Merge branch 'release/0.16.3' #16
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| name: CI/CD | |
| on: | |
| push: | |
| branches: [ "master", "develop" ] | |
| pull_request: | |
| branches: [ "master", "develop" ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| ci_pip: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Cleanup build folder 🧹 | |
| run: | | |
| ls -la ./ | |
| rm -rf ./* || true | |
| rm -rf ./.??* || true | |
| ls -la ./ | |
| - name: Setup Python 3.12 🐍 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - name: Setup backend 🏗️ | |
| run: | | |
| pip install uv | |
| uv pip install --system hatch pytest pytest-rerunfailures autoflake==1.7 isort==6.0 black==25.1 | |
| - name: Checkout 🛎️ | |
| uses: actions/checkout@v4 | |
| # Builds a wheel needed for the CD | |
| - name: Build wheel 🎡 | |
| run: hatch build -t wheel | |
| # Store the wheel in GitHub Actions | |
| - name: Upload artifact ❄️ | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: genomepy_wheel | |
| path: dist/ | |
| # Test if the created wheel can be installed | |
| - name: Install 🛠️ | |
| run: uv pip install --system dist/*.whl --force-reinstall | |
| - name: Unit tests 📜 | |
| run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py | |
| - name: Integration tests 📚 | |
| run: | | |
| genomepy --help | |
| genomepy annotation --help | |
| genomepy install --help | |
| genomepy search --help | |
| ci_conda: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Cleanup build folder 🧹 | |
| run: | | |
| ls -la ./ | |
| rm -rf ./* || true | |
| rm -rf ./.??* || true | |
| ls -la ./ | |
| - name: Checkout 🛎️ | |
| uses: actions/checkout@v4 | |
| - name: Setup backend 🏗️ | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: environment.yml | |
| miniforge-version: latest | |
| - name: Install 🛠️ | |
| run: pip install . --no-deps --ignore-installed | |
| - name: Unit tests 📜 | |
| run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py | |
| - name: Integration tests 📚 | |
| run: | | |
| genomepy --help | |
| genomepy annotation --help | |
| genomepy install --help | |
| genomepy search --help | |
| cd: | |
| needs: ci_pip | |
| runs-on: ubuntu-latest | |
| # Only run this job if new work is pushed to "master" | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| # # Only run this job on a tagged commit | |
| # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| steps: | |
| - name: Cleanup build folder 🧹 | |
| run: | | |
| ls -la ./ | |
| rm -rf ./* || true | |
| rm -rf ./.??* || true | |
| ls -la ./ | |
| - name: Setup Python 3.12 🐍 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - run: mkdir -p dist | |
| - name: Download artifact ❄️ | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: genomepy_wheel | |
| path: dist/ | |
| - name: Publish to PyPI 🚀 | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |