`pycistopic` 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.

[danli349]

Hello

When I run the Tutorials "https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html"

pycistopic tss gene_annotation_list | grep Human

/home/dan/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/__init__.py:3: 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.
  from pkg_resources import DistributionNotFound, get_distribution
hsapiens_gene_ensembl	Human genes (GRCh38.p14)

How should I solve this problem?
Thanks a lot

Best
Dan

[bmacnabb]

Hi Dan,

I encountered the same issue during the installation. To fix it, you can pin the version of setuptools in the requirements.txt file. Simply open that file with a text editor and add a line to specify the version of setuptools:
setuptools==79.0.1
worked for me.
Then re-run the installation step for the dependencies in the terminal so that the newer version of setuptools gets replaced by the deprecated one:
pip install -r requirements.txt --no-deps

Good luck!
Brendan

[danli349]

@bmacnabb I will try Thanks a lot.

[jingxinfu]

I had same error when trying to import scenicplus:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[2]import scenicplus

File ~/miniforge3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/__init__.py:1
----> [1]from pkg_resources import get_distribution, DistributionNotFound
      [3] try:
      [4]     __version__ = get_distribution("scenicplus").version

ModuleNotFoundError: No module named 'pkg_resources'