sbmlutils
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matthiaskoenig
Python utilities for SBML
Necessary to keep track of the sids and metaIds and allow access via these fields. This is especially important for more advanced model creation/manipulation.
The print options are very limited and complicated. This makes it difficult to investigate bugs and corner cases. - [ ] Use pydantic BaseModels for printing of complete information (`__repr__`)....
Currently some default timestamps are set. See https://github.com/sbmlteam/libsbml/issues/259
Add support in ModelCreator and parser - [x] key value pairs - [x] handle serialization to fbc-v2 and fbc-v3 - [x] FluxObjective - [x] UserDefinedConstraints - [ ] Model import...
Proper use of SBase required for all distrib classes.
Write documentation for - [ ] model creation (with all objects) - [ ] annotation - [ ] model import - [ ] model combination/merging
The models created with "SBML -> Model -> SBML -> SBMLInfo" must be valid. Currently issues with the new ModelEquation: ``` An error occurred. Please report this on https://github.com/matthiaskoenig/sbmlutils/issues/new so...
- [ ] SBML models must be imported to the internal model data structure - [ ] Test model import with the testsuite models
Merging of notes becomes important when importing models with existing notes. Combining Markdown and XML notes should work to not loose information. This is important for model import.
Currently a lot of duplicated code due to parallel developments 1. SBMLReport uses `SBML -> JSON` 2. SBMLParser & ModelFactory use `Model`, i.e., `SBML -> Model` This should be unified...