netneurotools

Useful tools from the Network Neuroscience Lab

https://github.com/netneurolab/netneurotools

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
3 of 12 committers (25.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary

Keywords

brain-imaging brain-networks hacktoberfest neuroimaging python

Keywords from Contributors

closember meta-analysis

Last synced: 6 months ago · JSON representation

Repository

Useful tools from the Network Neuroscience Lab

Basic Info

Host: GitHub
Owner: netneurolab
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://netneurolab.github.io/netneurotools
Size: 648 KB

Statistics

Stars: 78
Watchers: 6
Forks: 35
Open Issues: 12
Releases: 7

Topics

brain-imaging brain-networks hacktoberfest neuroimaging python

Created over 8 years ago · Last pushed 7 months ago

Metadata Files

Readme License

README.rst

netneurotools: Tools for network neuroscience
=============================================

|

.. .. image:: https://zenodo.org/badge/375755159.svg
..    :target: https://zenodo.org/badge/latestdoi/375755159
..    :alt: Zenodo record

.. image:: https://img.shields.io/pypi/v/netneurotools
   :target: https://pypi.python.org/pypi/netneurotools/
   :alt: Latest PyPI version

.. image:: https://img.shields.io/badge/docker-netneurolab/netneurotools-brightgreen.svg?logo=docker&style=flat
  :target: https://hub.docker.com/r/netneurolab/netneurotools/tags/
  :alt: Latest Docker image

.. image:: https://github.com/netneurolab/netneurotools/actions/workflows/tests.yml/badge.svg
  :target: https://github.com/netneurolab/netneurotools/actions/workflows/tests.yml
  :alt: run-tests status

.. image:: https://github.com/netneurolab/netneurotools/actions/workflows/docs.yml/badge.svg
  :target: https://netneurolab.github.io/netneurotools/
  :alt: deploy-docs status

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This toolbox is a collection of functions written in Python that get frequent
usage in the `Network Neuroscience Lab `_, housed in
the `Brain Imaging Centre `_ at
`McGill University `_.


.. _features:

Features
--------

Netneurotools provides a wide range of tools for network neuroscience research.

*  A range of useful datasets fetchers

*  Network construction: empirical and surrogate

*  Network (graph) metrics calculation: up-to-date and optimized

*  Brain and network visualization

*  Optimized statistics routines

*  Convenient interface for external tools

*  And much more!


Check out our `documentation `_
for more information!


.. _installation:

Installation
------------

You can install directly from PyPi with :code:`pip install netneurotools`.

This package is under active development. We recommend installing the latest version
with 

.. code-block:: bash

    pip install git+https://github.com/netneurolab/netneurotools.git


If you are looking for the earlier version of the toolbox before the recent breaking changes,
you can install it with

.. code-block:: bash

    pip install git+https://github.com/netneurolab/netneurotools.git@0.2.X


.. _development:

Development
-----------

This package has been developed by members of the Network Neuroscience Lab in
pursuit of their research. While we've made every effort to ensure these tools
work and have some documentation, there is always room for improvement! If
you've found a bug, are experiencing a problem, or have a question, create a
new `issue `_ with some
information about it and one of our team members will do our best to help you.


.. _licensing:

License Information
-------------------

This codebase is licensed under the 3-clause BSD license. The full license can
be found in the `LICENSE `_ file in the ``netneurotools`` distribution.

All trademarks referenced herein are property of their respective holders.

.. |sparkles| replace:: ✨

Owner

Name: Network Neuroscience Lab
Login: netneurolab
Kind: organization
Location: Montreal, Quebec

Website: https://netneurolab.github.io/
Repositories: 10
Profile: https://github.com/netneurolab

Network Neuroscience Lab at the MNI

GitHub Events

Total

Create event: 6
Issues event: 8
Release event: 1
Watch event: 17
Delete event: 4
Issue comment event: 5
Push event: 15
Pull request review event: 1
Pull request event: 26
Fork event: 3

Last Year

Create event: 6
Issues event: 8
Release event: 1
Watch event: 17
Delete event: 4
Issue comment event: 5
Push event: 15
Pull request review event: 1
Pull request event: 26
Fork event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 326
Total Committers: 12
Avg Commits per committer: 27.167
Development Distribution Score (DDS): 0.294

