pulling Chris' code to resolve errors #17
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Fix RAST parsing
bumped to version 0.4.0
Sync local dev branch with upstream changes Merging latest updates from upstream/dev to keep our fork in sync with the main repository. This brings in the latest features and bug fixes from the original project.
msatpcorrection.py default path + reactions pathways
…e, setting failure testing to false, and fixing report
changes in MSTemplate file to add additional biomass categories
…omes; fixing msexpression
gbff support
mstemplate biomass
# Conflicts: # modelseedpy/core/msatpcorrection.py # modelseedpy/core/msmodel.py # modelseedpy/core/mstemplate.py # setup.py
…simulation, biochemistry, and gapfilling
- Implements expression-constrained flux balance analysis - Handles genome-to-model and type transformations automatically - Integrates with ExpressionActivationPkg for optimization - Includes comprehensive NumPy-style docstring with examples - Adds 12 unit tests covering all functionality and edge cases - Validates thresholds, conditions, and model compatibility - Related to PRD 0001 and task list tasks-0001
…hat lack all dependencies
Fixed issue where reaction expression values were blank when converting from gene-level to reaction-level expression. The problem occurred when expression data was loaded without a genome or when model gene IDs didn't match genome feature IDs. The original code only searched through the genome object, failing to find genes with different ID formats (e.g., model has ACIAD#### but expression has ACIAD_RS#####). Changes: - First attempt direct lookup in self.features by gene ID - Fall back to genome search (which supports aliases) if direct lookup fails - This allows matching when gene IDs are identical, even without a genome - Maintains backward compatibility with genome-based alias resolution Fixes blank reaction expression values in genome-to-model conversion. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Integrates a new method to average expression data across replicates for each strain. This method: - Takes replicate columns (e.g., ACN2586_1, ACN2586_2) and averages them into single columns per strain - Properly uses MSCondition class instead of a fake ExpressionCondition - Returns a new MSExpression object with averaged data - Handles cases where replicates exist, single columns exist, or no data is found - Includes comprehensive logging and error handling This method is useful for preprocessing expression data before analysis.
…011CUoKZ7YGo72duYdrs7oTT Add average_expression_replicates method to MSExpression
…ance of claude web
…fixes to community and flexible biomass and thermo and adding features to msexpression
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Errors from phenotype simulating in the ASV Modeling Notebook made me realize that I may have an outdated version of MSpy from Chris' edits, and instead of me trying to debug everything