PyBIDS
PyBIDS: Python tools for BIDS datasets - Published in JOSS (2019)
Science Score: 95.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 12 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
✓Committers with academic emails
20 of 73 committers (27.4%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Keywords from Contributors
Scientific Fields
Repository
Python tools for querying and manipulating BIDS datasets.
Basic Info
- Host: GitHub
- Owner: bids-standard
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://bids-standard.github.io/pybids/
- Size: 11 MB
Statistics
- Stars: 247
- Watchers: 19
- Forks: 128
- Open Issues: 105
- Releases: 55
Topics
Metadata Files
README.md
PyBIDS
PyBIDS is a Python library to centralize interactions with datasets conforming BIDS (Brain Imaging Data Structure) format. For more information about BIDS visit https://bids.neuroimaging.io.
PyBIDS currently supports Python 3 on POSIX operating systems (including Mac OS). Windows is not officially supported, though most PyBIDS functionality will probably work fine.
Installation
PyBIDS is most easily installed from pip. To install the latest official release:
pip install pybids
Or, alternatively via conda:
conda install -c conda-forge pybids
If you want to live on the bleeding edge, you can install from master:
pip install git+https://github.com/bids-standard/pybids.git
Dependencies
PyBIDS has a number of dependencies. The core querying functionality requires only the BIDS-Validator package. However, most other modules require the core Python neuroimaging stack: numpy, scipy, pandas, and nibabel. The reports module additionally requires num2words. By default, all dependencies will be installed with pybids (if they aren't already available).
Usage
Get started by checking out the documentation!
Or you can start at our tutorial! You can run it interactively without installing anything via binder. Click on the link and then navigate to doc/examples/pybids_tutorial.md to explore.
Development and testing
PyBIDS uses tox to manage testing environments and ensure that the same commands can easily be run locally and in CI.
Install tox with:
pip install tox
To run tests with standard, minimal, or pre-release dependencies, use:
tox run -e [full|min|pre]
To run with a specific version, also specify py3X:
tox run -e py311-full
See tox documentation for more detail.
How to cite
To credit PyBIDS in your work, please cite both the JOSS paper and the Zenodo archive. The former provides a high level description of the package, and the latter points to a permanent record of all PyBIDS versions (we encourage you to cite the specific version you used). Example citations (for PyBIDS 0.9.3):
Yarkoni et al., (2019). PyBIDS: Python tools for BIDS datasets. Journal of Open Source Software, 4(40), 1294, https://doi.org/10.21105/joss.01294
Yarkoni, Tal, Markiewicz, Christopher J., de la Vega, Alejandro, Gorgolewski, Krzysztof J., Halchenko, Yaroslav O., Salo, Taylor, … Blair, Ross. (2019, August 8). bids-standard/pybids: 0.9.3 (Version 0.9.3). Zenodo. https://doi.org/10.5281/zenodo.3363985
Community guidelines
Bug reports, feedback, and other contributions to PyBIDS are welcome. To report a bug, request a feature, or raise a technical (non-usage-related) question for discussion, please open an issue on GitHub. Requests for support and questions about usage (where no bug is suspected) should be posted on the NeuroStars forum. For questions about the BIDS specification or BIDS-Validator, please see the corresponding repositories. For general BIDS-related discussion, see the bids-discussion mailing list.
Pull requests are always welcome. If you have any doubts about the suitability of a PR, or want to discuss implementation-related issues, feel free to open an issue for discussion.
