An sklearn installation error occurred while running setup.py in step-8 of FeTS 2022 Challenge Task 1.

[sunyeongan]

Describe the bug
A clear and concise description of what the bug is.
During step 8 in https://github.com/FeTS-AI/Challenge/tree/main/Task_1 , a sklearn installation error occurred while executing 'fets @ git+https://github.com/FETS-AI/Algorithms.git@fets_challenge', among install_requires in setup.py.

To Reproduce
Steps to reproduce the behavior:

1. Execute step8 (pip install .) command in https://github.com/FeTS-AI/Challenge/tree/main/Task_1
2. Error occurred at line 33 of the setup.py code https://github.com/FeTS-AI/Challenge/blob/main/Task_1/setup.py

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
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FeTS Version
Version information is found on Help > About

Desktop (please complete the following information):

• OS: window10
• Version : 22hz

Additional context
After cloning FeTS-AI/Algorithms to my GitHub, change sklearn in the 14th line code of https://github.com/sunyeongan/Algorithms/blob/master/setup.py to scikit-learn.

[sarthakpati]

Thanks for the report! Can you please put the PR so that we can record your contribution?

[sunyeongan]

When executing the command below
https://github.com/FeTS-AI/Challenge/blob/524d6b9f489ba852d601a437839abd937e5cab89/Task_1/README.md?plain=1#L29

Even after fixing it, a similar error occurs.

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [15 lines of output]
      The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
      rather than 'sklearn' for pip commands.

      Here is how to fix this error in the main use cases:
      - use 'pip install scikit-learn' rather than 'pip install sklearn'
      - replace 'sklearn' by 'scikit-learn' in your pip requirements files
        (requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
      - if the 'sklearn' package is used by one of your dependencies,
        it would be great if you take some time to track which package uses
        'sklearn' instead of 'scikit-learn' and report it to their issue tracker
      - as a last resort, set the environment variable
        SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error

      More information is available at
      https://github.com/scikit-learn/sklearn-pypi-package
      [end of output]

It seems like sklearn is being loaded again from somewhere. I haven't found out where that is yet. Does requirement.txt file exist?

[sarthakpati]

That's weird. I don't think a separate requirements.txt file exists, though.

[sunyeongan]

Found the problem.

Algorithms/setup.py

Line 14 in c46e968

install_requires=['protobuf', 'grpcio', 'tqdm', 'coloredlogs', 'nibabel', 'scikit-learn', 'nnUNet==1.6.6', 'batchgenerators==0.21', 'opencv-python', 'MedPy==0.4.0']

The version of nnUnet is version 1.6.6, and sklearn is used here.

https://github.com/MIC-DKFZ/nnUNet/releases/tag/v1.6.6

Version 1.7.0 of nnUnet uses scikit-learn. So, when I changed the nnUnet version of setup.py in the repository cloned from my GitHub to 1.7.0, the following error occurred.

Collecting dicom2nifti (from nnUNet==1.7.0->fets@ git+https://github.com/sunyeongan/Algorithms.git@6b1ee7dba53f84d068f58b2996393b7bb0c63c35->fets-challenge==2.0)
  Downloading dicom2nifti-2.4.10-py3-none-any.whl.metadata (1.3 kB)
INFO: pip is looking at multiple versions of nnunet to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install fets and fets-challenge because these package versions have conflicting dependencies.

The conflict is caused by:
    fets 0.0.1 depends on batchgenerators==0.21
    nnunet 1.7.0 depends on batchgenerators>=0.23

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

I think we need to change the version of nnUnet in setup.py to 1.7.0.
What do you think?

[sarthakpati]

If you can confirm that this will work as expected, then please put a PR in.