[WIP] Add new functions/methods to featurize module #1469
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Testing Linux | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| cache-dependency-path: pyproject.toml | |
| - uses: pre-commit/[email protected] | |
| test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} # enables conda/mamba env activation by reading bash profile | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| split: [1, 2, 3, 4, 5] | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba | |
| uses: mamba-org/setup-micromamba@main | |
| - name: Create mamba environment | |
| run: | | |
| micromamba create -n lobpy python=${{ matrix.python-version }} --yes | |
| - name: Install uv | |
| run: micromamba run -n lobpy pip install uv | |
| - name: Install LobsterPy and dependencies | |
| run: | | |
| micromamba activate lobpy | |
| uv pip install --upgrade pip | |
| uv pip install --editable '.[tests,featurizer]' | |
| - name: Test with pytest and coverage | |
| # run this locally to update tests durations | |
| # pytest --cov=lobsterpy --cov-append --splits 1 --group 1 --durations-path ./tests/test_data/.pytest-split-durations --store-durations | |
| env: | |
| MPLBACKEND: Agg # non-interactive backend for matplotlib | |
| run: | | |
| micromamba activate lobpy | |
| pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 5 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations | |
| - name: Upload coverage | |
| if: matrix.python-version == '3.10' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-${{ matrix.python-version }}-${{ matrix.split }} | |
| include-hidden-files: true | |
| overwrite: false | |
| path: ./.coverage | |
| - name: Upload test durations artifact | |
| if: matrix.python-version == '3.10' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-durations-${{ matrix.python-version }}-${{ matrix.split }} | |
| include-hidden-files: true | |
| path: ./tests/test_data/.pytest-split-durations | |
| coverage: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Coverage | |
| run: | | |
| python -m pip install coverage[toml] | |
| - name: Download coverage artifacts | |
| continue-on-error: true | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: coverage-3.10-* | |
| - name: Run coverage | |
| continue-on-error: true | |
| run: | | |
| coverage combine coverage*/.coverage* | |
| coverage report --show-missing | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: JaGeo/LobsterPy | |
| commit-durations: | |
| if: github.repository_owner == 'JaGeo' && github.ref == 'refs/heads/main' | |
| needs: test | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} # enables conda/mamba env activation by reading bash profile | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba | |
| uses: mamba-org/setup-micromamba@main | |
| - name: Create mamba environment | |
| run: | | |
| micromamba create -n lobpy_test python=3.10 --yes | |
| - name: Install uv | |
| run: micromamba run -n lobpy_test pip install uv | |
| - name: Install lobsterpy and dependencies | |
| run: | | |
| micromamba activate lobpy_test | |
| uv pip install --upgrade pip | |
| uv pip install -e .[tests,featurizer] | |
| - name: Download test duration artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: test-durations-* | |
| - name: Compute average of test durations | |
| run: | | |
| micromamba activate lobpy_test | |
| python3 .github/scripts/average_test_durations.py | |
| rm -rf test-durations-* | |
| - name: Create Pull Request to push consolidated test durations | |
| uses: peter-evans/create-pull-request@v7 | |
| with: | |
| commit-message: update test durations | |
| title: Update test durations file | |
| body: Auto updated test durations file | |
| branch: update-test-durations | |
| delete-branch: true | |
| base: main | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| cache-dependency-path: pyproject.toml | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[docs,featurizer] | |
| - name: Build | |
| run: sphinx-build -W docs _build |