build_check.yml

name: build_and_test

on:
  push:
    branches: 
      - master
  workflow_dispatch:

jobs:
  build_and_test:
    runs-on: ubuntu-20.04
    timeout-minutes: 60    
    steps:
      - uses: actions/checkout@v2
      - name: Setup conda, install packages, and test celloracle
        run: |
            sudo apt-get update
            sudo apt-get install -y bedtools
            wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
            bash miniconda.sh -b -p $HOME/miniconda
            source "$HOME/miniconda/etc/profile.d/conda.sh"
            hash -r
            conda config --set always_yes yes --set changeps1 no
            #conda update -q conda
            # Useful for debugging any issues with conda
            conda info -a
            # Create env
            conda create -q -n test-environment python=3.10
            # command to install dependencies
            conda activate test-environment
            conda install cython numpy pytest
            
            # Check pip
            echo pip_path
            which pip
            #Install fa2 for tutorial
            #pip install fa2
            # Install CellOracle
            pip install .
            # Show installed package
            conda list
            # command to run tests
            pytest -v