None: ... - def on_any_event(self, event) -> None: ... - -class NullWatcher: - def start(self) -> None: ... - def shutdown(self) -> None: ... - def watch_file(self, *args, **kwargs) -> None: ... - def watch_directory(self, *args, **kwargs) -> None: ... diff --git a/mypy-stubs/galaxy/util/web_compat.pyi b/mypy-stubs/galaxy/util/web_compat.pyi deleted file mode 100644 index 5feb5dd94..000000000 --- a/mypy-stubs/galaxy/util/web_compat.pyi +++ /dev/null @@ -1 +0,0 @@ -from galaxy.web_stack import register_postfork_function as register_postfork_function diff --git a/mypy-stubs/galaxy/util/xml_macros.pyi b/mypy-stubs/galaxy/util/xml_macros.pyi deleted file mode 100644 index 98b85f006..000000000 --- a/mypy-stubs/galaxy/util/xml_macros.pyi +++ /dev/null @@ -1,13 +0,0 @@ -from _typeshed import Incomplete - -def load_with_references(path): ... -def load(path): ... -def template_macro_params(root): ... -def raw_xml_tree(path): ... -def imported_macro_paths(root): ... - -class XmlMacroDef: - elements: Incomplete - parameters: Incomplete - def __init__(self, el) -> None: ... - def macro_tokens(self, expand_el): ... diff --git a/mypy-stubs/galaxy/util/yaml_util.pyi b/mypy-stubs/galaxy/util/yaml_util.pyi deleted file mode 100644 index a05e98ffa..000000000 --- a/mypy-stubs/galaxy/util/yaml_util.pyi +++ /dev/null @@ -1,11 +0,0 @@ -from _typeshed import Incomplete -from yaml import SafeLoader - -log: Incomplete - -class OrderedLoader(SafeLoader): - def __init__(self, stream) -> None: ... - def include(self, node): ... - -def ordered_load(stream, merge_duplicate_keys: bool = ...): ... -def ordered_dump(data, stream: Incomplete | None = ..., Dumper=..., **kwds): ... diff --git a/mypy-stubs/galaxy/util/zipstream.pyi b/mypy-stubs/galaxy/util/zipstream.pyi deleted file mode 100644 index 53b5be5fb..000000000 --- a/mypy-stubs/galaxy/util/zipstream.pyi +++ /dev/null @@ -1,20 +0,0 @@ -from .path import safe_walk as safe_walk -from _typeshed import Incomplete -from collections.abc import Generator - -class ZipstreamWrapper: - upstream_mod_zip: Incomplete - archive_name: Incomplete - archive: Incomplete - files: Incomplete - size: int - def __init__( - self, - archive_name: Incomplete | None = ..., - upstream_mod_zip: bool = ..., - upstream_gzip: bool = ..., - ) -> None: ... - def response(self) -> Generator[Incomplete, None, None]: ... - def get_headers(self): ... - def add_path(self, path, archive_name) -> None: ... - def write(self, path, archive_name: Incomplete | None = ...) -> None: ... diff --git a/mypy-stubs/networkx/algorithms/connectivity/edge_augmentation.pyi b/mypy-stubs/networkx/algorithms/connectivity/edge_augmentation.pyi index 8688890f4..cb446bd5a 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/edge_augmentation.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/edge_augmentation.pyi @@ -7,6 +7,8 @@ from typing import Any, Optional def is_k_edge_connected(G, k): ... def is_locally_k_edge_connected(G, s, t, k): ... -def k_edge_augmentation(G, k, avail: Optional[Any] = ..., weight: Optional[Any] = ..., partial: bool = ...): ... +def k_edge_augmentation( + G, k, avail: Optional[Any] = ..., weight: Optional[Any] = ..., partial: bool = ... +): ... -MetaEdge = namedtuple('MetaEdge', ) +# MetaEdge = namedtuple('MetaEdge', ) diff --git a/mypy-stubs/networkx/algorithms/connectivity/edge_kcomponents.pyi b/mypy-stubs/networkx/algorithms/connectivity/edge_kcomponents.pyi index bda3e5928..5aaa19809 100644 --- a/mypy-stubs/networkx/algorithms/connectivity/edge_kcomponents.pyi +++ b/mypy-stubs/networkx/algorithms/connectivity/edge_kcomponents.pyi @@ -9,9 +9,6 @@ def k_edge_subgraphs(G, k): ... def bridge_components(G): ... class EdgeComponentAuxGraph: - @classmethod - A: Any = ... - H: Any = ... def construct(EdgeComponentAuxGraph, G): ... def k_edge_components(self, k): ... def k_edge_subgraphs(self, k): ... diff --git a/mypy-stubs/prov/constants.py b/mypy-stubs/prov/constants.py new file mode 100644 index 000000000..f711d00dd --- /dev/null +++ b/mypy-stubs/prov/constants.py @@ -0,0 +1,217 @@ +from __future__ import absolute_import, division, print_function, unicode_literals + +from prov.identifier import Namespace + +__author__ = "Trung Dong Huynh" +__email__ = "trungdong@donggiang.com" + + +XSD = Namespace("xsd", "http://www.w3.org/2001/XMLSchema#") +PROV = Namespace("prov", "http://www.w3.org/ns/prov#") +XSI = Namespace("xsi", "http://www.w3.org/2001/XMLSchema-instance") + +# C1. Entities/Activities +PROV_ENTITY = PROV["Entity"] +PROV_ACTIVITY = PROV["Activity"] +PROV_GENERATION = PROV["Generation"] +PROV_USAGE = PROV["Usage"] +PROV_COMMUNICATION = PROV["Communication"] +PROV_START = PROV["Start"] +PROV_END = PROV["End"] +PROV_INVALIDATION = PROV["Invalidation"] + +# C2. Derivations +PROV_DERIVATION = PROV["Derivation"] + +# C3. Agents/Responsibility +PROV_AGENT = PROV["Agent"] +PROV_ATTRIBUTION = PROV["Attribution"] +PROV_ASSOCIATION = PROV["Association"] +PROV_DELEGATION = PROV["Delegation"] +PROV_INFLUENCE = PROV["Influence"] +# C4. Bundles +PROV_BUNDLE = PROV["Bundle"] +# C5. Alternate +PROV_ALTERNATE = PROV["Alternate"] +PROV_SPECIALIZATION = PROV["Specialization"] +PROV_MENTION = PROV["Mention"] +# C6. Collections +PROV_MEMBERSHIP = PROV["Membership"] + +PROV_N_MAP = { + PROV_ENTITY: "entity", + PROV_ACTIVITY: "activity", + PROV_GENERATION: "wasGeneratedBy", + PROV_USAGE: "used", + PROV_COMMUNICATION: "wasInformedBy", + PROV_START: "wasStartedBy", + PROV_END: "wasEndedBy", + PROV_INVALIDATION: "wasInvalidatedBy", + PROV_DERIVATION: "wasDerivedFrom", + PROV_AGENT: "agent", + PROV_ATTRIBUTION: "wasAttributedTo", + PROV_ASSOCIATION: "wasAssociatedWith", + PROV_DELEGATION: "actedOnBehalfOf", + PROV_INFLUENCE: "wasInfluencedBy", + PROV_ALTERNATE: "alternateOf", + PROV_SPECIALIZATION: "specializationOf", + PROV_MENTION: "mentionOf", + PROV_MEMBERSHIP: "hadMember", + PROV_BUNDLE: "bundle", +} + +# Records defined as subtypes in PROV-N but top level types in for example +# PROV XML also need a