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sbmlteam / libsbml

LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
https://sbml.org/software/libsbml
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libsbml 5.20.* python libraries miss symbols on win and mac distributions #340

Closed matthiaskoenig closed 10 months ago

matthiaskoenig commented 1 year ago

The Mac and Win releases miss the UnitDefinition_reorder, perhaps also other symbols/attributes in python

  File "C:\Users\Dsintara\.conda\envs\xresearch\lib\site-packages\sbmlsim\units.py", line 377, in udef_to_str
    libsbml.UnitDefinition_reorder(udef)
AttributeError: module 'libsbml' has no attribute 'UnitDefinition_reorder'

Workaround:

pip install python-libsbml==5.19.7

Things work on linux, but symbols are missing on mac and win.

fbergmann commented 1 year ago

This is due to how swig4 works these days. If you use UnitDefinition.reorder instead of UnitDefinition_reorder it will work.

matthiaskoenig commented 12 months ago

Hi Frank, thanks.

It is just confusing that I see the other symbols on linux and get this via autocomplete. So it is difficult to say which symbols should be different so that the code will work on mac and win also. For instance why is libsbml.UnitKind_toString not libsbml.UnitKind.toString but UnitDefinition_reorder is UnitDefinition.reorder?

I will close this as soon as tested on mac and win. Best Matthias

fbergmann commented 12 months ago

All the symbols with underscores were additionally produced by SWIG < 4, the others should have been available too. With SWIG 4 those underscore ones are no longer generated. I agree this is confusing. Sorry for the inconvenience. If you look into the site-packages/libsbml/__init__.py it will say which swig version was used to build it. If you need me to change something let me know.

fbergmann commented 10 months ago

I think this issue is resolved (@matthiaskoenig please feel free to reopen, if you think it needs an action)