DOC: Fix hyperlinks #41
Workflow file for this run
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| name: ARTKIT Release Pipeline | |
| on: | |
| push: | |
| branches: | |
| - 1.0.x | |
| - release/* | |
| pull_request: | |
| branches: | |
| - 1.0.x | |
| - release/* | |
| schedule: # runs on default branch | |
| - cron: "0 2 * * 1-5" # Every weekday at 2 AM | |
| env: | |
| project_name: artkit | |
| package_name: artkit | |
| jobs: | |
| code_quality_checks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Upgrade pip | |
| run: python -m pip install --upgrade pip | |
| - name: Run isort | |
| run: | | |
| python -m pip install isort~=5.12 | |
| python -m isort --check --diff . | |
| - name: Run black | |
| run: | | |
| python -m pip install black~=24.4.2 | |
| python -m black --check . | |
| - name: Run flake8 | |
| run: | | |
| python -m pip install flake8~=5.0 flake8-comprehensions~=3.10 | |
| python -m flake8 --config tox.ini -v . | |
| - name: Run mypy | |
| run: | | |
| python -m pip install mypy | |
| # add package dependencies for mypy | |
| dependencies=( | |
| fluxus~=1.0 | |
| gamma-pytools~=3.0 | |
| openai | |
| pandas-stubs | |
| pytest | |
| types-PyYAML | |
| aiohttp | |
| ) | |
| pip install "${dependencies[@]}" | |
| python -m mypy src --config-file pyproject.toml | |
| detect_build_config_changes: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| conda_build_config_changed: ${{ steps.diff.outputs.conda_build_config_changed }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Detect changes in build configuration | |
| id: diff | |
| run: | | |
| set -eux | |
| files_changed=$(git diff HEAD^ --name-only) | |
| echo "Files changed since last commit: ${files_changed}" | |
| n_files_changed=$(echo "${files_changed}" | grep -i -E 'meta\.yaml|pyproject\.toml|release-pipeline\.yml|tox\.ini|make\.py' | wc -l | xargs || true) | |
| if [ ${n_files_changed} -gt 0 ]; then | |
| build_changed=1 | |
| echo "build config has been changed" | |
| else | |
| build_changed=0 | |
| echo "build config is unchanged" | |
| fi | |
| echo "::set-output name=conda_build_config_changed::$build_changed" | |
| unit_tests: | |
| runs-on: ubuntu-latest | |
| needs: detect_build_config_changes | |
| if: ${{ needs.detect_build_config_changes.outputs.conda_build_config_changed == '1' }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Display directory contents | |
| run: ls ${{ github.workspace }} | |
| - name: Activate micromamba environment with pytest | |
| run: | | |
| set -eux | |
| # install micromamba | |
| curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba | |
| export MAMBA_ROOT_PREFIX=~/micromamba | |
| eval "$(./bin/micromamba shell hook -s posix)" | |
| # install the develop environment | |
| micromamba env create --yes --file environment.yml | |
| micromamba activate ${{ env.project_name }} | |
| export PYTHONPATH=${{ github.workspace }}/src/ | |
| export RUN_PACKAGE_VERSION_TEST=${{ env.project_name }} | |
| pytest \ | |
| --cov ${{ env.project_name }} \ | |
| --cov-config "tox.ini" \ | |
| --cov-report=xml:coverage.xml --cov-report=html:htmlcov \ | |
| --junitxml pytest.xml \ | |
| . -s | |
| - name: Publish test results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pytest-results | |
| path: pytest.xml | |
| - name: Publish code coverage results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: code-coverage-results | |
| path: coverage.xml | |
| conda_tox_essential: | |
| runs-on: ubuntu-latest | |
| needs: [detect_build_config_changes, code_quality_checks] | |
| if: ${{ needs.detect_build_config_changes.outputs.conda_build_config_changed == '1' && github.event_name != 'schedule' && !startsWith(github.head_ref, 'dev/') && !startsWith(github.ref, 'refs/heads/release/') }} | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| build-system: [conda, tox] | |
| pkg-dependencies: [max, min] | |
| exclude: | |
| - python-version: 3.11 | |
| build-system: conda | |
| pkg-dependencies: min | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Display directory contents | |
| run: ls ${{ github.workspace }} | |
| - name: Install and configure micromamba | |
| if: matrix.build-system == 'conda' | |
| run: | | |
| curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba | |
| export MAMBA_ROOT_PREFIX=~/micromamba | |
| eval "$(./bin/micromamba shell hook -s posix)" | |
| micromamba create -n build -y | |
| micromamba activate build | |
| micromamba install -y -c conda-forge boa~=0.14 toml~=0.10 flit~=3.6 packaging~=20.9 | |
| - name: Install dependencies using tox | |
| if: matrix.build-system == 'tox' | |
| run: | | |
| python -m pip install "toml~=0.10" | |
| python -m pip install "flit~=3.7" | |
| python -m pip install "tox~=3.25" | |
| - name: Build and test | |
| run: | | |
| set -eux | |
| if [ "${{ matrix.build-system }}" = "conda" ]; then | |
| export MAMBA_ROOT_PREFIX=~/micromamba | |
| eval "$(./bin/micromamba shell hook -s posix)" | |
| micromamba activate build | |
| fi | |
| echo "DIRNAME_WORKSPACE=$(dirname "${{ github.workspace }}")" >> $GITHUB_ENV | |
| export RUN_PACKAGE_VERSION_TEST=${{ env.project_name }} | |
| cd ${{ github.workspace }} | |
| ./make.py ${{ env.project_name }} ${{ matrix.build-system }} ${{ matrix.pkg-dependencies }} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.build-system }}_${{ matrix.pkg-dependencies }} | |
| path: ${{ env.DIRNAME_WORKSPACE }}/dist | |
| conda_tox_matrix: | |
| runs-on: ubuntu-latest | |
| needs: [detect_build_config_changes, code_quality_checks] | |
| if: startsWith(github.head_ref, 'dev/') || startsWith(github.ref, 'refs/heads/release/') || github.event_name == 'schedule' | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| build-system: [conda, tox] | |
| pkg-dependencies: [default, min, max] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Display directory contents | |
| run: ls ${{ github.workspace }} | |
| - name: Install and configure micromamba | |
| if: matrix.build-system == 'conda' | |
| run: | | |
| set -eux | |
| # install micromamba | |
| curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba | |
| export MAMBA_ROOT_PREFIX=~/micromamba | |
| eval "$(./bin/micromamba shell hook -s posix)" | |
| micromamba create -n build -y | |
| micromamba activate build | |
| micromamba install -y -c conda-forge boa~=0.14 toml~=0.10 flit~=3.6 packaging~=20.9 | |
| - name: Install dependencies using tox | |
| if: matrix.build-system == 'tox' | |
| run: | | |
| python -m pip install "toml~=0.10" | |
| python -m pip install "flit~=3.7" | |
| python -m pip install "tox~=3.25" | |
| - name: Build and test | |
| run: | | |
| set -eux | |
| if [ "${{ matrix.build-system }}" = "conda" ]; then | |
| export MAMBA_ROOT_PREFIX=~/micromamba | |
| eval "$(./bin/micromamba shell hook -s posix)" | |
| micromamba activate build | |
| fi | |
| echo "DIRNAME_WORKSPACE=$(dirname "${{ github.workspace }}")" >> $GITHUB_ENV | |
| export RUN_PACKAGE_VERSION_TEST=${{ env.project_name }} | |
| cd ${{ github.workspace }} | |
| ./make.py ${{ env.project_name }} ${{ matrix.build-system }} ${{ matrix.pkg-dependencies }} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.build-system }}_${{ matrix.pkg-dependencies }} | |
| path: ${{ env.DIRNAME_WORKSPACE }}/dist | |
| veracode_check: | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'schedule' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Prepare archive for Veracode | |
| shell: bash | |
| run: | | |
| set -eux | |
| eval "$(conda shell.bash hook)" | |
| cd ${{ github.workspace }} | |
| mkdir static_scan | |
| git archive --format=zip --output static_scan/archive.zip HEAD | |
| - name: Run Veracode Scan | |
| id: upload_and_scan | |
| uses: veracode/veracode-uploadandscan-action@master | |
| with: | |
| appname: 'artkit' | |
| version: '${{ github.run_number }}' | |
| filepath: 'static_scan/archive.zip' | |
| vid: '${{ secrets.VERACODE_API_ID }}' | |
| vkey: '${{ secrets.VERACODE_API_KEY }}' | |
| createprofile: false | |
| scanpollinginterval: '60' | |
| check_release: | |
| runs-on: ubuntu-latest | |
| needs: conda_tox_matrix | |
| if: startsWith(github.head_ref, 'dev/') || startsWith(github.ref, 'refs/heads/release/') | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Checkout artkit | |
| uses: actions/checkout@v4 | |
| with: | |
| path: artkit | |
| - name: Set env vars | |
| run: | | |
| pip install packaging~=20.9 | |
| export PYTHONPATH=${{ github.workspace }}/artkit/sphinx/make | |
