Merge branch 'main' of https://github.com/bids-standard/bids-website into 442-centralize-converters

iamdamion · iamdamion · commit dc736cd3967c · 2024-10-17T09:57:24.000-07:00
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,77 @@
+# Contributing to the BIDS website
+
+**Welcome to the BIDS website repository!**
+
+_We're so excited you're here and want to contribute._
+
+We hope that these guidelines are designed to make it as easy as possible to get involved.
+If you have any questions that aren't discussed below, please let us know
+by [opening an issue](https://github.com/bids-standard/bids-website/issues/new).
+
+If you are not familiar with Git ansd GitHub,
+check our [generic contributing guidelines](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html).
+
+If you want to contribute to the BIDS website,
+make sure you also read the instructions below.
+
+## Serving locally
+
+### Requirements
+
+- python >= 3.10
+
+Even though this is not required, having `make` installed
+will make it easier to easily serve the website locally.
+
+### Install and serve
+
+Fork and clone the repository and its submodules
+
+```bash
+git clone https://github.com/YOUR_USER_NAME/bids-website.git --recurse-submodules
+```
+
+Create a virtual environment using `conda`, `venv` of what other environment management tool you prefer.
+
+Install all the dependencies.
+
+```bash
+pip install -r requirements.txt
+```
+
+Generate all the content required for the build.
+
+```bash
+make update
+```
+
+Serve the website with the mkdocs.
+
+```bash
+mkdocs serve
+```
+
+## Maintenance
+
+### Requirements
+
+Same as for the install but you will also need to install `tox`.
+
+```bash
+pip install tox
+```
+<!-- TODO find minimal version of node and npm -->
+For some quality checks and rare operations, you will need node.js and npm.
+
+## Update all files
+
+```bash
+make update
+```
+
+## Run all formatting / linting tools
+
+```bash
+tox
+make remark
+```
diff --git a/README.md b/README.md
@@ -1,66 +1,43 @@
 [![Documentation Status](https://readthedocs.org/projects/bids-website/badge/?version=latest)](https://bids-website.readthedocs.io/en/latest/?badge=latest)
+[![Check Markdown links](https://github.com/bids-standard/bids-website/actions/workflows/check_md_links.yml/badge.svg?branch=main)](https://github.com/bids-standard/bids-website/actions/workflows/check_md_links.yml)
+[![Validation](https://github.com/bids-standard/bids-website/actions/workflows/validation.yml/badge.svg?branch=main)](https://github.com/bids-standard/bids-website/actions/workflows/validation.yml)
 
-# The one true BIDS website
+<img
+    src="https://github.com/bids-standard/bids-specification/blob/master/BIDS_logo/BIDS_logo_white_transparent_background_crop.png#gh-dark-mode-only"
+    alt="bids-logo"
+    width="600"
+/>
+<img
+    src="https://github.com/bids-standard/bids-specification/blob/master/BIDS_logo/BIDS_logo_black_transparent_background_crop.png#gh-light-mode-only"
+    alt="bids-logo"
+    width="600"
+/>
 
-View it here: https://bids-website.readthedocs.io/en/latest/?badge=latest
-
-## Serving locally
-
-### Requirements
-
-<!-- TODO determines minimum python version -->
-- python 3.X
-
-## Install
-
-Clone the repo and its submodules
-
-```bash
-git clone https://github.com/bids-standard/bids-website.git --recurse-submodules
-```
-
-Create a virtual environment using `conda`, `venv` of what other environment management tool you prefer.
+# BIDS website
 
-Install all the dependencies.
+<!-- This is the repository for the Brain Imaging Data Structure (BIDS) website that is hosted at <https://bids.neuroimaging.io>. -->
 
-```bash
-pip install -r requirements.txt
-```
-
-Generate all the content require for the build.
-
-```bash
-make update
-```
-
-Serve the website with the mkdocs.
-```bash
-mkdocs serve
-```
-
-## Maintenance
-
-### Requirements
-
-Same automation will work better if you are on unix system and have make.
+View it here: https://bids-website.readthedocs.io/en/latest/?badge=latest
 
-Same as for the install but you will also need to install `tox`.
+## Contributing to the BIDS website
 
-```bash
-pip install tox
-```
-<!-- TODO find minimal version of node and npm -->
-For some quality checks and rare operations, you will need node.js and npm.
+To contribute to the website,
+see our [contributing guidelines](./CONTRIBUTING.md)
+and please submit an [issue](https://github.com/bids-standard/bids-website/issues)
+or send a [pull request](https://github.com/bids-standard/bids-website/pulls) to this repository.
 
