This is a repository of analysis code for a paper in preparation. The repository includes:

• Jupyter notebooks that perform all of the analysis, from the raw data to the published figure
• a Python file containing some functions shared by the notebooks
• an environment.yml file that specifies that exact versions of all Python packages used in the analysis
• other YAML files containing experiment metadata

It does not contain the large data files. These should be downloaded separately from Google Drive or S3.

Review static (not runnable) copies of the notebooks here.

1. Download the data files and put them in the data/ directory (no subdirectories).

2. Install conda.

3. Open a terminal (command prompt) and use cd to change to the directory where these files are downloaded.

4. Install the required Python packages into a new "environment".

   conda-env create environment.yml
   

5. Activate the new environment. On Windows:

   activate pa
   

   On Mac/Linux:

   source activate pa
   

6. Start Jupyter notebook (formerly called IPython notebook).

   jupyter notebook
   

   This will open a browser tab where you can run and experiment with the notebooks.