test_and_deploy.yml

name: Test (and Deploy to PyPI on tag)

on:
  # Only run on pushes to main, or when version tags are pushed
  push:
    branches:
      - "main"
    tags:
      - "v**"
  # Run on all pull-requests
  pull_request:
  schedule:
  # Runs at 6:10am UTC on Monday
    - cron: '10 6 * * 1'
  # Allow workflow dispatch from GitHub
  workflow_dispatch:

concurrency:
  # Cancel this workflow if it is running,
  # and then changes are applied on top of the HEAD of the branch,
  # triggering another run of the workflow
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  linting:
    runs-on: ubuntu-latest
    name: Check Linting
    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: Run package tests
    timeout-minutes: 120
    runs-on: ${{ matrix.os }}
    env:
      KERAS_BACKEND: torch
      CELLFINDER_TEST_DEVICE: cpu
      # pooch cache dir
      BRAINGLOBE_TEST_DATA_DIR: "~/.pooch_cache"

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

    steps:
      - uses: actions/checkout@v4
      - name: Cache pooch data
        uses: actions/cache@v4
        with:
          path: "~/.pooch_cache"
          # hash on conftest in case url changes
          key: ${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/pooch_registry.txt') }}
      # Cache the tensorflow model so we don't have to remake it every time
      - name: Cache brainglobe directory
        uses: actions/cache@v3
        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
          key: brainglobe
      # Setup pyqt libraries
      - name: Setup qtpy libraries
        uses: tlambert03/setup-qt-libs@v1
      # Setup VTK with headless display
      - uses: pyvista/setup-headless-display-action@v2
      # Run all tests
      - uses: neuroinformatics-unit/actions/test@v2
        with:
          python-version: ${{ matrix.python-version }}
          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
          use-xvfb: true

      - 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

  test_numba_disabled:
    needs: [linting, manifest]
    name: Run tests with numba disabled
    timeout-minutes: 120
    runs-on: ubuntu-latest
    env:
      NUMBA_DISABLE_JIT: "1"
      PYTORCH_JIT: "0"
      # pooch cache dir
      BRAINGLOBE_TEST_DATA_DIR: "~/.pooch_cache"

    steps:
      - uses: actions/checkout@v4
      - name: Cache brainglobe directory
        uses: actions/cache@v3
        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
          key: brainglobe

      - name: Cache pooch data
        uses: actions/cache@v4
        with:
          path: "~/.pooch_cache"
          key: ${{ runner.os }}-3.10-${{ hashFiles('**/pooch_registry.txt') }}

      # Setup pyqt libraries
      - name: Setup qtpy libraries
        uses: tlambert03/setup-qt-libs@v1
      # Setup VTK with headless display
      - uses: pyvista/setup-headless-display-action@v2
      # Run test suite with numba disabled
      - uses: neuroinformatics-unit/actions/test@v2
        with:
          python-version: "3.12"
          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

  # Run brainglobe-workflows brainmapper-CLI tests to check for
  # breakages
  test_brainmapper_cli:
    needs: [linting, manifest]
    name: Run brainmapper tests to check for breakages
    timeout-minutes: 120
    runs-on: ubuntu-latest
    env:
      KERAS_BACKEND: torch
      CELLFINDER_TEST_DEVICE: cpu
    steps:
      - name: Cache brainglobe directory
        uses: actions/cache@v3
        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
          key: brainglobe
      - name: Checkout brainglobe-workflows
        uses: actions/checkout@v3
        with:
          repository: 'brainglobe/brainglobe-workflows'

      - name: Set up Python 3.12
        uses: actions/setup-python@v3
        with:
          python-version: "3.12"

      - name: Install test dependencies
        run: |
          python -m pip install --upgrade pip wheel
          # Install cellfinder from the latest SHA on this branch
          python -m pip install "cellfinder @ git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA"

          # Install checked out copy of brainglobe-workflows
          python -m pip install .[dev]

      - name: Run brainmapper tests in brainglobe-workflows
        run: |
          python -m pytest --color=yes -v tests/brainmapper


  build_sdist_wheel:
    name: Build source distribution
    needs: [test, test_numba_disabled]
    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_wheel]
    if: github.event_name == 'push' && github.ref_type == 'tag'
    runs-on: ubuntu-latest
    steps:
    - uses: neuroinformatics-unit/actions/upload_pypi@v2
      with:
        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}