[ENH] update FAQ for bids app (#533)

* fix

* mention bids apps spec

.github/ISSUE_TEMPLATE/bids_apps_submission.yml

@@ -11,10 +11,10 @@ body:
 -   type: markdown
     attributes:
         value: |
-            - Have you checked our [contributing guide](https://github.com/bids-apps/bids-apps.github.io/blob/master/CONTRIBUTING.md)?
+            - Have you checked our [contributing guide](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html)?
               It's a helpful resource.
 
-            - Have you checked our [FAQ](https://bids-apps.neuroimaging.io/dev_faq/)?
+            - Have you checked our [FAQ](https://bids-website.readthedocs.io/en/latest/faq/bids-apps.html)?
 
 -   type: textarea
     attributes:
@@ -30,7 +30,7 @@ body:
 
             More details here:
 
-            https://github.com/bids-apps/bids-apps.github.io/blob/761bcd927ddce83e80e9f898dce1864d9bcb9b04/_config.yml#L64
+            https://github.com/bids-standard/bids-website/blob/81c642691150e00c08ad4450dbdb05eb794f8f9a/data/tools/apps.yml#L3
 
             For example:
 

docs/collaboration/governance.md

@@ -60,7 +60,7 @@ users to confirm that a given dataset complies with the current edition
 of the standard, the [PyBIDS](https://github.com/bids-standard/pybids)
 Python and [bids-matlab](https://github.com/bids-standard/bids-matlab)
 libraries allow querying and manipulating BIDS-compliant datasets,
-[BIDS-Apps](https://bids-apps.neuroimaging.io/) for running portable
+[BIDS-Apps](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html) for running portable
 pipelines on validated BIDS datasets, and platforms like
 [OpenNeuro](https://openneuro.org/) store and serve BIDS datasets. Note
 that the associated software does not fall under the same governance

docs/collaboration/index.md

@@ -39,7 +39,7 @@ Below is a list of common resources where users can get involved in making the B
 There are so many ways to help us build this community.
 
 -   You could help someone else learn the benefits of BIDS by giving a talk in your local organization
--   Or you could work on [building a BIDS App](https://bids-apps.neuroimaging.io/){:target="_blank"}!
+-   Or you could work on [building a BIDS App](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html){:target="_blank"}!
 
 <b>The only requirement is that everyone who contributes adheres to our
 [BIDS Code of Conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md).</b>

docs/faq/bids-apps.md

@@ -1,96 +1,68 @@
-## Can I add more arguments to the API of my App?
+# BIDS apps
 
-Every BIDS App must use the mandatory arguments mentioned above, but you are
-free to add more that are specific to the task your App will perform.
+!!! note
 
-We recommend you follow the guidelines mentioned in the
-[BIDS extension proposal 027](https://bids.neuroimaging.io/bep027)
-for more information on specifying the API of your App.
+    Make sure to check out the [nipreps wesbite](https://www.nipreps.org/)
+    for more information on using and creating BIDS apps.
 
-## How can I check a version of a container I have available locally?
+!!! warning
 
-Inside each BIDS App there is a /version file with the version number.
+    If you are developing a BIDS app,
+    make sure to check the [BIDS apps specification](https://bids-standard.github.io/execution-spec/).
 
-This file is automatically populated with tag used to trigger the build on the CI server.
+## For users
 
-## How can I download a particular version of a BIDS App?
+### How can I check a version of a container I have available locally?
 
-All versions of BIDS Apps are archived on Docker Hub. To access a particular
-version you should refer to a specific Docker Hub tag. For example:
+For many bids-app you should be able to run something like:
 
 ```bash
-docker pull bids/example:v0.0.5
+docker run bids/example --version
 ```
 
-## How do I upload my BIDS App to the BIDS App Github org?
-
-You can release BIDS Apps using your own or your lab's account.
-However, if you want to be added to the BIDS docker hub,
-please message the [BIDS maintainers](mailto:bids.maintenance+apps@gmail.com)
-to have a repo created for you.
-
-If you base your code on <https://github.com/bids-apps/example> deployment on
-docker hub will happen automatically via Circle-ci.
-
-If you want your App to show on the BIDS App website
-[here](https://bids-apps.neuroimaging.io/apps/), you will in any case have to
-update the `_config.yml` in the
-[BIDS App website repository](https://github.com/bids-apps/bids-apps.github.io.git).
+Inside each BIDS App there is a `/version` file with the version number.
 
-## How should I version my BIDS App?
-
-Since most BIDS Apps are just thin wrappers around existing pipelines it would
-be most sensible to use the same version as the software they are wrapping.
+This file is automatically populated with tag used to trigger the build on the CI server.
 
