Better Handling of zero median values in Kernel Width #574
Workflow file for this run
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| name: gh-ci-checks | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.type }} | |
| cancel-in-progress: true | |
| on: | |
| pull_request: | |
| paths: | |
| - "**.py" | |
| - pyproject.toml | |
| - .github/workflows/main.yml | |
| push: | |
| branches: [main] | |
| paths: | |
| - "**.py" | |
| tags: | |
| - "v*.*.*" | |
| workflow_dispatch: | |
| jobs: | |
| style: | |
| timeout-minutes: 10 | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Install packages for Ubuntu | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install -r style_requirements.txt | |
| # check formatting of the code style | |
| - name: Check code formatting | |
| run: make pre-commit | |
| build: | |
| timeout-minutes: 15 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # upgrade to macos-latest when 3.10 is removed | |
| os: ["ubuntu-latest", "macos-13", "windows-latest"] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| name: build ${{ matrix.os }} - py${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: "x64" | |
| - name: Install and setup package | |
| run: | | |
| python -m pip install --progress-bar off .[build] | |
| - name: Test package install | |
| run: | | |
| python -c "import dodiscover; print(dodiscover.__version__)" | |
| - name: Remove package install | |
| run: | | |
| python -m pip uninstall -yq dodiscover | |
| - name: Build package | |
| run: python -m build | |
| - name: Upload package distribution files | |
| if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.11' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: package | |
| path: dist | |
| # | |
| # Test wheel-based Installation | |
| # | |
| - name: Install wheel | |
| run: pip install ./dist/*.whl | |
| - name: Test wheel install | |
| run: python -c "import dodiscover; print(dodiscover.__version__)" | |
| - name: Remove wheel install | |
| run: python -m pip uninstall -yq dodiscover | |
| # | |
| # Test sdist-based Installation | |
| # | |
| - name: Install sdist | |
| run: pip install ./dist/*.tar.gz | |
| - name: Test sdist install | |
| run: python -c "import dodiscover; print(dodiscover.__version__)" | |
| - name: Remove sdist install | |
| run: python -m pip uninstall -yq dodiscover | |
| test: | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
| # oldest and newest supported versions | |
| python-version: ["3.10", "3.11"] # TODO: update to 3.12 when statsmodels supports | |
| networkx: [stable, main] | |
| exclude: | |
| - { python-version: "3.10", os: "macos-latest" } | |
| include: | |
| - { python-version: "3.10", os: "macos-13" } | |
| name: Unit-test ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: "x64" | |
| - name: Install packages via pip | |
| run: | | |
| pip install --upgrade pip | |
| pip install numpy scipy networkx statsmodels | |
| - name: Install package | |
| run: | | |
| pip install .[test] | |
| pip install . | |
| - name: Install Networkx (main) | |
| if: "matrix.networkx == 'main'" | |
| run: | | |
| pip uninstall -yq networkx | |
| pip install --progress-bar off git+https://github.com/networkx/networkx | |
| - name: Run pytest | |
| run: | | |
| pytest --cov dodiscover ./tests/unit_tests/ | |
| - name: Upload coverage stats to codecov | |
| if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.10' && matrix.networkx == 'stable' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| integration_test: | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.11"] | |
| networkx: [main] | |
| name: Integration test ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: "x64" | |
| - name: Install packages for Ubuntu | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y graphviz optipng libxft2 graphviz-dev | |
| - name: Setup torch | |
| run: | | |
| sudo apt-get install nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc | |
| - name: Install packages via pip | |
| run: | | |
| pip install --upgrade pip | |
| pip install numpy scipy networkx statsmodels | |
| pip install .[test,doc] | |
| - name: Run pytest # headless via Xvfb on linux | |
| run: | | |
| pytest tests/integration_tests | |
| # release is ran when a release is made on Github | |
| release: | |
| name: Release | |
| runs-on: ubuntu-latest | |
| needs: [style, build, test] | |
| if: startsWith(github.ref, 'refs/tags/') | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip setuptools wheel | |
| python -m pip install --progress-bar off build twine | |
| - name: Prepare environment | |
| run: | | |
| echo "RELEASE_VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV | |
| echo "TAG=${GITHUB_REF#refs/tags/}" >> $GITHUB_ENV | |
| - name: Download package distribution files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: package | |
| path: dist | |
| # TODO: refactor scripts to generate release notes from `whats_new.rst` file instead | |
| # - name: Generate release notes | |
| # run: | | |
| # python scripts/release_notes.py > ${{ github.workspace }}-RELEASE_NOTES.md | |
| - name: Publish package to PyPI | |
| run: | | |
| twine upload -u ${{ secrets.PYPI_USERNAME }} -p ${{ secrets.PYPI_PASSWORD }} dist/* | |
| - name: Publish GitHub release | |
| uses: softprops/action-gh-release@v2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| # body_path: ${{ github.workspace }}-RELEASE_NOTES.md | |
| prerelease: ${{ contains(env.TAG, 'rc') }} | |
| files: | | |
| dist/* |