-## Update all files
+## Contributing to the BIDS specification
 
-```bash
-make update
-```
+The specification is hosted on [https://bids-specification.readthedocs.io](https://bids-specification.rtfd.io).
+To contribute to the specification,
+please submit an [issue](https://github.com/bids-standard/bids-specification/issues)
+or send a [pull request](https://github.com/bids-standard/bids-specification/pulls)
+on the [bids-specification](https://github.com/bids-standard/bids-specification) repository.
 
-## Run all formatting / linting tools
+## Asking questions about BIDS
 
-```bash
-tox
-make remark
-```
+If you have questions how to apply BIDS to your dataset,
+how to use a shared BIDS dataset,
+or about tools to convert and/or handle BIDS datasets,
+please see the [getting started section](https://bids-website.readthedocs.io/en/latest/getting_started/index.html) page,
+and our [FAQ](https://bids-website.readthedocs.io/en/latest/faq/index.html).
diff --git a/data/people/advisory.yml b/data/people/advisory.yml
@@ -101,7 +101,7 @@
         git: william_clarke
     -   name: Martin Wilson
         git: martin_wilson
-    
+
 # - title: BEP025 Medical Imaging Data Structure (MIDS)
 #   not included for now, as not merged into BIDS specification
 
diff --git a/data/working_groups.yml b/data/working_groups.yml
@@ -35,7 +35,7 @@
 #     url:
 #     chairs:
 #     -   name:
-#         email: 
+#         email:
 #     status: active
 
 -   title: Code of conducts amendments
diff --git a/docs/blog/posts/bids-news-september-2024.md b/docs/blog/posts/bids-news-september-2024.md
@@ -16,8 +16,8 @@ The BIDS Maintainers, Steering Group, working groups, and other contributors hav
 
 The BIDS specification has released a new minor version\! The highlights are:
 
-* Integrating BEP022 for Magnetic Resonance Spectroscopy  
-* Publishing the BIDS schema to [JavaScript Registry](https://jsr.io/@bids/schema)  
+* Integrating BEP022 for Magnetic Resonance Spectroscopy
+* Publishing the BIDS schema to [JavaScript Registry](https://jsr.io/@bids/schema)
 * For the full list of changes, you can read [the changelog](https://bids-specification.readthedocs.io/en/stable/CHANGES.html#v1100-2024-09-06)
 
 ## Schema-based BIDS validator deployed on validator site
@@ -46,9 +46,9 @@ BIDS continues to be featured in different venues. Our very own maintainer extra
 
 The BEPs carry on to help us all update the standard with new and previously unestablished data types and improvements. If there's a BEP here that affects you, consider getting involved by commenting on open Google Docs or GitHub pull requests or contacting the leads listed in the BEP. Here’s some of our newest BEPs.
 
-* [BEP041](https://bids.neuroimaging.io/bep041): Statistical Model (Taylor Salo)  
-* [BEP042](https://bids.neuroimaging.io/bep042): Electromyography (Seyed Yahya Shirazi)  
-* [BEP043](https://bids.neuroimaging.io/bep043): Term mapping (Chris Markiewicz & Eric Earl)  
+* [BEP041](https://bids.neuroimaging.io/bep041): Statistical Model (Taylor Salo)
+* [BEP042](https://bids.neuroimaging.io/bep042): Electromyography (Seyed Yahya Shirazi)
+* [BEP043](https://bids.neuroimaging.io/bep043): Term mapping (Chris Markiewicz & Eric Earl)
 * [BEP044](https://bids.neuroimaging.io/bep044): Stimuli (Seyed Yahya Shirazi)
 
 Other BEPs are listed on [the BIDS website](https://bids-website.readthedocs.io/en/latest/extensions/beps.html).
diff --git a/docs/collaboration/bids_github b/docs/collaboration/bids_github
@@ -1 +1 @@
-Subproject commit cee020f3f3970e31a5344bac6d2defc0209fb246
+Subproject commit 243a1bc511205fddee7be534e3cf0906016f3f1b
diff --git a/docs/collaboration/index.md b/docs/collaboration/index.md
@@ -1,6 +1,6 @@
 # Help make BIDS better!
 
-BIDS is informed, supported, and guided by its users. BIDS standards are intended to change and evolve as methods, resources, and the needs of the BIDS community changes. We encourage all researchers to contribute to the ongoing development of BIDS standards, be it through discussion on websites, the creation of new BIDS tools, or contributing to extending the BIDS specification through proposals. Below is a list of common resources where users can get involved in making the BIDS standard better! 
+BIDS is informed, supported, and guided by its users. BIDS standards are intended to change and evolve as methods, resources, and the needs of the BIDS community changes. We encourage all researchers to contribute to the ongoing development of BIDS standards, be it through discussion on websites, the creation of new BIDS tools, or contributing to extending the BIDS specification through proposals. Below is a list of common resources where users can get involved in making the BIDS standard better!
 
