test_and_deploy.yml

name: tests

on:
  push:
    branches: [ main ]
    tags:
      - '*'
  pull_request:
    branches: [ '*' ]

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]
    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: "3.9"
        - os: windows-latest
          python-version: "3.9"

    steps:
      - name: Cache tensorflow model
        uses: actions/cache@v3
        with:
          path: "~/.cellfinder"
          key: models-${{ hashFiles('~/.cellfinder/**') }}
      - uses: neuroinformatics-unit/actions/test@v2
        with:
          python-version: ${{ matrix.python-version }}


  # Run cellfinder tests to make sure cellfinder is still compatible
  # with cellfinder-core
  test_cellfinder:
    needs: [linting, manifest]
    name: Run cellfinder tests
    runs-on: ubuntu-latest
    steps:
      - name: Cache tensorflow model
        uses: actions/cache@v3
        with:
          path: "~/.cellfinder"
          key: models-${{ hashFiles('~/.cellfinder/**') }}

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

      - 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 cellfinder-core branch
          python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA
          # Install checked out copy of cellfinder
          python -m pip install .[dev]


      - name: Run cellfinder tests
        run: |
          python -m pytest --color=yes -v

  build_sdist_wheel:
    name: Build source distribution and wheel
    needs: [test, test_cellfinder]
    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 }}