[DOC] Update README.md (#588)

* Update README.md Add "How to cite" * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README.md * update citation * update version * update version * update README * update DOC README --------- Co-authored-by: Remi Gau <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
bids-standard · Nov 21, 2023 · 4a496e2 · 4a496e2
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diff --git a/CITATION.cff b/CITATION.cff
@@ -4,7 +4,7 @@ cff-version: 1.2.0
 
 title: bids-matlab
 
-version: 0.1.0dev
+version: 0.2.0
 
 license: MIT
 

diff --git a/Makefile b/Makefile
@@ -2,7 +2,7 @@
 clean:
 	rm version.txt
 
-version.txt: CITATION.cff
+version.txt: clean CITATION.cff
 	grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
 
 manual:

diff --git a/README.md b/README.md
@@ -68,7 +68,8 @@ addpath('bids-matlab');
 
 ### Get the latest features
 
-Stable versions should be fetched from a specific version tag.
+Stable versions should be fetched from a specific version tag
+or from the [Mathworkds file exchange](https://nl.mathworks.com/matlabcentral/fileexchange/93740-bids-matlab).
 
 A new version of BIDS matlab should be released for each new version of the BIDS specification
 to allow for a support of new BIDS datatypes or features.
@@ -85,14 +86,6 @@ Or clone it:
 git clone --branch main https://github.com/bids-standard/bids-matlab.git
 ```
 
-Or you can check it out the `main` branch
-after the adding this official bids-matlab repository as a remote.
-
-```
-git add remote upstream https://github.com/bids-standard/bids-matlab.git
-git checkout upstream/main
-```
-
 ## Features
 
 ### What this toolbox can do
@@ -231,6 +224,22 @@ on the brainhack mattermost
   [resting state analysis from OMEGA datasets](https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega#BIDS_specifications)
   )
 
+## How to cite
+To credit BIDS-Matlab in your work, please cite the [Zenodo archive](https://zenodo.org/record/5910584),
+which points to a permanent record of all BIDS-Matlab versions.
+We encourage you to mention the specific version you used.
+
+```bibtex
+@software{Gau_bids-matlab,
+author = {Gau, Rémi and Flandin, Guillaume and Janke, Andrew and Duval, Tanguy and Oostenveld, Robert and Madan, Christopher and Niso, Guiomar and Szczepanik, Michał and Mutsaerts, Henk and Beliy, Nikita and Norgaard, Martin and Pernet, Cyril and Chrisophe, Phillips and Shahzad, Iqra and  Botvinik-Nezer, Rotem and Barilari, Marco and Battal, Ceren and MacLean, Michèle and Caron-Guyon, Jeanne},
+license = {MIT},
+title = {{bids-matlab}},
+url = {https://github.com/bids-standard/bids-matlab},
+doi = https://doi.org/10.5281/zenodo.3363985
+}
+```
+
+
 ## Contributing
 
 If you want to contribute make sure to check our [contributing guidelines](CONTRIBUTING.md)

diff --git a/docs/source/general_information.md b/docs/source/general_information.md
@@ -1,17 +1,3 @@
-<!-- markdown-link-check-disable -->
-
-<!-- .. only:: html -->
-
-[![miss_hit](https://github.com/bids-standard/bids-matlab/actions/workflows/miss_hit.yml/badge.svg)](https://github.com/bids-standard/bids-matlab/actions/workflows/miss_hit.yml)
-[![tests_matlab](https://github.com/bids-standard/bids-matlab/actions/workflows/run_tests_matlab.yml/badge.svg)](https://github.com/bids-standard/bids-matlab/actions/workflows/run_tests_matlab.yml)
-[![tests_octave](https://github.com/bids-standard/bids-matlab/actions/workflows/run_tests_octave.yml/badge.svg)](https://github.com/bids-standard/bids-matlab/actions/workflows/run_tests_octave.yml)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/bids-standard/bids-matlab/main?urlpath=demos)
-[![View bids-matlab on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://nl.mathworks.com/matlabcentral/fileexchange/93740-bids-matlab)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5910584.svg)](https://doi.org/10.5281/zenodo.5910584)
-[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors-)
-
-<!-- markdown-link-check-enable -->
-
 # BIDS for MATLAB / Octave
 
 This repository aims at centralising MATLAB/Octave tools to interact with
@@ -178,41 +164,3 @@ removed.
   [group analysis from a MEG visual dataset](https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup),
   [resting state analysis from OMEGA datasets](https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega#BIDS_specifications)
   )
-
-## Contributors ✨
-
-Thanks goes to these wonderful people
-([emoji key](https://allcontributors.org/docs/en/emoji-key)):
-
-<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
-<!-- prettier-ignore-start -->
-<!-- markdownlint-disable -->
-<table>
-  <tr>
-    <td align="center"><a href="https://github.com/gllmflndn"><img src="https://avatars0.githubusercontent.com/u/5950855?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Guillaume</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=gllmflndn" title="Code">💻</a> <a href="#design-gllmflndn" title="Design">🎨</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=gllmflndn" title="Documentation">📖</a> <a href="#example-gllmflndn" title="Examples">💡</a> <a href="#ideas-gllmflndn" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-gllmflndn" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-gllmflndn" title="Maintenance">🚧</a> <a href="#question-gllmflndn" title="Answering Questions">💬</a> <a href="https://github.com/bids-standard/bids-matlab/pulls?q=is%3Apr+reviewed-by%3Agllmflndn" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=gllmflndn" title="Tests">⚠️</a></td>
