Atomizer fails on Python 3.12+: `ModuleNotFoundError: No module named 'imp'`

[wshlavacek]

Summary

The atomizer crashes immediately on Python 3.12+ because analyzeSBML.py imports the imp module, which was removed from the Python standard library in Python 3.12 (PEP 594, Python 3.12 changelog).

Environment

• Python: 3.12.12 (also affects 3.13+)
• PyBioNetGen: 0.7.9 (installed via uv pip install bionetgen)
• setuptools: 69.5.1 (needed for pkg_resources, which is also used by bionetgen/main.py)
• python-libsbml: 5.21.0
• OS: macOS Sonoma (arm64)

Steps to Reproduce

pip install bionetgen
bionetgen atomize -i model.xml -o output/

Error

Traceback (most recent call last):
  File ".../bin/bionetgen", line 10, in <module>
    sys.exit(main())
  File ".../bionetgen/main.py", line 631, in main
    app.run()
  File ".../cement/core/foundation.py", line 956, in run
    return_val = self.controller._dispatch()
  File ".../cement/ext/ext_argparse.py", line 835, in _dispatch
    return func()
  File ".../bionetgen/main.py", line 555, in atomize
    runAtomizeTool(self.app)
  File ".../bionetgen/core/main.py", line 95, in runAtomizeTool
    from bionetgen.atomizer import AtomizeTool
  File ".../bionetgen/atomizer/__init__.py", line 1, in <module>
    from .atomizeTool import AtomizeTool
  File ".../bionetgen/atomizer/atomizeTool.py", line 1, in <module>
    import bionetgen.atomizer.libsbml2bngl as ls2b
  File ".../bionetgen/atomizer/libsbml2bngl.py", line 15, in <module>
    import bionetgen.atomizer.atomizer.moleculeCreation as mc
  File ".../bionetgen/atomizer/atomizer/moleculeCreation.py", line 15, in <module>
    from . import analyzeSBML
  File ".../bionetgen/atomizer/atomizer/analyzeSBML.py", line 9, in <module>
    import imp
ModuleNotFoundError: No module named 'imp'

Root Cause

In atomizer/atomizer/analyzeSBML.py, line 9:

import imp

The imp module was deprecated in Python 3.4 and fully removed in Python 3.12 per PEP 594. The only usage appears to be imp.reload(), which should be replaced with importlib.reload().

Secondary Issue

There is also a related (but separate) issue: bionetgen/main.py line 21 uses:

from pkg_resources import packaging

The pkg_resources module requires setuptools to be installed, which is no longer bundled by default in Python 3.12+ virtual environments created by uv or with python -m venv. This is a separate bug from the imp issue but compounds the problem — even after manually installing setuptools<70 to get past pkg_resources, the atomizer still fails on the imp import.

Suggested Fix

In atomizer/atomizer/analyzeSBML.py, replace:

import imp

with:

import importlib

And replace any usage of imp.reload(module) with:

importlib.reload(module)

For the pkg_resources issue in bionetgen/main.py, consider replacing:

from pkg_resources import packaging

with:

from importlib.metadata import version

or using packaging directly (pip install packaging).

Impact

This blocks all SBML → BNGL conversion on Python 3.12+, which is the current stable Python release series. Users must downgrade to Python 3.11 to use the atomizer, which is increasingly impractical as the ecosystem moves forward.