Owner
- Name: Brain Imaging Data Structure
- Login: bids-standard
- Kind: organization
- Website: https://bids.neuroimaging.io
- Twitter: BIDSStandard
- Repositories: 47
- Profile: https://github.com/bids-standard
JOSS Publication
PyBIDS: Python tools for BIDS datasets
Authors
University of Texas at Austin
Stanford University
University of Texas at Austin
Stanford University
Florida International University
Dartmouth College
University of Texas at Austin
University of Oregon
McGill University
University of Southern California
Concordia University
National Institute of Mental Health
MRC Cognition and Brain Sciences Unit
Montreal Neurological Institute and Hospital
Alan Turing Institute
Montreal Neurological Institute and Hospital
Otto-von-Guericke University Magdeburg
CorticoMetrics LLC
Télécom ParisTech, France
Otto-von-Guericke University Magdeburg
Stanford University
Stanford University
Max Planck Institute for Human Development, Berlin, Germany
University of California at Berkeley
Queen Mary University London
INRIA
Rutgers University
National Institute of Mental Health
University of California at Berkeley
University of Lausanne
Stanford University
Editor
Christopher R. Madan
Tags
BIDS neuroimagingGitHub Events
Total
- Create event: 24
- Release event: 3
- Issues event: 27
- Watch event: 23
- Delete event: 16
- Issue comment event: 76
- Push event: 29
- Pull request review comment event: 5
- Pull request review event: 12
- Pull request event: 57
- Fork event: 5
Last Year
- Create event: 24
- Release event: 3
- Issues event: 27
- Watch event: 23
- Delete event: 17
- Issue comment event: 77
- Push event: 33
- Pull request review comment event: 5
- Pull request review event: 12
- Pull request event: 59
- Fork event: 5
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Tal Yarkoni | t****i@g****m | 717 |
| Christopher J. Markiewicz | m****z@s****u | 578 |
| Alejandro de la Vega | d****a@u****u | 381 |
| Krzysztof J. Gorgolewski | k****i@g****m | 77 |
| Taylor Salo | t****6@f****u | 72 |
| arokem | a****m@g****m | 64 |
| Remi Gau | r****u@h****m | 59 |
| Yaroslav O. Halchenko | d****n@o****m | 49 |
| dependabot[bot] | 4****] | 47 |
| Dimitri Papadopoulos Orfanos | 3****s | 37 |
| Oscar Esteban | c****e@o****s | 36 |
| James Kent | j****1@g****m | 29 |
| Hans Johnson | h****n@g****m | 28 |
| Krista DeStasio | k****o@g****m | 27 |
| Evgenii Kalenkovich | e****h@g****m | 24 |
| Dmitry Petrov | t****v@g****m | 17 |
| Dylan M. Nielson | D****n@n****v | 16 |
| Stefan Appelhoff | s****f@m****g | 15 |
| Peter Van Dyken | p****2@u****a | 14 |
| Mathias Goncalves | m****g@s****u | 11 |
| Shashank Bansal | s****6@g****m | 11 |
| Gregory Kiar | g****r@m****a | 8 |
| Johan Carlin | j****n@g****m | 8 |
| Satrajit Ghosh | s****a@m****u | 8 |
| Jake VanderPlas | j****p@u****u | 8 |
| Adina Wagner | a****r@t****e | 7 |
| Elizabeth DuPre | e****2@c****u | 7 |
| Kirstie Whitaker | k****1@c****k | 7 |
| Ali Khan | a****k@r****a | 6 |
| Andrew Janke | a****w@a****t | 6 |
| and 43 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 74
- Total pull requests: 260
- Average time to close issues: 11 months
- Average time to close pull requests: about 1 month
- Total issue authors: 49
- Total pull request authors: 24
- Average comments per issue: 2.99
- Average comments per pull request: 2.19
- Merged pull requests: 198
- Bot issues: 2
- Bot pull requests: 107
Past Year
- Issues: 17
- Pull requests: 95
- Average time to close issues: 9 days
- Average time to close pull requests: 6 days
- Issue authors: 16
- Pull request authors: 11
- Average comments per issue: 0.82
- Average comments per pull request: 1.25
- Merged pull requests: 73
- Bot issues: 2
- Bot pull requests: 45
Top Authors
Issue Authors
- effigies (6)
- adelavega (6)
- pvandyken (5)
- tsalo (4)
- bpinsard (4)
- oesteban (3)
- alperkent (2)
- MRIDude (2)
- dependabot[bot] (2)
- eulerleibniz (1)
- me-pic (1)
- Lestropie (1)
- maximemulder (1)
- wasciutto (1)
- musicinmybrain (1)
Pull Request Authors
- dependabot[bot] (98)
- effigies (57)
- Remi-Gau (22)
- DimitriPapadopoulos (17)
- adelavega (15)
- github-actions[bot] (9)
- akhanf (6)
- tsalo (5)
- oesteban (4)
- bpinsard (4)
- alperkent (3)
- cookpa (3)
- pvandyken (2)
- coryshain (2)
- fraimondo (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 56,670 last-month
- Total docker downloads: 28,429
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Total dependent packages: 51
(may contain duplicates) -
Total dependent repositories: 163
(may contain duplicates) - Total versions: 64
- Total maintainers: 4
pypi.org: pybids
bids: interface with datasets conforming to BIDS
- Homepage: https://github.com/bids-standard/pybids
- Documentation: https://pybids.readthedocs.io/
- License: The MIT License (MIT) Copyright (c) 2015-2016, Ariel Rokem, The University of Washington eScience Institute. Copyright (c) 2016--, PyBIDS developers, Planet Earth Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 0.19.0
published 10 months ago
Rankings
spack.io: py-pybids
bids: interface with datasets conforming to BIDS
- Homepage: https://github.com/bids-standard/pybids
- License: []
-
Latest release: 0.16.3
published about 2 years ago
Rankings
Maintainers (1)
Dependencies
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- bids-validator *
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- formulaic >=0.2.4, <0.6
- nibabel >=2.1
- num2words *
- numpy <1.25.0.dev0; python_version < '3.9'
- numpy *
- pandas >=0.23
- scipy *
- sqlalchemy <1.4.0.dev0
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