python-app.yaml

name: Python application

on: [pull_request]

jobs:
  monsdatest:   
    name: monsda-test 
    runs-on: "ubuntu-latest"
    defaults:
      run:
        shell: bash -el {0}
    # Docker Hub image that `postgres-job` executes in
    container: node:latest
    # service containers to run with `postgres-job`
    steps:      
      - uses: actions/checkout@master
        with:
          submodules: recursive
      - uses: conda-incubator/setup-miniconda@master
        with:
          miniconda-version: "latest"
          activate-environment: monsda-test
          environment-file: environment.yml
          python-version: 3.12.2
          channels: conda-forge,bioconda
          allow-softlinks: true
          channel-priority: flexible
          show-channel-urls: true
          use-only-tar-bz2: false
          auto-activate-base: false
      - name: build and install monsda
        run: |
          cd ${{ github.workspace }}
          echo "Build start"          
          python -m pip install --upgrade pip                
          python -m pip install build                                        
          python -m build
          pip install dist/*.whl
      - name: preparing test
        run: |          
          echo "Build finished, preparing tests"                     
          export a=$(monsda --version 2>&1 >/dev/null |sed 's/MONSDA version //g')          
          sed -i "s/\"VERSION\": \"FIXME\"/\"VERSION\": \"$a\"/g" tests/data/config_Test.json   
      - name: running test
        run: |   
          echo "Running tests" 
          cd ${{ github.workspace }}/tests
          ln -fs data/* .    
          mkdir -p CONDALIB
          monsda -j 6 -c config_Test.json --directory ${PWD} --use-conda --conda-prefix CONDALIB --save && echo "MONSDA test passed" || echo "MONSDA test failed"
          #chmod +x cicd_test.sh      
          #./cicd_test.sh