CI: Apply Copier template (#23)

* Add support for Python 3.10
* Add dependabot for Github Actions
* Use cache in Github Actions

Author: adrien-berchet

.copier-answers.yml

@@ -1,6 +1,6 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.9
+_commit: 0.1.26
 _src_path: [email protected]:neuromath/python-template.git
 author_email: ''
 author_name: Blue Brain Project, EPFL

.gitattributes

@@ -0,0 +1,3 @@
+*.asc linguist-detectable=false
+.auto-changelog-template.hbs linguist-detectable=false
+commitlint.config.js linguist-detectable=false

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Configure check for outdated GitHub Actions actions in workflows.
+  # See: https://docs.github.com/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+  - package-ecosystem: "github-actions"
+    directory: "/" # Check the repository's workflows under /.github/workflows/
+    schedule:
+      interval: "weekly"

.github/workflows/codeql.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  schedule:
+    - cron: '55 17 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/commitlint.yml

@@ -9,11 +9,11 @@ jobs:
     name: Check PR title
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-node@v3
         with:
-          node-version: '14'
+          node-version: '16'
       - run: npm install -g --force commitlint @commitlint/cli commitlint-plugin-cleanfeet
       - run: npm install conventional-changelog-conventionalcommits
       - run: touch .git/COMMIT_EDITMSG
-      - run: echo ${{ github.event.pull_request.title }} | commitlint
+      - run: echo "${{ github.event.pull_request.title }}" | commitlint

.github/workflows/publish-sdist.yml

@@ -10,15 +10,15 @@ jobs:
     name: Build and publish on PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Build a wheel and a source tarball
         run: |
-          pip install setuptools>=42 wheel setuptools_scm[toml]>=3.4
-          python setup.py sdist bdist_wheel
+          pip install setuptools>=42 build setuptools_scm[toml]>=3.4
+          python -m build -o dist
       - name: Publish distribution package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:

.github/workflows/run-tox.yml

@@ -13,32 +13,59 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Get current month
+      id: date
+      run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
+    - name: Cache APT Packages
+      uses: awalsh128/cache-apt-pkgs-action@latest
+      with:
+        packages: poppler-utils imagemagick
+        version: 1.0
+        execute_install_scripts: true
+    - name: Cache tox and precommit environments
+      uses: actions/cache@v3
+      with:
+        path: |
+          .tox
+          ~/.cache/pre-commit
+        key: ${{ runner.os }}-${{ matrix.python-version }}-${{ steps.date.outputs.date }}-${{ hashFiles('setup.py') }}-${{ hashFiles('.pre-commit-config.yaml') }}
+    - name: Install dependencies and register dot plugin
       run: |
-        sudo apt-get install -y poppler-utils imagemagick
         python -m pip install --upgrade pip setuptools
         pip install tox-gh-actions
+    - name: Clear results in tox environments
+      run: |
+        rm -rf .tox/*/tmp
     - name: Run tox
       run: |
         tox
     - name: JUnit Report Action
-      uses: mikepenz/action-junit-report@v3.2.0
+      uses: mikepenz/action-junit-report@v3
       if: always() # always run even if the previous step fails
       with:
         report_paths: 'reports/pytest-*.xml'
     - name: Upload to codecov
-      if: ${{matrix.python-version == '3.8'}}
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false
-        files: ./reports/coverage-py38.xml
+        files: ./reports/coverage-*.xml
         flags: pytest
-        name: "dir-content-diff-py38"
+        name: "dir-content-diff-py${{ matrix.python-version }}"
+    - name: Upload test artifacts
+      uses: actions/upload-artifact@v3
+      if: always()
+      with:
+        name: tests-${{ matrix.python-version }}
+        retention-days: 4
+        path: |
+          .tox/py*/tmp
+          docs/build
+          reports

.readthedocs.yml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.8"
+    python: "3.9"
 
 sphinx:
   configuration: docs/source/conf.py

pyproject.toml

@@ -15,7 +15,6 @@ target-version = [
     "py38",
     "py39",
 ]
-include = 'dir_content_diff\/.*\.py$|tests\/.*\.py$|docs\/source\/conf\.py$|setup\.py$'
 
 # PYDOCSTYLE
 [tool.pydocstyle]
@@ -25,7 +24,6 @@ add-ignore = [
     "D107",
 ]
 convention = "google"
-match = "[dir_content_diff, tests, docs/source/conf.py, setup.py]"
 
 # ISORT
 [tool.isort]

setup.py

@@ -1,7 +1,7 @@
 """Setup for the dir-content-diff package."""
 from pathlib import Path
 
-from setuptools import find_packages
+from setuptools import find_namespace_packages
 from setuptools import setup
 
 reqs = [
@@ -40,7 +40,7 @@
         "Source": "https://github.com/BlueBrain/dir-content-diff",
     },
     license="Apache License 2.0",
-    packages=find_packages(include=["dir_content_diff"]),
+    packages=find_namespace_packages(include=["dir_content_diff*"]),
     python_requires=">=3.8",
     use_scm_version=True,
     setup_requires=[
@@ -52,6 +52,10 @@
         "docs": doc_reqs + pandas_reqs,
         "test": test_reqs + pandas_reqs,
     },
+    entry_points={
+        "pytest11": ["dir-content-diff = dir_content_diff.pytest_plugin"],
+    },
+    include_package_data=True,
     classifiers=[
         "Development Status :: 4 - Beta",
         "Intended Audience :: Developers",
@@ -60,10 +64,7 @@
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Topic :: Software Development :: Libraries :: Python Modules",
     ],
-    include_package_data=True,
-    entry_points={
-        "pytest11": ["dir-content-diff = dir_content_diff.pytest_plugin"],
-    },
 )