bids2cite

Create a citation file for a BIDS dataset.

https://github.com/remi-gau/bids2cite

Science Score: 44.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary

Last synced: 7 months ago · JSON representation ·

Repository

Create a citation file for a BIDS dataset.

Basic Info

Host: GitHub
Owner: Remi-Gau
License: other
Language: Python
Default Branch: main
Homepage: https://bids2cite.readthedocs.io/en/latest/
Size: 451 KB

Statistics

Stars: 3
Watchers: 2
Forks: 1
Open Issues: 8
Releases: 3

Created over 3 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

bids2cite

Create a citation file for a BIDS dataset based on its dataset_description.json file.

Can also be used to interactively update references, authors and add a license to a dataset.

You can add references using their DOI or PMID, and add authors by using their ORCID.

This will also update the dataset_description.json by creating in a new file in a derivatives/bids2cite folder.

Visual demo

Installation

bash pip install bids2cite

For developers

Fork the repo and clone your fork.

bash pip install .[dev]

Basic tests can be run with:

bash make test make test-cli

Usage

Do not forget to check the online doc for more details.

Command line

The most basic usage is:

bash bids2cite path_to_bids_dataset

An example of call with all the options:

bash bids2cite "tests/bids" \ --keywords "foo, bar, me" \ --description "this is the description of my dataset" \ --authors_file "inputs/authors.tsv" \ --license "CC0-1.0" \ --verbose

--keywords, --license and --description allow you to pass keywords, license and description to add to the citation file.

With --skip-prompt you will skip the prompt to add information manually to the citation file.

--authors_file points to a TSV file containing potential authors to add citation file. This can be useful if you need to have a single file to keep track of several lab members and only pick the relevant ones to add to a given dataset.

This TSV file must at least have first_name and last_name columns, but can also include ORCID and affiliation columns.

Example

| firstname | lastname | ORCID | affiliation | | ---------- | --------- | ------------------- | ----------- | | Rémi | Gau | 0000-0002-1535-9767 | UCLouvain | | Mohamed | Rezk | 0000-0002-1866-8645 | UCLouvain |

There is a sample TSV in the inputs folder.

Type the following for more info on how to run it:

bash bids2cite --help

Python

If you need to incorporate this into a python script you can do like this:

```python from bids2cite.bids2cite import bids2cite from pathlib import Path

pathtobids_dataset = Path("path/to/bids/dataset")

bids2cite( bidsdir=pathtobidsdataset, description="add something", keywords=["foo", "bar"], skip_prompt=True, ) ```

More info in the doc

See also...

a BIDS dataset_description.json generator with a GUI
datalad-neuroimaging Pull Request to implement something similar to bids2cite in the datalad ecosysten

Owner

Name: Remi Gau
Login: Remi-Gau
Kind: user
Location: Louvain la neuve, Belgium
Company: Crossmodal perception plasticity lab

Website: https://remi-gau.github.io/
Twitter: RemiGau
Repositories: 70
Profile: https://github.com/Remi-Gau

Neuroimaging (high-res & laminar fMRI) and multisensory. Too much matlab and presentation and not enough R and python

Citation (CITATION.cff)

cff-version: 1.2.0

title: "bids2cite"

version: 0.1.0

abstract:
  "Adds a datacite file to a BIDS dataset."

message: "If you use this software, please cite it as below."

repository-code: "https://github.com/Remi-Gau/bids2cite.git"


contact:
  - affiliation: "Université catholique de Louvain"
    email: remi.gau@uclouvain.be
    family-names: Gau
    given-names: Rémi

authors:
  - family-names: "Gau"
    given-names: "Rémi"
    orcid: "https://orcid.org/0000-0002-1535-9767"
    affiliation: "Université catholique de Louvain"

license: GPL-3.0

keywords:
  - BIDS
  - brain imaging data structure
  - neuroimaging
  - automated pipeline
  - MRI
  - Python

GitHub Events

Total

Delete event: 17
Issue comment event: 18
Push event: 36
Pull request review event: 16
Pull request event: 38
Create event: 21

Last Year

Delete event: 17
Issue comment event: 18
Push event: 36
Pull request review event: 16
Pull request event: 38
Create event: 21

Committers

Last synced: about 3 years ago

All Time

Total Commits: 98
Total Committers: 2
Avg Commits per committer: 49.0
Development Distribution Score (DDS): 0.143

Top Committers

Name	Email	Commits
Remi Gau	r**u@h**m	84
pre-commit-ci[bot]	6**]@u**m	14

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 27
Total pull requests: 122
Average time to close issues: about 2 months
Average time to close pull requests: 3 days
Total issue authors: 2
Total pull request authors: 4
Average comments per issue: 0.11
Average comments per pull request: 0.61
Merged pull requests: 108
Bot issues: 0
Bot pull requests: 115

Past Year

Issues: 0
Pull requests: 42
Average time to close issues: N/A
Average time to close pull requests: 5 days
Issue authors: 0
Pull request authors: 3
Average comments per issue: 0
Average comments per pull request: 0.86
Merged pull requests: 37
Bot issues: 0
Bot pull requests: 41

View more stats

Top Authors

Issue Authors

Remi-Gau (26)
marcelzwiers (1)

Pull Request Authors

pre-commit-ci[bot] (108)
Remi-Gau (7)
dependabot[bot] (6)
sourcery-ai[bot] (1)

Top Labels

Issue Labels

enhancement (6) bug (3)

Pull Request Labels

dependencies (6) github_actions (6)

Packages

Total packages: 1
Total downloads:
- pypi 24 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

pypi.org: bids2cite

create a citation file for a BIDS dataset

Homepage: https://github.com/Remi-Gau/bids2cite
Documentation: https://bids2cite.readthedocs.io/
License: LGPL-3.0
Latest release: 0.1.1
published over 3 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 24 Last month

Rankings

Dependent packages count: 6.6%

Stargazers count: 25.5%

Average: 26.5%

Forks count: 30.5%

Dependent repos count: 30.6%

Downloads: 39.1%

Maintainers (1)

Remi-Gau

Last synced: 7 months ago

Dependencies

.github/workflows/check_md_links.yml actions

actions/checkout master composite
gaurav-nelson/github-action-markdown-link-check v1 composite

.github/workflows/package.yml actions

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

.github/workflows/test_and_coverage.yml actions

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

.github/workflows/validate_cff.yml actions

actions/checkout v3 composite
citation-file-format/cffconvert-github-action 2.0.0 composite

pyproject.toml pypi

cffconvert *
crossref-commons *
pandas *
requests *
rich *
rich_argparse *
ruamel.yaml *

bids2cite

Science Score: 44.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

bids2cite

Visual demo

Installation

For developers

Usage

Command line

Python

See also...

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: bids2cite

Rankings

Maintainers (1)

Dependencies