actions.yml

name: Continuous Integration / Deployment
on: [pull_request, push]

jobs:
  Format:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Apply formatting
        uses: github/super-linter@v4
        env:
          VALIDATE_ALL_CODEBASE: false
          VALIDATE_PYTHON_PYLINT: true
          VALIDATE_PYTHON_FLAKE8: true
          VALIDATE_PYTHON_ISORT: true
          DEFAULT_BRANCH: main
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          IGNORE_GITIGNORED_FILES: true

  Test_Linux:
    needs:
      - Format
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-variant: Mambaforge
          miniforge-version: 4.9.2-4
          use-mamba: true
          environment-file: envs/linux.yml
          use-only-tar-bz2: true
          auto-activate-base: false
          activate-environment: isicle
      
      - name: Install ISiCLE
        run: pip install --no-deps . 
    
      # - name: Test environment
      #   run: |
      #     pytest

  Test_Mac:
    needs:
      - Format
    runs-on: macos-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-variant: Mambaforge
          miniforge-version: 4.9.2-4
          use-mamba: true
          environment-file: envs/osx.yml
          use-only-tar-bz2: true
          auto-activate-base: false
          activate-environment: isicle
      
      - name: Install ISiCLE
        run: pip install --no-deps . 
    
      # - name: Test environment
      #   run: |
      #     pytest
  
  Deploy:
    needs:
      - Test_Linux
      - Test_Mac
    runs-on: ubuntu-latest
    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
    defaults:
      run:
        shell: bash -l {0}
    
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-variant: Mambaforge
          miniforge-version: 4.9.2-4
          use-mamba: true
          python-version: 3.9
          channels: conda-forge,bioconda
          use-only-tar-bz2: true
          auto-activate-base: true

      - name: Install dependencies
        run: |
          mamba install boa anaconda-client conda-verify

      - name: Build conda package
        run: |
          mkdir build/
          conda mambabuild conda-recipe/ --output-folder build/
          conda index build/

      - name: Convert to osx-64
        run: conda convert -p osx-64 build/linux-64/*.tar.bz2 -o build/

      - name: Upload packages
        env:
          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
        run: |
          anaconda upload build/linux-64/*.tar.bz2
          anaconda upload build/osx-64/*.tar.bz2