python-package-conda.yml

name: Python Package using Conda

on: [push]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH
    - name: Install dependencies
      run: |
        conda env create --file devtools/conda-envs/msanalysis_env.yaml --name msanalysis
        # Activate the test environment
        conda activate msanalysis
        # Build and install package
        python setup.py develop --no-deps
        cd patches
        python add_elements.py
        cd ..
    - name: Test with pytest
      run: |
        conda install pytest
        pytest -v --cov-config=.coveragec --cov=msanalysis msanalysis