-    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=Remi-Gau" title="Code">💻</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=Remi-Gau" title="Documentation">📖</a> <a href="#example-Remi-Gau" title="Examples">💡</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a> <a href="#question-Remi-Gau" title="Answering Questions">💬</a> <a href="https://github.com/bids-standard/bids-matlab/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=Remi-Gau" title="Tests">⚠️</a></td>
-    <td align="center"><a href="http://apjanke.net"><img src="https://avatars2.githubusercontent.com/u/2618447?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Andrew Janke</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=apjanke" title="Code">💻</a> <a href="#design-apjanke" title="Design">🎨</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=apjanke" title="Documentation">📖</a> <a href="#ideas-apjanke" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/bids-standard/bids-matlab/pulls?q=is%3Apr+reviewed-by%3Aapjanke" title="Reviewed Pull Requests">👀</a> <a href="#infra-apjanke" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
-    <td align="center"><a href="https://github.com/tanguyduval"><img src="https://avatars1.githubusercontent.com/u/7785316?v=4?s=100" width="100px;" alt=""/><br /><sub><b>tanguyduval</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=tanguyduval" title="Code">💻</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=tanguyduval" title="Documentation">📖</a> <a href="#ideas-tanguyduval" title="Ideas, Planning, & Feedback">🤔</a></td>
-    <td align="center"><a href="https://github.com/robertoostenveld"><img src="https://avatars1.githubusercontent.com/u/899043?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Robert Oostenveld</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=robertoostenveld" title="Code">💻</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=robertoostenveld" title="Documentation">📖</a> <a href="#ideas-robertoostenveld" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/bids-standard/bids-matlab/pulls?q=is%3Apr+reviewed-by%3Arobertoostenveld" title="Reviewed Pull Requests">👀</a></td>
-    <td align="center"><a href="http://www.cmadan.com"><img src="https://avatars0.githubusercontent.com/u/6385051?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Christopher Madan</b></sub></a><br /><a href="#content-cMadan" title="Content">🖋</a></td>
-    <td align="center"><a href="http://guiomarniso.com"><img src="https://avatars1.githubusercontent.com/u/4451818?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Julia Guiomar Niso Galán</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/pulls?q=is%3Apr+reviewed-by%3Aguiomar" title="Reviewed Pull Requests">👀</a></td>
-  </tr>
-  <tr>
-    <td align="center"><a href="https://github.com/mslw"><img src="https://avatars1.githubusercontent.com/u/11985212?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Michał Szczepanik</b></sub></a><br /><a href="#infra-mslw" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#ideas-mslw" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/bids-standard/bids-matlab/commits?author=mslw" title="Code">💻</a></td>
-    <td align="center"><a href="http://www.ExploreASL.org"><img src="https://avatars.githubusercontent.com/u/27774254?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Henk Mutsaerts</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=HenkMutsaerts" title="Code">💻</a> <a href="#ideas-HenkMutsaerts" title="Ideas, Planning, & Feedback">🤔</a></td>
-    <td align="center"><a href="https://github.com/nbeliy"><img src="https://avatars.githubusercontent.com/u/44231332?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Nikita Beliy</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=nbeliy" title="Code">💻</a> <a href="#ideas-nbeliy" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/bids-standard/bids-matlab/pulls?q=is%3Apr+reviewed-by%3Anbeliy" title="Reviewed Pull Requests">👀</a></td>
-    <td align="center"><a href="https://profiles.stanford.edu/martin-noergaard"><img src="https://avatars.githubusercontent.com/u/12412821?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Martin Norgaard</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/issues?q=author%3Amnoergaard" title="Bug reports">🐛</a> <a href="#ideas-mnoergaard" title="Ideas, Planning, & Feedback">🤔</a></td>
-    <td align="center"><a href="https://cpernet.github.io/"><img src="https://avatars.githubusercontent.com/u/4772878?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Cyril Pernet</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/commits?author=CPernet" title="Code">💻</a> <a href="#ideas-CPernet" title="Ideas, Planning, & Feedback">🤔</a></td>
-    <td align="center"><a href="http://www.giga.uliege.be"><img src="https://avatars.githubusercontent.com/u/2011934?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Christophe Phillips</b></sub></a><br /><a href="#ideas-ChristophePhillips" title="Ideas, Planning, & Feedback">🤔</a></td>
-    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars.githubusercontent.com/u/10451654?v=4?s=100" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/pulls?q=is%3Apr+reviewed-by%3ACerenB" title="Reviewed Pull Requests">👀</a></td>
-  </tr>
-</table>
-
-<!-- markdownlint-restore -->
-<!-- prettier-ignore-end -->
-
-<!-- ALL-CONTRIBUTORS-LIST:END -->
-
-This project follows the
-[all-contributors](https://github.com/all-contributors/all-contributors)
-specification. Contributions of any kind welcome!
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-v0.1.0dev
+v0.2.0