nipype

Workflows and interfaces for neuroimaging packages

https://github.com/nipy/nipype

Science Score: 59.0%

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

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
62 of 257 committers (24.1%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.6%) to scientific vocabulary

Keywords

big-data brain-imaging brainweb data-science dataflow dataflow-programming neuroimaging python workflow-engine

Keywords from Contributors

bids fmri fmri-preprocessing closember neuroscience quality-reporter quality-control mri eeg prediction

Last synced: 6 months ago · JSON representation

Repository

Workflows and interfaces for neuroimaging packages

Basic Info

Host: GitHub
Owner: nipy
License: other
Language: Python
Default Branch: master
Homepage: https://nipype.readthedocs.org/en/latest/
Size: 75.6 MB

Statistics

Stars: 792
Watchers: 49
Forks: 536
Open Issues: 431
Releases: 49

Topics

big-data brain-imaging brainweb data-science dataflow dataflow-programming neuroimaging python workflow-engine

Created over 15 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Zenodo

README.rst

========================================================
NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
========================================================

.. image:: https://travis-ci.org/nipy/nipype.svg?branch=master
  :target: https://travis-ci.org/nipy/nipype

.. image:: https://circleci.com/gh/nipy/nipype/tree/master.svg?style=svg
  :target: https://circleci.com/gh/nipy/nipype/tree/master

.. image:: https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg
  :target: https://codecov.io/gh/nipy/nipype

.. image:: https://api.codacy.com/project/badge/Grade/452bfc0d4de342c99b177d2c29abda7b
  :target: https://www.codacy.com/app/nipype/nipype?utm_source=github.com&utm_medium=referral&utm_content=nipy/nipype&utm_campaign=Badge_Grade

.. image:: https://img.shields.io/pypi/v/nipype.svg
    :target: https://pypi.python.org/pypi/nipype/
    :alt: Latest Version

.. image:: https://img.shields.io/pypi/pyversions/nipype.svg
    :target: https://pypi.python.org/pypi/nipype/
    :alt: Supported Python versions

.. image:: https://img.shields.io/pypi/status/nipype.svg
    :target: https://pypi.python.org/pypi/nipype/
    :alt: Development Status

.. image:: https://img.shields.io/pypi/l/nipype.svg
    :target: https://pypi.python.org/pypi/nipype/
    :alt: License

.. image:: https://img.shields.io/badge/gitter-join%20chat%20%E2%86%92-brightgreen.svg?style=flat
    :target: http://gitter.im/nipy/nipype
    :alt: Chat

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.596855.svg
   :target: https://doi.org/10.5281/zenodo.596855
   :alt: Citable DOI

Current neuroimaging software offer users an incredible opportunity to
analyze data using a variety of different algorithms. However, this has
resulted in a heterogeneous collection of specialized applications
without transparent interoperability or a uniform operating interface.

*Nipype*, an open-source, community-developed initiative under the
umbrella of NiPy, is a Python project that provides a uniform interface
to existing neuroimaging software and facilitates interaction between
these packages within a single workflow. Nipype provides an environment
that encourages interactive exploration of algorithms from different
packages (e.g., SPM, FSL, FreeSurfer, AFNI, Slicer, ANTS), eases the
design of workflows within and between packages, and reduces the
learning curve necessary to use different packages. Nipype is creating a
collaborative platform for neuroimaging software development in a
high-level language and addressing limitations of existing pipeline
systems.

*Nipype* allows you to:

* easily interact with tools from different software packages
* combine processing steps from different software packages
* develop new workflows faster by reusing common steps from old ones
* process data faster by running it in parallel on many cores/machines
* make your research easily reproducible
* share your processing workflows with the community

Documentation
-------------

Please see the ``doc/README.txt`` document for information on our
documentation.

Website
-------

Information specific to Nipype is located here::

    http://nipy.org/nipype

Python 2 Statement
------------------

Python 2.7 reaches its end-of-life in January 2020, which means it will
*no longer be maintained* by Python developers. `Many projects
`__ are removing support in advance of this
deadline, which will make it increasingly untenable to try to support
Python 2, even if we wanted to.

The final series with 2.7 support is 1.3.x. If you have a package using
Python 2 and are unable or unwilling to upgrade to Python 3, then you
should use the following `dependency
`__ for
Nipype::

    nipype<1.4

Bug fixes will be accepted against the ``maint/1.3.x`` branch.

Support and Communication
-------------------------

If you have a problem or would like to ask a question about how to do something in Nipype please open an issue to
`NeuroStars.org `_ with a *nipype* tag. `NeuroStars.org `_  is a
platform similar to StackOverflow but dedicated to neuroinformatics.

To participate in the Nipype development related discussions please use the following mailing list::

       http://mail.python.org/mailman/listinfo/neuroimaging

Please add *[nipype]* to the subject line when posting on the mailing list.

