<commit_before>Setup development environment
=============================

Date: Jul 23, 2015

  1. Install [anaconda](http://continuum.io/downloads)

  2. Create __imodels__ environment:
  
  		$ conda create -n imodels python=3.4
  		
  3. Activate __imodels__ environment:

        $ source activate imodels
        
  4. Install some conda packages:
  
        $ conda install pkgconfig matplotlib networkx ipython ipython-notebook
        $ conda install -c omnia mdtraj
        
  5. Patch _mdtraj_ with [this patch](https://github.com/mdtraj/mdtraj/pull/896/files).
  
  		$ cd /path/to/anaconda/envs/imodels/lib/python3.4/site-packages/mdtraj/html
  		$ subl trajectory_widget.py
  		
  6. Clone [Intermol](https://github.com/shirtsgroup/InterMol), [foyer](https://github.com/iModels/foyer) and [mbuild](https://github.com/iModels/mbuild) projects and setup them:
  
  		$ cd /path/to/your/projects/
  		$ git clone https://github.com/shirtsgroup/InterMol.git
  		$ git clone https://github.com/iModels/foyer.git
  		$ git clone https://github.com/iModels/mbuild.git

	##### Intermol
  		$ cd Intermol
  		$ git checkout forcetype
  		$ python setup.py develop
  		
  	##### foyer
  		$ cd foyer
  		$ python setup.py develop
  		
  	##### mbuild
  		$ cd mbuild
  		$ python setup.py develop
  	
  	<commit_msg>foyer/intermol optional<commit_after>Setup development environment
=============================

Date: Jul 23, 2015

  1. Install [anaconda](http://continuum.io/downloads)

  2. Create __imodels__ environment:
  
  		$ conda create -n imodels python=3.4
  		
  3. Activate __imodels__ environment:

        $ source activate imodels
        
  4. Install some conda packages:
  
        $ conda install pkgconfig matplotlib networkx ipython ipython-notebook
        $ conda install -c omnia mdtraj
        
  5. Patch _mdtraj_ with [this patch](https://github.com/mdtraj/mdtraj/pull/896/files).
  
  		$ cd /path/to/anaconda/envs/imodels/lib/python3.4/site-packages/mdtraj/html
  		$ subl trajectory_widget.py
  		
  6. Clone [mbuild](https://github.com/iModels/mbuild) and set it up:
  
  		$ cd /path/to/your/projects/
  		$ git clone https://github.com/iModels/mbuild.git
  		$ cd mbuild
  		$ python setup.py develop


  7. __[Optional]__ Clone [Intermol](https://github.com/shirtsgroup/InterMol) and [foyer](https://github.com/iModels/foyer) and set them up:

  		$ cd /path/to/your/projects/
  		$ git clone https://github.com/shirtsgroup/InterMol.git
  		$ git clone https://github.com/iModels/foyer.git

	##### Intermol
  		$ cd Intermol
  		$ git checkout forcetype
  		$ python setup.py develop
  		
  	##### foyer
  		$ cd foyer
  		$ python setup.py develop  	
  	
{'fraction_non_alphanumeric': 0.13306152705707933, 'fraction_numerical': 0.014455151964418088, 'mean_word_length': 2.722758620689655, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 14, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, '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': '75817', 'n_tokens_mistral': 1035, 'n_tokens_neox': 966, 'n_words': 199}