Past Year

Commits: 14
Committers: 1
Avg Commits per committer: 14.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Ross Markello	r**o@g**m	230
Zhen-Qi Liu	l**7@g**m	40
Vincent Bazinet	v**t@m**a	22
justinehansen	j**n@m**a	12
Golia Shafiei	g**i@m**a	11
Kendra Oudyk	3****k	3
Golia Shafiei	3****i	2
Kendra Oudyk	k**k@g**m	2
vincent bazinet	a**e@h**m	1
gkiar	g**7@g**m	1
vincent bazinet	v**t@h**m	1
Vincent Bazinet	4****z	1

Committer Domains (Top 20 + Academic)

mail.mcgill.ca: 3

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 26
Total pull requests: 115
Average time to close issues: 4 months
Average time to close pull requests: 30 days
Total issue authors: 16
Total pull request authors: 11
Average comments per issue: 1.12
Average comments per pull request: 1.23
Merged pull requests: 102
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 20
Average time to close issues: about 2 months
Average time to close pull requests: 10 days
Issue authors: 4
Pull request authors: 3
Average comments per issue: 0.5
Average comments per pull request: 0.1
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

rmarkello (5)
liuzhenqi77 (4)
VinceBaz (3)
athantas95 (2)
ghisvail (2)
KirstenPeterson (1)
kuffmode (1)
balandongiv (1)
avaruuser (1)
ReinderVosDeWael (1)
giuliabaracc (1)
dzodkin33 (1)
gkiar (1)
weimath (1)
yusaiwen (1)

Pull Request Authors

rmarkello (51)
liuzhenqi77 (42)
VinceBaz (12)
fmilisav (6)
gshafiei (4)
justinehansen (4)
eric2302 (3)
NicolasGensollen (2)
koudyk (1)
pvandyken (1)
gkiar (1)

Top Labels

Issue Labels

enhancement (3) bug (1)

Pull Request Labels

hacktoberfest-accepted (9) enhancement (2)

Packages

Total packages: 2
Total downloads:
- pypi 4,858 last-month

Total dependent packages: 6
(may contain duplicates)
Total dependent repositories: 10
(may contain duplicates)
Total versions: 8
Total maintainers: 5

pypi.org: netneurotools

A toolbox for network neuroscience

Homepage: https://github.com/netneurolab/netneurotools
Documentation: https://netneurotools.readthedocs.io/
License: BSD 3-Clause License Copyright (c) 2018, Network Neuroscience Lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Latest release: 0.2.5
published over 1 year ago

Versions: 7
Dependent Packages: 6
Dependent Repositories: 10
Downloads: 4,846 Last month

Rankings

Dependent packages count: 1.6%

Dependent repos count: 4.6%

Average: 6.6%

Forks count: 7.6%

Downloads: 9.5%

Stargazers count: 9.8%

Maintainers (4)

rossmarkello jhansen liuzhenqi77 vincebaz

Last synced: 6 months ago

pypi.org: netneurotools-scipyfix

Commonly used tools in the Network Neuroscience Lab

Homepage: https://github.com/netneurolab/netneurotools
Documentation: https://netneurotools-scipyfix.readthedocs.io/
License: BSD-3
Latest release: 0.0.0
published about 2 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 12 Last month

Rankings

Forks count: 7.7%

Stargazers count: 9.9%

Dependent packages count: 10.1%

Average: 23.7%

Dependent repos count: 67.3%

Maintainers (1)

1NC-K_ou1

Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi

pillow *
pytest-doctestplus *
sphinx >=1.2
sphinx-gallery *
sphinx_rtd_theme *

requirements.txt pypi

bctpy *
matplotlib *
matplotlib >=3.3.0
nibabel *
nilearn *
numpy >=1.16
scikit-learn *
scipy >=1.4.0
tqdm *

.github/workflows/tests.yml actions

actions/checkout v4 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
codecov/codecov-action v3 composite

pyproject.toml pypi

setup.py pypi

.github/workflows/docker-release.yml actions

actions/checkout v4 composite
docker/build-push-action v2.10.0 composite
docker/login-action v1.14.1 composite
docker/metadata-action v3.8.0 composite

.github/workflows/docs.yml actions

actions/checkout v4 composite
actions/deploy-pages v2 composite
actions/setup-python v4 composite
actions/upload-pages-artifact v2 composite

environment.yml conda

matplotlib
nibabel
nilearn
numpy >=1.16
pip
python >=3.6
scikit-learn
scipy >=1.4.0

Dockerfile docker

python 3.9.7-slim build