-For example in case of HCP Pipelines this would be `v3.17.0`.
+## How can I download a particular version of a BIDS App?
 
-## How to tag a new release?
+All versions of BIDS Apps are archived on Docker Hub. To access a particular
+version you should refer to a specific Docker Hub tag. For example:
 
 ```bash
-git tag v0.0.1
-git push
+docker pull bids/example:v0.0.5
 ```
 
-## I want to release a new version of a BIDS App, but the pipeline version is the same?
-
-This can happen when only the runscript or the Dockerfile changed?
-According to semantic versioning we should use the `+` signed followed by the build number.
-Unfortunately Docker Hub does not support semantic versioning.
-The best option is to use the `-` sign followed by the build number.
-For example `v3.17.0-3`.
+## What do the analysis levels (`participant` and `group`) mean?
 
-## Is it mandatory to first check the dataset validity using the BIDS-validator?
+Generally, `participant` means individual level analysis (for instance: single subject).
+The `group` level analysis can be thought of as the second step,
+where the input becomes the output of the `participant` level analysis.
 
-It is an extremely helpful feature to have validation of the dataset as part of your tool.
-However, it's not considered mandatory.
-For instance: many Apps will
-simply fail with an error message if the dataset is not BIDS compliant.
+For example, generating statistic maps of each subject's brain could be considered `participant`,
+while generating the average of these maps across the dataset could be considered `group`.
 
-## Is there a BIDS App template?
+## For developers
 
-Have a look at the
-[example BIDS App repository](https://github.com/bids-apps/example). A
-minimalist example of a BIDS App consisting of a Dockerfile and a simple entry
-point script (written in this case in Python) accepting the standard BIDS Apps
-command line arguments.
+### Getting started
 
-## What do the analysis levels (`participant` and `group`) mean?
+#### Is there a BIDS App template?
 
-Generally, `participant` means individual level analysis (for instance: single
-subject) The group level analysis can be thought of as the second step, where
-the input becomes the output of the `participant` level analysis.
+Have a look at the
+[example BIDS App repository](https://github.com/bids-apps/example).
+A minimalist example of a BIDS App consisting of a Dockerfile
+and a simple entry point script (written in this case in Python)
+accepting the standard BIDS Apps command line arguments.
 
-For example, generating statistic maps of each subject's brain could be
-considered `participant`, while generating the average of these maps across the
-dataset could be considered `group`.
+#### Which container should I use to start building my app?
 
-## What do we do if our application does not have any use for the group level analysis?
+The only minimum requirements of a BIDS App's container is its ability to run your pipeline.
+So for example, if your App is mostly Python based it should be sufficient
+to start with any image that has Python and include your environment dependencies.
 
-If your pipeline has no need for group level analysis, it is fine if it is only
-valid for the analysis_level argument (see
-[fmriprep](https://fmriprep.readthedocs.io/en/latest/usage.html))
+### API
 
-## What should the API of my BIDS App look like?
+#### What should the API of my BIDS App look like?
 
 The obligatory arguments of the API of any BIDS App are:
 
