PyBioNetGen fails with setuptools ≥81 (Python 3.12)

[wshlavacek]

Summary

PyBioNetGen 0.8.3 fails to run when installed in an environment with
modern setuptools (≥81).
The failure is due to removal of pkg_resources from setuptools, while
PyBioNetGen still imports:

from pkg_resources import packaging

This causes a runtime ModuleNotFoundError.

---

Environment

• macOS (Darwin)
• Python 3.12
• PyBioNetGen 0.8.3
• setuptools 82.0.1
• Installed in a clean virtual environment

---

Error

Running:

bionetgen --version

Produces:

Traceback (most recent call last):
 File ".../.venv/bin/bionetgen", line 4, in <module>
 from bionetgen.main import main
 File ".../site-packages/bionetgen/main.py", line 21, in <module>
 from pkg_resources import packaging
ModuleNotFoundError: No module named 'pkg_resources'

Direct import also fails:

python -c "import pkg_resources"

ModuleNotFoundError: No module named 'pkg_resources'

---

Root Cause

As of setuptools 81+, pkg_resources has been removed.

PyBioNetGen currently imports:

from pkg_resources import packaging

This dependency no longer works with modern Python packaging stacks.

---

Temporary Workaround

Downgrade setuptools:

pip install "setuptools<81"

After downgrading, PyBioNetGen runs normally.

---

Proposed Fix

Replace usage of:

from pkg_resources import packaging

With:

from packaging import version

And add packaging as a direct dependency in pyproject.toml or
setup.py.

This removes reliance on deprecated pkg_resources and restores
compatibility with modern setuptools and Python 3.12+.

---

Impact

• Breaks fresh Python 3.12 installations
• Breaks modern virtual environments
• Affects users using uv, pip, conda, or other modern packaging
  toolchains

---

Recommendation

• Remove dependency on pkg_resources
• Depend directly on packaging
• Add CI testing against Python 3.12 and latest setuptools

[akutuva21]

Should be fixed in #63