cicd.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Python package

on:
  push:
    branches: [ "main", "release" ]
  pull_request:
    branches: [ "main", "release" ]

jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
    - name: Set up Python 3.10
      uses: actions/setup-python@v3
      with:
        python-version: "3.10"
    - name: Set up pre-commit
      run: python -m pip install pre-commit && pre-commit install
    - name: Run pre-commit
      run: pre-commit run --all-files

  test:
    runs-on: ubuntu-latest
    needs: lint
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.10", "3.11"]

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install ".[test]"
    - name: Test with pytest
      run: |
        pytest
    - name: Codecov
      # You may pin to the exact commit or the version.
      # uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
      env:
        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
      uses: codecov/codecov-action@v3.1.4
      with:
        # Specify whether the Codecov output should be verbose
        verbose: true # optional

  docker_test:
    runs-on: ubuntu-latest
    needs: [lint]
    steps:
    - uses: actions/checkout@v3
    - name: Set up Python
      uses: actions/setup-python@v3
      with:
        python-version: '3.10'
    - name: Install dependencies
      run: |
        python -m pip install ".[build]"
    - name: build wheel
      run: python -m build
    - name: Set up Docker Buildx
      uses: docker/setup-buildx-action@v2
    # Docker Setup
    - name: Build Docker image
      id: dockerbuild
      run: |
        docker build -t ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") .

    # Quick test on the docker image
    - name: Test Docker image
      run: |
        docker run --rm -v ${PWD}:/data/ \
          ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") \
          flimsay fill_blib /data/tests/unit_tests/data/test.blib /data/out.blib


  publish:
    runs-on: ubuntu-latest
    if: startsWith(github.event_name, 'push') && startsWith(github.ref, 'refs/heads/release')
    needs: [lint, test, docker_test]

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python
      uses: actions/setup-python@v3
      with:
        python-version: '3.10'
    - name: Install dependencies
      run: |
        python -m pip install ".[build]"

    - name: Set up quarto
      uses: quarto-dev/quarto-actions/setup@v2
    - name: Render README
      run: quarto render README.qmd
    - name: build wheel
      run: python -m build
    - name: pypi-publish
      uses: pypa/gh-action-pypi-publish@v1.8.8
      with:
        # Password for your PyPI user or an access token
        password: ${{ secrets.PYPI_TOKEN }} # optional
        # The target directory for distribution
        packages-dir: dist # optional
        # Show verbose output.
        verbose: true # optional, default is false
        skip-existing: true

    - name: Set up Docker Buildx
      uses: docker/setup-buildx-action@v2

    - name: Login to the GitHub Container Registry
      uses: docker/login-action@v2
      with:
        registry: ghcr.io
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    # Docker Setup
    - name: Build Docker image
      id: dockerbuild
      run: |
        docker build -t ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") .

    # Quick test on the docker image
    - name: Test Docker image
      run: |
        docker run --rm -v ${PWD}:/data/ ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") \
          flimsay fill_blib /data/tests/unit_tests/data/test.blib /data/out.blib

    # Publish Docker
    - name: Push the Docker image to the GHCR
      id: ghcr_push
      run: |
          docker push ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)")