test_and_deploy.yml

name: tests

on:
  push:
    branches:
      - "main"
    tags:
      - "v**"
  pull_request:
  schedule:
  # Runs at 6:10am UTC on Monday
    - cron: '10 6 * * 1'
  workflow_dispatch:

jobs:
  linting:
    name: Check Linting
    runs-on: ubuntu-latest
    steps:
      - uses: neuroinformatics-unit/actions/lint@v2

  manifest:
    name: Check Manifest
    runs-on: ubuntu-latest
    steps:
      - uses: neuroinformatics-unit/actions/check_manifest@v2

  test:
    needs: [linting, manifest]
    name: ${{ matrix.os }} py${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}

    strategy:
      matrix:
        # Run all supported Python versions on linux
        os: [ubuntu-latest]
        python-version: ["3.10", "3.11", "3.12"]
        # Include one windows and two macOS (intel based and arm based) runs
        include:
          - os: macos-13
            python-version: "3.12"
          - os: macos-latest
            python-version: "3.12"
          - os: windows-latest
            python-version: "3.12"

    steps:
      - name: Cache data
        uses: actions/cache@v4
        with:
          path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually
            ~/.brainglobe
            !~/.brainglobe/atlas.tar.gz
          # hash on conftest in case url changes
          key: brainglobe-dir-${{ runner.os }}${{ hashFiles('**/conftest.py') }}


      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      # these libraries enable testing on Qt on linux
      - uses: pyvista/setup-headless-display-action@v2
        with:
          qt: true
      # Run tests
      - uses: neuroinformatics-unit/actions/test@v2
        with:
          python-version: ${{ matrix.python-version }}
          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}

  test_numba_disabled:
    needs: [ linting, manifest ]
    name: Run tests with numba disabled
    runs-on: ubuntu-latest
    env:
      NUMBA_DISABLE_JIT: "1"


    steps:
      - name: Cache data
        uses: actions/cache@v4
        with:
          path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually
            ~/.brainglobe
            !~/.brainglobe/atlas.tar.gz
          # hash on conftest in case url changes
          key: brainglobe-dir-${{ runner.os }}${{ hashFiles('**/conftest.py') }}

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"
      # these libraries enable testing on Qt on linux
      - uses: pyvista/setup-headless-display-action@v2
        with:
          qt: true
      # Run test suite with numba disabled
      - uses: neuroinformatics-unit/actions/test@v2
        with:
          python-version: "3.11"
          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
          codecov-flags: "numba"


      - name: Notify slack on scheduled failure
        if: failure() && github.event_name == 'schedule'
        uses: ravsamhq/notify-slack-action@v2
        with:
          status: ${{ job.status }} # required
          notify_when: 'failure'
        env:
          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_NOTIFYBOT_WEBHOOK_URL }} # required


  build_sdist_wheels:
    name: Build source distribution
    needs: [test]
    if: github.event_name == 'push' && github.ref_type == 'tag'
    runs-on: ubuntu-latest
    steps:
    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2

  upload_all:
    name: Publish build distributions
    needs: [build_sdist_wheels]
    runs-on: ubuntu-latest
    steps:
    - uses: neuroinformatics-unit/actions/upload_pypi@v2
      with:
        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}