You can even hangout with the Nipype developers in their
`Gitter `_ channel or in the BrainHack `Slack `_ channel. (Click `here `_ to join the Slack workspace.)


Contributing to the project
---------------------------

If you'd like to contribute to the project please read our `guidelines `_. Please also read through our `code of conduct `_.

Owner

Name: NIPY developers
Login: nipy
Kind: organization

Website: http://nipy.org
Repositories: 38
Profile: https://github.com/nipy

GitHub Events

Total

Create event: 16
Release event: 5
Issues event: 20
Watch event: 47
Delete event: 10
Issue comment event: 79
Push event: 31
Pull request review comment event: 25
Pull request review event: 29
Pull request event: 58
Fork event: 13

Last Year

Create event: 16
Release event: 5
Issues event: 20
Watch event: 47
Delete event: 10
Issue comment event: 79
Push event: 31
Pull request review comment event: 25
Pull request review event: 29
Pull request event: 58
Fork event: 13

Committers

Last synced: over 2 years ago

All Time

Total Commits: 11,681
Total Committers: 257
Avg Commits per committer: 45.451
Development Distribution Score (DDS): 0.808

Past Year

Commits: 104
Committers: 21
Avg Commits per committer: 4.952
Development Distribution Score (DDS): 0.596

Top Committers

Name	Email	Commits
Satrajit Ghosh	s**h@g**m	2,244
Oscar Esteban	c**e@o**s	1,529
Krzysztof J. Gorgolewski	k**i@g**m	1,520
Christopher J. Markiewicz	e**s@g**m	1,097
Christopher Burns	c**s@b**u	464
Mathias Goncalves	g**s@g**m	277
Dorota Jarecka	d**a@g**m	241
Erik Ziegler	e**d@g**m	221
Shoshana Berleant	b**t@s**u	206
David Ellis	d**0@g**m	199
Cindee Madison	c**e@b**u	181
Michael Waskom	m**m@g**m	163
Michael Philipp Notter	m**r@h**m	141
Basille Pinsard	b**d@u**a	139
Alexandre M. Savio	a**o@g**m	124
Daniel Clark	d**7@g**m	113
Yaroslav Halchenko	d**n@o**m	102
Dav Clark	d**k@b**u	102
Fred Loney	l**f@o**u	90
Kesshi Jordan	K**n@u**u	86
Martin Norgaard	m**d@n**k	76
Michael Dayan	m**h@g**m	75
Salma Bougacha	s**a@h**m	63
Hans Johnson	h**n@u**u	61
Blake Dewey	b**y@j**u	55
Benjamin Yvernault	b**t@g**m	54
Horea Christian	h**t@y**m	51
Carlo Hamalainen	c**o@c**t	50
Ben Cipollini	b**i@c**g	50
Taylor Salo	t**6@f**u	49
and 227 more...

Committer Domains (Top 20 + Academic)

berkeley.edu: 5 mit.edu: 5 inria.fr: 4 fiu.edu: 4 uiowa.edu: 4 ucl.ac.uk: 2 dartmouth.edu: 2 flywheel.io: 2 icm-institute.org: 2 gmx.de: 2 cea.fr: 2 nih.gov: 2 childrens.harvard.edu: 2 stanford.edu: 2 cbs.mpg.de: 2 uniklinikum-dresden.de: 1 charite.de: 1 mcw.edu: 1 mail.tau.ac.il: 1 cornell.edu: 1 uw.edu: 1 uni-heidelberg.de: 1 umassmed.edu: 1 mail.utexas.edu: 1 sydney.edu.au: 1 cs.washington.edu: 1 mymail.pomona.edu: 1 jhu.edu: 1 ucsf.edu: 1 ohsu.edu: 1 tuebingen.mpg.de: 1 wisc.edu: 1 vu.nl: 1 nmr.mgh.harvard.edu: 1 univ-amu.fr: 1 wustl.edu: 1 birch.pst.ed.ac.uk: 1 mcgill.ca: 1 mailbox.tu-berlin.de: 1 newcastle.edu.au: 1 mail.nih.gov: 1 cam.ac.uk: 1 mailbox.tu-dresden.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 126
Total pull requests: 184
Average time to close issues: 8 months
Average time to close pull requests: 9 months
Total issue authors: 82
Total pull request authors: 55
Average comments per issue: 2.1
Average comments per pull request: 2.27
Merged pull requests: 125
Bot issues: 0
Bot pull requests: 16

Past Year

Issues: 16
Pull requests: 54
Average time to close issues: 6 days
Average time to close pull requests: 9 days
Issue authors: 14
Pull request authors: 13
Average comments per issue: 1.75
Average comments per pull request: 1.37
Merged pull requests: 43
Bot issues: 0
Bot pull requests: 5

