test_and_deploy.yml

name: tests

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:
  # 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
    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
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # Run all supported Python versions on linux
        os: [ubuntu-latest]
        python-version: ["3.8", "3.9", "3.10"]
        # Include one windows, one macos run
        include:
        - os: macos-latest
          python-version: "3.10"
        - os: windows-latest
          python-version: "3.10"

    steps:
      # Cache the tensorflow model so we don't have to remake it every time
      - name: Cache tensorflow model
        uses: actions/cache@v3
        with:
          path: "~/.cellfinder"
          key: models-${{ hashFiles('~/.cellfinder/**') }}
      # 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 }}
          use-xvfb: true

  # Run brainglobe-workflows cellfinder-CLI tests to check for
  # breakages
  test_cellfinder_cli:
    needs: [linting, manifest]
    name: Run cellfinder CLI to check for breakages
    runs-on: ubuntu-latest
    steps:
      - name: Cache tensorflow model
        uses: actions/cache@v3
        with:
          path: "~/.cellfinder"
          key: models-${{ hashFiles('~/.cellfinder/**') }}

      - name: Checkout brainglobe-workflows
        uses: actions/checkout@v3
        with:
          repository: 'brainglobe/brainglobe-workflows'

      - name: Set up Python 3.10
        uses: actions/setup-python@v3
        with:
          python-version: "3.10"

      - name: Install test dependencies
        run: |
          python -m pip install --upgrade pip wheel
          # Install latest SHA on this brainglobe-workflows branch
          python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA
          # Install checked out copy of brainglobe-workflows
          python -m pip install .[dev]

      - name: Run cellfinder CLI test of brainglobe-workflows
        run: |
          python -m pytest --color=yes -v tests/cellfinder

  build_sdist_wheel:
    name: Build source distribution and wheel
    needs: [test, test_cellfinder_cli]
    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: actions/download-artifact@v3
      with:
        name: artifact
        path: dist
    - uses: pypa/gh-action-pypi-publish@v1.5.0
      with:
        user: __token__
        password: ${{ secrets.TWINE_API_KEY }}