Merge branch 'master' into patch-1

Author: edavidaja

.github/workflows/main.yml

@@ -5,6 +5,8 @@ on:
     tags: ['*']
   pull_request:
     branches: [master]
+  workflow_dispatch:
+
 permissions:
   id-token: write
   contents: write
@@ -14,7 +16,7 @@ jobs:
       matrix:
         # TODO: work on windows-latest compatibility?
         os: [ubuntu-latest]
-        python-version: ['3.5', '3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         include:
         - os: macos-latest
           python-version: '3.9'
@@ -28,10 +30,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - run: pip install -r requirements.txt
     - run: pip freeze
-    - if: matrix.python-version > '3.5'
-      run: make fmt
-    - if: matrix.python-version >= '3.6'
-      run: make lint
+    - run: make fmt
+    - run: make lint
     - run: python setup.py --version
     - run: make test-${{ matrix.python-version }}
   prerelease-test:

.github/workflows/snyk.yml

@@ -0,0 +1,30 @@
+name: snyk
+on:
+  schedule:
+    - cron: "0 10 * * 1" # Monday @ 10am UTC
+  workflow_dispatch:
+
+env:
+  SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
+  SNYK_ORG: rstudio-connect
+  SNYK_PROJECT: rsconnect-python
+
+jobs:
+  python-dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Run Snyk on dependencies
+        uses: snyk/actions/python@master
+        with:
+          command: monitor
+          args: --file=setup.py --print-deps --project-name=${{ env.SNYK_PROJECT }} --org=${{ env.SNYK_ORG }}
+  python-code:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Run Snyk static analysis
+        uses: snyk/actions/python@master
+        with:
+          command: code test
+          args: --project-name=${{ env.SNYK_PROJECT }} --org=${{ env.SNYK_ORG }} rsconnect/

CONTRIBUTING.md

@@ -5,7 +5,7 @@ tooling](https://packaging.python.org/guides/tool-recommendations/).
 
 To get started, you'll want to:
 - clone the repo into a project directory
-- setup a virtual 3.5+ python environment in the project directory
+- setup a virtual 3.7+ python environment in the project directory
 - activate that virtual environment
 - install the dependencies
 - validate your build environment with some sample commands

Makefile

@@ -35,10 +35,10 @@ SOURCE_DATE_EPOCH := $(shell date +%s)
 export SOURCE_DATE_EPOCH
 
 .PHONY: all-tests
-all-tests: all-images test-3.5 test-3.6 test-3.7 test-3.8 test-3.9 test-3.10
+all-tests: all-images test-3.7 test-3.8 test-3.9 test-3.10
 
 .PHONY: all-images
-all-images: image-3.5 image-3.6 image-3.7 image-3.8 image-3.9 image-3.10
+all-images: image-3.7 image-3.8 image-3.9 image-3.10
 
 image-%:
 	docker build -t rsconnect-python:$* --build-arg BASE_IMAGE=python:$*-slim .
@@ -62,9 +62,6 @@ mock-test-%: clean-stores
 fmt-%:
 	$(RUNNER) 'black .'
 
-.PHONY: fmt-3.5
-fmt-3.5: .fmt-unsupported
-
 .PHONY: .fmt-unsupported
 .fmt-unsupported:
 	@echo ERROR: This python version cannot run the fmting tools
@@ -83,9 +80,6 @@ lint-%:
 	$(RUNNER) 'flake8 tests/'
 	$(RUNNER) 'mypy -p rsconnect'
 
-.PHONY: lint-3.5
-lint-3.5: .lint-unsupported
-
 .PHONY: .lint-unsupported
 .lint-unsupported:
 	@echo ERROR: This python version cannot run the linting tools

README.md

@@ -2,9 +2,7 @@
 
 !!! warning
 
-    As of version 1.7.0, rsconnect-python requires Python version 3.5 or higher. Please see the
-    [official announcement](https://www.rstudio.com/blog/rstudio-connect-2021-08-python-updates/)
-    for details about this decision.
+    As of version 1.14.0, rsconnect-python requires Python version 3.7 or higher.
 
 This package provides a CLI (command-line interface) for interacting
 with and deploying to Posit Connect. This is also used by the

requirements.txt

@@ -1,4 +1,4 @@
-black==22.3.0; python_version >= '3.6'
+black==22.3.0
 click>=7.0.0
 coverage
 flake8
@@ -8,13 +8,12 @@ importlib-metadata
 ipykernel
 ipython
 jupyter_client
-mypy; python_version >= '3.6'
+mypy
 nbconvert
-pyjwt>=2.4.0; python_version >= '3.6'
-pyjwt; python_version < '3.6'
+pyjwt>=2.4.0
 pytest
 pytest-cov
-pytest-mypy; python_version >= '3.5'
+pytest-mypy
 semver>=2.0.0,<3.0.0
 setuptools_scm
 six>=1.14.0

