<commit_before>language: python
cache:
  directories:
    - $HOME/.cache/pip
python:
  - "2.7"
  - "3.5"
before_install:
  - sudo add-apt-repository --yes ppa:webupd8team/java
  - sudo apt-get update
  - echo debconf shared/accepted-oracle-license-v1-1 select true | sudo debconf-set-selections
  - echo debconf shared/accepted-oracle-license-v1-1 seen true | sudo debconf-set-selections
  - pip install numpy scipy sympy cython==0.23.5 nose lxml matplotlib==1.5.0 pandas
  - sudo pip2 install numpy
install:
  # INDRA dependencies
  - sudo apt-get install libstdc++6
  - sudo apt-get install graphviz
  - sudo apt-get install oracle-java8-installer
  - sudo update-java-alternatives -s java-8-oracle
  - sudo apt-get install oracle-java8-set-default
  - export JAVA_HOME="/usr/lib/jvm/java-8-oracle/"
  - pip install pygraphviz pydot jsonschema coverage python-coveralls boto3 sqlalchemy psycopg2-binary pgcopy nose-timer flask
  - pip install doctest-ignore-unicode
  - pip install git+https://github.com/pybel/pybel.git@master
  - wget http://sorger.med.harvard.edu/data/bachman/Phosphorylation_site_dataset.tsv --directory-prefix=indra/resources/ -nv
  # PySB and dependencies
  - wget "http://www.csb.pitt.edu/Faculty/Faeder/wp-content/uploads/2017/04/BioNetGen-2.2.6-stable_Linux.tar.gz" -O bionetgen.tar.gz -nv
  - tar xzf bionetgen.tar.gz
  - export BNGPATH=`pwd`/BioNetGen-2.2.6-stable
  - pip install git+https://github.com/pysb/pysb.git
  # Biopax/Paxtools dependencies
  - pip install jnius-indra
  # Download a number of useful resource files for testing purposes
  - pip install .[all]
  - cd indra/benchmarks/assembly_eval/batch4
  - wget http://sorger.med.harvard.edu/data/bachman/trips_reach_batch4.gz -nv
  - tar -xf trips_reach_batch4.gz
  - cd $TRAVIS_BUILD_DIR
  - wget http://sorger.med.harvard.edu/data/bachman/reach-82631d-biores-e9ee36.jar -nv
  - export REACHPATH=$TRAVIS_BUILD_DIR/reach-82631d-biores-e9ee36.jar
  # Get a daily updated Eidos jar for testing
  - wget http://sorger.med.harvard.edu/data/bgyori/eidos.jar -nv
  - export EIDOSPATH=$TRAVIS_BUILD_DIR/eidos.jar
  - pip install pycodestyle
  # TEES
  - if [[ "$TRAVIS_EVENT_TYPE" == "cron" ]]; then
        export RUN_SLOW=true;<commit_msg>Fix PySB version since it's temporarily broken<commit_after>language: python
cache:
  directories:
    - $HOME/.cache/pip
python:
  - "2.7"
  - "3.5"
before_install:
  - sudo add-apt-repository --yes ppa:webupd8team/java
  - sudo apt-get update
  - echo debconf shared/accepted-oracle-license-v1-1 select true | sudo debconf-set-selections
  - echo debconf shared/accepted-oracle-license-v1-1 seen true | sudo debconf-set-selections
  - pip install numpy scipy sympy cython==0.23.5 nose lxml matplotlib==1.5.0 pandas
  - sudo pip2 install numpy
install:
  # INDRA dependencies
  - sudo apt-get install libstdc++6
  - sudo apt-get install graphviz
  - sudo apt-get install oracle-java8-installer
  - sudo update-java-alternatives -s java-8-oracle
  - sudo apt-get install oracle-java8-set-default
  - export JAVA_HOME="/usr/lib/jvm/java-8-oracle/"
  - pip install pygraphviz pydot jsonschema coverage python-coveralls boto3 sqlalchemy psycopg2-binary pgcopy nose-timer flask
  - pip install doctest-ignore-unicode
  - pip install git+https://github.com/pybel/pybel.git@master
  - wget http://sorger.med.harvard.edu/data/bachman/Phosphorylation_site_dataset.tsv --directory-prefix=indra/resources/ -nv
  # PySB and dependencies
  - wget "http://www.csb.pitt.edu/Faculty/Faeder/wp-content/uploads/2017/04/BioNetGen-2.2.6-stable_Linux.tar.gz" -O bionetgen.tar.gz -nv
  - tar xzf bionetgen.tar.gz
  - export BNGPATH=`pwd`/BioNetGen-2.2.6-stable
  - pip install pysb==1.6.0
  # Biopax/Paxtools dependencies
  - pip install jnius-indra
  # Download a number of useful resource files for testing purposes
  - pip install .[all]
  - cd indra/benchmarks/assembly_eval/batch4
  - wget http://sorger.med.harvard.edu/data/bachman/trips_reach_batch4.gz -nv
  - tar -xf trips_reach_batch4.gz
  - cd $TRAVIS_BUILD_DIR
  - wget http://sorger.med.harvard.edu/data/bachman/reach-82631d-biores-e9ee36.jar -nv
  - export REACHPATH=$TRAVIS_BUILD_DIR/reach-82631d-biores-e9ee36.jar
  # Get a daily updated Eidos jar for testing
  - wget http://sorger.med.harvard.edu/data/bgyori/eidos.jar -nv
  - export EIDOSPATH=$TRAVIS_BUILD_DIR/eidos.jar
  - pip install pycodestyle
  # TEES
  - if [[ "$TRAVIS_EVENT_TYPE" == "cron" ]]; then
        export RUN_SLOW=true;
{'fraction_non_alphanumeric': 0.11766024204392649, 'fraction_numerical': 0.025324966382787986, 'mean_word_length': 3.4674674674674675, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 3, 'lorem ipsum': 0, 'www.': 2, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6662259', 'n_tokens_mistral': 1748, 'n_tokens_neox': 1659, 'n_words': 333}