`libsbml.writeMathMLWithNamespaceToString` leaks memory

[dweindl]

It looks like libsbml.writeMathMLWithNamespaceToString leaks memory:

$ valgrind --leak-check=full python -c "import libsbml; libsbml.writeMathMLWithNamespaceToString(libsbml.ASTNode(), libsbml.SBMLNamespaces(3, 2))"
# output
==320841== Memcheck, a memory error detector
==320841== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al.
==320841== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info
==320841== Command: python -c import\ libsbml;\ libsbml.writeMathMLWithNamespaceToString(libsbml.ASTNode(),\ libsbml.SBMLNamespaces(3,\ 2))
==320841== 
==320841== 
==320841== HEAP SUMMARY:
==320841==     in use at exit: 483,812 bytes in 20 blocks
==320841==   total heap usage: 65,487 allocs, 65,467 frees, 151,614,594 bytes allocated
==320841== 
==320841== 90 bytes in 1 blocks are definitely lost in loss record 5 of 15
==320841==    at 0x484A858: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==320841==    by 0x9D4621F: safe_strdup (in lib/python3.13/site-packages/libsbml/_libsbml.cpython-313-x86_64-linux-gnu.so)
==320841==    by 0x9D3BF12: writeMathMLWithNamespaceToString (in lib/python3.13/site-packages/libsbml/_libsbml.cpython-313-x86_64-linux-gnu.so)
==320841==    by 0x95DB9CC: _wrap_writeMathMLWithNamespaceToString (in lib/python3.13/site-packages/libsbml/_libsbml.cpython-313-x86_64-linux-gnu.so)
==320841==    by 0x58D527: ??? (in /usr/bin/python3.13)
==320841==    by 0x54AB72: _PyObject_MakeTpCall (in /usr/bin/python3.13)
==320841==    by 0x567183: _PyEval_EvalFrameDefault (in /usr/bin/python3.13)
==320841==    by 0x65B4DC: PyEval_EvalCode (in /usr/bin/python3.13)
==320841==    by 0x67C201: ??? (in /usr/bin/python3.13)
==320841==    by 0x67810D: ??? (in /usr/bin/python3.13)
==320841==    by 0x66A1C5: ??? (in /usr/bin/python3.13)
==320841==    by 0x66A0D0: ??? (in /usr/bin/python3.13)
==320841== 
==320841== LEAK SUMMARY:
==320841==    definitely lost: 90 bytes in 1 blocks
==320841==    indirectly lost: 0 bytes in 0 blocks
==320841==      possibly lost: 0 bytes in 0 blocks
==320841==    still reachable: 483,690 bytes in 18 blocks
==320841==         suppressed: 32 bytes in 1 blocks
==320841== Reachable blocks (those to which a pointer was found) are not shown.
==320841== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==320841== 
==320841== For lists of detected and suppressed errors, rerun with: -s
==320841== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)

python-libsbml==5.20.5 with Python 3.13.3 on Ubuntu 25.04.

[fbergmann]

@dweindl agreed, please use writeMathMLToStdString all toString methods from libsbml should be used with caution. That being said, we should annotate the swig bindings for those methods.

[dweindl]

Thanks, Frank. I don't see writeMathMLToStdString in the Python library, though (AttributeError: module 'libsbml' has no attribute 'writeMathMLToStdString').

[luciansmith]

Looking at the code, I think 'writeMathMLToStdString' will also leak, too. But that could be fixed in libsbml; the other leak is probably an issue with SWIG?

EDIT: nope, no leaks with the other version. But it looks like we don't expose it to the python bindings.

[dweindl]

the other leak is probably an issue with SWIG?

Yes, I think %newobject writeMathMLWithNamespaceToString; is missing below https://github.com/sbmlteam/libsbml/blob/31a6ce30cd484fbb8470cb9779c5092a92aa0ddb/src/bindings/swig/libsbml.i#L396.

[dweindl]

But it looks like we don't expose it to the python bindings.

Yup, #ifndef SWIG: https://github.com/sbmlteam/libsbml/blob/31a6ce30cd484fbb8470cb9779c5092a92aa0ddb/src/sbml/math/MathML.h#L87-L102