python-package-conda.yml

name: Python Package using Conda

on: [push, pull_request]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
      matrix:
        python-version: [3.7]       

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH
    - name: Install dependencies
      run: |
        conda config --add channels defaults
        conda config --add channels bioconda
        conda config --add channels conda-forge
        # conda config --set channel_priority flexible
        # conda env update --file environment.yml --name base
        conda create -n test-environment stream r-stringi python=${{ matrix.python-version }}
        source activate test-environment
        # conda install stream
        python -m pip install --upgrade pip
        pip install -e .
#     - name: Lint with flake8
#       run: |
#         conda install flake8
#         # stop the build if there are Python syntax errors or undefined names
#         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
#         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
#         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test
      run: |
        source activate test-environment
        stream_run_test