.travis.yml

language: python
cache:
  directories:
    - $HOME/.cache/pip
    - $HOME/.pybel
    - $HOME/build/bgyori/indra/cache/geonames/index
python:
  - "3.6"
services:
  # Enable plotting on fake display
  - xvfb
before_install:
  - sudo apt-get update
  - sudo apt-get install openjdk-8-jdk
  - sudo apt-get install libstdc++6 graphviz
install:
  # Install test/Travis-specific dependencies not covered elsewhere
  - pip install pydot jsonschema coverage
        nose-timer doctest-ignore-unicode awscli pycodestyle
  - mkdir -p $HOME/.pybel/data
  - aws s3 cp s3://bigmech/travis/pybel_cache.db $HOME/.pybel/data/ --no-sign-request  --source-region us-east-1
  - mkdir -p $HOME/.indra/bio_ontology/1.1
  - aws s3 cp s3://bigmech/travis/mock_ontology.pkl $HOME/.indra/bio_ontology/1.1/bio_ontology.pkl --no-sign-request  --source-region us-east-1
  # PySB and dependencies
  - wget "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.4.0/BioNetGen-2.4.0-Linux.tgz" -O bionetgen.tar.gz -nv
  - tar xzf bionetgen.tar.gz
  - export BNGPATH=`pwd`/BioNetGen-2.4.0
  - pip install git+https://github.com/pysb/pysb.git
  # Temporary fix. Ensure cython is installed before pyjnius
  - pip install cython
  # Now install INDRA with all its extras
  - pip install .[all]
  - aws s3 cp s3://bigmech/travis/reach-82631d-biores-e9ee36.jar . --no-sign-request  --source-region us-east-1
  - export REACHPATH=$TRAVIS_BUILD_DIR/reach-82631d-biores-e9ee36.jar
  - aws s3 cp s3://bigmech/travis/eidos.jar . --no-sign-request --source-region us-east-1
  - export EIDOSPATH=$TRAVIS_BUILD_DIR/eidos.jar
  - aws s3 cp s3://bigmech/travis/Phosphorylation_site_dataset.tsv indra/resources/ --no-sign-request  --source-region us-east-1
  # 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
  # Install nose notify
  - mkdir $HOME/.nose_notify;
  - git clone https://github.com/pagreene/nose-notify.git $HOME/.nose_notify;
  - export PYTHONPATH=$PYTHONPATH:$HOME/.nose_notify;
  # Download adeft models
  - python -m adeft.download
script:
  # Credit: https://graysonkoonce.com/getting-the-current-branch-name-during-a-pull-request-in-travis-ci/
  - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
  - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH, PR=$PR, BRANCH=$BRANCH"
  - echo "$TRAVIS_EVENT_TYPE"
  - export TEES_PATH=~/TEES
  - export PYTHONPATH=$PYTHONPATH:$TRAVIS_BUILD_DIR
  - export _JAVA_OPTIONS="-Xmx4g -Xms1g"
  # These are files that are ignored so that doctests don't fail
  - export NOSE_IGNORE_FILES="find_full_text_sentence.py";
  # Set nose attributes based on the context in which we are running
  - export NOSEATTR="!notravis";
  - if [[ $TRAVIS_PULL_REQUEST != "false" ]]; then
      export NOSEATTR="!nonpublic,$NOSEATTR";
    fi
  - if [[ $RUN_SLOW != "true" ]]; then
      export NOSEATTR="!slow,$NOSEATTR";
    fi
  - if [[ $TRAVIS_EVENT_TYPE != "cron" ]]; then
      export NOSEATTR="!cron,$NOSEATTR";
    fi
  - echo $NOSEATTR
  # Now run all INDRA tests
  - cd $TRAVIS_BUILD_DIR
  - python -u -m nose_notify --slack_hook $SLACK_NOTIFY_HOOK --label "$TRAVIS_REPO_SLUG - $TRAVIS_BRANCH"
    indra -v -a $NOSEATTR --exclude='.*tees.*' --exclude='.*eidos.*' --exclude='.*isi.*'
        --ignore-files='.*test_reach.py' --ignore-files='.*test_live_curation.py'
        --with-coverage --cover-inclusive --cover-package=indra
        --with-doctest --with-doctest-ignore-unicode --with-timer --timer-top-n 10
        --processes=0
  # First run TEES and Eidos tests separately for technical reasons
  - 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;
  - python -m nose_notify indra/tests/test_eidos.py --slack_hook $SLACK_NOTIFY_HOOK
    --label "$TRAVIS_REPO_SLUG - $TRAVIS_BRANCH" -v -a $NOSEATTR;
  - python -m nose_notify indra/tests/test_live_curation.py
    --slack_hook $SLACK_NOTIFY_HOOK
    --label "$TRAVIS_REPO_SLUG - $TRAVIS_BRANCH" -v -a $NOSEATTR;
  - python -m nose_notify indra/tests/test_reach.py
    --slack_hook $SLACK_NOTIFY_HOOK
    --label "$TRAVIS_REPO_SLUG - $TRAVIS_BRANCH" -v -a $NOSEATTR;
  # 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
  # Run assembly benchmarks
  - cd $TRAVIS_BUILD_DIR/indra/benchmarks/assembly_eval/batch4
  - |
    if [[ $TRAVIS_EVENT_TYPE == "cron" ]]; then
      # Download a number of useful resource files for testing purposes
      aws s3 cp s3://bigmech/travis/trips_reach_batch4.gz .  --no-sign-request  --source-region us-east-1
      tar -xf trips_reach_batch4.gz
      python run_combined.py
    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;