bctpy 0.6.1

Description:

bctpy 0.6.1

# Brain Connectivity Toolbox for Python version 0.6.1
Author: Roan LaPlante <[email protected]>
Tested against python 3.7+.
## Copyright information
This program strictly observes the tenets of fundamentalist Theravada Mahasi
style Buddhism. Any use of this program in violation of these aforementioned
tenets or in violation of the principles described in the Visuddhimagga Sutta
is strictly prohibited and punishable by extensive Mahayana style practice.
By being or not being mindful of the immediate present moment sensations
involved in the use of this program, you confer your acceptance of these terms
and conditions.
Note that the observation of the tenets of fundamentalist Theravada Mahasi
style Buddhism and the Visuddhimagga Sutta is optional as long as the terms and
conditions of the GNU GPLv3+ are upheld.
## Packages used
BCTPY is written in pure python and requires only scipy and numpy. scipy is required for a couple of functions for its statistical and linear algebra
packages which have some features not available in numpy alone. If you don’t
have scipy, most functions that do not need scipy functionality will still work.
Note that graphs must be passed in as numpy.array rather than numpy.matrix. Other constraints/edge cases of the adjacency matrices (e.g. self-loops, negative weights) behave similarly to the matlab functions.
A small number of functions also depend on networkx. This notably includes Network-Based Statistic, a nonparametric test for differences in undirected weighted graphs from different populations. Ideally this dependency should be removed in the future.
Nosetests is used for the test suite. The test suite is not complete.
## About bctpy and other authors
BCT is a matlab toolbox with many graph theoretical measures off of which bctpy
is based. I did not write BCT (apart from small bugfixes I have submitted)
and a quality of life improvements that I have taken liberties to add.
With few exceptions, bctpy is a direct translation of matlab code to python.
bctpy should be considered beta software, with BCT being the gold standard by
comparison. I did my best to test all functionality in bctpy, but much of it is
arcane math that flies over the head of this humble programmer. There are
bugs lurking in bctpy, the question is not whether but how many. If you locate
bugs, please consider submitting pull requests.
Many thanks to Stefan Fuertinger for his assistance tracking down a number of
bugs. Stefan Fuertinger has a similar software package dealing with brain
network functionality at http://research.mssm.edu/simonyanlab/analytical-tools/
Many thanks to Chris Barnes for his assistance in documenting a number of issues and facilitating a number of test cases.
Credit for writing BCT (the matlab version) goes to the following list of
authors, especially Olaf Sporns and Mika Rubinov.

Olaf Sporns
Mikail Rubinov
Yusuke Adachi
Andrea Avena
Danielle Bassett
Richard Betzel
Joaquin Goni
Alexandros Goulas
Patric Hagmann
Christopher Honey
Martijn van den Heuvel
Rolf Kotter
Jonathan Power
Murray Shanahan
Andrew Zalesky

In order to be a bit more compact I have removed the accreditations from the
docstrings each functions. This does not in any way mean that I wish to take
credit from the individual contributions. I have moved these accreditations
to the credits file.