Fix for #117 #208
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| name: Test and release | |
| on: | |
| push: | |
| jobs: | |
| test: | |
| name: Run unit tests on the ontology | |
| if: "!contains(github.event.head_commit.message, '[Skip CI]')" | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Check out the repository | |
| - name: Checkout repo | |
| uses: actions/checkout@master | |
| with: | |
| fetch-depth: 1 | |
| # Install the requirements for the tests | |
| - name: Install Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.9' | |
| - name: Setup pip cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: /opt/hostedtoolcache/Python | |
| key: ${{ runner.os }}-pip-${{ hashFiles('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install pip and setuptools | |
| run: | | |
| python -m pip install --upgrade pip==23.0.0 | |
| python -m pip install --upgrade pip==23.0.0 | |
| - name: Install the Python KiSAO package | |
| working-directory: libkisao/python | |
| run: | | |
| cp ../../kisao.owl kisao/ | |
| python -m pip install .[all] | |
| # Lint the package | |
| - name: Install flake8 | |
| run: python -m pip install flake8 | |
| - name: Lint the package | |
| working-directory: libkisao/python | |
| run: python -m flake8 | |
| # Run the tests | |
| - name: Install the requirements for the tests | |
| working-directory: libkisao/python | |
| run: | | |
| python -m pip install pytest pytest-cov | |
| python -m pip install -r tests/requirements.txt | |
| - name: Run the tests | |
| working-directory: libkisao/python | |
| run: python -m pytest tests/ --cov | |
| # Compile documentation | |
| - name: Install the requirements for compiling the documentation | |
| working-directory: libkisao/python | |
| run: python -m pip install -r docs-src/requirements.txt | |
| - name: Compile the documentation | |
| working-directory: libkisao/python | |
| run: | | |
| sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc | |
| mkdir -p docs-src/_static | |
| sphinx-build docs-src docs | |
| - name: Compile a report of the substitutability among algorithms | |
| working-directory: libkisao/python | |
| shell: python | |
| run: | | |
| import kisao.utils | |
| import os | |
| report = kisao.utils.get_algorithm_substitution_matrix() | |
| report.to_csv(os.path.join('docs', 'algorithm-substitutability.csv')) | |
| - name: Upload the coverage report to Codecov | |
| if: false | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: unittests | |
| file: ./libkisao/python/coverage.xml | |
| getMainBranchHeadRevision: | |
| name: Get the head revision of the main branch | |
| if: startsWith(github.ref, 'refs/tags/') | |
| runs-on: ubuntu-latest | |
| outputs: | |
| mainBranchHeadRevision: ${{ steps.get-main-branch.outputs.mainBranchHeadRevision }} | |
| steps: | |
| - name: Clone repository | |
| run: | | |
| git clone https://${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} . | |
| - id: get-main-branch | |
| name: Determine main branch | |
| run: | | |
| mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD | cut -d '/' -f 4) | |
| mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch}) | |
| echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT | |
| determineIfReleaseNeeded: | |
| name: Determine if the package should be released | |
| needs: | |
| - getMainBranchHeadRevision | |
| if: startsWith(github.ref, 'refs/tags/') | |
| runs-on: ubuntu-latest | |
| outputs: | |
| release: ${{ steps.determine-if-release-needed.outputs.release }} | |
| steps: | |
| # Check out the repository | |
| - name: Checkout repo | |
| uses: actions/checkout@master | |
| with: | |
| fetch-depth: 1 | |
| - id: determine-if-release-needed | |
| name: Determine if a release should be made | |
| run: | | |
| release="0" | |
| if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then | |
| echo "First check passed" | |
| tag_hash=$(git rev-parse "${{ github.ref }}") | |
| echo "tag_hash: $tag_hash" | |
| if [ "$tag_hash" == "${{ needs.getMainBranchHeadRevision.outputs.mainBranchHeadRevision }}" ]; then | |
| echo "Second check passed" | |
| release="1" | |
| fi | |
| fi | |
| echo "release=$release" >> $GITHUB_OUTPUT | |
| echo "release=$release" | |
| commitCompiledDocumentation: | |
| name: Commit and push compiled documentation to GitHub | |
| needs: | |
| - test | |
| - determineIfReleaseNeeded | |
| if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1' | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Check out the repository | |
| - name: Checkout repo | |
| uses: actions/checkout@master | |
| with: | |
| fetch-depth: 1 | |
| # ref: dev | |
| # token: ${{ secrets.ADMIN_GITHUB_TOKEN }} | |
| # Install the requirements for the tests | |
| - name: Install Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.9' | |
| - name: Setup pip cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: /opt/hostedtoolcache/Python | |
| key: ${{ runner.os }}-pip-${{ hashFiles('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install pip and setuptools | |
| run: | | |
| python -m pip install --upgrade pip==23.0.0 | |
| python -m pip install --upgrade pip==23.0.0 | |
| - name: Install the Python KiSAO package | |
| working-directory: libkisao/python | |
| run: | | |
| cp ../../kisao.owl kisao/ | |
| python -m pip install .[all] | |
| - name: Install the requirements for compiling the documentation | |
| working-directory: libkisao/python | |
| run: python -m pip install -r docs-src/requirements.txt | |
| - name: Compile the documentation | |
| working-directory: libkisao/python | |
