main.yml

name: CI-CD

# only run on pushes to main or pull requests
on:
  push:
    # push to any branch *
    branches: [ "*" ]
  pull_request:
    branches: [ main , development ]

jobs:
  ################################################################################################
  # Unit-Tests: Run unit tests using pytest
  ################################################################################################
  Unit-Tests:
    runs-on: ${{ matrix.os }}
    timeout-minutes: 15 # Consider increasing timeout
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, macos-14] # , windows-latest removed for now
        env: ["py310", "py311", "py312"]

    steps:
      - uses: actions/checkout@v4

      - name: Install Pixi
        uses: prefix-dev/setup-pixi@v0.8.1
        with:
          environments: ${{ matrix.env }}
          pixi-version: v0.36.0
          cache: true
          locked: false # wont be the same because of the tag

      - name: Run pytest
        run: |
          pixi run -e ${{ matrix.env }} test

      - name: Upload coverage report artifact to be used by Codecov
        # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12
        if: matrix.os == 'ubuntu-latest' && matrix.env == 'py312'
        uses: actions/upload-artifact@v4
        with:
          name: coverage-report
          path: coverage-report
  Build-Documentation:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Install Pixi
        uses: prefix-dev/setup-pixi@v0.8.1
        with:
          environments: docs
          pixi-version: v0.36.0
          cache: true
          locked: false # wont be the same because of the tag

      - name: Build documentation
        run: |
          pixi run -e docs doc-build

  Code-Coverage:
    needs: Unit-Tests
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v3

      - name: Download coverage.xml artifact
        uses: actions/download-artifact@v2
        with:
          name: coverage-report
          path: coverage-report

      - name: Use Codecov to track coverage
        uses: codecov/codecov-action@v3
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: ./coverage-report/coverage.xml
          fail_ci_if_error: true
          verbose: true
          name: codecov-umbrella


#   Continuous-Deployment:
#     permissions:
#         contents: write
#         packages: write
#         issues: write
#         pull-requests: write

#     needs: [Unit-Tests]

#     # if pulling to main, deploy to PyPI
#     if: github.ref == 'refs/heads/main'

#     # Set up operating system
#     runs-on: ubuntu-latest

#     outputs:
#       released: ${{ steps.release.outputs.released }}
#       version: ${{ steps.release.outputs.version }}
#       tag: ${{ steps.release.outputs.tag }}

#     # Define job steps
#     steps:
#     - name: Set up Python 3.12
#       uses: actions/setup-python@v2
#       with:
#         python-version: 3.12

#     - name: Check-out repository
#       uses: actions/checkout@v2
#       with:
#         fetch-depth: 0

#     - name: Python Semantic Release
#       id: release
#       uses: python-semantic-release/python-semantic-release@master
#       with:
#         github_token: ${{ secrets.GITHUB_TOKEN }}

#   Publish-To-PyPi:
#     needs: Continuous-Deployment
#     if: needs.Continuous-Deployment.outputs.released == 'true'
#     runs-on: ubuntu-latest
#     steps:
#       - name: Checkout the code with tag ${{ needs.Continuous-Deployment.outputs.tag }}
#         uses: actions/checkout@v3
#         with:
#           ref: ${{ needs.Continuous-Deployment.outputs.tag }}

#       - name: Set up Python 3.12
#         uses: actions/setup-python@v4
#         with:
#           python-version: 3.12

#       - name: Install Package-Building Tool
#         run:
#           python3 -m pip install build twine

#       - name: Build package
#         run:
#           python3 -m build --sdist --wheel --outdir dist/

#       - name: Publish to PyPI
#         uses: pypa/gh-action-pypi-publish@release/v1
#         with:
#           verbose: true
#           user: __token__
#           password: ${{ secrets.PYPI_API_TOKEN }}

#   Build-Docker-Images:
#     needs: Continuous-Deployment
#     if: needs.Continuous-Deployment.outputs.released == 'true'
#     runs-on: ubuntu-latest
#     steps:
#       - name: Checkout code
#         uses: actions/checkout@v3
#         with:
#           ref: ${{ needs.Continuous-Deployment.outputs.tag }}

#       - name: Set up QEMU
#         uses: docker/setup-qemu-action@v3

#       - name: Set up Docker Buildx
#         uses: docker/setup-buildx-action@v3

#       - name: Login to Docker Hub
#         uses: docker/login-action@v3
#         with:
#           username: ${{ secrets.DOCKERHUB_USERNAME }}
#           password: ${{ secrets.DOCKERHUB_TOKEN }}

#       - name: Login to the GitHub Container Registry
#         uses: docker/login-action@v3
#         with:
#           registry: ghcr.io
#           username: ${{ github.actor }}
#           password: ${{ secrets.GITHUB_TOKEN }}

#       - name: Extract metadata (tags, labels) for Docker
#         id: meta
#         uses: docker/metadata-action@v3
#         with:
#           images: |
#             ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
#             ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}

#       - name: Build and push Docker images
#         uses: docker/build-push-action@v5
#         with:
#           context: .
#           platforms: linux/amd64,linux/arm64
#           file: ./Dockerfile
#           push: true
#           tags: |
#             ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
#             ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
#             ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
#             ghcr.io/${{ github.repository }}/nbiatoolkit:latest
#           labels: ${{ steps.meta.outputs.labels }}

#   Test-PyPi-Install:
#     needs: Publish-To-PyPi
#     runs-on: ${{ matrix.os }}
#     strategy:
#       matrix:
#         os: [ubuntu-latest, macos-latest, macos-14]
#         python-version: ["3.12", "3.11", "3.10"]

#     steps:
#       - uses: actions/checkout@v3

#       - name: Set up Python ${{ matrix.python-version }}
#         uses: actions/setup-python@v4
#         with:
#           python-version: ${{ matrix.python-version }}

#       - name: Install using PyPi
#         run: |
#           pip install nbiatoolkit==${{ needs.Continuous-Deployment.outputs.version }}
#           NBIAToolkit

#   Test-Docker-Image:
#     needs: Build-Docker-Images
#     runs-on: ${{ matrix.os }}
#     strategy:
#       matrix:
#         os: [ubuntu-latest, macos-latest]

#     steps:
#       - name: Setup Docker to pull images
#         uses: docker/setup-buildx-action@v3

#       - name: Install using Docker
#         run: |
#           docker pull ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }};
#           docker run --rm ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} NBIAToolkit