python-package-conda.yml

name: freyja CI
on: 
  push:
    branches: [ main ]
  pull_request:
    
jobs:
  testsuite:
    runs-on: ubuntu-latest
      
    steps:
      # Downloads a copy of the code in your repository before running CI tests
      - name: Check out repository code
        uses: actions/checkout@v2

      - name: Setup for conda
        uses: conda-incubator/setup-miniconda@v2
        with:        
          auto-update-conda: true
          channels: bioconda,conda-forge
          channel-priority: true
          python-version: 3.7
          activate-environment: test
      
      - name: Install
        shell: bash -l {0}
        run: |
          conda install -n base conda-libmamba-solver
          conda config --set solver libmamba
          conda config --add channels bioconda
          conda config --add channels conda-forge          
          conda install --yes --file ci/conda_requirements.txt
          pip install -e . --no-deps 
          
      - name: Test
        shell: bash -l {0}
        run: |
          conda activate test
          make test

  lint:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: flake8
      uses: actions/setup-python@v2
      with:
        python-version: 3.7
    - name: install dependencies
      run: python -m pip install --upgrade pip
    - name: lint
      run: |
        pip install -q flake8
        make lint