python-tiledbsoma-ml.yml

name: python-tiledbsoma-ml

on:
  pull_request:
    branches: ["*"]
    paths:
      - "!**"
      - "other_packages/python/tiledbsoma_ml/**"
      - ".github/workflows/python-tiledbsoma-ml.yml"

  push:
    branches: [main]
    paths:
      - "!**"
      - "other_packages/python/tiledbsoma_ml/**"
      - ".github/workflows/python-tiledbsoma-ml.yml"

  workflow_dispatch:

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Restore pre-commit cache
        uses: actions/cache@v4
        with:
          path: ~/.cache/pre-commit
          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}

      - name: Install pre-commit
        run: pip -v install pre-commit

      - name: Run pre-commit hooks on all files
        run: pre-commit run -v -a

  tests:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip
          cache-dependency-path: python-spec/requirements-py${{ matrix.python-version }}.txt

      - name: Install prereqs
        working-directory: ./other_packages/python/tiledbsoma_ml/
        run: |
          pip install --upgrade pip wheel pytest pytest-cov setuptools
          pip install .

      - name: Run tests
        run: |
          PYTHONPATH=$(pwd)/other_packages/python/tiledbsoma_ml python -m pytest \
            --cov=other_packages/python/tiledbsoma_ml/src \
            --cov-report=xml other_packages/python/tiledbsoma_ml/tests \
            -v

      - name: Report coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          flags: python
          # Although Codecov isn't supposed to require an auth token for public repos like this one,
          # the uploader can be unreliable without one; see
          #     https://github.com/codecov/codecov-action/issues/557#issuecomment-1216749652
          # As of this writing (8 Nov 2022) the CODECOV_TOKEN was generated by @aaronwolen in his
          # Codecov settings page for this repo, then filled into the GitHub Actions secrets.
          token: ${{ secrets.CODECOV_TOKEN }}

  build:
    # for now, just do a test build to ensure that it works
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Set up environment
        working-directory: ./other_packages/python/tiledbsoma_ml/
        run: |
          pip install --upgrade build pip wheel setuptools setuptools-scm
          python -m build .