feat: Add FROG report generation to workflows (Resolves #21)#44
Open
dyrpsf wants to merge 1 commit into
Open
Conversation
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.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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
frog: Falseparameter to thehqtbYAML configuration files (default, advanced, and basic) under theanalysisstep.runfunction insrc/specimen/hqtb/core/analysis.pyto accept thegenerate_frogboolean.fbc_curation.run_frogfunction. It creates a dedicatedFROG_reportdirectory within the analysis output folder and saves the report there.fbc_curationimport in atry-exceptblock so that if a user hasn't installed the package, it gracefully logs an error and skips the step without crashing the entire workflow.about-pipeline.rstdocumentation.Testing
fbc_curationis not installed (falls back to logging an error).