Update Input Datatype Details and Fix Sorting Features on BIDS-Apps Page

[rcruces]

First of all, we’d like to thank you for the effort you’ve put into the new website; it looks fantastic.

Our teams, Hippunfold and Micapipe, noticed that the “Status of the Latest Docker Image” table on the BIDS-Apps page currently lacks input datatype details for both tools, and “uses raw” is marked as “no.” We were wondering if this information is automatically pulled from the Docker hub or the GitHub repository and if there’s a way we could update it ourselves to correct the information.

The intended entries should be as follows:

App	Input Datatype	Uses Raw	Use Derivatives
hippunfold	anat	YES	NO
micapipe	anat, dwi, func	YES	YES (could use FreeSurfer/FastSurfer derivatives)

  Additionally, we observed that the sorting features for “Number of Docker Pulls” and “Image Size” don’t appear to be working as expected. One last issue is that the table width does not fit the screen, and one column is missing even when adjusting the zoom or switching browsers.

Could you also clarify what “status unstable” means on the table "Status of the default branch on the source repository"?

Thanks again!

[Remi-Gau]

thanks for getting in touch and for the feedback

if there’s a way we could update it ourselves to correct the information.

most of the metadata for the bids apps is stored in this file: https://github.com/bids-standard/bids-website/blob/main/data/tools/apps.yml

can I let you update the info with a pull request? it'd be MUCH appreciated.

[Remi-Gau]

the sorting features for “Number of Docker Pulls” and “Image Size” don’t appear to be working as expected.

yup that's a bug I have noticed but forgot to open an issue for

I suspect that the sorting is done based on the name of the svg image represented in the 'badge' rather than by the actual number (or something like this)

Not had the time properly investigate or fix.

[Remi-Gau]

Could you also clarify what “status unstable” means on the table "Status of the default branch on the source repository"?

ah yeah that's underexplained at the moment: we should add some info

so the status of the latest image should mean: if I pull the latest 'stable' version from dockerhub and run the test contained in the repo: do they pass?

the unstable table is meant to represent the status of the bids-app on the default branch of the repo. with every commit or pull request merge we run the following tests:

• try to build the docker image
• try to use that image to run the bids app on some lightweight bids dataset
• if that passes we push that image to dockerhub with an 'unstable' tag (can be useful if users want to check the bleeding edge version of an app that has not yet been released)
• if any of those fail then this table should let us know about it

as you can see this is still work in progress

[Remi-Gau]

Could you also clarify what “status unstable” means on the table "Status of the default branch on the source repository"?

So I quickly looked.

It seems that micapipe has no test set up to run in continuous integration in the repo, so we should probably have some "not available" for this case.

For hippunfold I guess the workflow that could be used for 'unstable' would be this one: https://github.com/khanlab/hippunfold/actions/workflows/python-testing.yml

[rcruces]

Thank you for your quick reply, good luck fixing the bugs of the website. We updated the apps info in the apps.yml see the PR 568 . We'll work on a CI for micapipe. we've tried before but github actions crashed because the container was quite big. so we need to use a different strategy. Do you have any suggestion? We'll follow up the hippunfold ci @jordandekraker

[Remi-Gau]

github actions crashed because the container was quite big. so we need to use a different strategy. Do you have any suggestion?

a lot of bids apps use circle-CI to run their CI: not sure how big your image is but this could maybe work.

worth checking how much circle-CI allows you