mapping. +ADDITIONAL_N_MAP = { + PROV["Revision"]: "wasRevisionOf", + PROV["Quotation"]: "wasQuotedFrom", + PROV["PrimarySource"]: "hadPrimarySource", + PROV["SoftwareAgent"]: "softwareAgent", + PROV["Person"]: "person", + PROV["Organization"]: "organization", + PROV["Plan"]: "plan", + PROV["Collection"]: "collection", + PROV["EmptyCollection"]: "emptyCollection", +} + +# Maps qualified names from the PROV namespace to their base class. If it +# has no baseclass it maps to itsself. This is needed for example for PROV +# XML (de)serializer where extended types are used a lot. +PROV_BASE_CLS = { + PROV_ENTITY: PROV_ENTITY, + PROV_ACTIVITY: PROV_ACTIVITY, + PROV_GENERATION: PROV_GENERATION, + PROV_USAGE: PROV_USAGE, + PROV_COMMUNICATION: PROV_COMMUNICATION, + PROV_START: PROV_START, + PROV_END: PROV_END, + PROV_INVALIDATION: PROV_INVALIDATION, + PROV_DERIVATION: PROV_DERIVATION, + PROV["Revision"]: PROV_DERIVATION, + PROV["Quotation"]: PROV_DERIVATION, + PROV["PrimarySource"]: PROV_DERIVATION, + PROV_AGENT: PROV_AGENT, + PROV["SoftwareAgent"]: PROV_AGENT, + PROV["Person"]: PROV_AGENT, + PROV["Organization"]: PROV_AGENT, + PROV_ATTRIBUTION: PROV_ATTRIBUTION, + PROV_ASSOCIATION: PROV_ASSOCIATION, + PROV["Plan"]: PROV_ENTITY, + PROV_DELEGATION: PROV_DELEGATION, + PROV_INFLUENCE: PROV_INFLUENCE, + PROV_ALTERNATE: PROV_ALTERNATE, + PROV_SPECIALIZATION: PROV_SPECIALIZATION, + PROV_MENTION: PROV_MENTION, + PROV["Collection"]: PROV_ENTITY, + PROV["EmptyCollection"]: PROV_ENTITY, + PROV_MEMBERSHIP: PROV_MEMBERSHIP, + PROV_BUNDLE: PROV_ENTITY, +} + +# Identifiers for PROV's attributes +PROV_ATTR_ENTITY = PROV["entity"] +PROV_ATTR_ACTIVITY = PROV["activity"] +PROV_ATTR_TRIGGER = PROV["trigger"] +PROV_ATTR_INFORMED = PROV["informed"] +PROV_ATTR_INFORMANT = PROV["informant"] +PROV_ATTR_STARTER = PROV["starter"] +PROV_ATTR_ENDER = PROV["ender"] +PROV_ATTR_AGENT = PROV["agent"] +PROV_ATTR_PLAN = PROV["plan"] +PROV_ATTR_DELEGATE = PROV["delegate"] +PROV_ATTR_RESPONSIBLE = PROV["responsible"] +PROV_ATTR_GENERATED_ENTITY = PROV["generatedEntity"] +PROV_ATTR_USED_ENTITY = PROV["usedEntity"] +PROV_ATTR_GENERATION = PROV["generation"] +PROV_ATTR_USAGE = PROV["usage"] +PROV_ATTR_SPECIFIC_ENTITY = PROV["specificEntity"] +PROV_ATTR_GENERAL_ENTITY = PROV["generalEntity"] +PROV_ATTR_ALTERNATE1 = PROV["alternate1"] +PROV_ATTR_ALTERNATE2 = PROV["alternate2"] +PROV_ATTR_BUNDLE = PROV["bundle"] +PROV_ATTR_INFLUENCEE = PROV["influencee"] +PROV_ATTR_INFLUENCER = PROV["influencer"] +PROV_ATTR_COLLECTION = PROV["collection"] + +# Literal properties +PROV_ATTR_TIME = PROV["time"] +PROV_ATTR_STARTTIME = PROV["startTime"] +PROV_ATTR_ENDTIME = PROV["endTime"] + + +PROV_ATTRIBUTE_QNAMES = { + PROV_ATTR_ENTITY, + PROV_ATTR_ACTIVITY, + PROV_ATTR_TRIGGER, + PROV_ATTR_INFORMED, + PROV_ATTR_INFORMANT, + PROV_ATTR_STARTER, + PROV_ATTR_ENDER, + PROV_ATTR_AGENT, + PROV_ATTR_PLAN, + PROV_ATTR_DELEGATE, + PROV_ATTR_RESPONSIBLE, + PROV_ATTR_GENERATED_ENTITY, + PROV_ATTR_USED_ENTITY, + PROV_ATTR_GENERATION, + PROV_ATTR_USAGE, + PROV_ATTR_SPECIFIC_ENTITY, + PROV_ATTR_GENERAL_ENTITY, + PROV_ATTR_ALTERNATE1, + PROV_ATTR_ALTERNATE2, + PROV_ATTR_BUNDLE, + PROV_ATTR_INFLUENCEE, + PROV_ATTR_INFLUENCER, + PROV_ATTR_COLLECTION, +} +PROV_ATTRIBUTE_LITERALS = {PROV_ATTR_TIME, PROV_ATTR_STARTTIME, PROV_ATTR_ENDTIME} + +# Set of formal attributes of PROV records +PROV_ATTRIBUTES = PROV_ATTRIBUTE_QNAMES | PROV_ATTRIBUTE_LITERALS +PROV_RECORD_ATTRIBUTES = list((attr, str(attr)) for attr in PROV_ATTRIBUTES) + +PROV_RECORD_IDS_MAP = dict( + (PROV_N_MAP[rec_type_id], rec_type_id) for rec_type_id in PROV_N_MAP +) +PROV_ID_ATTRIBUTES_MAP = dict( + (prov_id, attribute) for (prov_id, attribute) in PROV_RECORD_ATTRIBUTES +) +PROV_ATTRIBUTES_ID_MAP = dict( + (attribute, prov_id) for (prov_id, attribute) in PROV_RECORD_ATTRIBUTES +) + +# Extra definition for convenience +PROV_TYPE = PROV["type"] +PROV_LABEL = PROV["label"] +PROV_VALUE = PROV["value"] +PROV_LOCATION = PROV["location"] +PROV_ROLE = PROV["role"] + +PROV_QUALIFIEDNAME = PROV["QUALIFIED_NAME"] + +# XSD DATA TYPES +XSD_ANYURI = XSD["anyURI"] +XSD_QNAME = XSD["QName"] +XSD_DATETIME = XSD["dateTime"] +XSD_TIME = XSD["time"] +XSD_DATE = XSD["date"] +XSD_STRING = XSD["string"] +XSD_BOOLEAN = XSD["boolean"] +# All XSD Integer types +XSD_INTEGER = XSD["integer"] +XSD_LONG = XSD["long"] +XSD_INT = XSD["int"] +XSD_SHORT = XSD["short"] +XSD_BYTE = XSD["byte"] +XSD_NONNEGATIVEINTEGER = XSD["nonNegativeInteger"] +XSD_UNSIGNEDLONG = XSD["unsignedLong"] +XSD_UNSIGNEDINT = XSD["unsignedInt"] +XSD_UNSIGNEDSHORT = XSD["unsignedShort"] +XSD_UNSIGNEDBYTE = XSD["unsignedByte"] +XSD_POSITIVEINTEGER = XSD["positiveInteger"] +XSD_NONPOSITIVEINTEGER = XSD["nonPositiveInteger"] +XSD_NEGATIVEINTEGER = XSD["negativeInteger"] +# All XSD real number types +XSD_FLOAT = XSD["float"] +XSD_DOUBLE = XSD["double"] +XSD_DECIMAL = XSD["decimal"] diff --git a/mypy-stubs/prov/constants.pyi b/mypy-stubs/prov/constants.pyi deleted file mode 100644 index ac0d7582d..000000000 --- a/mypy-stubs/prov/constants.pyi +++ /dev/null @@ -1,90 +0,0 @@ -from _typeshed import Incomplete -from prov.identifier import Namespace as Namespace - -XSD: Incomplete -PROV: Incomplete -XSI: Incomplete -PROV_ENTITY: Incomplete -PROV_ACTIVITY: Incomplete -PROV_GENERATION: Incomplete -PROV_USAGE: Incomplete -PROV_COMMUNICATION: Incomplete -PROV_START: Incomplete -PROV_END: Incomplete -PROV_INVALIDATION: Incomplete -PROV_DERIVATION: Incomplete -PROV_AGENT: Incomplete -PROV_ATTRIBUTION: Incomplete -PROV_ASSOCIATION: Incomplete -PROV_DELEGATION: Incomplete -PROV_INFLUENCE: Incomplete -PROV_BUNDLE: Incomplete -PROV_ALTERNATE: Incomplete -PROV_SPECIALIZATION: Incomplete -PROV_MENTION: Incomplete -PROV_MEMBERSHIP: Incomplete -PROV_N_MAP: Incomplete -ADDITIONAL_N_MAP: Incomplete -PROV_BASE_CLS: Incomplete -PROV_ATTR_ENTITY: Incomplete -PROV_ATTR_ACTIVITY: Incomplete -PROV_ATTR_TRIGGER: Incomplete -PROV_ATTR_INFORMED: Incomplete -PROV_ATTR_INFORMANT: Incomplete -PROV_ATTR_STARTER: Incomplete -PROV_ATTR_ENDER: Incomplete -PROV_ATTR_AGENT: Incomplete -PROV_ATTR_PLAN: Incomplete -PROV_ATTR_DELEGATE: Incomplete -PROV_ATTR_RESPONSIBLE: Incomplete -PROV_ATTR_GENERATED_ENTITY: Incomplete -PROV_ATTR_USED_ENTITY: Incomplete -PROV_ATTR_GENERATION: Incomplete -PROV_ATTR_USAGE: Incomplete -PROV_ATTR_SPECIFIC_ENTITY: Incomplete -PROV_ATTR_GENERAL_ENTITY: Incomplete -PROV_ATTR_ALTERNATE1: Incomplete -PROV_ATTR_ALTERNATE2: Incomplete -PROV_ATTR_BUNDLE: Incomplete -PROV_ATTR_INFLUENCEE: Incomplete -PROV_ATTR_INFLUENCER: Incomplete -PROV_ATTR_COLLECTION: Incomplete -PROV_ATTR_TIME: Incomplete -PROV_ATTR_STARTTIME: Incomplete -PROV_ATTR_ENDTIME: Incomplete -PROV_ATTRIBUTE_QNAMES: Incomplete -PROV_ATTRIBUTE_LITERALS: Incomplete -PROV_ATTRIBUTES: Incomplete -PROV_RECORD_ATTRIBUTES: Incomplete -PROV_RECORD_IDS_MAP: Incomplete -PROV_ID_ATTRIBUTES_MAP: Incomplete -PROV_ATTRIBUTES_ID_MAP: Incomplete -PROV_TYPE: Incomplete -PROV_LABEL: Incomplete -PROV_VALUE: Incomplete -PROV_LOCATION: Incomplete -PROV_ROLE: Incomplete -PROV_QUALIFIEDNAME: Incomplete -XSD_ANYURI: Incomplete -XSD_QNAME: Incomplete -XSD_DATETIME: Incomplete -XSD_TIME: Incomplete -XSD_DATE: Incomplete -XSD_STRING: Incomplete -XSD_BOOLEAN: Incomplete -XSD_INTEGER: Incomplete -XSD_LONG: Incomplete -XSD_INT: Incomplete -XSD_SHORT: Incomplete -XSD_BYTE: Incomplete -XSD_NONNEGATIVEINTEGER: Incomplete -XSD_UNSIGNEDLONG: Incomplete -XSD_UNSIGNEDINT: Incomplete -XSD_UNSIGNEDSHORT: Incomplete -XSD_UNSIGNEDBYTE: Incomplete -XSD_POSITIVEINTEGER: Incomplete -XSD_NONPOSITIVEINTEGER: Incomplete -XSD_NEGATIVEINTEGER: Incomplete -XSD_FLOAT: Incomplete -XSD_DOUBLE: Incomplete -XSD_DECIMAL: Incomplete diff --git a/mypy-stubs/prov/dot.pyi b/mypy-stubs/prov/dot.pyi index 9ac52aee0..02b896e20 100644 --- a/mypy-stubs/prov/dot.pyi +++ b/mypy-stubs/prov/dot.pyi @@ -1,29 +1,27 @@ from _typeshed import Incomplete -from prov.model import ( - Identifier as Identifier, - PROV_ACTIVITY as PROV_ACTIVITY, - PROV_AGENT as PROV_AGENT, - PROV_ALTERNATE as PROV_ALTERNATE, - PROV_ASSOCIATION as PROV_ASSOCIATION, - PROV_ATTRIBUTE_QNAMES as PROV_ATTRIBUTE_QNAMES, - PROV_ATTRIBUTION as PROV_ATTRIBUTION, - PROV_BUNDLE as PROV_BUNDLE, - PROV_COMMUNICATION as PROV_COMMUNICATION, - PROV_DELEGATION as PROV_DELEGATION, - PROV_DERIVATION as PROV_DERIVATION, - PROV_END as PROV_END, - PROV_ENTITY as PROV_ENTITY, - PROV_GENERATION as PROV_GENERATION, - PROV_INFLUENCE as PROV_INFLUENCE, - PROV_INVALIDATION as PROV_INVALIDATION, - PROV_MEMBERSHIP as PROV_MEMBERSHIP, - PROV_MENTION as PROV_MENTION, - PROV_SPECIALIZATION as PROV_SPECIALIZATION, - PROV_START as PROV_START, - PROV_USAGE as PROV_USAGE, - ProvException as ProvException, - sorted_attributes as sorted_attributes, -) +from prov.model import PROV_ACTIVITY as PROV_ACTIVITY +from prov.model import PROV_AGENT as PROV_AGENT +from prov.model import PROV_ALTERNATE as PROV_ALTERNATE +from prov.model import PROV_ASSOCIATION as PROV_ASSOCIATION +from prov.model import PROV_ATTRIBUTE_QNAMES as PROV_ATTRIBUTE_QNAMES +from prov.model import PROV_ATTRIBUTION as PROV_ATTRIBUTION +from prov.model import PROV_BUNDLE as PROV_BUNDLE +from prov.model import PROV_COMMUNICATION as PROV_COMMUNICATION +from prov.model import PROV_DELEGATION as PROV_DELEGATION +from prov.model import PROV_DERIVATION as PROV_DERIVATION +from prov.model import PROV_END as PROV_END +from prov.model import PROV_ENTITY as PROV_ENTITY +from prov.model import PROV_GENERATION as PROV_GENERATION +from prov.model import PROV_INFLUENCE as PROV_INFLUENCE +from prov.model import PROV_INVALIDATION as PROV_INVALIDATION +from prov.model import PROV_MEMBERSHIP as PROV_MEMBERSHIP +from prov.model import PROV_MENTION as PROV_MENTION +from prov.model import PROV_SPECIALIZATION as PROV_SPECIALIZATION +from prov.model import PROV_START as PROV_START +from prov.model import PROV_USAGE as PROV_USAGE +from prov.model import Identifier as Identifier +from prov.model import ProvException as ProvException +from prov.model import sorted_attributes as sorted_attributes DOT_PROV_STYLE: Incomplete ANNOTATION_STYLE: Incomplete diff --git a/mypy-stubs/prov/model.pyi b/mypy-stubs/prov/model.pyi index 28595adca..0ce442677 100644 --- a/mypy-stubs/prov/model.pyi +++ b/mypy-stubs/prov/model.pyi @@ -1,11 +1,12 @@ +import types from datetime import datetime -from typing import Any, Dict, List, Set, Tuple +from typing import IO, Any, Dict, Iterable, List, Set, Tuple from _typeshed import Incomplete from prov.constants import * + # from prov import Error as Error, serializers as serializers -from prov.identifier import Identifier as Identifier -from prov.identifier import Namespace as Namespace +from prov.identifier import Identifier, Namespace, QualifiedName logger: Incomplete @@ -16,19 +17,24 @@ XSD_DATATYPE_PARSERS: Incomplete # def first(a_set): ... +_attributes_type = Dict[str | Identifier, Any] | List[Tuple[str | Identifier, Any]] + class ProvRecord: FORMAL_ATTRIBUTES: Incomplete def __init__( - self, bundle: str, identifier: str, attributes: Dict[str, str] | None = ... + self, + bundle: str, + identifier: Identifier | str, + attributes: Dict[str, str] | None = ..., ) -> None: ... def __hash__(self) -> int: ... def copy(self) -> ProvRecord: ... def get_type(self) -> str: ... def get_asserted_types(self) -> Set[str]: ... - def add_asserted_type(self, type_identifier: str) -> None: ... + def add_asserted_type(self, type_identifier: str | QualifiedName) -> None: ... def get_attribute(self, attr_name: str) -> Set[str]: ... @property - def identifier(self) -> str: ... + def identifier(self) -> Identifier: ... @property def attributes(self) -> List[Tuple[str, str]]: ... @property @@ -43,7 +49,10 @@ class ProvRecord: def label(self) -> str: ... @property def value(self) -> str: ... - def add_attributes(self, attributes: Dict[str, str]) -> None: ... + def add_attributes( + self, + attributes: _attributes_type, + ) -> None: ... def __eq__(self, other: Any) -> bool: ... def get_provn(self) -> str: ... def