Python 3.14 compatibility: ValueError: argument groups cannot be nested

[federedef]

Hi,

I'm trying to use pyensembl with Python 3.14.3, but the CLI fails immediately when running:

pyensembl install --release 75 --species homo_sapiens

I get the following output:

/federogc/dev_py/venvs/pets_env/lib/python3.14/site-packages/pyensembl/shell.py:43: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
Traceback (most recent call last):
File "/federogc/dev_py/venvs/pets_env/bin/pyensembl", line 3, in
from pyensembl.shell import run
File "/federogc/dev_py/venvs/pets_env/lib/python3.14/site-packages/pyensembl/shell.py", line 74, in
release_group = root_group.add_argument_group()
File "/soft_bio_267/programs/x86_64/pyenv/.pyenv/versions/3.14.3/lib/python3.14/argparse.py", line 1791, in add_argument_group
raise ValueError('argument groups cannot be nested')
ValueError: argument groups cannot be nested

It looks like Python 3.14 no longer allows nested argument groups in argparse, causing the CLI to fail during initialization.

Additionally, there is a warning about pkg_resources being deprecated and scheduled for removal in future versions of Setuptools.

Is Python 3.14 currently supported? If not, are there any plans to add compatibility?

Thank you!

[iskandr]

Thanks for the report! Which version of pyensembl are you running (pip show pyensembl)?

I believe this specific argument groups cannot be nested error was already fixed in v2.6.2 (see #318). Your traceback shows root_group.add_argument_group() and import pkg_resources in shell.py, both of which were removed by that fix, so it looks like you may be on a pre-2.6.2 build. Upgrading should resolve it:

pip install -U pyensembl

If you still hit the error on the latest release, let me know and I'll reopen and dig in.

[federedef]

Thanks for the quick response!

You were right. The issue turned out to be that I was using an older version of VarCode, which in turn depended on an older version of pyensembl (pre-2.6.2). After updating VarCode and its dependencies, the problem is now resolved.

Thanks again for your help!