rsconnect/api.py

@@ -852,7 +852,7 @@ def validate_app_mode(self, *args, **kwargs):
                     existing_app_mode = AppModes.get_by_cloud_name(app.json_data["mode"])
                 else:
                     raise RSConnectException("Unable to infer Connect client.")
-            if existing_app_mode and app_mode != existing_app_mode:
+            if existing_app_mode and existing_app_mode not in (None, AppModes.UNKNOWN, app_mode):
                 msg = (
                     "Deploying with mode '%s',\n"
                     + "but the existing deployment has mode '%s'.\n"

rsconnect/bundle.py

@@ -14,6 +14,7 @@
 from pprint import pformat
 from collections import defaultdict
 from mimetypes import guess_type
+from pathlib import Path
 import click
 
 
@@ -33,7 +34,7 @@
 
 # From https://github.com/rstudio/rsconnect/blob/485e05a26041ab8183a220da7a506c9d3a41f1ff/R/bundle.R#L85-L88
 # noinspection SpellCheckingInspection
-directories_to_ignore = [
+directories_ignore_list = [
     ".Rproj.user/",
     ".env/",
     ".git/",
@@ -47,6 +48,7 @@
     "rsconnect/",
     "venv/",
 ]
+directories_to_ignore = {Path(d) for d in directories_ignore_list}
 
 
 # noinspection SpellCheckingInspection
@@ -423,17 +425,20 @@ def make_notebook_html_bundle(
     return bundle_file
 
 
-def keep_manifest_specified_file(relative_path):
+def keep_manifest_specified_file(relative_path, ignore_path_set=directories_to_ignore):
     """
     A helper to see if the relative path given, which is assumed to have come
     from a manifest.json file, should be kept or ignored.
 
     :param relative_path: the relative path name to check.
     :return: True, if the path should kept or False, if it should be ignored.
     """
-    for ignore_me in directories_to_ignore:
-        if relative_path.startswith(ignore_me):
+    p = Path(relative_path)
+    for parent in p.parents:
+        if parent in ignore_path_set:
             return False
+    if p in ignore_path_set:
+        return False
     return True
 
 
@@ -550,56 +555,6 @@ def list_environment_dirs(directory):
     return envs
 
 
-def _create_api_file_list(
-    directory,  # type: str
-    requirements_file_name,  # type: str
-    extra_files=None,  # type: typing.Optional[typing.List[str]]
-    excludes=None,  # type: typing.Optional[typing.List[str]]
-):
-    # type: (...) -> typing.List[str]
-    """
-    Builds a full list of files under the given directory that should be included
-    in a manifest or bundle.  Extra files and excludes are relative to the given
-    directory and work as you'd expect.
-
-    :param directory: the directory to walk for files.
-    :param requirements_file_name: the name of the requirements file for the current
-    Python environment.
-    :param extra_files: a sequence of any extra files to include in the bundle.
-    :param excludes: a sequence of glob patterns that will exclude matched files.
-    :return: the list of relevant files, relative to the given directory.
-    """
-    # Don't let these top-level files be added via the extra files list.
-    extra_files = extra_files or []
-    skip = [requirements_file_name, "manifest.json"]
-    extra_files = sorted(list(set(extra_files) - set(skip)))
-
-    # Don't include these top-level files.
-    excludes = list(excludes) if excludes else []
-    excludes.append("manifest.json")
-    excludes.append(requirements_file_name)
-    excludes.extend(list_environment_dirs(directory))
-    glob_set = create_glob_set(directory, excludes)
-
-    file_list = []
-
-    for subdir, dirs, files in os.walk(directory):
-        for file in files:
-            abs_path = os.path.join(subdir, file)
-            rel_path = os.path.relpath(abs_path, directory)
-
-            if keep_manifest_specified_file(rel_path) and (rel_path in extra_files or not glob_set.matches(abs_path)):
-                file_list.append(rel_path)
-                # Don't add extra files more than once.
-                if rel_path in extra_files:
-                    extra_files.remove(rel_path)
-
-    for rel_path in extra_files:
-        file_list.append(rel_path)
-
-    return sorted(file_list)
-
-
 def make_api_manifest(
     directory: str,
     entry_point: str,
@@ -624,7 +579,17 @@ def make_api_manifest(
     if is_environment_dir(directory):
         excludes = list(excludes or []) + ["bin/", "lib/"]
 
