pyxnat

XNAT in Python

Science Score: 23.0%

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
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.zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
9 of 34 committers (26.5%) 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 (14.4%) to scientific vocabulary

Keywords from Contributors

neuroimaging brain-imaging brainweb dataflow-programming workflow-engine dataflow quality-control neuroscience fmri medical-imaging

Last synced: 10 months ago · JSON representation

Repository

XNAT in Python

Basic Info

Host: GitHub
Owner: pyxnat
License: other
Language: Python
Default Branch: master
Homepage: https://pyxnat.github.io/pyxnat
Size: 7.96 MB

Statistics

Stars: 76
Watchers: 10
Forks: 67
Open Issues: 13
Releases: 8

Created almost 16 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog License

README.rst

=======
pyxnat
=======

..  image:: https://github.com/pyxnat/pyxnat/actions/workflows/ci.yml/badge.svg
     :target: https://github.com/pyxnat/pyxnat/actions/workflows/ci.yml
.. image:: https://coveralls.io/repos/github/pyxnat/pyxnat/badge.svg?branch=master
    :target: https://coveralls.io/github/pyxnat/pyxnat?branch=master
.. image:: https://img.shields.io/pypi/dm/pyxnat.svg
    :target: https://pypi.org/project/pyxnat/
.. image:: https://img.shields.io/pypi/pyversions/pyxnat.svg
    :target: https://pypi.org/project/pyxnat
.. image:: https://img.shields.io/pypi/v/pyxnat.svg
    :target: https://pypi.org/project/pyxnat

.. image:: https://gitlab.com/xgrg/tweetit/-/raw/master/resources/008-pyxnat-v1.4.gif?inline=false

Where to get it
===============

The source code is currently hosted on GitHub at:
https://github.com/pyxnat/pyxnat

Binary installers for the latest released version are available at the `Python
package index `_. **pyxnat** can be installed
using ``pip`` with the following command::

    pip install pyxnat

Dependencies
============

- `requests `_ v2.20 or higher
- `python-lxml `_ v4.3.2 or higher recommended, earlier versions may work.

For development purposes:

- `pytest `_ v7.1 or higher
- `coverage `_ v3.6 or higher

See the `full installation instructions `_
for recommended and optional dependencies.

Installation from sources
=========================

To install **pyxnat** from source, from the ``pyxnat`` directory (same one
where you found this file after cloning the git repo), execute::

    python setup.py install


Documentation
=============

The official documentation is hosted at: https://pyxnat.github.io/pyxnat

Running the test suite
=========================

Until v1.1 tests were exclusively performed on `XNAT Central `_
using a dedicated user account (``nosetests``). Yet some tests were not allowed to
run due to restricted permissions.
In v1.1, tests were restructured and were directed to two independent XNAT
instances based on permission level. Hence `XNAT Central `_
is still used for most tests with read access whereas other tests requiring
write permissions are run on a local XNAT instance in a Docker container.

Consequently, running the test suite now requires the following:

  - *pytest* v7.1+
  - *coverage* v3.6+
  - *docker* v18+

Setting up a local Docker-powered XNAT instance may be achieved easily using
``docker-compose`` and any available recipe. We recommend the one from the
`following repository `_
(maintained by the XNAT team). Once the repository cloned, run the following
command (possibly as ``sudo``) ::

  docker-compose up -d

After a couple of minutes, the XNAT instance should be up and running locally.
You may check it out visiting http://localhost.

The script ``tests/setup_xnat.py`` may then be executed to populate the local
instance before running the tests.

Finally run the tests with the following command (from the root of the project)::

    pytest --cov pyxnat

The file ``.github/workflows/ci.yml`` (used for CI) features these described
steps and may be referred to for further information.


Building the documentation
==========================

Building the docs requires to have `setuptools `_
and `sphinx `_ (v2.0+) installed.
Then run the command::

    python setup.py build_sphinx

The docs are built in the ``build/sphinx/html`` folder.

Contribute to **pyxnat**
=========================

To contribute to **pyxnat**, first create an account on `GitHub
`_. Once this is done, fork the `pyxnat repository
`_ to have you own repository,
clone it using ``git clone`` on the computers where you want to work. Make
changes in your clone, push them to your GitHub fork, test them
on several computers and when you are happy with them, send a `pull
request `_ to the main repository.

License
=======

`BSD 3 `_

Owner

Name: pyxnat
Login: pyxnat
Kind: organization

Website: https://pyxnat.github.io/pyxnat/
Repositories: 2
Profile: https://github.com/pyxnat

GitHub Events

Total

Create event: 5
Release event: 1
Issues event: 5
Watch event: 3
Issue comment event: 2
Push event: 16
Pull request review comment event: 8
Pull request review event: 11
Pull request event: 16
Fork event: 4

Last Year

Create event: 5
Release event: 1
Issues event: 5
Watch event: 3
Issue comment event: 2
Push event: 16
Pull request review comment event: 8
Pull request review event: 11
Pull request event: 16
Fork event: 4

Committers

Last synced: over 2 years ago

All Time

Total Commits: 529
Total Committers: 34
Avg Commits per committer: 15.559
Development Distribution Score (DDS): 0.645

Past Year

Commits: 19
Committers: 2
Avg Commits per committer: 9.5
Development Distribution Score (DDS): 0.053

