run_coverage.yml

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 }}
    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
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
    env:
      OS: ${{ matrix.os }}
      PYTHON: '3.12'
    steps:
      - name: Cancel non-latest runs
        uses: styfle/cancel-workflow-action@0.11.0
        with:
          all_but_latest: true
          access_token: ${{ github.token }}

      - uses: actions/checkout@v4
        with:
          submodules: 'recursive'
          fetch-depth: 0  # tags are required for versioneer to determine the version

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: ${{ env.PYTHON }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install -r requirements-dev.txt -r requirements.txt

      # - name: Install optional dependencies
      #   if: ${{ matrix.opt_req }}
      #   run: python -m pip install -r requirements-opt.txt

      - name: Install package
        run: |
          python -m pip install -e .  # must install in editable mode for coverage to find sources
          python -m pip list

      - name: Run unit tests and generate coverage report
        run: |
          python -m coverage run test.py --pynwb
          python -m coverage xml  # codecov uploader requires xml format
          python -m coverage report -m

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          flags: unit
          files: coverage.xml
          fail_ci_if_error: true
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

      - name: Run integration tests and generate coverage report
        run: |
          python -m coverage run -p test.py --integration --validation-module --backwards
          # validation CLI tests generate separate .coverage files that need to be merged
          python -m coverage combine
          python -m coverage xml  # codecov uploader requires xml format
          python -m coverage report -m

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          flags: integration
          files: coverage.xml
          fail_ci_if_error: true
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}