| package_path=${{ github.workspace }}/${{ env.project_name }}/src/${{ env.project_name }} | |
| version=$(python -c "import make_util; print(make_util.get_package_version(package_path='$package_path'))") | |
| echo "current_version=$version" >> $GITHUB_ENV | |
| if [ ${{ github.event_name }} == 'pull_request' ]; then | |
| echo "BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV | |
| else | |
| ref=${{ github.ref }} | |
| branch_name=${ref/refs\/heads\//} | |
| echo "BRANCH_NAME=$branch_name" >> $GITHUB_ENV | |
| fi | |
| - name: Check version consistency | |
| run: | | |
| set -eux | |
| python -m pip install toml~=0.10.2 packaging~=20.9 | |
| cd ${{ github.workspace }}/artkit | |
| python <<EOF | |
| from os import environ | |
| from make import ToxBuilder | |
| branch = "${{ env.BRANCH_NAME }}" | |
| print(f"Checking package version consistency with branch: {branch}") | |
| assert (branch.startswith("release/") or branch.startswith("dev/") or branch=="1.0.x" | |
| ), "This check should only run on versioned branches – check pipeline." | |
| if branch=="1.0.x": | |
| branch_version = branch[:-2] | |
| package_version = ToxBuilder("${{ env.project_name }}", "default").package_version | |
| assert package_version.startswith(branch_version), f"Package version '{package_version}' does not match '{branch_version}' from branch." | |
| else: | |
| branch_version = branch.split("/", maxsplit=1)[1] | |
| package_version = ToxBuilder("${{ env.project_name }}", "default").package_version | |
| assert ( | |
| package_version == branch_version | |
| ), f"Package version '{package_version}' does not match '{branch_version}' from branch." | |
| print("Check passed.") | |
| EOF | |
| release: | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.head_ref, 'dev/') || startsWith(github.ref, 'refs/heads/release/') | |
| needs: check_release | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Checkout artkit | |
| uses: actions/checkout@v4 | |
| with: | |
| path: artkit | |
| - name: Get package version | |
| run: | | |
| set -eux | |
| echo "Getting version" | |
| pip install packaging~=20.9 | |
| export PYTHONPATH=${{ github.workspace }}/artkit/sphinx/make | |
| package_path=${{ github.workspace }}/${{ env.project_name }}/src/${{ env.project_name }} | |
| version=$(python -c "import make_util; print(make_util.get_package_version(package_path='$package_path'))") | |
| echo "current_version=$version" >> $GITHUB_ENV | |
| echo "Detecting pre-release ('dev' or 'rc' in version)" | |
| prerelease=False | |
| [[ $version == *dev* ]] && prerelease=True && echo "Development release identified" | |
| [[ $version == *rc* ]] && prerelease=True && echo "Pre-release identified" | |
| echo "is_prerelease=$prerelease" >> $GITHUB_ENV | |
| echo "DIRNAME_WORKSPACE=$(dirname "${{ github.workspace }}")" >> $GITHUB_ENV | |
| - name: Download Tox Build Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: tox_default | |
| path: ${{ env.DIRNAME_WORKSPACE }}/dist | |
| - name: Download Conda Build Artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: conda_default | |
| path: ${{ env.DIRNAME_WORKSPACE }}/dist | |
| - name: Publish to PyPi (Tox) | |
| if: startsWith(github.ref, 'refs/heads/release/') | |
| env: | |
| FLIT_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
| FLIT_USERNAME: __token__ | |
| run: | | |
| set -eux | |
| cd ${{ github.workspace }}/${{ env.project_name }} | |
| pip install flit | |
| flit install | |
| flit publish | |
| echo "pypi_published=True" >> $GITHUB_ENV | |
| - name: Publish to Anaconda (Conda) | |
| if: startsWith(github.ref, 'refs/heads/release/') | |
| env: | |
| CONDA_TOKEN: ${{ secrets.CONDA_TOKEN }} | |
| run: | | |
| set -eux | |
| cd ${{ env.DIRNAME_WORKSPACE }} | |
| eval "$(conda shell.bash hook)" | |
| conda install -y anaconda-client | |
| anaconda -t ${CONDA_TOKEN} upload --user bcgx --force ${{ env.DIRNAME_WORKSPACE }}/dist/conda/noarch/${{ env.package_name }}-*.tar.bz2 | |
| anaconda logout | |
| echo "conda_published=True" >> $GITHUB_ENV | |
| - name: GitHub Release | |
| if: startsWith(github.ref, 'refs/heads/release/') | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| tag_name: ${{ env.current_version }} | |
| files: | | |
