fs-license is bound twice in the generated invocation; the YAML comment is stale
- Dominant language
- Python
- Stars
- 1
- Forks
- 4
- Avg merge
- 15h 39m
- Merged PRs (30d)
- 24
Description
The rendered `bids-fmriprep_zip.sh` binds the FreeSurfer license **twice**: once emitted by babs itself, and once from our pipeline `singularity_args`. Observed in the 2026-07-19 Unity run:
```
-B /license.txt:/SGLR/FREESURFER_HOME/license.txt
```
Same source, same destination, so **nothing breaks** — the duplicate bind only produces a warning. But it means **current babs main does auto-bind the fs-license**, and the comment in the fmriprep/mriqc pipeline YAMLs — "BABS rewrites `--fs-license-file` ... does NOT auto-bind, so we bind manually" — is stale.
## Cleanup
Drop the manual `-B .../license.txt:/SGLR/FREESURFER_HOME/license.txt` from the fmriprep + mriqc `singularity_args`, and correct the comment.
## Why it is not a quick commit
Verification needs a **real fmriprep or mriqc run** to confirm babs's own bind is sufficient. The e2e uses simbids, which does not consume a FreeSurfer license, so the local suite cannot exercise it natively (a hacked-up simbids config could approximate it). So this waits for a run that already needs doing, rather than motivating one.
Also a concrete data point for the pipeline-vs-cluster config composition question, which already carries the fs-license rewrite as a case.
Contributor guide
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Research direction
Inspect the fmriprep and mriqc pipeline YAMLs, focusing on singularity_args and the stale fs-license comment; compare their output with the generated bids-fmriprep_zip.sh invocation. Remove the duplicate bind and confirm with a real fmriprep or mriqc run that babs's auto-bind is sufficient.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell, yaml
- Domain
- devops, infrastructure
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100