is_element(self) -> bool: ... @@ -54,7 +63,7 @@ class ProvElement(ProvRecord): self, bundle: "ProvBundle", identifier: str, - attributes: Dict[str, str] | None = ..., + attributes: _attributes_type, ) -> None: ... def is_element(self) -> bool: ... @@ -66,13 +75,13 @@ class ProvEntity(ProvElement): self, activity: str, time: datetime | str | None = ..., - attributes: Dict[str, str] | List[Tuple[str, str]] | None = ..., + attributes: _attributes_type | None = None, ) -> ProvGeneration: ... def wasInvalidatedBy( self, activity: str, time: datetime | str | None = ..., - attributes: Dict[str, str] | List[Tuple[str, str]] | None = ..., + attributes: _attributes_type | None = None, ) -> ProvInvalidation: ... def wasDerivedFrom( self, @@ -80,12 +89,12 @@ class ProvEntity(ProvElement): activity: str | None = ..., generation: Incomplete | None = ..., usage: Incomplete | None = ..., - attributes: Incomplete | None = ..., + attributes: _attributes_type | None = None, ) -> ProvDerivation: ... def wasAttributedTo( self, agent: str, - attributes: Dict[str, str] | List[Tuple[str, str]] | None = ..., + attributes: _attributes_type | None = None, ) -> ProvAttribution: ... def alternateOf(self, alternate2: str) -> ProvElement: ... def specializationOf(self, generalEntity: str) -> ProvSpecialization: ... @@ -96,29 +105,39 @@ class ProvActivity(ProvElement): def set_time( self, startTime: Incomplete | None = ..., endTime: Incomplete | None = ... ) -> None: ... - def get_startTime(self): ... - def get_endTime(self): ... + def get_startTime(self) -> datetime: ... + def get_endTime(self) -> datetime: ... def used( - self, entity, time: Incomplete | None = ..., attributes: Incomplete | None = ... - ): ... - def wasInformedBy(self, informant, attributes: Incomplete | None = ...): ... + self, + entity: str, + time: datetime | str | None = ..., + attributes: _attributes_type | None = None, + ) -> ProvActivity: ... + def wasInformedBy( + self, + informant: str, + attributes: _attributes_type | None = None, + ) -> ProvActivity: ... def wasStartedBy( self, - trigger, - starter: Incomplete | None = ..., - time: Incomplete | None = ..., - attributes: Incomplete | None = ..., - ): ... + trigger: str, + starter: str | None = ..., + time: datetime | str | None = ..., + attributes: _attributes_type | None = None, + ) -> ProvActivity: ... def wasEndedBy( self, - trigger, - ender: Incomplete | None = ..., - time: Incomplete | None = ..., - attributes: Incomplete | None = ..., - ): ... + trigger: str, + ender: str | None = ..., + time: datetime | str | None = ..., + attributes: _attributes_type | None = None, + ) -> ProvActivity: ... def wasAssociatedWith( - self, agent, plan: Incomplete | None = ..., attributes: Incomplete | None = ... - ): ... + self, + agent: str, + plan: str | None = ..., + attributes: _attributes_type | None = None, + ) -> ProvActivity: ... class ProvGeneration(ProvRelation): FORMAL_ATTRIBUTES: Incomplete @@ -144,10 +163,10 @@ class ProvDerivation(ProvRelation): class ProvAgent(ProvElement): def actedOnBehalfOf( self, - responsible, - activity: Incomplete | None = ..., - attributes: Incomplete | None = ..., - ): ... + responsible: str, + activity: str | None = ..., + attributes: _attributes_type | None = ..., + ) -> ProvAgent: ... class ProvAttribution(ProvRelation): FORMAL_ATTRIBUTES: Incomplete @@ -176,251 +195,269 @@ class ProvMembership(ProvRelation): PROV_REC_CLS: Incomplete DEFAULT_NAMESPACES: Incomplete -class NamespaceManager(dict): - parent: Incomplete - def __init__( - self, - namespaces: Incomplete | None = ..., - default: Incomplete | None = ..., - parent: Incomplete | None = ..., - ) -> None: ... - def get_namespace(self, uri): ... - def get_registered_namespaces(self): ... - def set_default_namespace(self, uri) -> None: ... - def get_default_namespace(self): ... - def add_namespace(self, namespace): ... - def add_namespaces(self, namespaces) -> None: ... - def valid_qualified_name(self, qname): ... - def get_anonymous_identifier(self, local_prefix: str = ...): ... - class ProvBundle: def __init__( self, - records: Incomplete | None = ..., - identifier: Incomplete | None = ..., - namespaces: Incomplete | None = ..., - document: Incomplete | None = ..., + records: Iterable[ProvRecord] | None = ..., + identifier: str | None = ..., + namespaces: Iterable[Namespace] | None = ..., + document: ProvDocument | None = ..., ) -> None: ... @property - def namespaces(self): ... + def namespaces(self) -> Set[Namespace]: ... @property - def default_ns_uri(self): ... + def default_ns_uri(self) -> str | None: ... @property - def document(self): ... + def document(self) -> ProvDocument | None: ... @property - def identifier(self): ... + def identifier(self) -> str | None: ... @property - def records(self): ... - def set_default_namespace(self, uri) -> None: ... - def get_default_namespace(self): ... - def add_namespace(self, namespace_or_prefix, uri: Incomplete | None = ...): ... - def get_registered_namespaces(self): ... - def valid_qualified_name(self, identifier): ... - def get_records(self, class_or_type_or_tuple: Incomplete | None = ...): ... - def get_record(self, identifier): ... - def is_document(self): ... - def is_bundle(self): ... - def has_bundles(self): ... + def records(self) -> List[ProvRecord]: ... + def set_default_namespace(self, uri: Namespace) -> None: ... + def get_default_namespace(self) -> Namespace: ... + def add_namespace( + self, namespace_or_prefix: Namespace | str, uri: str | None = ... + ) -> Namespace: ... + def get_registered_namespaces(self) -> Iterable[Namespace]: ... + def valid_qualified_name( + self, identifier: QualifiedName | Tuple[str, Identifier] + ) -> QualifiedName | None: ... + def get_records( + self, + class_or_type_or_tuple: type + | types.UnionType + | Tuple[type | types.UnionType | Tuple[Any, ...], ...] + | None = ..., + ) -> List[ProvRecord]: ... + def get_record( + self, identifier: Identifier | None + ) -> ProvRecord | List[ProvRecord] | None: ... + def is_document(self) -> bool: ... + def is_bundle(self) -> bool: ... + def has_bundles(self) -> bool: ... @property - def bundles(self): ... - def get_provn(self, _indent_level: int = ...): ... - def __eq__(self, other): ... - def __ne__(self, other): ... - __hash__: Incomplete - def unified(self): ... - def update(self, other) -> None: ... + def bundles(self) -> Iterable[ProvBundle]: ... + def get_provn(self, _indent_level: int = ...) -> str: ... + def unified(self) -> ProvBundle: ... + def update(self, other: ProvBundle) -> None: ... def new_record( self, - record_type, - identifier, - attributes: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... - def add_record(self, record): ... - def entity(self, identifier, other_attributes: Incomplete | None = ...): ... + record_type: PROV_REC_CLS, + identifier: str, + attributes: _attributes_type | None = None, + other_attributes: _attributes_type | None = None, + ) -> ProvRecord: ... + def add_record(self, record: ProvRecord) -> ProvRecord: ... + def entity( + self, + identifier: str | QualifiedName, + other_attributes: _attributes_type | None = None, + ) -> ProvEntity: ... def activity( self, - identifier, - startTime: Incomplete | None = ..., - endTime: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + identifier: str | QualifiedName, + startTime: datetime | str | None = ..., + endTime: datetime | str | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvActivity: ... def generation( self, - entity, - activity: Incomplete | None = ..., - time: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + entity: ProvEntity | str, + activity: ProvActivity | str | None = ..., + time: datetime | str | None = ..., + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvGeneration: ... def usage( self, - activity, - entity: Incomplete | None = ..., - time: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + activity: ProvActivity | str, + entity: ProvEntity | str | None = ..., + time: datetime | str | None = ..., + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvUsage: ... def start( self, - activity, - trigger: Incomplete | None = ..., - starter: Incomplete | None = ..., - time: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + activity: ProvActivity | ProvAgent | str, + trigger: ProvEntity | None = ..., + starter: ProvActivity | ProvAgent | str | None = ..., + time: datetime | str | None = ..., + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvStart: ... def end( self, - activity, - trigger: Incomplete | None = ..., - ender: Incomplete | None = ..., - time: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + activity: ProvActivity | str, + trigger: ProvEntity | None = ..., + ender: ProvActivity | str | None = ..., + time: datetime | str | None = ..., + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvEnd: ... def invalidation( self, - entity, - activity: Incomplete | None = ..., - time: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + entity: ProvEntity | str, + activity: ProvActivity | str | None = ..., + time: datetime | str | None = ..., + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvInvalidation: ... def communication( self, - informed, - informant, - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... - def agent(self, identifier, other_attributes: Incomplete | None = ...): ... + informed: ProvActivity | str, + informant: ProvActivity | str, + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvCommunication: ... + def agent( + self, + identifier: Identifier | str, + other_attributes: _attributes_type | None = None, + ) -> ProvAgent: ... def attribution( self, - entity, - agent, - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + entity: ProvEntity | str, + agent: ProvAgent | str, + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvAttribution: ... def association( self, - activity, - agent: Incomplete | None = ..., - plan: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + activity: ProvActivity | str, + agent: ProvAgent | str | None = ..., + plan: ProvEntity | str | None = ..., + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvAssociation: ... def delegation( self, - delegate, - responsible, - activity: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + delegate: ProvAgent | str, + responsible: ProvAgent | str, + activity: ProvActivity | str | None = ..., + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvDelegation: ... def influence( self, - influencee, - influencer, - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + influencee: ProvEntity | ProvActivity | ProvAgent | str, + influencer: ProvEntity | ProvActivity | ProvAgent | str, + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvInfluence: ... def derivation( self, - generatedEntity, - usedEntity, - activity: Incomplete | None = ..., - generation: Incomplete | None = ..., + generatedEntity: ProvEntity | str, + usedEntity: ProvEntity | str, + activity: ProvActivity | str | None = ..., + generation: ProvActivity | str | None = ..., usage: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvDerivation: ... def revision( self, - generatedEntity, - usedEntity, - activity: Incomplete | None = ..., - generation: Incomplete | None = ..., + generatedEntity: ProvEntity | str, + usedEntity: ProvEntity | str, + activity: ProvActivity | str | None = ..., + generation: ProvActivity | str | None = ..., usage: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvRecord: ... def quotation( self, - generatedEntity, - usedEntity, - activity: Incomplete | None = ..., - generation: Incomplete | None = ..., + generatedEntity: ProvEntity | str, + usedEntity: ProvEntity | str, + activity: ProvActivity | str | None = ..., + generation: ProvActivity | str | None = ..., usage: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvRecord: ... def primary_source( self, - generatedEntity, - usedEntity, - activity: Incomplete | None = ..., - generation: Incomplete | None = ..., + generatedEntity: ProvEntity | str, + usedEntity: ProvEntity | str, + activity: ProvActivity | str | None = ..., + generation: ProvActivity | str | None = ..., usage: Incomplete | None = ..., - identifier: Incomplete | None = ..., - other_attributes: Incomplete | None = ..., - ): ... - def specialization(self, specificEntity, generalEntity): ... - def alternate(self, alternate1, alternate2): ... - def mention(self, specificEntity, generalEntity, bundle): ... - def collection(self, identifier, other_attributes: Incomplete | None = ...): ... - def membership(self, collection, entity): ... + identifier: Identifier | None = ..., + other_attributes: _attributes_type | None = None, + ) -> ProvRecord: ... + def specialization( + self, specificEntity: ProvEntity | str, generalEntity: ProvEntity | str + ) -> ProvRecord: ... + def alternate( + self, alternate1: ProvEntity | str, alternate2: ProvEntity | str + ) -> ProvRecord: ... + def mention( + self, + specificEntity: ProvEntity | str, + generalEntity: ProvEntity | str, + bundle: Incomplete, + ) -> ProvRecord: ... + def collection( + self, + identifier: str, + other_attributes: _attributes_type | None, + ) -> ProvRecord: ... + def membership( + self, collection: ProvRecord, entity: ProvEntity | str + ) -> ProvRecord: ... def plot( self, - filename: Incomplete | None = ..., + filename: str | None = ..., show_nary: bool = ..., use_labels: bool = ..., show_element_attributes: bool = ..., show_relation_attributes: bool = ..., ) -> None: ... - wasGeneratedBy: Incomplete - used: Incomplete - wasStartedBy: Incomplete - wasEndedBy: Incomplete - wasInvalidatedBy: Incomplete - wasInformedBy: Incomplete - wasAttributedTo: Incomplete - wasAssociatedWith: Incomplete - actedOnBehalfOf: Incomplete - wasInfluencedBy: Incomplete - wasDerivedFrom: Incomplete - wasRevisionOf: Incomplete - wasQuotedFrom: Incomplete - hadPrimarySource: Incomplete - alternateOf: Incomplete - specializationOf: Incomplete - mentionOf: Incomplete - hadMember: Incomplete + wasGeneratedBy = generation + used = usage + wasStartedBy = start + wasEndedBy = end + wasInvalidatedBy = invalidation + wasInformedBy = communication + wasAttributedTo = attribution + wasAssociatedWith = association + actedOnBehalfOf = delegation + wasInfluencedBy = influence + wasDerivedFrom = derivation + wasRevisionOf = revision + wasQuotedFrom = quotation + hadPrimarySource = primary_source + alternateOf = alternate + specializationOf = specialization + mentionOf = mention + hadMember = membership class ProvDocument(ProvBundle): def __init__( - self, records: Incomplete | None = ..., namespaces: Incomplete | None = ... + self, + records: Iterable[ProvRecord] | None = ..., + namespaces: Iterable[Namespace] | None = ..., ) -> None: ... - def __eq__(self, other): ... - def is_document(self): ... - def is_bundle(self): ... - def has_bundles(self): ... + def is_document(self) -> bool: ... + def is_bundle(self) -> bool: ... + def has_bundles(self) -> bool: ... @property - def bundles(self): ... - def flattened(self): ... - def unified(self): ... - def update(self, other) -> None: ... - def add_bundle(self, bundle, identifier: Incomplete | None = ...) -> None: ... - def bundle(self, identifier): ... + def bundles(self) -> Iterable[ProvBundle]: ... + def flattened(self) -> ProvDocument: ... + def unified(self) -> ProvDocument: ... + def update(self, other: ProvDocument | ProvBundle) -> None: ... + def add_bundle( + self, bundle: ProvBundle, identifier: Incomplete | None = ... + ) -> None: ... + def bundle(self, identifier: Identifier) -> ProvBundle: ... def serialize( - self, destination: Incomplete | None = ..., format: str = ..., **args - ): ... + self, destination: IO[Any] | None = ..., format: str = ..., **args: Any + ) -> str | None: ... @staticmethod def deserialize( - source: Incomplete | None = ..., - content: Incomplete | None = ..., + source: IO[Any] | str | None = ..., + content: str | None = ..., format: str = ..., - **args - ): ... + **args: Any + ) -> ProvDocument: ... -def sorted_attributes(element, attributes): ... +def sorted_attributes(element: ProvElement, attributes: List[str]) -> List[str]: ... diff --git a/mypy-stubs/pydot.pyi b/mypy-stubs/pydot.pyi index 871b3ba80..93464c1d4 100644 --- a/mypy-stubs/pydot.pyi +++ b/mypy-stubs/pydot.pyi @@ -34,7 +34,7 @@ class InvocationException(Exception): class Node(Common): obj_dict: Any def __init__( - self, name: str = ..., obj_dict: Any | None = ..., **attrs: Dict[str, str] + self, name: str = ..., obj_dict: Any | None = ..., **attrs: str ) -> None: ... def set_name(self, node_name: str) -> None: ... def get_name(self) -> str: ... diff --git a/mypy-stubs/rdflib/graph.pyi b/mypy-stubs/rdflib/graph.pyi index 7852c81c6..23c2e6e1f 100644 --- a/mypy-stubs/rdflib/graph.pyi +++ b/mypy-stubs/rdflib/graph.pyi @@ -1,7 +1,20 @@ -from typing import Any, Iterable, Iterator, List, Optional, Set, Tuple, Union, overload +import pathlib +from typing import ( + IO, + Any, + Iterable, + Iterator, + List, + Optional, + Set, + Tuple, + Union, + overload, +) from rdflib import query from rdflib.collection import Collection +from rdflib.paths import Path from rdflib.resource import Resource from rdflib.term import BNode, Identifier, Node @@ -37,6 +50,12 @@ class Graph(Node): Optional[Identifier], ], ) -> Iterator[Tuple[Identifier, Identifier, Identifier]]: ... + def __getitem__( + self, item: slice | Path | Node + ) -> Iterator[ + Tuple[Identifier, Identifier, Identifier] | Tuple[Identifier, identifier] | Node + ]: ... + def __contains__(self, triple: Any) -> bool: ... def __add__(self, other: Any) -> Graph: ... def set(self, triple: Any) -> None: ... def subjects( @@ -47,7 +66,7 @@ class Graph(Node): ) -> Iterable[Node]: ... def objects( self, subject: Optional[Any] = ..., predicate: Optional[Any] = ... - ) -> Iterable[Node]: ... + ) -> Iterable[Identifier]: ... def subject_predicates(self, object: Optional[Any] = ...) -> None: ... def subject_objects(self, predicate: Optional[Any] = ...) -> None: ... def predicate_objects(self, subject: Optional[Any] = ...) -> None: ... @@ -87,13 +106,61 @@ class Graph(Node): ) -> Any: ... def namespaces(self) -> Iterator[Tuple[Any, Any]]: ... def absolutize(self, uri: Any, defrag: int = ...) -> Any: ... + + # no destination and non-None positional encoding + @overload + def serialize( + self, + destination: None, + format: str, + base: Optional[str], + encoding: str, + **args: Any, + ) -> bytes: ... + + # no destination and non-None keyword encoding + @overload def serialize( self, - destination: Optional[Any] = ..., + destination: None = ..., format: str = ..., - base: Optional[Any] = ..., - encoding: Optional[Any] = ..., - **args: Any + base: Optional[str] = ..., + *, + encoding: str, + **args: Any, + ) -> bytes: ... + + # no destination and None encoding + @overload + def serialize( + self, + destination: None = ..., + format: str = ..., + base: Optional[str] = ..., + encoding: None = ..., + **args: Any, + ) -> str: ... + + # non-None destination + @overload + def serialize( + self, + destination: Union[str, pathlib.PurePath, IO[bytes]], + format: str = ..., + base: Optional[str] = ..., + encoding: Optional[str] = ..., + **args: Any, + ) -> "Graph": ... + + # fallback + @overload + def serialize( + self, + destination: Optional[Union[str, pathlib.PurePath, IO[bytes]]] = ..., + format: str = ..., + base: Optional[str] = ..., + encoding: Optional[str] = ..., + **args: Any, ) -> Union[bytes, str, "Graph"]: ... def parse( self, @@ -103,7 +170,7 @@ class Graph(Node): location: Optional[Any] = ..., file: Optional[Any] = ..., data: Optional[Any] = ..., - **args: Any + **args: Any, ) -> "Graph": ... def load( self, source: Any, publicID: Optional[Any] = ..., format: str = ... @@ -116,7 +183,7 @@ class Graph(Node): initNs: Optional[Any] = ..., initBindings: Optional[Any] = ..., use_store_provided: bool = ..., - **kwargs: Any + **kwargs: Any, ) -> query.Result: ... def update( self, @@ -125,7 +192,7 @@ class Graph(Node): initNs: Optional[Any] = ..., initBindings: Optional[Any] = ..., use_store_provided: bool = ..., - **kwargs: Any + **kwargs: Any, ) -> Any: ... def n3(self) -> str: ... def isomorphic(self, other: Any) -> bool: ... @@ -177,7 +244,7 @@ class ConjunctiveGraph(Graph): location: Optional[Any] = ..., file: Optional[Any] = ..., data: Optional[Any] = ..., - **args: Any + **args: Any, ) -> Graph: ... class Seq: diff --git a/mypy-stubs/rdflib/namespace/__init__.pyi b/mypy-stubs/rdflib/namespace/__init__.pyi index 2ecbc29db..e5342fd9b 100644 --- a/mypy-stubs/rdflib/namespace/__init__.pyi +++ b/mypy-stubs/rdflib/namespace/__init__.pyi @@ -36,11 +36,15 @@ class Namespace(str): def title(self) -> URIRef: ... def term(self, name: Any) -> URIRef: ... def __getitem__(self, key: Any) -> URIRef: ... + def __getattr__(self, name: str) -> URIRef: ... class URIPattern(str): def format(self, *args: Any, **kwargs: Any) -> str: ... -class DefinedNamespaceMeta(type): ... +class DefinedNamespaceMeta(type): + def __getitem__(cls, name: Any, default: Any | None = ...) -> URIRef: ... + def __getattr__(cls, name: Any) -> URIRef: ... + def __contains__(cls, item: Any) -> bool: ... class DefinedNamespace(metaclass=DefinedNamespaceMeta): def __init__(self) -> None: ... diff --git a/mypy-stubs/rdflib/query.pyi b/mypy-stubs/rdflib/query.pyi index 2b73dafe9..db0d89290 100644 --- a/mypy-stubs/rdflib/query.pyi +++ b/mypy-stubs/rdflib/query.pyi @@ -1,5 +1,22 @@ from io import BufferedIOBase -from typing import Any, Dict, Optional, Union +from typing import Any, Dict, Iterator, List, Optional, Tuple, overload + +from rdflib import URIRef, Variable +from typing_extensions import SupportsIndex + +class ResultRow: # Tuple[Variable, URIRef]): + def __new__( + cls, values: Dict[Variable, URIRef], labels: List[Variable] + ) -> ResultRow: ... + def __getattr__(self, name: str) -> Any: ... + @overload + def __getitem__(self, name: str) -> URIRef: ... + @overload + def __getitem__(self, __x: SupportsIndex) -> Variable | URIRef: ... + @overload + def __getitem__(self, __x: slice) -> Tuple[Variable | URIRef, ...]: ... + def get(self, name: str, default: Any | None = ...) -> URIRef: ... + def asdict(self) -> Dict[Variable, URIRef]: ... class Result: type: Any @@ -8,16 +25,17 @@ class Result: graph: Any def __init__(self, type_: str) -> None: ... bindings: Any + def __iter__(self) -> Iterator[bool | ResultRow]: ... @staticmethod def parse( - source: Any | None = ..., - format: Any | None = ..., - content_type: Any | None = ..., + source: str | None = ..., + format: str | None = ..., + content_type: str | None = ..., **kwargs: Any - ) -> Any: ... + ) -> Result: ... def serialize( self, - destination: Optional[Union[str, BufferedIOBase]] = ..., + destination: str | BufferedIOBase | None = ..., encoding: str = ..., format: str = ..., **args: Any diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 03b54d81e..7dd7790df 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -4,7 +4,7 @@ import sys import urllib from pathlib import Path -from typing import Any, Generator +from typing import IO, Any, Generator, cast import arcp import bagit @@ -286,15 +286,15 @@ def check_bagit(base_path: Path) -> None: assert not list(missing_tagfiles), "Some files only in tagmanifest" bag.validate() # TODO: Check other bag-info attributes - assert arcp.is_arcp_uri(bag.info.get("External-Identifier")) + assert arcp.is_arcp_uri(cast(str, bag.info.get("External-Identifier"))) def find_arcp(base_path: Path) -> str: # First try to find External-Identifier bag = bagit.Bag(str(base_path)) - ext_id = bag.info.get("External-Identifier") + ext_id = cast(str, bag.info.get("External-Identifier")) if arcp.is_arcp_uri(ext_id): - return str(ext_id) + return ext_id raise Exception("Can't find External-Identifier") @@ -326,7 +326,7 @@ def check_ro(base_path: Path, nested: bool = False) -> None: g.parse(data=jsonld, format="json-ld", publicID=base) if os.environ.get("DEBUG"): print("Parsed manifest:\n\n") - g.serialize(sys.stdout, format="ttl") + g.serialize(cast(IO[bytes], sys.stdout), format="ttl") _ro = None for _ro in g.subjects(ORE.isDescribedBy, URIRef(base)): @@ -338,19 +338,19 @@ def check_ro(base_path: Path, nested: bool = False) -> None: profile = dc break assert profile is not None, "Can't find profile with dct:conformsTo" - assert profile == URIRef(provenance_constants.CWLPROV_VERSION), ( - "Unexpected cwlprov version " + profile - ) + assert profile == URIRef( + provenance_constants.CWLPROV_VERSION + ), f"Unexpected cwlprov version {profile}" paths = [] externals = [] for aggregate in g.objects(_ro, ORE.aggregates): - if not arcp.is_arcp_uri(aggregate): + if not arcp.is_arcp_uri(cast(str, aggregate)): externals.append(aggregate) # Won't check external URIs existence here # TODO: Check they are not relative! continue - lfile = _arcp2file(base_path, aggregate) + lfile = _arcp2file(base_path, cast(str, aggregate)) paths.append(os.path.relpath(lfile, base_path)) assert os.path.isfile(lfile), f"Can't find aggregated {lfile}" @@ -451,7 +451,7 @@ def check_prov( g.parse(file=f, format="nt", publicID=arcp_root) if os.environ.get("DEBUG"): print("Parsed %s:\n\n" % prov_file) - g.serialize(sys.stdout, format="ttl") + g.serialize(cast(IO[bytes], sys.stdout), format="ttl") runs = set(g.subjects(RDF.type, WFPROV.WorkflowRun)) # main workflow run URI (as urn:uuid:) should correspond to arcp uuid part From ba9d7e42e87bcf51fd35c2b251f4d8268c575126 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Mon, 1 Aug 2022 17:51:40 +0200 Subject: [PATCH 5/8] needed until there is a new release of galaxy-tool-util with updated types --- cwltool/software_requirements.py | 2 +- mypy.ini | 6 ++++++ test-requirements.txt | 1 + tests/test_dependencies.py | 2 +- 4 files changed, 9 insertions(+), 2 deletions(-) diff --git a/cwltool/software_requirements.py b/cwltool/software_requirements.py index d80eb66ba..37eafd0b6 100644 --- a/cwltool/software_requirements.py +++ b/cwltool/software_requirements.py @@ -151,7 +151,7 @@ def get_container_from_software_requirements( [DOCKER_CONTAINER_TYPE], tool_info ) if container_description: - return container_description.identifier + return cast(Optional[str], container_description.identifier) return None diff --git a/mypy.ini b/mypy.ini index 0694696ec..ae17b1e0b 100644 --- a/mypy.ini +++ b/mypy.ini @@ -14,3 +14,9 @@ ignore_errors = True [mypy-past.builtins.*] ignore_missing_imports = True + +[mypy-galaxy.tool_util.*] +ignore_missing_imports = True + +[mypy-cwltool.software_requirements] +warn_unused_ignores= False diff --git a/test-requirements.txt b/test-requirements.txt index 434506ab3..c955c702d 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -7,3 +7,4 @@ pytest-cov arcp >= 0.2.0 rdflib-jsonld>=0.4.0, <= 0.6.1;python_version<='3.6' -rrequirements.txt +galaxy-tool-util >= 21.1.0 diff --git a/tests/test_dependencies.py b/tests/test_dependencies.py index 534dd4d5c..f26e45d5e 100644 --- a/tests/test_dependencies.py +++ b/tests/test_dependencies.py @@ -11,7 +11,7 @@ deps = None # type: Optional[ModuleType] try: - from galaxy.tool_util import deps + from galaxy.tool_util import deps # type: ignore[no-redef] except ImportError: pass From 649f03be4a09bd68f14b6814063e4bd40a8b92bd Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Mon, 1 Aug 2022 18:02:54 +0200 Subject: [PATCH 6/8] add missing rdflib.paths type hints --- mypy-stubs/rdflib/paths.pyi | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 mypy-stubs/rdflib/paths.pyi diff --git a/mypy-stubs/rdflib/paths.pyi b/mypy-stubs/rdflib/paths.pyi new file mode 100644 index 000000000..de350b131 --- /dev/null +++ b/mypy-stubs/rdflib/paths.pyi @@ -0,0 +1,29 @@ +from collections.abc import Generator +from typing import Any, Callable, Union + +from rdflib.term import Node as Node +from rdflib.term import URIRef as URIRef + +ZeroOrMore: str +OneOrMore: str +ZeroOrOne: str + +class Path: + __or__: Callable[[Path, Union["URIRef", "Path"]], "AlternativePath"] + __invert__: Callable[[Path], "InvPath"] + __neg__: Callable[[Path], "NegatedPath"] + __truediv__: Callable[[Path, Union["URIRef", "Path"]], "SequencePath"] + __mul__: Callable[[Path, str], "MulPath"] + def __hash__(self) -> int: ... + def __eq__(self, other: Any) -> bool: ... + def __lt__(self, other: Any) -> bool: ... + def __le__(self, other: Any) -> bool: ... + def __ne__(self, other: Any) -> bool: ... + def __gt__(self, other: Any) -> bool: ... + def __ge__(self, other: Any) -> bool: ... + +class InvPath(Path): ... +class SequencePath(Path): ... +class AlternativePath(Path): ... +class MulPath(Path): ... +class NegatedPath(Path): ... From b727704664c69e2224bfb5001e235cbcf97afca7 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Mon, 1 Aug 2022 18:09:47 +0200 Subject: [PATCH 7/8] fix for py3.6 --- mypy-stubs/prov/model.pyi | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/mypy-stubs/prov/model.pyi b/mypy-stubs/prov/model.pyi index 0ce442677..57ac5cb1e 100644 --- a/mypy-stubs/prov/model.pyi +++ b/mypy-stubs/prov/model.pyi @@ -1,4 +1,3 @@ -import types from datetime import datetime from typing import IO, Any, Dict, Iterable, List, Set, Tuple @@ -225,8 +224,8 @@ class ProvBundle: def get_records( self, class_or_type_or_tuple: type - | types.UnionType - | Tuple[type | types.UnionType | Tuple[Any, ...], ...] + | type[int | str] + | Tuple[type | type[int | str] | Tuple[Any, ...], ...] | None = ..., ) -> List[ProvRecord]: ... def get_record( From 59db016399df87bce9ec0353322e85dba9fc4397 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Mon, 1 Aug 2022 18:44:59 +0200 Subject: [PATCH 8/8] fixup --- MANIFEST.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/MANIFEST.in b/MANIFEST.in index 8e2a853da..08a85b4ec 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -3,7 +3,7 @@ include MANIFEST.in include LICENSE.txt include *requirements.txt mypy.ini tox.ini include gittaggers.py Makefile cwltool.py -recursive-include mypy-stubs *.pyi +recursive-include mypy-stubs *.pyi *.py include tests/* include tests/tmp1/tmp2/tmp3/.gitkeep include tests/tmp4/alpha/*