| run: | | |
| sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc | |
| mkdir -p docs-src/_static | |
| sphinx-build docs-src docs | |
| - name: Compile a report of the substitutability among algorithms | |
| working-directory: libkisao/python | |
| shell: python | |
| run: | | |
| import kisao.utils | |
| import os | |
| report = kisao.utils.get_algorithm_substitution_matrix() | |
| report.to_csv(os.path.join('docs', 'algorithm-substitutability.csv')) | |
| # If new tag, commit and push documentation | |
| - name: Configure Git | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "SED-ML bot" | |
| git config pull.rebase false | |
| - id: commit-docs | |
| name: Commit the compiled documentation | |
| working-directory: libkisao/python | |
| run: | | |
| git stash | |
| git pull | |
| set +e | |
| git stash pop | |
| git add docs | |
| git commit -m "Updated compiled documentation [Skip CI]" | |
| git checkout . | |
| git clean -f -d | |
| if [[ $? = 0 ]]; then | |
| docsChanged=1 | |
| else | |
| docsChanged=0 | |
| fi | |
| echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT | |
| - name: Push the compiled documentation | |
| if: startsWith(github.ref, 'refs/tags/') && steps.commit-docs.outputs.docsChanged == '1' | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.ADMIN_GITHUB_TOKEN }} | |
| branch: ${{ steps.get-main-branch.outputs.mainBranch }} | |
| createGitHubRelease: | |
| name: Create GitHub release | |
| needs: | |
| - test | |
| - determineIfReleaseNeeded | |
| if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@master | |
| with: | |
| fetch-depth: 1 | |
| # ref: dev | |
| # token: ${{ secrets.ADMIN_GITHUB_TOKEN }} | |
| - name: Merge dev branch into deploy branch | |
| uses: devmasx/[email protected] | |
| with: | |
| type: now | |
| target_branch: deploy | |
| github_token: ${{ secrets.ADMIN_GITHUB_TOKEN }} | |
| - id: get-version | |
| name: Get version number | |
| env: | |
| TAG: ${{ github.ref }} | |
| run: | | |
| version="${TAG/refs\/tags\//}" | |
| echo "version=$version" >> $GITHUB_OUTPUT | |
| - name: Create GitHub release | |
| uses: "marvinpinto/action-automatic-releases@latest" | |
| with: | |
| repo_token: "${{ secrets.ADMIN_GITHUB_TOKEN }}" | |
| draft: false | |
| prerelease: false | |
| automatic_release_tag: ${{ steps.get-version.outputs.version }} | |
| releaseToBioPortal: | |
| name: Release version to BioPortal | |
| needs: | |
| - test | |
| - determineIfReleaseNeeded | |
| if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@master | |
| - name: Install jq | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y --no-install-recommends jq moreutils | |
| - name: Prepare BioPortal submission | |
| env: | |
| TAG: ${{ github.ref }} | |
| run: | | |
| version="${TAG/refs\/tags\//}" | |
| released=$(date --iso-8601=second) | |
| cp .github/workflows/BioPortal-submission.json .github/workflows/BioPortal-submission-version.json | |
| jq \ | |
| ".pullLocation = \"https://raw.githubusercontent.com/SED-ML/KiSAO/${version}/kisao.owl\"" \ | |
| .github/workflows/BioPortal-submission-version.json | sponge .github/workflows/BioPortal-submission-version.json | |
| jq \ | |
| ".version = \"${version}\"" \ | |
| .github/workflows/BioPortal-submission-version.json | sponge .github/workflows/BioPortal-submission-version.json | |
| jq \ | |
| ".released = \"${released}\"" \ | |
| .github/workflows/BioPortal-submission-version.json | sponge .github/workflows/BioPortal-submission-version.json | |
| - name: Submit to BioPortal | |
| run: | | |
| curl -X POST \ | |
| -H "Authorization: apikey token=${{ secrets.BIOPORTAL_API_KEY }}" \ | |
| -H "Content-Type: application/json" \ | |
| -H "Accept: application/json" \ | |
| -d @.github/workflows/BioPortal-submission-version.json \ | |
| http://data.bioontology.org/ontologies/KISAO/submissions | |
| echo | |
| releaseToPyPI: | |
| name: Release version to PyPI | |
| needs: | |
| - test | |
| - determineIfReleaseNeeded | |
| if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1' | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Check out the repository | |
| - name: Checkout repo | |
| uses: actions/checkout@master | |
| with: | |
| fetch-depth: 1 | |
| # Install the requirements for the tests | |
| - name: Install Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.9' | |
| - name: Setup pip cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: /opt/hostedtoolcache/Python | |
| key: ${{ runner.os }}-pip-${{ hashFiles('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install pip | |
| run: | | |
| python -m pip install --upgrade pip==23.0.0 | |
| python -m pip install --upgrade pip==23.0.0 | |
| # Create PyPI release | |
| - name: Create PyPI release | |
| working-directory: libkisao/python | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | |
| run: | | |
| # Install pandoc | |
| sudo apt-get update -y | |
| sudo apt-get install -y --no-install-recommends wget | |
| wget "https://github.com/jgm/pandoc/releases/download/3.1.3/pandoc-3.1.3-1-amd64.deb" -O /tmp/pandoc.deb | |
| sudo dpkg -i /tmp/pandoc.deb | |
| rm /tmp/pandoc.deb | |
| # Copy OWL file and LICENSE so it can be bundled into the Python package | |
| cp ../../kisao.owl kisao/ | |
| cp ../../LICENSE . | |
| # Convert README to .rst format | |
| pandoc --from=gfm --output=README.rst --to=rst README.md | |
| # Install twine | |
| python -m pip install wheel twine | |
| # Create packages to upload to PyPI | |
| python setup.py sdist | |
| python setup.py bdist_wheel | |
| # Upload packages to PyPI | |
| twine upload dist/* |