wedap 0.0.0

weighted ensemble data analysis and plotting

wedap

Weighted Ensemble data analysis and plotting.

This repository is currently under development.

Requirements

• Numpy
• Matplotlib
• H5py
• Moviepy
• Scipy
• Gooey
• tqdm

GUI

wedap has a GUI built using Gooey which can be launched by running pythonw wedap.py (on MacOSX) or python wedap.py with no arguments. If you wish to use the command line interface instead include the --ignore-gooey flag.

Installation

I recommend first installing dependencies via conda, especially gooey. To install the dependencies into your python env via pip or conda:

conda env create --name wedap --file requirements.txt
conda activate wedap
conda install -c conda-forge gooey
pip install wedap

Or update an existing environmnent:

conda activate ENV_NAME
conda env update ENV_NAME --file requirements.txt
conda install -c conda-forge gooey
pip install wedap

Or pip install (you may have issues pip installing wxPython):

pip install gooey
pip install wedap

If you have the repository cloned, go into the main wedap directory:

pip install gooey
pip install .

Note that gooey is kindof troublesome to pip install in some systems, which is why it's not included in the requirements (although it is required). I am trying to fix this but for now I reccomend conda installing gooey.

Examples

After installation, to run the CLI version and view available options:

wedap --ignore-gooey --help

To start the GUI simply input:

wedap

To visualize the evolution of the pcoord for the example p53.h5 file via CLI:

wedap --ignore-gooey -h5 /path/to/h5/p53.h5

To do the same with the API:

import wedap
import matplotlib.pyplot as plt

wedap.H5_Plot(h5="/path/to/h5/p53.h5", data_type="evolution").plot()
plt.show()

Contributing

Features should be developed on branches. To create and switch to a branch, use the command:

git checkout -b new_branch_name

To switch to an existing branch, use:

git checkout branch_name

To submit your feature to be incorporated into the main branch, you should submit a Pull Request. The repository maintainers will review your pull request before accepting your changes.

Copyright

Copyright (c) 2022, Darian Yang