Top Committers

Name	Email	Commits
Yannick Schwartz	y**z@c**r	188
xgrg	g**o@g**m	163
jhuguetn	j**n@g**m	55
Just, David J. (Dave)	D**t@g**m	24
David Just	j**d@m**u	13
Christian Haselgrove	c**e@u**u	12
bud42	b**2@g**m	11
marinagrprat	m**a@b**g	6
Deech	d**h@d**)	5
Yaroslav Halchenko	d**n@o**m	5
Scott Burns	s**s@g**m	4
Stephan Gerhard	g**t@u**h	4
Rick Herrick	r**k@g**m	4
Satrajit Ghosh	s**a@m**u	4
John Flavin	f**j@g**m	3
Baris Kanber	b**r@u**k	2
Rick Herrick	r**k@w**u	2
Jordi Huguet	j**t@a**l	2
Aditya Siram	a**a@a**)	2
roelant001	r**r@h**m	2
Kevin A. Archie	k**e@w**u	2
Kevin A. Archie	k**e@a**u	2
Christoph Kolbitsch	c**h@p**e	2
Dom McIntyre	d**e@h**m	2
Nolan Nichols	n**s@g**m	1
koekie	m**k@e**l	1
Victor Férat	v**t@l**r	1
DavidJJ	d**b@g**m	1
Yannick Schwartz	y**3@i**)	1
FredLoney	l**f@o**u	1
and 4 more...

Committer Domains (Top 20 + Academic)

wustl.edu: 2 cea.fr: 1 mayo.edu: 1 umassmed.edu: 1 barcelonabeta.org: 1 deech-thinkpad-x200.(none): 1 onerussian.com: 1 unidesign.ch: 1 mit.edu: 1 ucl.ac.uk: 1 amc.nl: 1 aditya-desktop.(none): 1 alumni.caltech.edu: 1 ptb.de: 1 erasmusmc.nl: 1 live.fr: 1 is140727.(none): 1 ohsu.edu: 1 biac.duke.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 42
Total pull requests: 103
Average time to close issues: over 1 year
Average time to close pull requests: about 1 month
Total issue authors: 28
Total pull request authors: 15
Average comments per issue: 2.36
Average comments per pull request: 0.6
Merged pull requests: 78
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 21
Average time to close issues: 28 days
Average time to close pull requests: 15 days
Issue authors: 3
Pull request authors: 4
Average comments per issue: 0.67
Average comments per pull request: 0.1
Merged pull requests: 16
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jhuguetn (11)
zswgzx (3)
yarikoptic (3)
alexpron (1)
samiraepp (1)
rb643 (1)
Phildrummer (1)
andersonwinkler (1)
Pkaps25 (1)
gkowalski (1)
FredLoney (1)
raamana (1)
ghammad (1)
DavidJJ (1)
emollier (1)

Pull Request Authors

jhuguetn (51)
xgrg (29)
anaharrismatnez (10)
Udolf15 (3)
emollier (2)
Pkaps25 (2)
scandel (2)
marinagrprat (2)
a-detiste (2)
onealbao (1)
vferat (1)
sburns (1)
locastre (1)
ckolbPTB (1)
ayan-b (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 319,271 last-month
Total docker downloads: 3,067

Total dependent packages: 12
(may contain duplicates)
Total dependent repositories: 875
(may contain duplicates)
Total versions: 57
Total maintainers: 5

pypi.org: pyxnat

XNAT in Python

Homepage: https://github.com/pyxnat/pyxnat
Documentation: https://pyxnat.readthedocs.io/
License: BSD
Latest release: 1.6.3
published over 1 year ago

Versions: 34
Dependent Packages: 10
Dependent Repositories: 873
Downloads: 319,117 Last month
Docker Downloads: 3,067

Rankings

Dependent repos count: 0.4%

Dependent packages count: 1.0%

Downloads: 1.0%

Docker downloads count: 1.9%

Average: 3.0%

Forks count: 5.5%

Stargazers count: 8.3%

Maintainers (5)

jhuguetn xgrg DavidJ schwarty Rick.Herrick

Last synced: 11 months ago

pypi.org: bbrc-pyxnat

XNAT in Python

Homepage: https://github.com/pyxnat/pyxnat
Documentation: https://bbrc-pyxnat.readthedocs.io/
License: BSD
Latest release: 1.6.3
published over 1 year ago

Versions: 23
Dependent Packages: 2
Dependent Repositories: 2
Downloads: 154 Last month

Rankings

Dependent packages count: 3.1%

Forks count: 5.5%

Stargazers count: 8.3%

Average: 9.3%

Dependent repos count: 11.6%

Downloads: 18.1%

Maintainers (2)

jhuguetn xgrg

Last synced: 11 months ago

Dependencies

requirements-dev.txt pypi

coverage >=3.6
coveralls *
future >=0.16
lxml >=4.3.2
matplotlib >=2.2
networkx >=2.2
nose >=1.2.1
pandas >=0.24
pathlib >=1.0.1
requests >=2.20
six >=1.15

requirements.txt pypi

future >=0.16
lxml >=4.3.2
pathlib >=1.0.1
requests >=2.20
six >=1.15

setup.py pypi

future >=0.16
lxml >=4.3
pathlib >=1.0
requests >=2.20
six >=1.15

.github/workflows/ci.yml actions

actions/checkout v3 composite
actions/setup-python v3 composite

.github/workflows/docs.yml actions

actions/checkout v3 composite
actions/setup-python v3 composite