@@ -104,20 +76,59 @@ with an API call that would look like this:
 app_name bids_dir output_dir analysis_level
 ```
 
-## When is a new image deposited to Docker Hub?
+#### What do we do if my application does not have any use for the group level analysis?
 
-Even though Docker image is being build on the CI server each time
-you push a commit to the repository it is not automatically being pushed to Docker Hub.
-Only if you tag a commit, push the tag to GitHub,
-and the tests you configured pass a new image will be deposited in Docker Hub.
+If your pipeline has no need for group level analysis,
+it is fine if it is only valid for the analysis_level argument
+(see [fmriprep](https://fmriprep.readthedocs.io/en/latest/usage.html)).
 
-## Where can I can data to test my app
+#### Can I add more arguments to the API of my App?
+
+Every BIDS App must use the mandatory arguments mentioned above,
+but you are free to add more that are specific to the task your App will perform.
+
+We recommend you follow the guidelines mentioned in the [BIDS apps specification](https://bids-standard.github.io/execution-spec/)
+for more information on specifying the API of your App.
+
+### Testing
+
+#### Where can I can get data to test my app?
 
 For both lightweight and full datasets to test your BIDS App, you can choose
 from one of these
 [example datasets](https://bids-standard.github.io/bids-starter-kit/dataset_examples.html)
 
-## Where should I describe changes between versions?
+#### Is it mandatory to first check the dataset validity using the BIDS-validator?
+
+It is an extremely helpful feature to have validation of the dataset as part of your tool.
+However, it's not considered mandatory.
+For instance: many Apps will simply fail with an error message if the dataset is not BIDS compliant.
+
+### Version
+
+#### How should I version my BIDS App?
+
+Since most BIDS Apps are just thin wrappers around existing pipelines it would
+be most sensible to use the same version as the software they are wrapping.
+
+For example in case of HCP Pipelines this would be `v3.17.0`.
+
+#### How to tag a new release?
+
+```bash
+git tag v0.0.1
+git push
+```
+
+#### I want to release a new version of a BIDS App, but the pipeline version is the same?
+
+This can happen when only the runscript or the Dockerfile changed?
+According to semantic versioning we should use the `+` signed followed by the build number.
+Unfortunately Docker Hub does not support semantic versioning.
+The best option is to use the `-` sign followed by the build number.
+For example `v3.17.0-3`.
+
+#### Where should I describe changes between versions?
 
 After tagging a new release it is important to provide a list of changes
 on the GitHub Releases page.
@@ -126,13 +137,25 @@ It accepts markdown syntax and allows you to explain in detail what has changed.
 
 Here's an [example](https://github.com/bids-apps/example/releases).
 
-## Which container should I use to start building my app?
+### Deplopying
+
+#### How do I upload my BIDS App to the BIDS App Github org?
 
-The only minimum requirements of a BIDS App's container is its ability to run
-your pipeline. So for example, if your App is mostly Python based it should be
-sufficient to start with any image that has Python and include your environment
-dependencies.
+You can release BIDS Apps using your own or your lab's account.
+However, if you want to be added to the BIDS docker hub,
+please message the [BIDS maintainers](mailto:bids.maintenance+apps@gmail.com)
+to have a repo created for you.
+
+If you base your code on <https://github.com/bids-apps/example> deployment
+on docker hub will happen automatically via Circle-ci.
 
-<hr>
+If you want your App to show on the [BIDS website](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html),
+you will have to update the `data/tools/apps.yml` in the
+[BIDS website repository](https://github.com/bids-standard/bids-website/tree/main).
 
-Generated by [FAQtory](https://github.com/willmcgugan/faqtory)
+#### When is a new image deposited to Docker Hub?
+
+Even though Docker image is being build on the CI server each time
+you push a commit to the repository it is not automatically being pushed to Docker Hub.
+Only if you tag a commit, push the tag to GitHub,
+and the tests you configured pass a new image will be deposited in Docker Hub.

docs/faq/bids-extensions.md

@@ -17,7 +17,3 @@ See
 [bids-specification issue #1177](https://github.com/bids-standard/bids-specification/issues/1177)
 for an example of the reasoning that led to the application of an entity
 previously used for functional data to anatomical MRI.
-
-<hr>
-
-Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

docs/faq/eeg.md

@@ -36,7 +36,3 @@ This is the case for Biosemi, as further documented on
 For a formatted example on how to deal with this in the BIDS context,
 please see this
 [template](https://github.com/bids-standard/bids-starter-kit/blob/main/templates/sub-01/ses-01/eeg/sub-01_ses-01_task-ReferenceExample_eeg.json).
-
-<hr>
-
-Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

docs/faq/general.md

@@ -182,7 +182,3 @@ page dedicated to this topic.
 
 If you plan to put your dataset on [openneuro](https://openneuro.org/),
 you should use a CC0 or a PDDL license as explained in their [FAQ](https://openneuro.org/faq).
-
-<hr>
-
-Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

docs/faq/mri.md

@@ -89,7 +89,3 @@ Otherwise you can also use:
 
 -   [Fieldtrip](http://www.fieldtriptoolbox.org/faq/how_can_i_anonymize_an_anatomical_mri/) under matlab can do it.
 -   SPM8 and SPM12: when in the batch editor go to: `SPM menu --> Util --> Deface`
-
-<hr>
-
-Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

docs/faq/phenotype.md

@@ -17,7 +17,3 @@ Yes, open this
 [epilepsyClassification2017](https://github.com/bids-standard/bids-starter-kit/blob/main/interactiveTreeVisualization/epilepsyClassification2017/tree.html)
 and follow the examples in the
 [phenotype templates](https://github.com/bids-standard/bids-starter-kit/tree/main/templates/phenotype).
-
-<hr>
-
-Generated by [FAQtory](https://github.com/willmcgugan/faqtory)

docs/impact/index.md

@@ -77,7 +77,7 @@ You can also find them [in the specification](https://bids-specification.readthe
 | statistical model | ![PyPI - Downloads](https://img.shields.io/pypi/dm/bsmschema)                                                            |
 
 For the number of docker pulls of the BIDS apps, please check the
-[BIDS app dashboard](https://bids-apps.neuroimaging.io/apps/).
+[BIDS app dashboard](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html).
 
 ### Contributors