tests.yml

name: Check resource validity and run tests

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    steps:
    - name: Check out repo
      uses: actions/checkout@v2
    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: 3.9
    - name: Install dependencies
      run: |
        sudo apt-get install libstdc++6 python3-dev graphviz libgraphviz-dev pkg-config
        pip install future requests pygraphviz
        pip install mypy pytest-cov
        pip install .[all]
        git clone https://github.com/sorgerlab/indra.git $HOME/indra
        pip install bel_resources==0.0.3
    - name: Check references and export generation
      run: |
        export PYTHONPATH=$PYTHONPATH:$HOME/indra
        python check_references.py
        python export/relations_graph.py
        python export/obo.py
        python export/hgnc_ids.py
        python export/belns.py
        python export/reach_bioresources.py
    - name: Check that exports are up to date
      run: |
        export belns_diff=$(git diff -U0 export/famplex.belns | egrep "^[\+-][^\+-]")
        export belns=$(echo "$belns_diff" | egrep -v "^[\+-](VersionString|CreatedDateTime)")
        export obo_diff=$(git diff -U0 export/famplex.obo | egrep "^[\+-][^\+-]")
        export obo=$(echo "$obo_diff" | egrep -v "^[\+-]date")
        export hgnc=$(git diff -U0 export/hgnc_symbol_map.csv | egrep "^[\+-][^\+-]")
        export reach=$(git diff -U0 export/famplex_groundings.tsv | egrep "^[\+-][^\+-]")
        if [[ ! -z $belns ]] || [[ ! -z $obo ]] || [[ ! -z $hgnc ]] || [[ ! -z $reach ]]; then
          echo "FAIL exports have not been updated";
          echo $belns;
          echo $obo;
          echo $hgnc;
          echo $reach;
          exit 1;
        fi
    - name: Run package unit tests
      run: |
        mypy famplex/api.py famplex/graph.py famplex/load.py
        cd $HOME
        pytest --cov=famplex --pyargs famplex.tests