Properly Separating samples and drug omics file generation for beatam… #30
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| name: Python package tests | |
| on: | |
| push: | |
| branches: [ builder_branch_JJ ] | |
| jobs: | |
| test: | |
| if: github.actor != 'github-actions[bot]' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| test-file: [ | |
| 'test_download_and_load_beataml.py', | |
| 'test_download_and_load_cell_line.py', | |
| 'test_download_beataml_cli.py', | |
| 'test_download_cell_line_cli.py', | |
| 'test_download_and_load_cptac.py', | |
| 'test_download_and_load_hcmi.py', | |
| 'test_download_cptac_cli.py', | |
| 'test_download_hcmi_cli.py' | |
| ] | |
| outputs: | |
| result: ${{ steps.test-outcome.outcome }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install pytest-xdist | |
| - name: Install as package | |
| run: | | |
| pip install . | |
| - name: Run test | |
| id: test-outcome | |
| run: | | |
| pytest -n 4 tests/${{ matrix.test-file }} | |
| build-and-publish: | |
| if: github.actor != 'github-actions[bot]' | |
| needs: test | |
| runs-on: ubuntu-latest | |
| environment: build | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Fetch tags from main branch | |
| run: | | |
| git fetch origin 'refs/tags/*:refs/tags/*' | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel twine packaging | |
| - name: Update version | |
| run: | | |
| # Extract the current version from setup.py | |
| CURRENT_VERSION=$(grep -oP "version='\K[0-9]+\.[0-9]+\.[0-9]+" setup.py) | |
| echo "Current version: $CURRENT_VERSION" | |
| # Fetch tags and get the latest tag, removing the 'v' prefix | |
| git fetch --tags | |
| LATEST_TAG=$(git describe --tags `git rev-list --tags --max-count=1` | sed 's/^v//') | |
| echo "Latest tag: $LATEST_TAG" | |
| # Use Python to compare versions | |
| HIGHER_VERSION=$(python -c "from packaging.version import parse as parse_version; \ | |
| current = parse_version('$CURRENT_VERSION'); \ | |
| latest = parse_version('$LATEST_TAG'); \ | |
| print(current if current > latest else latest)") | |
| echo "Higher version: $HIGHER_VERSION" | |
| # If current version is higher, increment patch version in setup.py | |
| if [ "$CURRENT_VERSION" == "$HIGHER_VERSION" ]; then | |
| IFS='.' read -r -a VERSION_PARTS <<< "$CURRENT_VERSION" | |
| PATCH=$((VERSION_PARTS[2] + 1)) | |
| NEW_VERSION="${VERSION_PARTS[0]}.${VERSION_PARTS[1]}.$PATCH" | |
| echo "Incremented version: $NEW_VERSION" | |
| sed -i "s/version='\([0-9]\+\.[0-9]\+\.\)[0-9]\+'/version='\1$PATCH'/" setup.py | |
| # Commit and push the updated setup.py | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Action" | |
| git add setup.py | |
| git commit -m "Increment version number to $NEW_VERSION [skip ci]" | |
| git push | |
| else | |
| echo "No version increment needed" | |
| fi | |
| - name: Build local and publish to PyPI | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN_SECRET }} | |
| run: | | |
| python setup.py sdist bdist_wheel | |
| twine upload dist/* --verbose | |