Add mapping for CHD #166
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| 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 |