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bioconda release broken due to setuptools not being shipped with python 3.12 anymore #403

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njohner opened this issue Jul 31, 2024 · 0 comments

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@njohner
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njohner commented Jul 31, 2024

When installing the latest bioconda release in a fresh environment, Python 3.12 will get installed and checkm will fail with the following error:

Traceback (most recent call last):
  File "/home/njohner/bin/miniconda3/envs/test_checkm/bin/checkm", line 38, in <module>
    from checkm import main
  File "/home/njohner/bin/miniconda3/envs/test_checkm/lib/python3.12/site-packages/checkm/main.py", line 22, in <module>
    from checkm.defaultValues import DefaultValues
  File "/home/njohner/bin/miniconda3/envs/test_checkm/lib/python3.12/site-packages/checkm/defaultValues.py", line 23, in <module>
    from checkm.checkmData import DBManager
  File "/home/njohner/bin/miniconda3/envs/test_checkm/lib/python3.12/site-packages/checkm/checkmData.py", line 25, in <module>
    from pkg_resources import resource_filename
ModuleNotFoundError: No module named 'pkg_resources'

pkg_resources is deprecated and removed in Python 3.12.

I could fix the issue either by setting the python version to 3.7 or lower or by adding a dependency to setuptools.

njohner added a commit to metagenlab/zDB that referenced this issue Jul 31, 2024
Newer versions of python do not include setuptools anymore, which
breaks checkm. I have also opened an issue with checkm as I think
they should fix that (Ecogenomics/CheckM#403).
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