Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.9%) to scientific vocabulary
Last synced: 7 months ago
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Repository
BIDS Stats Models Specification
Basic Info
- Host: GitHub
- Owner: bids-standard
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://bids-standard.github.io/stats-models
- Size: 8.31 MB
Statistics
- Stars: 2
- Watchers: 7
- Forks: 9
- Open Issues: 30
- Releases: 1
Created almost 4 years ago
· Last pushed 10 months ago
Metadata Files
Readme
License
Citation
README.md
BIDS Stats Models Specification
This repository is intended to be the authoritative reference for the BIDS Stats Models specification. It consists of two parts:
1) bsmschema, a Pydantic description of the
BIDS Stats Models files, which can be used as a schema validator or generate JSON
schema for independent validation.
2) specification, a JupyterBook website that includes
more human readable introductions and explanations, as well as a reference document
for bsmschema.
Installing bsmschema
From the Python package index
pip install bsmschema
From source
git clone https://github.com/bids-standard/stats-models.git
pip install stats-models/bsmschema
You may wish to install in editable mode, to ensure that your changes get propagated without reinstalling:
pip install -e stats-models/bsmschema
How to run schema validator
python
from bsmschema.models import BIDSStatsModel
BIDSStatsModel.parse_file('stats-models/specification/examples/model-example_smdl.json')
Building the documentation locally
We recommend using the uv tool to ensure reproducible builds.
1) Build the schema files to ensure the local validator will work:
uv run -m bsmschema specification/schema
1) Build the JupyterBook:
uv run jb build specification
1) Serve the built website:
uv run -m http.server -d specification/_build/html/
Note that this will start a long-running web-server that will occupy your terminal.
Ctrl-C quits.
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
Citation (CITATION.cff)
# schema: https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
cff-version: 1.2.0
title: "BIDS Stats Models Specification"
version: 1.0.0-rc2
abstract: BIDS Stats Models Specification.
message: "If you are using the BIDS stats model, please cite it as below."
repository-code: "https://github.com/bids-standard/stats-models.git"
# identifiers:
# - description: This is the collection of archived snapshots of all releases of BIDSpm
# type: doi
# value: "10.5281/zenodo.3554331"
contact:
- family-names: Markiewicz
given-names: Christopher J.
website: https://github.com/effigies
email: effigies@gmail.com
- family-names: de la Vega
given-names: Alejandro
website: https://github.com/adelavega
email: aleph4@gmail.com
orcid: https://orcid.org/0000-0001-9062-3778
authors:
# TEMPLATE
# - family-names: XXX
# given-names: XXX
# affiliation: XXX
# website: XXX
# email: XXX@XXX.XXX
# orcid: "https://orcid.org/XXXX-XXXX-XXXX-XXXX"
# Sorted alphabetically except for the 1rst and last authors
- family-names: Markiewicz
given-names: Christopher J.
website: https://github.com/effigies
email: markiewicz@stanford.edu
orcid: https://orcid.org/0000-0002-6533-164X
affiliation: Stanford University
- family-names: Bansal
given-names: Shashank
website: https://shashankbansal6.github.io/
email: shashankbansal56@gmail.com
orcid: https://orcid.org/0000-0002-1252-8772
affiliation: UCSD Bioengineering
- family-names: Blair
given-names: Ross W.
website: https://github.com/rwblair
- family-names: Bottenhorn
given-names: Katherine
website: https://github.com/62442katieb
orcid: https://orcid.org/0000-0002-7796-8795
affiliation: Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA USA
email: bottenho@usc.edu
- family-names: Chen
given-names: Gang
website: https://github.com/afni-gangc
orcid: https://orcid.org/0000-0002-2960-089X
affiliation:
National Institutes of Health, Scientific and Statistical Computing Core,
NIMH, Bethesda, MD 20892, USA
email: gangchen@mail.nih.gov
- family-names: Dafflon
given-names: Jessica
website: https://jessicadafflon.github.io/
- family-names: Esteban
given-names: Oscar
website: http://www.axonlab.org
orcid: https://orcid.org/0000-0001-8435-6191
affiliation:
Department of Radiology, Lausanne University Hospital and University of Lausanne,
Lausanne, Switzerland
email: phd@oscaresteban.es
- family-names: Gau
given-names: Rémi
affiliation: Université catholique de Louvain
email: remi.gau@uclouvain.be
orcid: "https://orcid.org/0000-0002-1535-9767"
- family-names: Gorgolewski
given-names: Krzysztof Jacek
website: https://chrisgorgolewski.org
orcid: https://orcid.org/0000-0003-3321-7583
- family-names: Halchenko
given-names: Yaroslav
affiliation: Dartmouth College
website: https://centerforopenneuroscience.org/whoweare#yaroslav_o_halchenko_
orcid: "https://orcid.org/0000-0003-3456-2493"
- family-names: Johnson
given-names: Timothy
affiliation: University of Michigan, Biostatistics
email: tdjtdj@umich.edu
website: https://sph.umich.edu/faculty-profiles/johnson-timothy.html
- family-names: Kent
given-names: James
affiliation:
Psychoinformatics Laboratory at the University of Texas at Austin
website: https://jdkent.github.io/
email: jamesdkent21@gmail.com
- family-names: Maumet
given-names: Camille
website: https://camillemaumet.com/
orcid: https://orcid.org/0000-0002-6290-553X
affiliation: Inria, Univ Rennes, CNRS, Inserm, Rennes, 35042, France
- family-names: Mumford
given-names: Jeanette
website: https://github.com/jmumford
email: jeanette.mumford@gmail.com
- family-names: Narayan
given-names: Manjari
email: manjari@alumni.rice.edu
- family-names: Nichols
given-names: Thomas E.
