`confuse` release breaking CI

[j-c-c]

A confuse release yesterday is breaking our CI: https://github.com/ComputationalCryoEM/ASPIRE-Python/actions/runs/21454969722/job/61871169791?pr=1357

It looks like we're not pulling in a typing_extensions dependency of confuse. Looking into it and will submit a fix shortly.

[j-c-c]

Ok, this appears to be a bug on confuse's end. They attempt to import typing_extensions without including it in the package dependencies.

If I simply try to install confuse and import it I get the same error:

(base) ☁  ASPIRE-python.confuse_bug [develop] ⚡  conda activate confuse_install

(confuse_install) ☁  ASPIRE-python.confuse_bug [develop] ⚡  pip install confuse
Collecting confuse
  Using cached confuse-2.2.0-py3-none-any.whl.metadata (4.0 kB)
Collecting pyyaml (from confuse)
  Using cached pyyaml-6.0.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.4 kB)
Using cached confuse-2.2.0-py3-none-any.whl (27 kB)
Using cached pyyaml-6.0.3-cp311-cp311-macosx_11_0_arm64.whl (175 kB)
Installing collected packages: pyyaml, confuse
Successfully installed confuse-2.2.0 pyyaml-6.0.3

(confuse_install) ☁  ASPIRE-python.confuse_bug [develop] ⚡  pip freeze         
confuse==2.2.0
packaging @ file:///opt/miniconda3/conda-bld/packaging_1761049079066/work
PyYAML==6.0.3

(confuse_install) ☁  ASPIRE-python.confuse_bug [develop] ⚡  python -c "import confuse"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/carmichael/opt/miniconda3/envs/confuse_install/lib/python3.11/site-packages/confuse/__init__.py", line 3, in <module>
    from .core import *  # noqa: F403
    ^^^^^^^^^^^^^^^^^^^
  File "/Users/carmichael/opt/miniconda3/envs/confuse_install/lib/python3.11/site-packages/confuse/core.py", line 37, in <module>
    from typing_extensions import Self
ModuleNotFoundError: No module named 'typing_extensions'

[j-c-c]

Looks like confuse has resolved this issue in their recent release: https://github.com/beetbox/confuse/releases/tag/v2.2.1

Will pick this up and unpin the version.

[j-c-c]

Resolved by #1400. Colsing.