Recreate the figures from https://www.biorxiv.org/content/10.1101/505032v3 in 4 easy steps!

N.B.: Before following any of these steps, I'd recommend activating a Python virtualenv. It won't affect how easy it is to run this project, probably, but it will make your life easier after you've forgotten about this project and moved on to other Python packages.

(To view API documentation for this project online, please go here.)

Figure Creation

1. To create the figures, first install the deepcell-kiosk-figure-generation package using the included setup.py file with the command pip install -e ..
2. Place all JSON benchmarking data in a top-level folder inside the project. (The project comes with a new_data folder containing default data for this purpose, but feel to throw this data away and replace it with your own, or put yours in an entirely new folder.)
3. Edit the global attributes in figure_generation/graph_creation.py to suit your tastes. (The global attributes should all be documented at the top of figure_generation/graph_creation.py.)
4. Execute python3 ./figure_generation/graph_creation.py.

Note that we did a significant amount of aesthetic primping in Illustrator to the figures generated from the included default data before we put them in the paper, but the data is all the same.

Documentation

If you want to create a local copy of the documentation for this project (instead of viewing the online version, linked above), follow these steps:

1. First, install the package with the docs dependencies included: pip install -e .[docs]. (It's ok if you've already installed without the docs dependencies; there won't be any conflict if you use this command after that.)
2. Move into the docs directory.
3. Execute sphinx-build -b html . ./_build/. Assuming no errors were encountered, there should be a series of HTML files in the docs/_build directory that contain the project's documentation. To view them, simply open docs/_build/index.html with a web browser. N.B.: If step 3 hits an error, it probably indicates that you already had Sphinx installed, and you're just a little unlucky today. Make sure your system is using the Python3 version of Sphinx. If it isn't, delete those Sphinx files or edit your PYTHONPATH to point to the Python3 Sphinx version. (On Debian-based Linux distributions, you can delete these files by executing apt-get remove python2-sphinx.

requirements.txt vs. setup.py

I don't expect any users to need requirements.txt right now. Instead, the project should be installed using pip install -e ., which uses setup.py. I'm keeping requirements.txt around for now, though, in case it comes in handy later for some reason. Also, since figure_generation/graph_creation.py is essentially the entrypoint for the entire module and it uses absolute (from figure_generation.figures import ...) instead of relative (from .figures import ...) imports, it's necessary for install the deepcell-kiosk-figure-generation package (using setup.py), and installing package using only requirements.txt wouldn't be sufficient.