hdmf/.github/workflows/run_coverage.yml at dev · hdmf-dev/hdmf · GitHub

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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:

permissions:
  contents: read

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: '3.14'
    steps:
      - name: Checkout repo with submodules
        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
        with:
          persist-credentials: false
          submodules: 'recursive'
          fetch-depth: 0  # tags are required to determine the version

      - name: Set up Python
        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1  # v6.3.0
        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 --group test .

      - name: Install package with optional dependencies
        if: ${{ matrix.opt_req }}
        run: |
          python -m pip install --group test ".[tqdm,sparse,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
        # immutable release (see .github/zizmor.yml for the policy exception)
        uses: codecov/codecov-action@v7.0.0
        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-python3.14-ros3  , python-ver: "3.14", os: ubuntu-latest }
    steps:
      - name: Checkout repo with submodules
        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
        with:
          persist-credentials: false
          submodules: 'recursive'
          fetch-depth: 0  # tags are required to determine the version

      - name: Set up Conda
        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5  # v4.0.1
        with:
          auto-update-conda: true
          activate-environment: ros3
          environment-file: environment-ros3.yml
          python-version: ${{ matrix.python-ver }}
          channels: conda-forge
          auto-activate: false

      - name: Install run dependencies
        run: |
          python -m pip install .
          python -m 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: |
          python -m pytest --cov --cov-report=xml --cov-report=term tests/unit/test_io_hdf5_streaming.py

      - name: Upload coverage to Codecov
        # immutable release (see .github/zizmor.yml for the policy exception)
        uses: codecov/codecov-action@v7.0.0
        with:
          fail_ci_if_error: true
          files: ./coverage.xml
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}