Lock the shapely version

[celeron533]

shapely 2.0.0 changed the API which causes test fail.

This issue first appeared in: https://github.com/didymo/OnkoDICOM/actions/runs/3955459739

[celeron533]

Migrating to Shapely 1.8 / 2.0 https://shapely.readthedocs.io/en/stable/migration.html

[sjswerdloff]

Sklearn vs scikit-learn was a build failure Is shapely dependent on sklearn? Did shapely also change its dependency in 2.0 to scikit-learn

[celeron533]

Sklearn vs scikit-learn was a build failure Is shapely dependent on sklearn? Did shapely also change its dependency in 2.0 to scikit-learn

the output from my repo's github action looks good as the following

Collecting sklearn
  Downloading sklearn-0.0.post1.tar.gz (3.6 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting imblearn

while here it is shown as below even they are in the same version

Collecting sklearn
  Downloading sklearn-0.0.post1.tar.gz (3.6 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [18 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

      If the previous advice does not cover your use case, feel free to report it at
      https://github.com/scikit-learn/sklearn-pypi-package/issues/new
      [end of output]

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

[celeron533]

@sjswerdloff updated the dependency of scikit-learn in requirement.txt. The item in pyproject.toml is already up-to-date.