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:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # os: [ubuntu-latest]
        # python-version: ["3.12"]
        os: [ubuntu-latest, macos-latest, macos-14]
        python-version: ["3.12", "3.11"]

    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 poetry
        uses: snok/install-poetry@v1

      - name: Install dependencies
        run: poetry install

      - name: Test with pytest
        run: |
          # Github action runners now have 4 cores
          poetry run pytest -s -v -n 4 --cov --cov-report xml:coverage-report/coverage.xml

      - 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.python-version == '3.12'
        uses: actions/upload-artifact@v2
        with:
          name: coverage-report
          path: coverage-report

  Codecov:
    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

  Build-Documentation:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v3

      - name: Set up Python 3.10
        uses: actions/setup-python@v4
        with:
          python-version: 3.10.4

      - name: Install poetry
        uses: snok/install-poetry@v1

      - name: Install dependencies
        run: poetry install

      - name: Build documentation
        run: |
          pip install -r docs/requirements.txt
          pip install .
          make html --directory=docs

  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

    # 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: Install poetry
      uses: snok/install-poetry@v1

    - name: Install package
      run: poetry install

   # This action uses Python Semantic Release v8
   # What this action does:
   # - Determines the next version number based on the commit history
    # - Creates a new tag with the new version number
    # - Pushes the new tag to GitHub
    # - Creates a GitHub release with the new version number
    - name: Python Semantic Release
      id: release
      uses: python-semantic-release/python-semantic-release@master
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}

    - name: Test Outputs of semantic release step
      run: |
        echo "${{ steps.release.outputs.released }}"
        echo "${{ steps.release.outputs.version }}"
        echo "${{ steps.release.outputs.tag }}"

    - name: Install packaging-related tool
      run:
        python3 -m pip install build twine

    # Build Package step:
    # After semantic release, we should have a new tag if the commit history
    # has been updated. If there isnt a new tag, then we dont need to build
    # a new package. If there is a new tag, then we need to build a new package
    # and publish it to PyPI
    - name: Build package
      if: steps.release.outputs.released == 'true'
      run: |
        poetry version ${{ steps.release.outputs.version }}
        python -m build --sdist --wheel --outdir dist/ .

    - name: Publish package distributions to PyPI
      if: steps.release.outputs.released == 'true'
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        verbose: true
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}

    - name: Set up QEMU
      if: steps.release.outputs.released == 'true'
      uses: docker/setup-qemu-action@v3

    - name: Set up Docker Buildx
      if: steps.release.outputs.released == 'true'
      uses: docker/setup-buildx-action@v3

    - name: Login to Docker Hub
      if: steps.release.outputs.released == 'true'
      uses: docker/login-action@v3
      with:
        username: ${{ secrets.DOCKERHUB_USERNAME }}
        password: ${{ secrets.DOCKERHUB_TOKEN }}

    - name: Login to the GitHub Container Registry
      if: steps.release.outputs.released == 'true'
      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: |
          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ steps.release.outputs.tag }}
          ghcr.io/${{ github.repository }}/nbiatoolkit:${{ steps.release.outputs.tag }}

    - name: Build
      if: steps.release.outputs.released == 'true'
      uses: docker/build-push-action@v5
      with:
        context: .
        platforms: linux/amd64,linux/arm64
        file: ./Dockerfile
        push: true
        tags: |
          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ steps.release.outputs.tag }}
          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
          ghcr.io/${{ github.repository }}/nbiatoolkit:${{ steps.release.outputs.tag }}
          ghcr.io/${{ github.repository }}/nbiatoolkit:latest
        labels: ${{ steps.meta.outputs.labels }}

  test_install_withPyPi:
    needs: Continuous-Deployment
    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;
          NBIAToolkit


  test_image_with_new_tag:
    needs: Continuous-Deployment
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v3

      - name: Test Image With new Tag
        run: |
          # test image with latest tag
          docker run --rm \
            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ steps.release.outputs.tag }} \
            NBIAToolkit


  test_image_with_latest_tag:
    needs: Continuous-Deployment
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v2

      - name: Test Image with "latest" Tag
        run: |
          docker run --rm \
            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
            NBIAToolkit

  Update-README:
    needs: Continuous-Deployment
    runs-on: ubuntu-latest
    # if: jobs.Continuous-Deployment.outputs.released == 'true'
    steps:
      - name: Checkout code
        uses: actions/checkout@v3

      - name: Get Current branch
        run: |
          echo "Current branch is: ${{ github.ref }}"
          echo "Current branch is: ${{ github.head_ref }}"
          echo "Current branch is: ${{ github.base_ref }}"
          echo "Current branch is: ${{ github.event_name }}"

          # if main, then git pull main
          if [ "${{ github.ref }}" == "refs/heads/main" ]; then
              git pull origin main
          fi

          # fix diverged branch
          git fetch origin ${{ github.head_ref }}
          git checkout ${{ github.head_ref }}

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

      - name: Install using PyPi
        run: |
          # update pip
          pip install .
          NBIAToolkit

      - name: Update README code block
        run: |
          awk '/``` bash NBIAToolkit-Output/ {
            print "``` bash NBIAToolkit-Output";
            print "> NBIAToolkit --version";
            system("NBIAToolkit --version");
            f=1;
            next
            } f && /```/ {
              print "```";
              f=0;
              next
            } !f' README.md > temp && mv temp README.md

      - name: Commit and push changes
        run: |
          LATEST_TAG=$(curl -s \
              "https://api.github.com/repos/${{ github.repository }}/releases/latest" \
              | jq -r .tag_name | sed 's/^v//')
          echo "LATEST_TAG=${LATEST_TAG}"
          # Check for changes
          if [[ $(git status --porcelain) ]]; then
              # Changes are present
              echo "Changes found. Committing and pushing..."

              git config --global user.name 'jjjermiah'
              git config --global user.email 'jjjermiah@users.noreply.github.com'

              # Add all changes
              git add .

              # Commit with a timestamp
              git commit -m "chore: Update README: $LATEST_TAG"

              # Push changes to the remote repository
              # if github.head_ref is not null
              # then push to the branch
              # else push to the base branch
              if [ -n "${{ github.head_ref }}" ]; then
                  git push origin HEAD:${{ github.head_ref }}
              else
                  git push origin HEAD:${{ github.ref }}
              fi


              echo "Changes committed and pushed successfully."
          else
              # No changes
              echo "No changes found. Nothing to commit or push."
          fi