feat: Integrate simularium file generation in exec combine function

ssandrews / Smoldyn

Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions

GNU General Public License v3.0

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Closed AlexPatrie closed 9 months ago

AlexPatrie commented 9 months ago

What does this PR do?:

Adds biosimulators-simularium>=0.5.24 as a dependency for the Python bindings of Smoldyn.
Implements Simularium file generation inside the body of the exec_sedml_docs_in_combine_archive function within the smoldyn.biosimulators.combine.py Python binding.
Adds a test for the aforementioned content.