<commit_before>language: c
install:
    - sudo apt-get update -qq
    - sudo apt-get install -qq python-dev python-pip python-yaml g++
    - sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
    - sudo apt-get install -qq swig doxygen
    - sudo pip install conda
    - sudo conda init
    - conda create --yes --name test numpy scipy pytables numexpr nose pandas cython statsmodels pandas patsy pyyaml matplotlib pip netCDF4 pyflakes
    - export PATH="$HOME/envs/test/bin/:$PATH"
    - pip install -q mdtraj git+git://github.com/rmcgibbo/simtk.unit
    
script:
    - git clone https://github.com/SimTk/openmm.git
    - cd openmm
    - cmake -DCMAKE_INSTALL_PREFIX=~/OpenMM .
    - make
    - make install
    - export LD_LIBRARY_PATH=~/OpenMM/lib/
    - export OPENMM_LIB_PATH=~/OpenMM/lib/
    - export OPENMM_INCLUDE_PATH=~/OpenMM/include/
    - cd python
    - python setup.py install
    - cd ../../
    - python setup.py install
    - nosetests
    - nosetests tests/test_alchemy.py

after_script:
    - pyflakes yank/*.py<commit_msg>Now use conda for installation of openmm, and clone repex from github.<commit_after>language: c
install:
    - sudo apt-get update -qq
    - sudo apt-get install -qq python-dev python-pip python-yaml g++
    - sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
    - sudo apt-get install -qq swig doxygen
    - sudo pip install conda
    - sudo conda init
    - conda create --yes --name test numpy scipy pytables numexpr nose pandas cython statsmodels pandas patsy pyyaml matplotlib pip netCDF4 pyflakes
    - export PATH="$HOME/envs/test/bin/:$PATH"
    - conda config --add channels http://conda.binstar.org/rmcgibbo
    - conda install mdtraj openmm
    - pip install pymbar
    - pip install -q mdtraj git+git://github.com/rmcgibbo/simtk.unit
    
script:
    - git clone <EMAIL>:choderalab/repex.git
    - cd repex
    - python setup.py install
    - cd ..
    - python setup.py install
    - nosetests
    - nosetests tests/test_alchemy.py

after_script:
    - pyflakes yank/*.py
{'fraction_non_alphanumeric': 0.09621993127147767, 'fraction_numerical': 0.0029455081001472753, 'mean_word_length': 2.5259515570934257, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 1, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7263917', 'n_tokens_mistral': 723, 'n_tokens_neox': 682, 'n_words': 197}