[pre-commit.ci] pre-commit autoupdate (#1236) #2531
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| name: Run code coverage | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| tags-ignore: # exclude tags created by "ci_addons publish_github_release" | |
| - 'latest' | |
| - 'latest-tmp' | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| run-coverage: | |
| name: ${{ matrix.os }}, opt reqs ${{ matrix.opt_req }} | |
| runs-on: ${{ matrix.os }} | |
| # TODO handle forks | |
| # run pipeline on either a push event or a PR event on a fork | |
| # if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}-${{ matrix.opt_req }} | |
| cancel-in-progress: true | |
| strategy: | |
| matrix: | |
| include: | |
| - { os: ubuntu-latest , opt_req: true } | |
| - { os: ubuntu-latest , opt_req: false } | |
| - { os: windows-latest, opt_req: false } | |
| - { os: macos-latest , opt_req: false } | |
| env: # used by codecov-action | |
| OS: ${{ matrix.os }} | |
| PYTHON: '3.12' # TODO: Update to 3.13 when linkml and its deps support 3.13 | |
| steps: | |
| - name: Checkout repo with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required to determine the version | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON }} | |
| - name: Upgrade pip | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install package | |
| if: ${{ ! matrix.opt_req }} | |
| run: | | |
| python -m pip install ".[test]" | |
| - name: Install package with optional dependencies | |
| if: ${{ matrix.opt_req }} | |
| run: | | |
| python -m pip install ".[test,tqdm,zarr,termset]" | |
| - name: Run tests and generate coverage report | |
| run: | | |
| # coverage is configured in pyproject.toml | |
| # codecov uploader requires xml format | |
| python -m pip list | |
| pytest --cov --cov-report=xml --cov-report=term | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| files: ./coverage.xml | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| run-ros3-coverage: | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} # necessary for conda | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { name: linux-python3.13-ros3 , python-ver: "3.13", os: ubuntu-latest } | |
| steps: | |
| - name: Checkout repo with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required to determine the version | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| activate-environment: ros3 | |
| environment-file: environment-ros3.yml | |
| python-version: ${{ matrix.python-ver }} | |
| channels: conda-forge | |
| auto-activate-base: false | |
| - name: Install run dependencies | |
| run: | | |
| pip install . | |
| pip list | |
| - name: Conda reporting | |
| run: | | |
| conda info | |
| conda config --show-sources | |
| conda list --show-channel-urls | |
| - name: Run ros3 tests # TODO include gallery tests after they are written | |
| run: | | |
| pytest --cov --cov-report=xml --cov-report=term tests/unit/test_io_hdf5_streaming.py | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| files: ./coverage.xml | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |