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This repository may be downloaded by using a command line interface: 1. installing osfclient - `conda install osfclient` - or `pip install osfclient` 2. cloning `osf -p 2wf6g clone` All data analysis and representation was accomplished using `Python 3.6.5` with a single script `figures.py`. We use a library called `WrightTools` to aid in data import and representation. In order to execute `figures.py`, `WrightTools` should be installed. This can be accomplished with `conda` or `pip`. - `conda install WrightTools=3.1.3` - `pip install WrightTools==3.1.3` in which the version of `WrightTools` that was used in the workup is installed (newer versions are available). The entire project (excluding simulation fitting) may be built by simply running `python build.py` in a command line. `build.py` will generate a new `wt5` files (our implementation of the excellent `hdf5` data format) and then read the data from the `wt5` files to make figures. Simulation fitting takes ~50 hrs and may be accomplished by running the `.py` files present in the `simulation` directory. Note, these simulations could likely be optimized significantly by rewriting the code for the non-general case. ## Instructions for figure generation In order to run our figure generation script, the following ought to be accomplished: 0. Obtain [`Python 3.6`](www.python.org) or later. (see Note 1 at bottom) 1. Obtain the [SciPy software stack](www.scipy.org/install.html). (see Note 1 at bottom) 2. Obtain `WrightTools`. The easiest ways to get the current stable version is to use pip or conda from your command line. `pip install wrighttools` or `conda install wrighttools`. (see Note 2 at bottom) 3. Run the `figures.py` script. ## Notes 1. We find it easiest to use the excellent, free [Anaconda distribution](www.continuum.io/downloads) to get Python and the SciPy stack on our machines. 2. Alternatively, you can clone from [GitHub](github.com/wright-group/WrightTools) and ensure that it is located in your PYTHONPATH. This folder should be downloaded and then the user should run `python setup.py install` while in the same directory as the WrightTools `setup.py` script. 3. If additional aid or description is needed, don't hesitate to email Darien Morrow at darienmorrow@gmail.com (permanent) or dmorrow3@wisc.edu (current institution).