Increase Gilda requirement #1211
Workflow file for this run
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| name: Tests | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup java | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 8 | |
| - name: Install dependencies | |
| run: | | |
| echo $GITHUB_EVENT_NAME | |
| sudo apt-get update | |
| sudo apt-get install libstdc++6 graphviz python3-dev libgraphviz-dev pkg-config | |
| # Install test/CI-specific dependencies not covered elsewhere | |
| pip install --upgrade pip setuptools wheel | |
| pip install pytest pytest-cov pydot jsonschema awscli pycodestyle | |
| mkdir -p $HOME/.pybel/data | |
| wget -nv https://bigmech.s3.amazonaws.com/travis/pybel_cache.db -O $HOME/.pybel/data/pybel_cache.db | |
| # PySB and dependencies | |
| wget "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.4.0/BioNetGen-2.4.0-Linux.tgz" -O bionetgen.tar.gz -nv | |
| tar xzf bionetgen.tar.gz | |
| pip install git+https://github.com/pysb/pysb.git | |
| # Temporary fix. Ensure cython is installed before pyjnius | |
| pip install "cython<3" | |
| # Now install INDRA with all its extras | |
| pip install .[all] | |
| # Run slow tests only if we're in the cron setting | |
| #- | | |
| # if [[ $TRAVIS_EVENT_TYPE == "cron" ]]; then | |
| # export RUN_SLOW=true; | |
| # fi | |
| # Install TEES only if slow tests are being run | |
| #- | | |
| # if [[ $RUN_SLOW == "true" ]]; then | |
| # sudo pip2 install numpy | |
| # sudo apt-get --yes install ruby; | |
| # aws s3 cp s3://bigmech/travis/TEES.tar.bz2 . --no-sign-request --no-sign-request; | |
| # tar xjf TEES.tar.bz2; | |
| # mv TEES ~/TEES; | |
| # export TEES_SETTINGS=~/TEES/tees_local_settings.py | |
| # fi | |
| # Download adeft models | |
| python -m adeft.download | |
| python -m gilda.resources | |
| # Get INDRA World | |
| git clone https://github.com/indralab/indra_world.git | |
| # Download Reach | |
| wget -nv https://bigmech.s3.amazonaws.com/travis/reach-82631d-biores-e9ee36.jar | |
| # Get INDRA Bioontology | |
| BIOONTOLOGY_VERSION=$(python -m indra.ontology.bio version) | |
| echo $BIOONTOLOGY_VERSION | |
| mkdir -p $HOME/.indra/bio_ontology/$BIOONTOLOGY_VERSION | |
| wget -nv https://bigmech.s3.amazonaws.com/travis/bio_ontology/$BIOONTOLOGY_VERSION/mock_ontology.pkl -O $HOME/.indra/bio_ontology/$BIOONTOLOGY_VERSION/bio_ontology.pkl | |
| - name: Run unit tests | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| INDRA_DB_REST_URL: ${{ secrets.INDRA_DB_REST_URL }} | |
| INDRA_DB_REST_API_KEY: ${{ secrets.INDRA_DB_REST_API_KEY }} | |
| ELSEVIER_API_KEY: ${{ secrets.ELSEVIER_API_KEY }} | |
| ELSEVIER_INST_KEY: ${{ secrets.ELSEVIER_INST_KEY }} | |
| BIOGRID_API_KEY: ${{ secrets.BIOGRID_API_KEY }} | |
| run: | | |
| # Set pytest attributes based on the context in which we are running | |
| export PYTESTMARKS="(not nogha) and (not slow) and (not cron)" | |
| export PYTESTMARKS=$(if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then echo $PYTESTMARKS "and (not nonpublic)"; else echo $PYTESTMARKS; fi) | |
| export PYTHONPATH=$PYTHONPATH:`pwd`/indra_world | |
| export _JAVA_OPTIONS="-Xmx4g -Xms1g" | |
| export BNGPATH=`pwd`/BioNetGen-2.4.0 | |
| export REACHPATH=`pwd`/reach-82631d-biores-e9ee36.jar | |
| export CLASSPATH=$REACHPATH | |
| # These are files that are ignored so that doctests don't fail | |
| #export NOSE_IGNORE_FILES="find_full_text_sentence.py"; | |
| #- cd $TRAVIS_BUILD_DIR | |
| # Now run all INDRA tests | |
| pytest -v -m "$PYTESTMARKS" --ignore-glob='*tees*' --ignore-glob='*isi*' --ignore-glob='*test_reach*' --cov=indra --cov-report=term-missing --doctest-modules --durations=10 --continue-on-collection-errors indra/tests | |
| pytest -v -m "$PYTESTMARKS" indra/tests/test_reach.py | |
| # TEES tests | |
| #- python -m nose_notify indra/tests/test_tees.py --slack_hook $SLACK_NOTIFY_HOOK | |
| # --label "$TRAVIS_REPO_SLUG - $TRAVIS_BRANCH" -v -a $NOSEATTR --process-restartworker; | |
| # Run NL model examples only when the environmental variable | |
| # RUN_NL_MODELS is set to true in the Travis build | |
| # NOTE: if blocks in Travis DO NOT FAIL even if there is | |
| # and error in one of the commands inside. Therefore passing | |
| # alone does not mean that all the operations inside were | |
| # successful. Rather, the log needs to be inspected and compared | |
| # to desired behavior. | |
| #- | | |
| # if [[ $RUN_NL_MODELS == "true" ]]; then | |
| # cd $TRAVIS_BUILD_DIR/models | |
| # python hello_indra.py | |
| # cd $TRAVIS_BUILD_DIR/models/p53_model | |
| # python run_p53_model.py noplot | |
| # cd $TRAVIS_BUILD_DIR/models/braf_model | |
| # python assemble_model.py | |
| # cd $TRAVIS_BUILD_DIR/models/ras_pathway | |
| # python run_ras_pathway.py trips | |
| # fi | |
| #- cd $TRAVIS_BUILD_DIR | |
| # Run code style report on diff | |
| #- git remote set-branches --add origin master | |
| #- git fetch | |
| #- git diff origin/master | pycodestyle --diff > pep8.txt; cat pep8.txt; |