cgatcore_python.yml

name: cgatcore

on: [push, pull_request]

jobs:
  build:
    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest", "macos-latest"]
        python-version: ["3.10", "3.11", "3.12"]

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v3

      - name: Cache conda
        uses: actions/cache@v3
        env:
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-core.yml') }}

      - name: Set installer URL
        id: set-installer-url
        run: |
          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
            echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" >> $GITHUB_ENV
          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
            echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh" >> $GITHUB_ENV
          fi

      - uses: conda-incubator/setup-miniconda@v2
        with:
          installer-url: ${{ env.installer-url }}
          python-version: ${{ matrix.python-version }}
          channels: conda-forge, bioconda, defaults
          channel-priority: true
          activate-environment: cgat-core
          environment-file: conda/environments/cgat-core.yml

      - name: Configure Conda Paths
        run: echo "/usr/share/miniconda3/condabin" >> $GITHUB_PATH

      - name: Show conda
        run: |
          conda info
          conda list

      - name: Debug Python Environment
        run: |
          python --version
          pip list
          openssl version

      - name: Test
        run: |
          pip install .
          ./all-tests.sh


  deploy_docs:
    name: Deploy MkDocs Documentation
    runs-on: ubuntu-latest
    needs: build

    steps:
      - uses: actions/checkout@v3

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

      - name: Install MkDocs and Dependencies
        run: |
          pip install mkdocs mkdocs-material mkdocstrings[python]

      - name: Build and Deploy MkDocs Site
        run: mkdocs gh-deploy --force --clean
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}