Halla install, sklearn

Downstream analysis and statistics HAllA
1

Hello,
It seems that ‘sklearn’ PyPI package is deprecated, but Halla install fails without it. Any suggestions to overcome this? Thank you!!

Error:
#$ pip install halla --no-binary :all:

Collecting halla

Using cached HAllA-0.8.20.tar.gz (35 kB)

Preparing metadata (setup.py) … done

Requirement already satisfied: jenkspy>=0.1.5 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (0.4.0)

Requirement already satisfied: matplotlib>=3.3.0 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (3.5.3)

Requirement already satisfied: numpy>=1.19.0 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (1.21.6)

Requirement already satisfied: pandas>=1.0.5 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (1.3.5)

Requirement already satisfied: PyYAML>=5.4 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (6.0.1)

Requirement already satisfied: rpy2>=3.3.5 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (3.5.16)

Requirement already satisfied: scikit-learn>=0.23.1 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (1.0.2)

Requirement already satisfied: scipy>=1.5.1 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (1.7.3)

Requirement already satisfied: seaborn>=0.10.1 in /miniconda3/envs/omics/lib/python3.7/site-packages (from halla) (0.12.2)

Collecting sklearn>=0.0 (from halla)

Using cached sklearn-0.0.post12.tar.gz (2.6 kB)

Preparing metadata (setup.py) … error

error: subprocess-exited-with-error

× 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]

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.

2

Hi Emilia
I guess the real fix would be for maintianers to update sklearn referrals in the package,but in the meanwhile, setting:

export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
worked for me
Had a bunch of other issues as well , posted them here HALLA 0.8.20 installation issues