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Neuropycon package of functions for electrophysiology analysis, can be used from ephypype and nipype

Home Page: https://neuropycon.github.io/graphpype/

License: BSD 3-Clause "New" or "Revised" License

Python 99.47% Dockerfile 0.53%

connectivity graph-analysis electrophysiology

graphpype's Introduction

https://travis-ci.org/neuropycon/graphpype.svg?branch=master

graphpype

Neuropycon project for graph analysis, can be used from ephypype and nipype

Documentation

https://neuropycon.github.io/graphpype/

Installation

pip install https://api.github.com/repos/neuropycon/graphpype/zipball/master

Or with pip:

pip install graphpype

Radatools

You should add all the directories from radatools to the PATH env variable:

Download radatools sotware:

http://deim.urv.cat/~sergio.gomez/radatools.php#download

Download and extract the zip file
Add following lines in your .bashrc:

For radatools 3.2

RADA_PATH=/home/david/Tools/Software/radatools-3.2-linux32

(replace /home/david/Tools/Software by your path to radatools)

export PATH=$PATH:$RADA_PATH/01-Prepare_Network/

export PATH=$PATH:$RADA_PATH/02-Find_Communities/

export PATH=$PATH:$RADA_PATH/03-Reformat_Results

export PATH=$PATH:$RADA_PATH/04-Other_Tools/

For radatools 4.0

RADA_PATH=/home/david/Tools/Software/radatools-4.0-linux64

(replace /home/david/Tools/Software by your path to radatools)

export PATH=$PATH:$RADA_PATH/Network_Tools

export PATH=$PATH:$RADA_PATH/Network_Properties

export PATH=$PATH:$RADA_PATH/Communities_Detection

export PATH=$PATH:$RADA_PATH/Communities_Tools

For radatools 5.0

RADA_PATH=/home/david/Tools/Software/radatools-5.0-linux64

(replace /home/david/Tools/Software by your path to radatools)

export PATH=$PATH:$RADA_PATH/Network_Tools

export PATH=$PATH:$RADA_PATH/Network_Properties

export PATH=$PATH:$RADA_PATH/Communities_Detection

export PATH=$PATH:$RADA_PATH/Communities_Tools

graphpype's People

Contributors

Stargazers

Watchers

Forkers

davidmeunier79 nagyistge dmalt etiennecmb annapasca neuroidss lqcheng2017 forksbot acamargofb dalerxli isak-h47

graphpype's Issues

Question about RADA_PATH

How can I create this environment (RADA_PATH)? because it is not in my conda and was not created by the previously suggested commands:
pip install graphpype (this command is not working in my conda shell, several errors are shown along the way of installing the packages)

$ pip install https://api.github.com/repos/neuropycon/graphpype/zipball/master (this apparently didn't throw any errors)

add circleci to build docs automatically

Getting Error: OSError: No command "List_To_Net.exe"

When running the tutorial, the compiler return the following error

RuntimeError: Workflow did not execute cleanly. Check log for details
210818-01:18:44,747 nipype.workflow INFO:
	 ***********************************
210818-01:18:44,748 nipype.workflow ERROR:
	 could not run node: graph_analysis.graph_den_pipe_den_0_05.prep_rada.a0
210818-01:18:44,748 nipype.workflow INFO:
	 crashfile: /home/cisir2/Documents/rpb/driving_eeg_graph_theory/src_code/crash-20210818-011842-cisir2-prep_rada.a0-8daddd78-7be8-4af3-8d15-fb29ec1769af.pklz
210818-01:18:44,748 nipype.workflow ERROR:
	 could not run node: graph_analysis.graph_den_pipe_den_0_05.prep_rada.a1
210818-01:18:44,748 nipype.workflow INFO:
	 crashfile: /home/cisir2/Documents/rpb/driving_eeg_graph_theory/src_code/crash-20210818-011842-cisir2-prep_rada.a1-e9758268-ee46-4863-910e-48dd60f6679f.pklz
210818-01:18:44,748 nipype.workflow INFO:
	 ***********************************

May I why this arise?

Some of the setup
Ubuntu 16.04
radatools-5.2-linux64

Python 3.9

bctpy==0.5.2
certifi==2021.5.30
charset-normalizer==2.0.4
ci-info==0.2.0
click==8.0.1
cycler==0.10.0
ephypype @ git+https://github.com/neuropycon/ephypype.git@976f66e640b5f0ffc1a7be77c2c0f0db79c61554
etelemetry==0.2.2
filelock==3.0.12
freetype-py==2.2.0
graphpype @ git+https://github.com/balandongiv/graphpype.git@7bce7c7b78793adcea6758d8e1355bb8ccb3558d
h5py==3.3.0
hsluv==5.0.2
idna==3.2
isodate==0.6.0
kiwisolver==1.3.1
lxml==4.6.3
matplotlib==3.4.3
mne @ https://github.com/mne-tools/mne-python/archive/main.zip
networkx==2.6.2
nibabel==3.2.1
nipype @ git+https://github.com/nipy/nipype.git@7080ef9edd0fe095323a90b0b77be7a0b73824a5
numpy==1.21.2
packaging==21.0

pandas

the version should be updated

The version is incorrect here: https://github.com/neuropycon/graphpype/blob/master/setup.py#L9

The development version should have a different version number.

igraph package on which graphpype depends seems to be obsolete

I've been trying to build neuropycon documentation and sphinx threw this error:

DeprecationWarning                        Traceback (most recent call last)
<ipython-input-1-73ffca960e68> in <module>()
----> 1 import igraph

/home/dmalt/Code/python/neuropycon/neuropycon/lib/python2.7/site-packages/igraph/__init__.py in <module>()
      6 __license__ = "MIT"
      7 
----> 8 raise DeprecationWarning("To avoid name collision with the igraph project, "
      9                          "this visualization library has been renamed to "
     10                          "'jgraph'. Please upgrade when convenient.")

DeprecationWarning: To avoid name collision with the igraph project, this visualization library has been renamed to 'jgraph'. Please upgrade when convenient

Should igraph be substituted with jgraph?

installation with pip install . doesn't work

Had to use pip install --editable . instead.
Readme installation instructions should be fixed.

libtk8.6.so error at import

On my archlinux after installation

import graphpype

results into
ImportError: libtk8.6.so: cannot open shared object file: No such file or directory
after installing tk package this issue was resolved.
tk dependency should be added to dependencies list in installation instruction.
Does it work on ubuntu out of the box?

Requirements too specific?

The install requirements of this package state very specific versions for various packages:

    install_requires=['numpy>=1.3.0',
                      'statsmodels==0.8.0',
                      'patsy==0.5.1',
                      'nipype',
                      'configparser',
                      "pandas==0.23.4",
                      "xlwt",
                      'networkx==1.9',
                      "matplotlib==2.2.3",
                      "bctpy"]

Is it really necessary that the user has these specfic versions installed? If not, better to relax the version requirements, as this will cause pip to either freak out or overwrite whatever version the user already had.

neuropycon / graphpype Goto Github PK

graphpype's Introduction

graphpype

Documentation

Installation

Radatools

For radatools 3.2

For radatools 4.0

For radatools 5.0

graphpype's People

Contributors

Stargazers

Watchers

Forkers

graphpype's Issues

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