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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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bioconda release broken due to setuptools not being shipped with python 3.12 anymore #403

Open njohner opened 3 months ago

njohner commented 3 months ago

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.