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https://github.com/Remi-Gau/bids2cite
Create a citation file for a BIDS dataset.
https://github.com/Remi-Gau/bids2cite
Last synced: about 1 month ago
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Create a citation file for a BIDS dataset.
- Host: GitHub
- URL: https://github.com/Remi-Gau/bids2cite
- Owner: Remi-Gau
- License: other
- Created: 2022-10-09T17:08:12.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-11-04T22:20:45.000Z (about 1 month ago)
- Last Synced: 2024-11-08T19:45:03.746Z (about 1 month ago)
- Language: Python
- Homepage: https://bids2cite.readthedocs.io/en/latest/
- Size: 460 KB
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
- awesome-bids - bids2cite
README
[](https://github.com/Remi-Gau/bids2cite/actions/workflows/test.yml)
[](https://codecov.io/gh/Remi-Gau/bids2cite)
[](https://results.pre-commit.ci/latest/github/Remi-Gau/bids2cite/main)
[](https://bids2cite.readthedocs.io/en/latest/?badge=latest)
[](https://badge.fury.io/py/bids2cite)
# 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
[](https://www.youtube.com/embed/BXSW5KGoQRY)
## 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](https://bids2cite.readthedocs.io) 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**
| first_name | last_name | 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](https://github.com/Remi-Gau/bids2cite/tree/main/inputs).
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
path_to_bids_dataset = Path("path/to/bids/dataset")
bids2cite(
bids_dir=path_to_bids_dataset,
description="add something",
keywords=["foo", "bar"],
skip_prompt=True,
)
```
More info in the
[doc](https://bids2cite.readthedocs.io/en/latest/bids2cite.html#bids2cite.bids2cite.main)
## See also...
- [a BIDS dataset_description.json generator with a GUI](https://github.com/tolik-g/BIDS_GUI_dataset_description)
- datalad-neuroimaging
[Pull Request](https://github.com/bids-standard/bids-specification/issues/901)
to implement something similar to bids2cite in the datalad ecosysten