tests.yml

name: Tests
on: [push, pull_request]
jobs:
  tests:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13-dev']
        # https://numpy.org/neps/nep-0029-deprecation_policy.html
        numpy-version: ['1.22', 'latest', 'dev']
        exclude:
          - python-version: '3.12'
            numpy-version: '1.22'
          - python-version: '3.13-dev'
            numpy-version: '1.22'
      fail-fast: false
    steps:
      - uses: actions/checkout@v2
      - uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install Dependencies
        run: |
          set -x
          set -e
          python -m pip install -r requirements-dev.txt
          if [[ ${{ matrix.numpy-version }} == 'latest' ]]; then
              python -m pip install --upgrade numpy
          elif [[ ${{ matrix.numpy-version }} == 'dev' ]]; then
              python -m pip install --pre --upgrade --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
          else
              python -m pip install --upgrade numpy==${{ matrix.numpy-version }}.*
          fi
      - name: Test Installation
        run: |
          python -m pip install --verbose .
        # COVERAGE_CORE=sysmon does not work with Cython. Since coverage is
        # really slow without it (see
        # https://github.com/nedbat/coveragepy/issues/1665), just omit Cython
        # coverage in 3.12. Hopefully by the time it is our minimal version it
        # will work with Cython, or trace coverage will be faster again.
      - name: Set CYTHON_COVERAGE=1
        run: echo "CYTHON_COVERAGE=1" >> $GITHUB_ENV
        if: matrix.python-version != '3.12' && matrix.python-version != '3.13-dev'
      - name: Disable Coverage Plugin
        run: sed -i '/plugins = Cython.Coverage/d' .coveragerc
        if: matrix.python-version == '3.12' || matrix.python-version == '3.13-dev'
      - name: In-place build
        run: |
          python setup.py clean
          python setup.py build_ext --inplace
      - name: Run Doctests
        run: |
          ./run_doctests
        # A NumPy 2.0 compatible skimage doesn't support 3.9, and we need a
        # version of matplotlib that requires NumPy 1.23. Easiest to just
        # skip this for now.
        if: matrix.numpy-version != 'dev' && matrix.python-version != '3.9' && matrix.numpy-version != '1.22'
      - name: Run Slotscheck
        run: |
          python -m slotscheck ndindex
      # Enable experimental faster sys.monitoring coverage for Python 3.12
      - name: Set COVERAGE_CORE=sysmon
        run: echo "COVERAGE_CORE=sysmon" >> $GITHUB_ENV
        if: matrix.python-version == '3.12' || matrix.python-version == '3.13-dev'
      - name: Run Tests
        run: |
          set -x
          set -e

          python -We:invalid -We::SyntaxWarning -m compileall -f -q ndindex/
          # The coverage requirement check is done by the coverage report line below
          PYTEST_FLAGS="$PYTEST_FLAGS -v --cov-fail-under=0";
          pytest $PYTEST_FLAGS
          # Coverage. This also sets the failing status if the
          # coverage is not 100%. Travis sometimes cuts off the last command, which is
          # why we print stuff at the end.
          if ! coverage report -m; then
              echo "Coverage failed";
              false;
          else
              echo "Coverage passed";
          fi;