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feat: Add FROG report generation to workflows (Resolves #21)#44

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draeger-lab:devfrom
dyrpsf:feature/issue-21-frog-report
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feat: Add FROG report generation to workflows (Resolves #21)#44
dyrpsf wants to merge 1 commit into
draeger-lab:devfrom
dyrpsf:feature/issue-21-frog-report

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@dyrpsf dyrpsf commented Jul 16, 2026

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Description

This PR addresses Issue #21 by adding an optional step to generate a FROG (Flux balance constraint Report Objective Generation) report at the end of the analysis pipeline[cite: 11].

Key Changes

  • Configurations: Added the frog: False parameter to the hqtb YAML configuration files (default, advanced, and basic) under the analysis step.
  • Core Logic: Updated the run function in src/specimen/hqtb/core/analysis.py to accept the generate_frog boolean.
  • FROG Generation: Integrated the fbc_curation.run_frog function. It creates a dedicated FROG_report directory within the analysis output folder and saves the report there.
  • Safe Import: Wrapped the fbc_curation import in a try-except block so that if a user hasn't installed the package, it gracefully logs an error and skips the step without crashing the entire workflow.
  • Documentation: Removed the "future update" placeholder for FROG in the about-pipeline.rst documentation.

Testing

  • Verified that the workflow continues without errors when fbc_curation is not installed (falls back to logging an error).

Resolves draeger-lab#21. Adds the generate_frog / rog parameter to configuration files and triggers the fbc_curation FROG report generation during the analysis step if enabled.
@dyrpsf dyrpsf mentioned this pull request Jul 16, 2026
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