 <u>Neurostars Website</u>
 
diff --git a/docs/getting_started/bids_apps/tutorial.md b/docs/getting_started/bids_apps/tutorial.md
@@ -41,23 +41,17 @@ the docker image will be automatically downloaded from Docker Hub.
 
 ## Running a BIDS App on a cluster (HPC)
 
-Before a BIDS App can be run on a cluster,
-it first needs to be saved to an Apptainer-compatible image file.1
-This step needs to be performed outside of the cluster (for example on a laptop) and requires Docker:
+HPC clusters typically require Apptainer/Singularity rather than Docker.
+Apptainer (and later versions of Singularity) directly support [Docker/OCI images](https://apptainer.org/docs/user/latest/docker_and_oci.html).
 
 ```bash
-docker run --privileged -ti --rm  \
-    -v /var/run/docker.sock:/var/run/docker.sock \
-    -v /home/srycajal/apptainer_images:/output \
-    singularityware/docker2singularity \
-    bids/example:0.0.4
+apptainer build bids-example-0.0.7.sif docker://bids/example:0.0.7
 ```
 
-Where `/home/srycajal/apptainer_images` is a path where the image will be stored.
 After transferring the .img file to a cluster it can be run like any other executable:
 
 ```bash
-./bids_example-0.0.4.img /bids_dataset /outputs participant --participant_label 01
+./bids_example-0.0.7.img /bids_dataset /outputs participant --participant_label 01
 ```
 
 ## Helpful links
diff --git a/docs/getting_started/folders_and_files/files.md b/docs/getting_started/folders_and_files/files.md
@@ -736,4 +736,4 @@ in which case those values are listed in <code>&lt;&gt;</code>, separated by <co
 </ul>
 
 </details>
-<!-- MICR TEMPLATE ENDS HERE: do not edit manually -->
+<!-- MICR TEMPLATE ENDS HERE: do not edit manually -->
diff --git a/docs/getting_started/folders_and_files/index.md b/docs/getting_started/folders_and_files/index.md
@@ -1 +1,4 @@
-A BIDS dataset basically consists of a collection of folders and files.
+# BIDS Folders and Files
+
+A BIDS dataset consists of a collection of folders and files that are organized and named in compliance with the BIDS specification.
+The following sections provide more information on how to properly organize and name your data.
diff --git a/docs/getting_started/index.md b/docs/getting_started/index.md
@@ -1,5 +1,5 @@
 # Unsure how to get started using BIDS with your current data?
 
-BIDS, at its core, is a set of guidelines for naming and organizing neuroimaging files that is intended to standardize many processes in neuroimaging research and foster a data ecosystem that makes collaboration and data sharing easy. For newcomers to BIDS standards, getting used to these file standards can be overwhelming, especially when considering organizational changes and file edits that are needed to convert datasets into BIDS format. 
+BIDS, at its core, is a set of guidelines for naming and organizing neuroimaging files that is intended to standardize many processes in neuroimaging research and foster a data ecosystem that makes collaboration and data sharing easy. For newcomers to BIDS standards, getting used to these file standards can be overwhelming, especially when considering organizational changes and file edits that are needed to convert datasets into BIDS format.
 
-The following resources were developed to help newcomers to the BIDS standards learn how BIDS data are organized, provide information through publications and presentations, and provide a set of tutorials that are intended to help you get started using BIDS. 
+The following resources were developed to help newcomers to the BIDS standards learn how BIDS data are organized, provide information through publications and presentations, and provide a set of tutorials that are intended to help you get started using BIDS.
diff --git a/docs/getting_started/resources/index.md b/docs/getting_started/resources/index.md
@@ -0,0 +1,7 @@
+# BIDS Resources
+
+The following collection of resources have been compiled to help you get started with BIDS.
+The links section has links to software tools for working with BIDS datasets.
+The glossary section has explanations of common BIDS "jargon".
+The dependencies section provides an overview of software and programming languages commonly used with BIDS.
+The talks and slides page has links to some recent presentations about using BIDS file organization and BIDS tools.
diff --git a/docs/getting_started/resources/talks.md b/docs/getting_started/resources/talks.md
@@ -1,6 +1,7 @@
 # Talks and slides
 