-    relevant_files = _create_api_file_list(directory, environment.filename, extra_files, excludes)
+    extra_files = extra_files or []
+    skip = [environment.filename, "manifest.json"]
+    extra_files = sorted(list(set(extra_files) - set(skip)))
+
+    # Don't include these top-level files.
+    excludes = list(excludes) if excludes else []
+    excludes.append("manifest.json")
+    excludes.append(environment.filename)
+    excludes.extend(list_environment_dirs(directory))
+
+    relevant_files = create_file_list(directory, extra_files, excludes)
     manifest = make_source_manifest(app_mode, environment, entry_point, None, image)
 
     manifest_add_buffer(manifest, environment.filename, environment.contents)
@@ -655,6 +620,8 @@ def make_html_bundle_content(
     """
     extra_files = list(extra_files) if extra_files else []
     entrypoint = entrypoint or infer_entrypoint(path=path, mimetype="text/html")
+    if not entrypoint:
+        raise RSConnectException("Unable to find a valid html entry point.")
 
     if path.startswith(os.curdir):
         path = relpath(path)
@@ -667,37 +634,15 @@ def make_html_bundle_content(
 
     extra_files = extra_files or []
     skip = ["manifest.json"]
-    extra_files = sorted(list(set(extra_files) - set(skip)))
+    extra_files = sorted(set(extra_files) - set(skip))
 
     # Don't include these top-level files.
     excludes = list(excludes) if excludes else []
     excludes.append("manifest.json")
     if not isfile(path):
         excludes.extend(list_environment_dirs(path))
-    glob_set = create_glob_set(path, excludes)
-
-    file_list = []
 
-    for rel_path in extra_files:
-        file_list.append(rel_path)
-
-    if isfile(path):
-        file_list.append(path)
-    else:
-        for subdir, dirs, files in os.walk(path):
-            for file in files:
-                abs_path = os.path.join(subdir, file)
-                rel_path = os.path.relpath(abs_path, path)
-
-                if keep_manifest_specified_file(rel_path) and (
-                    rel_path in extra_files or not glob_set.matches(abs_path)
-                ):
-                    file_list.append(rel_path)
-                    # Don't add extra files more than once.
-                    if rel_path in extra_files:
-                        extra_files.remove(rel_path)
-
-    relevant_files = sorted(file_list)
+    relevant_files = create_file_list(path, extra_files, excludes)
     manifest = make_html_manifest(entrypoint, image)
 
     for rel_path in relevant_files:
@@ -706,6 +651,48 @@ def make_html_bundle_content(
     return manifest, relevant_files
 
 
+def create_file_list(
+    path: str,
+    extra_files: typing.List[str] = None,
+    excludes: typing.List[str] = None,
+) -> typing.List[str]:
+    """
+    Builds a full list of files under the given path that should be included
+    in a manifest or bundle.  Extra files and excludes are relative to the given
+    directory and work as you'd expect.
+
+    :param path: a file, or a directory to walk for files.
+    :param extra_files: a sequence of any extra files to include in the bundle.
+    :param excludes: a sequence of glob patterns that will exclude matched files.
+    :return: the list of relevant files, relative to the given directory.
+    """
+    extra_files = extra_files or []
+    excludes = excludes if excludes else []
+    glob_set = create_glob_set(path, excludes)
+    exclude_paths = {Path(p) for p in excludes}
+    file_set = set()  # type: typing.Set[str]
+    file_set.union(extra_files)
+
+    if isfile(path):
+        file_set.add(path)
+        return sorted(file_set)
+
+    for subdir, dirs, files in os.walk(path):
+        if Path(subdir) in exclude_paths:
+            continue
+        for file in files:
+            abs_path = os.path.join(subdir, file)
+            rel_path = os.path.relpath(abs_path, path)
+
+            if Path(abs_path) in exclude_paths:
+                continue
+            if keep_manifest_specified_file(rel_path, exclude_paths | directories_to_ignore) and (
+                rel_path in extra_files or not glob_set.matches(abs_path)
+            ):
+                file_set.add(rel_path)
+    return sorted(file_set)
+
+
 def infer_entrypoint(path, mimetype):
     if os.path.isfile(path):
         return path
@@ -823,25 +810,9 @@ def _create_quarto_file_list(
     excludes = list(excludes) if excludes else []
     excludes.append("manifest.json")
     excludes.extend(list_environment_dirs(directory))
-    glob_set = create_glob_set(directory, excludes)
-
-    file_list = []
-
-    for subdir, dirs, files in os.walk(directory):
-        for file in files:
-            abs_path = os.path.join(subdir, file)
-            rel_path = os.path.relpath(abs_path, directory)
-
-            if keep_manifest_specified_file(rel_path) and (rel_path in extra_files or not glob_set.matches(abs_path)):
-                file_list.append(rel_path)
-                # Don't add extra files more than once.
-                if rel_path in extra_files:
-                    extra_files.remove(rel_path)
-
-    for rel_path in extra_files:
-        file_list.append(rel_path)
 
-    return sorted(file_list)
+    file_list = create_file_list(directory, extra_files, excludes)
+    return file_list
 
 
 def make_quarto_manifest(