Fixes for dicot pipeline #243
Workflow file for this run
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| # Continuous integration | |
| name: CI | |
| on: | |
| pull_request: | |
| types: [opened, reopened, synchronize] | |
| paths: | |
| - "sleap_roots/**" | |
| - "tests/**" | |
| - ".github/workflows/ci.yml" | |
| - "environment.yml" | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - "sleap_roots/**" | |
| - "tests/**" | |
| - ".github/workflows/ci.yml" | |
| - "environment.yml" | |
| jobs: | |
| # Lint with black and docstring check with pydocstyle | |
| lint: | |
| # This job runs: | |
| # | |
| # 1. Linting with black | |
| # | |
| # 2. Docstring style checking with pydocstyle | |
| # Note: This uses Google-style docstring convention | |
| # Ref: https://google.github.io/styleguide/pyguide.html | |
| name: Lint | |
| runs-on: "ubuntu-22.04" | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| pip install --editable .[dev] | |
| - name: Run Black | |
| run: | | |
| black --check sleap_roots tests | |
| - name: Run pydocstyle | |
| run: | | |
| pydocstyle --convention=google sleap_roots/ | |
| # Tests with pytest | |
| tests: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-22.04", "windows-2022"] | |
| python: [3.9] | |
| name: Tests (${{ matrix.os }}, Python ${{ matrix.python }}) | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| - name: Setup Micromamba | |
| # https://github.com/mamba-org/setup-micromamba | |
| # Note: Set channel-priority in .condarc if needed | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| cache-environment-key: environment-${{ hashFiles('environment.yml') }}-${{ hashFiles('pyproject.toml') }} | |
| init-shell: >- | |
| bash | |
| powershell | |
| post-cleanup: all | |
| - name: Print environment info | |
| shell: bash -l {0} | |
| run: | | |
| which python | |
| micromamba info | |
| micromamba list | |
| pip freeze | |
| - name: Test with pytest | |
| if: ${{ !(startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9) }} | |
| shell: bash -l {0} | |
| run: | | |
| pytest | |
| - name: Test with pytest (with coverage) | |
| if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }} | |
| shell: bash -l {0} | |
| run: | | |
| pytest --cov=sleap_roots --cov-report=xml tests/ | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v3 | |
| if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }} | |
| with: | |
| fail_ci_if_error: true | |
| verbose: false |