Fix subject_selection_flag

[tientong98]

Closes #307.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 80.78%. Comparing base (5a89bec) to head (c6f549d).

Files with missing lines	Patch %	Lines
babs/generate_bidsapp_runscript.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #308      +/-   ##
==========================================
- Coverage   80.83%   80.78%   -0.06%     
==========================================
  Files          16       16              
  Lines        1508     1509       +1     
  Branches      234      234              
==========================================
  Hits         1219     1219              
- Misses        181      182       +1     
  Partials      108      108              

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[Copilot]

Pull Request Overview

This PR fixes the handling of subject selection flags in the bidsapp run script, ensuring that a dynamic flag value is used instead of a hardcoded one.

• Replaces the hardcoded "--participant-label" in the shell template with the variable subject_selection_flag.
• Updates the Python script to include subject_selection_flag in the template context with a default value.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
babs/templates/bidsapp_run.sh.jinja2	Uses subject_selection_flag variable instead of the hardcoded flag in the command line.
babs/generate_bidsapp_runscript.py	Introduces and passes subject_selection_flag (with default value) in the generation context.

Comments suppressed due to low confidence (2)

babs/templates/bidsapp_run.sh.jinja2:69

• Ensure that subject_selection_flag is consistently provided to avoid any scenarios where the flag might be missing at runtime.

{{ subject_selection_flag }} "${subid}"

babs/generate_bidsapp_runscript.py:62

• [nitpick] Consider expanding the comment to document under what circumstances subject_selection_flag may be overridden, ensuring clarity for future maintainers.

subject_selection_flag = '--participant-label'  # default value