website: http://nisox.org
orcid: https://orcid.org/0000-0002-4516-5103
affiliation: University of Oxford, Big Data Institute, Oxford, OX3 7LF, UK
email: thomas.nichols@BDI.OX.AC.UK
- family-names: Nielson
given-names: Dylan
affiliation:
Machine Learning Team at the National Institute of Mental Health
website: https://github.com/Shotgunosine
- family-names: Niso
given-names: Guiomar
website: http://guiomarniso.com
orcid: https://orcid.org/0000-0001-5872-8924
affiliation: Instituto Cajal, CSIC, Spain
email: guiomar.niso@ctb.upm.es
- family-names: Ombao
given-names: Hernando
affiliation: KAUST, Saudi Arabia
website: https://cemse.kaust.edu.sa/biostats
email: hernando.ombao@kaust.edu.sa
orcid: https://orcid.org/0000-0001-7020-8091
- family-names: Poldrack
given-names: Russell A.
website: http://www.poldracklab.org
orcid: https://orcid.org/0000-0001-6755-0259
affiliation: Stanford University, Stanford, CA 94305 USA
email: russpold@stanford.edu
- family-names: Poline
given-names: Jean-Baptiste
website: https://github.com/jbpoline
orcid: https://orcid.org/0000-0002-9794-749X
- family-names: Thirion
given-names: Bertrand
website: https://github.com/bthirion
orcid: https://orcid.org/0000-0001-5018-7895
- family-names: de la Vega
given-names: Alejandro
website: https://github.com/adelavega
- family-names: Yarkoni
given-names: Tal
email: tyarkoni@gmail.com
license: CC-BY-4.0
keywords:
- BIDS
- brain imaging data structure
- statistical modeling
- general linear model
GitHub Events
Total
- Release event: 1
- Delete event: 4
- Issue comment event: 5
- Member event: 1
- Push event: 13
- Pull request event: 10
- Create event: 5
Last Year
- Release event: 1
- Delete event: 4
- Issue comment event: 5
- Member event: 1
- Push event: 13
- Pull request event: 10
- Create event: 5
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 47
- Total pull requests: 56
- Average time to close issues: 10 months
- Average time to close pull requests: 8 days
- Total issue authors: 6
- Total pull request authors: 9
- Average comments per issue: 1.64
- Average comments per pull request: 1.68
- Merged pull requests: 51
- Bot issues: 0
- Bot pull requests: 7
Past Year
- Issues: 0
- Pull requests: 13
- Average time to close issues: N/A
- Average time to close pull requests: 18 minutes
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.15
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 7
Top Authors
Issue Authors
- Remi-Gau (16)
- effigies (11)
- adelavega (11)
- chrisgorgo (7)
- jdkent (1)
- Shotgunosine (1)
Pull Request Authors
- effigies (26)
- Remi-Gau (8)
- dependabot[bot] (7)
- adelavega (4)
- bendhouseart (3)
- rwblair (3)
- Shotgunosine (3)
- yarikoptic (1)
- DimitriPapadopoulos (1)
Top Labels
Issue Labels
website (3)
documentation (3)
good first issue (1)
question (1)
Pull Request Labels
dependencies (7)
github_actions (7)
Packages
- Total packages: 1
-
Total downloads:
- pypi 514 last-month
- Total dependent packages: 1
- Total dependent repositories: 2
- Total versions: 6
- Total maintainers: 1
pypi.org: bsmschema
A Pydantic schema for BIDS Stats Models
- Homepage: https://bids-standard.github.io/stats-models/
- Documentation: https://bsmschema.readthedocs.io/
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While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright 2022 BIDS Stats Models Contributors Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
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Latest release: 0.1.1
published 10 months ago
Rankings
Dependent packages count: 4.7%
Downloads: 6.4%
Forks count: 11.4%
Dependent repos count: 11.6%
Average: 14.6%
Stargazers count: 38.8%
Maintainers (1)
Last synced:
7 months ago
Dependencies
requirements.txt
pypi
- autodoc_pydantic *
- black *
- jupyter-book >=0.13
- jupytext *
- pandas *
- sphinxcontrib-matlabdomain *
.github/workflows/codespell.yml
actions
- actions/checkout v3 composite
- codespell-project/actions-codespell v1 composite
.github/workflows/gh-pages.yml
actions
- actions/checkout v3 composite
- actions/setup-python v4 composite
- peaceiris/actions-gh-pages v3 composite
.github/workflows/package.yml
actions
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
bsmschema/pyproject.toml
pypi
- pydantic !=2.0a1