View more stats

Top Authors

Issue Authors

effigies (7)
GalKepler (6)
JohannesWiesner (6)
TheChymera (5)
oesteban (4)
yarikoptic (4)
mnoergaard (4)
zachlindsey (3)
mauriliogenovese (3)
fladd (3)
lamaresh (3)
lukevano (2)
sulantha2006 (2)
man-shu (2)
stepantikhomirov (2)

Pull Request Authors

DimitriPapadopoulos (43)
effigies (41)
dependabot[bot] (19)
mauriliogenovese (16)
GalKepler (6)
zachlindsey (6)
mgxd (5)
yarikoptic (5)
mnoergaard (5)
hjmjohnson (4)
shnizzedy (3)
TheChymera (3)
salma1601 (3)
manuegrx (3)
hstojic (2)

Top Labels

Issue Labels

help-wanted (4) bug (3) good-first-issue (2) nipype 2.0 (1) doc (1) discussion (1) enhancement (1) question (1) faq (1)

Pull Request Labels

dependency (16) orphaned (3) dependencies (3) github_actions (3) bug (2) 0 - Backlog (2) 2 - Working <= 5 (2) in-progress (2) nipype 2.0 (2) 1 - Ready (2) blocked (1) maintenance (1)

Packages

Total packages: 5
Total downloads:
- pypi 353,495 last-month
Total docker downloads: 20,836

Total dependent packages: 49
(may contain duplicates)
Total dependent repositories: 1,112
(may contain duplicates)
Total versions: 123
Total maintainers: 6

pypi.org: nipype

Neuroimaging in Python: Pipelines and Interfaces

Homepage: http://nipy.org/nipype
Documentation: https://nipype.readthedocs.io/
License: Apache License, 2.0
Latest release: 1.10.0
published 11 months ago

Versions: 68
Dependent Packages: 45
Dependent Repositories: 1,107
Downloads: 353,301 Last month
Docker Downloads: 20,836

Rankings

Dependent packages count: 0.3%

Dependent repos count: 0.3%

Average: 0.7%

Downloads: 1.1%

Docker downloads count: 1.2%

Maintainers (4)

cjmarkie filo mgxd satra

Last synced: 6 months ago

proxy.golang.org: github.com/nipy/nipype

Documentation: https://pkg.go.dev/github.com/nipy/nipype#section-documentation
License: other
Latest release: v1.0.0
published about 8 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 6 months ago

spack.io: py-nipype

Neuroimaging in Python: Pipelines and Interfaces.

Homepage: https://github.com/nipy/nipype
License: []
Latest release: 1.8.6
published almost 3 years ago

Versions: 6
Dependent Packages: 3
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 3.9%

Average: 7.9%

Stargazers count: 8.8%

Dependent packages count: 19.0%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

pypi.org: nipype-ancp

Neuroimaging in Python: Pipelines and Interfaces

Homepage: http://nipy.org/nipype
Documentation: https://nipype-ancp.readthedocs.io/
License: Apache License, 2.0
Latest release: 0.1.0
published 7 months ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 194 Last month

Rankings

Forks count: 3.0%

Stargazers count: 3.3%

Dependent packages count: 8.7%

Average: 16.0%

Dependent repos count: 49.2%

Maintainers (1)

KarelLopezVilaret

Last synced: 6 months ago

conda-forge.org: nipype

Homepage: https://github.com/nipy/nipype
License: Apache-2.0
Latest release: 1.8.5
published over 3 years ago

Versions: 45
Dependent Packages: 1
Dependent Repositories: 5

Rankings

Forks count: 7.4%

Dependent repos count: 14.8%

Stargazers count: 15.4%

Average: 16.7%

Dependent packages count: 29.0%

Last synced: 6 months ago

Dependencies

.github/workflows/contrib.yml actions

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

.github/workflows/tests.yml actions

actions/checkout v3 composite
actions/download-artifact v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
codecov/codecov-action v3 composite
pypa/gh-action-pypi-publish release/v1 composite

doc/requirements.txt pypi

dipy *
ipython *
matplotlib *
nbsphinx *
niflow-nipype1-workflows *
sphinx >=2.1.2
sphinx-argparse *
sphinxcontrib-apidoc *
sphinxcontrib-napoleon *

requirements.txt pypi

click >=6.6.0
etelemetry >=0.2.0
filelock >=3.0.0
networkx >=2.0
nibabel >=2.1.0
numpy >=1.13
numpy >=1.15.3
packaging *
prov >=1.5.2
pydot >=1.2.3
python-dateutil >=2.2
rdflib >=5.0.0
scipy >=0.14
simplejson >=3.8.0
traits >=4.6,

.github/workflows/codespell.yml actions

actions/checkout v3 composite
codespell-project/actions-codespell v1 composite