-You can find curated list of talks and slides:
+BIDS-related talks and presentations are ongoing.
+Two great resources for curated lists of talks and slides are:
 
 -   [on this project on OSF](https://osf.io/yn93h/)
 -   [organized by playlist on the BIDS youtube channel](https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw/playlists)
diff --git a/docs/getting_started/tutorials/conversion/index.md b/docs/getting_started/tutorials/conversion/index.md
@@ -0,0 +1,4 @@
+# BIDS Conversion
+
+We know that converting datasets to BIDS organization comes with some challenges, including file reorganization and renaming.
+The following guides can help.
diff --git a/docs/getting_started/tutorials/index.md b/docs/getting_started/tutorials/index.md
@@ -1,5 +1,9 @@
 # Tutorials
 
+Many BIDS tutorials have been created by the greater BIDS community and a selection are linked here.
+We aim to add more high-quality tutorials to this list as new tutorials are created and the maintainers become aware of them.
+Let us know about tutorials that are missing from this list by submitting a [request on github](https://github.com/bids-standard/bids-website/issues) to add them to this website.
+
 ## Video tutorials
 
 Check out the
diff --git a/docs/standards/bids_app_specification/contributors.md b/docs/standards/bids_app_specification/contributors.md
@@ -1,6 +1,6 @@
 # Contributing
 
-The following list of contributors have donated countless hours to the development of BIDS standards and BIDS Apps. If you would like to get involved and are able to donate time to advancing the BIDS standards, please look into submitting or contributing a current BIDS Extension Proposal [BEPs](/extensions/index.html) or contact one of the contributors below. 
+The following list of contributors have donated countless hours to the development of BIDS standards and BIDS Apps. If you would like to get involved and are able to donate time to advancing the BIDS standards, please look into submitting or contributing a current BIDS Extension Proposal [BEPs](/extensions/index.html) or contact one of the contributors below.
 
 ## Lead Contributors
 
diff --git a/docs/standards/index.md b/docs/standards/index.md
@@ -1,3 +1,3 @@
 # BIDS Standards
 
-The current set of BIDS Standards provide outlines and guidance for file naming and organization, statistical modeling of neuroimaging data, and applications created to be used with BIDS data. These standards are intended to be updated and evolve as methods and data types change, but current documentation on BIDS standards can be found in the sections below. 
+The current set of BIDS Standards provide outlines and guidance for file naming and organization, statistical modeling of neuroimaging data, and applications created to be used with BIDS data. These standards are intended to be updated and evolve as methods and data types change, but current documentation on BIDS standards can be found in the sections below.
diff --git a/docs/tools/bids-apps.md b/docs/tools/bids-apps.md
@@ -1,5 +1,5 @@
 # BIDS Apps
 
-BIDS Apps are typically docker or singularity images that allow you to seamlessly run many applications without the need to installing all dependencies, and are generally guaranteed to run on your data, provided your data is BIDS compliant. Below is a list of many commonly used BIDS Apps. 
+BIDS Apps are typically docker or singularity images that allow you to seamlessly run many applications without the need to installing all dependencies, and are generally guaranteed to run on your data, provided your data is BIDS compliant. Below is a list of many commonly used BIDS Apps.
 
 {{ MACROS___generate_apps_table() }}
diff --git a/docs/tools/index.md b/docs/tools/index.md
@@ -4,7 +4,7 @@ There is a rich ecosystem of tools to help you work with BIDS datasets.
 
 - Converters: There are many [converters](./converters/index.md)
 to help you go from your sourcedata to have a BIDS dataset.
-- BIDS Validator: The [BIDS validator](./validator.md) is there to ensure that your BIDS dataset is valid and will work with BIDS Apps without any obvious issues. 
+- BIDS Validator: The [BIDS validator](./validator.md) is there to ensure that your BIDS dataset is valid and will work with BIDS Apps without any obvious issues.
 - BIDS Apps: You can use [BIDS apps](./bids-apps.md)
 (automated pipelines that can be used as Docker or Apptainer images)
 to process your BIDS datasets.
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,6 +1,6 @@
 ---
 site_name: The Brain Imaging Data Structure (BIDS)
-repo_url: https://github.com/bids-standard/bids-website.git
+repo_url: https://github.com/bids-standard/bids-website/tree/main
 site_url: https://bids-website.readthedocs.io
 
 plugins:
diff --git a/specification b/specification
@@ -1 +1 @@
-Subproject commit 3fc4f65e94ddf48123bd9db08fb19a48ab566262
+Subproject commit 8692e1fd12c82201eb63ae8a7098f3a77a4ee1bc
