From 03f19549c56f9ebf9f3500fc7c225e49ae71faa5 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Wed, 13 Oct 2021 02:39:50 +0530 Subject: [PATCH 1/5] Fix dependencies in requirements-dev.txt --- requirements-dev.txt | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index 212a1bd44f..04522714c4 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -2,14 +2,13 @@ # See that file for comments about the need/usage of each dependency. aesara>=2.1.0 -arviz>=0.11.2 +arviz>=0.11.4 cachetools cloudpickle fastprogress>=0.2.0 h5py>=2.7 ipython>=7.16 myst-nb -nbsphinx>=0.4 numpy>=1.15.0 numpydoc>=0.9 pandas @@ -20,6 +19,8 @@ pytest>=3.0 recommonmark>=0.4 scipy>1.4.1 sphinx-autobuild>=0.7 +sphinx-design +sphinx-notfound-page sphinx-panels sphinx>=1.5 typing-extensions>=3.7.4 From bc0138ef50ce87dcb6b314baf8e42cd017385f83 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Wed, 13 Oct 2021 02:59:34 +0530 Subject: [PATCH 2/5] Fix dependencies in conda files --- conda-envs/environment-test-py37.yml | 5 ++++- conda-envs/environment-test-py38.yml | 5 ++++- conda-envs/environment-test-py39.yml | 5 ++++- requirements-dev.txt | 3 ++- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/conda-envs/environment-test-py37.yml b/conda-envs/environment-test-py37.yml index 2331d2a253..e1335823e9 100644 --- a/conda-envs/environment-test-py37.yml +++ b/conda-envs/environment-test-py37.yml @@ -4,7 +4,7 @@ channels: - defaults dependencies: - aesara>=2.1.0 -- arviz>=0.11.2 +- arviz>=0.11.4 - cachetools>=4.2.1 - cloudpickle - fastprogress>=0.2.0 @@ -25,7 +25,10 @@ dependencies: - recommonmark>=0.4 - scipy>1.4.1 - sphinx-autobuild>=0.7 +- sphinx-notfound-page - sphinx-panels - sphinx>=1.5 - typing-extensions - watermark +- pip: + - sphinx-design diff --git a/conda-envs/environment-test-py38.yml b/conda-envs/environment-test-py38.yml index feacd5b59d..f7245b9761 100644 --- a/conda-envs/environment-test-py38.yml +++ b/conda-envs/environment-test-py38.yml @@ -4,7 +4,7 @@ channels: - defaults dependencies: - aesara>=2.1.0 -- arviz>=0.11.2 +- arviz>=0.11.4 - cachetools>=4.2.1 - cloudpickle - fastprogress>=0.2.0 @@ -26,7 +26,10 @@ dependencies: - recommonmark>=0.4 - scipy>1.4.1 - sphinx-autobuild>=0.7 +- sphinx-notfound-page - sphinx-panels - sphinx>=1.5 - typing-extensions>=3.7.4 - watermark +- pip: + - sphinx-design diff --git a/conda-envs/environment-test-py39.yml b/conda-envs/environment-test-py39.yml index 3ff4e75a77..41452495e8 100644 --- a/conda-envs/environment-test-py39.yml +++ b/conda-envs/environment-test-py39.yml @@ -4,7 +4,7 @@ channels: - defaults dependencies: - aesara>=2.1.0 -- arviz>=0.11.2 +- arviz>=0.11.4 - cachetools - cloudpickle - fastprogress>=0.2.0 @@ -26,7 +26,10 @@ dependencies: - recommonmark>=0.4 - scipy>1.4.1 - sphinx-autobuild>=0.7 +- sphinx-notfound-page - sphinx-panels - sphinx>=1.5 - typing-extensions>=3.7.4 - watermark +- pip: + - sphinx-design diff --git a/requirements-dev.txt b/requirements-dev.txt index 04522714c4..2a651941e2 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -6,9 +6,10 @@ arviz>=0.11.4 cachetools cloudpickle fastprogress>=0.2.0 -h5py>=2.7 +h5py ipython>=7.16 myst-nb +nbsphinx>=0.4 numpy>=1.15.0 numpydoc>=0.9 pandas From 941cb3b585bafa9d7a70078f5fe8653d28320da6 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Wed, 13 Oct 2021 03:04:34 +0530 Subject: [PATCH 3/5] Fix pre-commit one more time --- requirements-dev.txt | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index 2a651941e2..f8da663dee 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -3,13 +3,12 @@ aesara>=2.1.0 arviz>=0.11.4 -cachetools +cachetools>=4.2.1 cloudpickle fastprogress>=0.2.0 h5py -ipython>=7.16 +ipython myst-nb -nbsphinx>=0.4 numpy>=1.15.0 numpydoc>=0.9 pandas From b820b7d28c80dee30430691c1245234a24ab75b5 Mon Sep 17 00:00:00 2001 From: "Oriol (ZBook)" Date: Thu, 14 Oct 2021 02:25:02 +0300 Subject: [PATCH 4/5] update and reduce environment files --- .pre-commit-config.yaml | 2 +- conda-envs/environment-dev-py37.yml | 5 ++--- conda-envs/environment-dev-py38.yml | 5 ++--- conda-envs/environment-dev-py39.yml | 3 +-- conda-envs/environment-test-py37.yml | 12 +----------- conda-envs/environment-test-py38.yml | 13 +------------ conda-envs/environment-test-py39.yml | 13 +------------ conda-envs/windows-environment-dev-py38.yml | 1 - conda-envs/windows-environment-test-py38.yml | 11 +---------- requirements-dev.txt | 4 +--- 10 files changed, 11 insertions(+), 58 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 286aecd9f5..0f2cebd113 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -52,7 +52,7 @@ repos: - id: pip-from-conda additional_dependencies: [pyyaml] entry: python scripts/generate_pip_deps_from_conda.py - files: ^conda-envs/ + files: ^conda-envs/environment-dev-py.+.yml$ language: python name: Generate pip dependency from conda - id: no-relative-imports diff --git a/conda-envs/environment-dev-py37.yml b/conda-envs/environment-dev-py37.yml index 7d58f7c851..a3e14c419a 100644 --- a/conda-envs/environment-dev-py37.yml +++ b/conda-envs/environment-dev-py37.yml @@ -1,3 +1,4 @@ +# "dev" conda envs are to be used by devs in setting their local environments name: pymc-dev-py37 channels: - conda-forge @@ -8,7 +9,7 @@ dependencies: - cachetools>=4.2.1 - cloudpickle - fastprogress>=0.2.0 -- h5py +- h5py>=2.7 - ipython - myst-nb - numpy>=1.15 @@ -20,13 +21,11 @@ dependencies: - pytest>=3.0 - python-graphviz - python=3.7 -- recommonmark>=0.4 - scipy>1.4.1 - sphinx-autobuild>=0.7 - sphinx-notfound-page - sphinx-panels - sphinx>=1.5 - typing-extensions -- watermark - pip: - sphinx-design diff --git a/conda-envs/environment-dev-py38.yml b/conda-envs/environment-dev-py38.yml index 7a6cd883a4..b0bb7b4922 100644 --- a/conda-envs/environment-dev-py38.yml +++ b/conda-envs/environment-dev-py38.yml @@ -1,3 +1,4 @@ +# "dev" conda envs are to be used by devs in setting their local environments name: pymc-dev-py38 channels: - conda-forge @@ -8,7 +9,7 @@ dependencies: - cachetools>=4.2.1 - cloudpickle - fastprogress>=0.2.0 -- h5py +- h5py>=2.7 - ipython - myst-nb - numpy>=1.15.0 @@ -20,13 +21,11 @@ dependencies: - pytest>=3.0 - python-graphviz - python=3.8 -- recommonmark>=0.4 - scipy>1.4.1 - sphinx-autobuild>=0.7 - sphinx-notfound-page - sphinx-panels - sphinx>=1.5 - typing-extensions>=3.7.4 -- watermark - pip: - sphinx-design diff --git a/conda-envs/environment-dev-py39.yml b/conda-envs/environment-dev-py39.yml index 151f28b98b..a8e929b112 100644 --- a/conda-envs/environment-dev-py39.yml +++ b/conda-envs/environment-dev-py39.yml @@ -1,3 +1,4 @@ +# "dev" conda envs are to be used by devs in setting their local environments name: pymc-dev-py39 channels: - conda-forge @@ -20,13 +21,11 @@ dependencies: - pytest>=3.0 - python-graphviz - python=3.9 -- recommonmark>=0.4 - scipy>1.4.1 - sphinx-autobuild>=0.7 - sphinx-notfound-page - sphinx-panels - sphinx>=1.5 - typing-extensions>=3.7.4 -- watermark - pip: - sphinx-design diff --git a/conda-envs/environment-test-py37.yml b/conda-envs/environment-test-py37.yml index e1335823e9..6e7b26f6a8 100644 --- a/conda-envs/environment-test-py37.yml +++ b/conda-envs/environment-test-py37.yml @@ -1,3 +1,4 @@ +# "test" conda envs are used to set up our CI environment in GitHub actions name: pymc-test-py37 channels: - conda-forge @@ -12,23 +13,12 @@ dependencies: - ipython - libblas=*=*mkl - mkl-service -- myst-nb - numpy>=1.15.0 -- numpydoc>=0.9 - pandas=0.24 - pre-commit>=2.8.0 -- pydata-sphinx-theme - pytest-cov>=2.5 - pytest>=3.0 - python-graphviz - python=3.7 -- recommonmark>=0.4 - scipy>1.4.1 -- sphinx-autobuild>=0.7 -- sphinx-notfound-page -- sphinx-panels -- sphinx>=1.5 - typing-extensions -- watermark -- pip: - - sphinx-design diff --git a/conda-envs/environment-test-py38.yml b/conda-envs/environment-test-py38.yml index f7245b9761..1db9766278 100644 --- a/conda-envs/environment-test-py38.yml +++ b/conda-envs/environment-test-py38.yml @@ -1,3 +1,4 @@ +# "test" conda envs are used to set up our CI environment in GitHub actions name: pymc-test-py38 channels: - conda-forge @@ -12,24 +13,12 @@ dependencies: - ipython - libblas=*=*mkl - mkl-service -- myst-nb -- nbsphinx>=0.4 - numpy>=1.15.0 -- numpydoc>=0.9 - pandas - pre-commit>=2.8.0 -- pydata-sphinx-theme - pytest-cov>=2.5 - pytest>=3.0 - python-graphviz - python=3.8 -- recommonmark>=0.4 - scipy>1.4.1 -- sphinx-autobuild>=0.7 -- sphinx-notfound-page -- sphinx-panels -- sphinx>=1.5 - typing-extensions>=3.7.4 -- watermark -- pip: - - sphinx-design diff --git a/conda-envs/environment-test-py39.yml b/conda-envs/environment-test-py39.yml index 41452495e8..8aedc89930 100644 --- a/conda-envs/environment-test-py39.yml +++ b/conda-envs/environment-test-py39.yml @@ -1,3 +1,4 @@ +# "test" conda envs are used to set up our CI environment in GitHub actions name: pymc-test-py39 channels: - conda-forge @@ -12,24 +13,12 @@ dependencies: - ipython>=7.16 - libblas=*=*mkl - mkl-service -- myst-nb -- nbsphinx>=0.4 - numpy>=1.15.0 -- numpydoc>=0.9 - pandas - pre-commit>=2.8.0 -- pydata-sphinx-theme - pytest-cov>=2.5 - pytest>=3.0 - python-graphviz - python=3.9 -- recommonmark>=0.4 - scipy>1.4.1 -- sphinx-autobuild>=0.7 -- sphinx-notfound-page -- sphinx-panels -- sphinx>=1.5 - typing-extensions>=3.7.4 -- watermark -- pip: - - sphinx-design diff --git a/conda-envs/windows-environment-dev-py38.yml b/conda-envs/windows-environment-dev-py38.yml index 4d1b7166ad..77616756d9 100644 --- a/conda-envs/windows-environment-dev-py38.yml +++ b/conda-envs/windows-environment-dev-py38.yml @@ -25,7 +25,6 @@ dependencies: - pydata-sphinx-theme - pytest-cov>=2.5 - pytest>=3.0 -- recommonmark>=0.4 - sphinx-autobuild>=0.7 - sphinx-notfound-page - sphinx-panels diff --git a/conda-envs/windows-environment-test-py38.yml b/conda-envs/windows-environment-test-py38.yml index 944ac67d15..646bb2d01b 100644 --- a/conda-envs/windows-environment-test-py38.yml +++ b/conda-envs/windows-environment-test-py38.yml @@ -20,17 +20,8 @@ dependencies: - python-graphviz - scipy>1.4.1 - typing-extensions>=3.7.4 -# Extra stuff for dev, testing and docs build +# Extra stuff for testing - ipython>=7.16 -- myst-nb -- nbsphinx>=0.4 -- numpydoc>=0.9 - pre-commit>=2.8.0 -- pydata-sphinx-theme - pytest-cov>=2.5 - pytest>=3.0 -- recommonmark>=0.4 -- sphinx-autobuild>=0.7 -- sphinx-panels -- sphinx>=1.5 -- watermark diff --git a/requirements-dev.txt b/requirements-dev.txt index f8da663dee..d7691ddb7c 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -6,7 +6,7 @@ arviz>=0.11.4 cachetools>=4.2.1 cloudpickle fastprogress>=0.2.0 -h5py +h5py>=2.7 ipython myst-nb numpy>=1.15.0 @@ -16,7 +16,6 @@ pre-commit>=2.8.0 pydata-sphinx-theme pytest-cov>=2.5 pytest>=3.0 -recommonmark>=0.4 scipy>1.4.1 sphinx-autobuild>=0.7 sphinx-design @@ -24,4 +23,3 @@ sphinx-notfound-page sphinx-panels sphinx>=1.5 typing-extensions>=3.7.4 -watermark From 0698b06786ca11cf9bbafb67745542c589dfe29d Mon Sep 17 00:00:00 2001 From: "Oriol (ZBook)" Date: Thu, 14 Oct 2021 02:45:04 +0300 Subject: [PATCH 5/5] unpin pandas --- conda-envs/environment-test-py37.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-envs/environment-test-py37.yml b/conda-envs/environment-test-py37.yml index 6e7b26f6a8..cb979c85ad 100644 --- a/conda-envs/environment-test-py37.yml +++ b/conda-envs/environment-test-py37.yml @@ -14,7 +14,7 @@ dependencies: - libblas=*=*mkl - mkl-service - numpy>=1.15.0 -- pandas=0.24 +- pandas>=0.24 - pre-commit>=2.8.0 - pytest-cov>=2.5 - pytest>=3.0