Introduces SBML parsing and modern CLI functionality #37
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YagmurSimsekk wants to merge 7 commits intoDILiS-lab:mainfrom
Open
Introduces SBML parsing and modern CLI functionality #37YagmurSimsekk wants to merge 7 commits intoDILiS-lab:mainfrom
YagmurSimsekk wants to merge 7 commits intoDILiS-lab:mainfrom
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- Implement SBML Level 2/3 parsing with units handling - Include boundary species filtering for ODE models - Add BioModels Database API integration for model download from CLI - Create structured data export (CSV, JSON, NPZ formats) - Add CLI commands for parsing and BioModels database access
- Updated validation logic and type code check - Fixed _get_rule_type_name() mapping - Added comprehensive ODE detection helpers - Added rate rule support and proper method naming - Added rate rule execution in ODE derivatives - fix trailing whitespace and EOF newlines
- fixes SBMLSystemModel parameter naming to use SBML names instead of artificial prefixes - resolve local parameter conflicts with global parameters in kinetic law evaluation
Supports multiple solver methods: lsoda, scipy, newton, bounded
Local parameters are now included in generated datasets but kept constant to avoid biologicall impossible parameter combinations. Only species initial conditions are varied for dataset generation. Add function definition detection Add LSODA → bounded solver fallback for better convergence
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