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Migrate to using extended version of rapidjson/python-rapidjson for serialization and add support for models written in Julia
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@langmm langmm released this 17 Apr 18:45
· 106 commits to main since this release
v1.9.0
270e65a
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  • Added Julia interface with units implemented via Unitful
  • Added Julia versions of examples
  • Dropped support for Python 3.5
  • Changed rapidjson submodule to extended version
  • Vendor python-rapidjson extension
  • Removed jsonschema requirement
  • Updated yggdrasil to use the vendored rapidjson for serialization, validation, normalization, and units
  • Removed majority of datatypes submodule. rapidjson should be used for type validation, normalization, and serialization
  • Removed C and C++ API for AsciiFile and AsciiTable
  • Changed how tables are parsed such that rows in single column tables will be read as arrays unless otherwise specified via the YAML option 'transform: select_scalar'
  • Updated utility scripts and package parameters to build extension
  • Changed native string types in languages to be used for JSON string values
  • In C, C++, and Fortran, if Python objects will be sent/received the model must initialize Python via "init_python_API()" (a subroutine in Fortran).If a model is a wrapped function, this will be added automatically.
  • Change all JSON serialization to use rapidjson, removing JSONDecoder, JSONEncoder, & JSONEncoderReadable in the process.
  • C++ interface now expects C++ classes for generic, array, object, ply, & obj types. Send methods should pass pointers to these objects. Formatted_io examples for these types have been updated to reflect these changes.
  • Unpinned libroadrunner dependency for SBML
  • Removed the 'serializer_class' and 'serializer_kwargs' from accepted communication keyword arguments. Serializer classes can be accessed via the seritype string associated with them in the schema and keyword arguments for serializer construction can be passed in a dictionary via 'serializer'.
  • Removed 'typedef' attribute from serializer class, 'datatype' should be used instead
  • Removed use of 'header_kwargs' keyword argument from serializer 'serialize' method. Use 'metadata' instead.
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