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Teichlab / Genes2Genes

Aligning gene expression trajectories of single-cell reference and query systems
https://teichlab.github.io/Genes2Genes/
MIT License
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ERROR: Can not execute `setup.py` since setuptools is not available in the build environment. #5

Closed danli349 closed 1 month ago

danli349 commented 1 month ago

Hello:

When I install genes2genes, 

python -m pip install genes2genes

There is an error:

Collecting genes2genes
  Using cached genes2genes-0.2.0-py3-none-any.whl.metadata (6.7 kB)
Requirement already satisfied: anndata in ./.local/lib/python3.8/site-packages (from genes2genes) (0.9.2)
Requirement already satisfied: regex in ./miniconda3/lib/python3.8/site-packages (from genes2genes) (2021.4.4)
Requirement already satisfied: tabulate in ./miniconda3/lib/python3.8/site-packages (from genes2genes) (0.8.10)
Requirement already satisfied: gseapy in ./miniconda3/lib/python3.8/site-packages (from genes2genes) (0.10.4)
Collecting blitzgsea (from genes2genes)
  Using cached blitzgsea-1.3.47-py3-none-any.whl
Requirement already satisfied: torch in ./.local/lib/python3.8/site-packages (from genes2genes) (2.4.1)
Requirement already satisfied: scipy in ./.local/lib/python3.8/site-packages (from genes2genes) (1.10.1)
Requirement already satisfied: scikit-learn in ./.local/lib/python3.8/site-packages (from genes2genes) (1.3.2)
Requirement already satisfied: tqdm in ./.local/lib/python3.8/site-packages (from genes2genes) (4.66.5)
Requirement already satisfied: matplotlib in ./.local/lib/python3.8/site-packages (from genes2genes) (3.7.5)
Requirement already satisfied: numpy<2 in ./miniconda3/lib/python3.8/site-packages (from genes2genes) (1.24.4)
Collecting pandas>=2.0.3 (from genes2genes)
  Using cached pandas-2.0.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Requirement already satisfied: seaborn>=0.12.2 in ./.local/lib/python3.8/site-packages (from genes2genes) (0.13.2)
Collecting leven (from genes2genes)
  Using cached leven-1.0.4.tar.gz (20 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [1 lines of output]
      ERROR: Can not execute `setup.py` since setuptools is not available in the build environment.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
~$ python -V
Python 3.8.5

How can I fix it? Thanks a lot

ktpolanski commented 1 month ago

Created fresh environment, modifying version to match the one specified here exactly. Cannot replicate. Everything runs fine and installs fine and loads fine.

conda create --name g2g python=3.8.5
conda activate g2g
pip install genes2genes

I'd like to point out you have some packages in ./.local/lib/python3.8/site-packages and others in ./miniconda3/lib/python3.8/site-packages. Seems there's something strange about your setup.

danli349 commented 1 month ago

@ktpolanski Thanks for helping. I can install genes2genes in a new conda environment, the error only occurs in the base environment.