| ${{ github.workspace }}/tox_default/tox/${{ env.package_name }}-*.tar.gz | |
| ${{ env.DIRNAME_WORKSPACE }}/dist/conda/noarch/${{ env.package_name }}-*.tar.bz2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_REPOSITORY: ${{ github.repository }} | |
| release_name: ${{ env.project_name }} ${{ env.current_version }} | |
| body: | | |
| This is the ${{ env.current_version }} release of ${{ env.package_name }}. | |
| You can upgrade your current pip installation via | |
| pip install --upgrade ${{ env.package_name }} | |
| Your conda package can be upgraded by running | |
| conda install -c conda-forge -c bcgx ${{ env.package_name }} | |
| draft: true | |
| prerelease: ${{ env.is_prerelease }} | |
| docs: | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.head_ref, 'dev/') || startsWith(github.ref, 'refs/heads/release/') | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Retrieve current documentation versions from github-pages | |
| run: | | |
| set -eux | |
| if git show-ref --verify --quiet refs/heads/github-pages; then | |
| echo "Checking out github-pages" | |
| git fetch origin github-pages --depth=1 | |
| git checkout --track origin/github-pages | |
| else | |
| echo "Branch github-pages does not exist. Creating and checking out..." | |
| git checkout -b github-pages | |
| fi | |
| # make sure we have a docs directory | |
| mkdir -p docs/docs-version | |
| echo "Current documentation contents:" | |
| ls docs/docs-version | |
| # create staging area | |
| mkdir -p ${{ github.workspace }}/staging | |
| # copy the current documentation versions to the staging area | |
| cp -r docs/docs-version ${{ github.workspace }}/staging/docs-version.bak | |
| - name: Build latest documentation | |
| run: | | |
| set -eux | |
| if [ "${{ github.event_name }}" == 'pull_request' ]; then | |
| BRANCH_NAME=${{ github.head_ref }} | |
| else | |
| BRANCH_NAME=${{ github.ref_name }} | |
| fi | |
| echo "Checking out $BRANCH_NAME" | |
| git fetch origin $BRANCH_NAME --depth=1 | |
| git checkout $BRANCH_NAME | |
| # install micromamba | |
| curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba | |
| export MAMBA_ROOT_PREFIX=~/micromamba | |
| eval "$(./bin/micromamba shell hook -s posix)" | |
| # install the docs environment | |
| micromamba env create -n docs --yes --file environment.yml | |
| micromamba activate docs | |
| export PYTHONPATH=${{ github.workspace }}/src/ | |
| python sphinx/make.py html | |
| - name: Merge previous and latest docs | |
| run: | | |
| set -eux | |
| export MAMBA_ROOT_PREFIX=~/micromamba | |
| eval "$(./bin/micromamba shell hook -s posix)" | |
| # install the tree utility | |
| sudo apt-get install -y tree | |
| echo "Restoring previous documentation to the docs directory" | |
| pwd # /home/runner/work/artkit/artkit | |
| mkdir -p docs | |
| mv ${{ github.workspace }}/staging/docs-version.bak docs/docs-version | |
| ls docs/docs-version | |
| mkdir -p ${{ github.workspace }}/sphinx/build/ | |
| micromamba activate docs | |
| python sphinx/make.py prepare_docs_deployment | |
| echo "Current docs contents:" | |
| tree docs | |
| mv ${{ github.workspace }}/docs staging/docs | |
| - name: Archive docs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ env.project_name }}_docs | |
| path: ${{ github.workspace }}/staging/docs | |
| - name: Publish docs to branch github-pages | |
| if: startsWith(github.ref, 'refs/heads/release/') | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| current_version: ${{ env.current_version}} | |
| run: | | |
| set -eux | |
| echo "Adjusting git credentials" | |
| git config --global user.name "GitHub Actions" | |
| git config --global user.email "[email protected]" | |
| git checkout github-pages | |
| echo "Exporting version as env var" | |
| pip install packaging~=20.9 | |
| export PYTHONPATH=${{ github.workspace }}/sphinx/make | |
| package_path="${{ github.workspace }}/src/${{ env.project_name }}" | |
| version=$(python -c "import make_util; print(make_util.get_package_version(package_path='$package_path'))") | |
| rm -rf docs | |
| mv staging/docs . | |
| git add docs | |
| git status | |
| git commit -m "Publish GitHub Pages [skip ci]" | |
| git tag -a -m "Release version $version" $version | |
| git push -f --set-upstream origin github-pages |