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How to reproduce paper results

Open SZ-qing opened this issue 1 year ago • 5 comments

Hi,I am reproducing the results of your article, but I have encountered some environmental problems.

As described in https://github.com/theislab/scgen-reproducibility, I recreated a virtual environment called scgen-reproduce with packages tensorflow, scanpy, numpy, matplotlib, scipy, and wget. Then follow the prompts to cd to the code path and run the following command line: python ModelTrainer.py all [all datas have been downloaded ] , but an error is encountered:

_Traceback (most recent call last): File "", line 1, in File "/public/home/nierq01/platform/scGen/reproduce/scgen-reproducibility-master/code/scgen/init.py", line 19, in version = get_version(file) File "/public/home/nierq01/anaconda3/envs/scgen-reproduce/lib/python3.7/site-packages/get_version/init.py", line 280, in get_version raise NoVersionFound(Source.all, msg) get_version.NoVersionFound: No version found:

  • Directory name: name of directory “/public/home/nierq01/platform/scGen/reproduce/scgen-reproducibility-master/code” does not contain a valid version.
  • VCS: could not find VCS from directory “/public/home/nierq01/platform/scGen/reproduce/scgen-reproducibility-master/code”.
  • Package metadata: could not find distribution “scgen”._

What I understand is that when reproducing the results, you don't have to install scgen yourself in the python environment, right?

SZ-qing avatar May 06 '23 07:05 SZ-qing