Error while installing with Pip

[dhondta]

$ pip -q install --user --no-warn-script-location --break-system-packages --upgrade scikit-learn-extra
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [60 lines of output]
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      import sys
      from time import time
      
      from libc.math cimport exp, log, sqrt, pow, fabs
      cimport numpy as np
      from numpy.math cimport INFINITY
      ^
      ------------------------------------------------------------
      
      sklearn_extra/robust/_robust_weighted_estimator_helper.pyx:18:0: 'numpy/math.pxd' not found
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      import sys
      from time import time
      
      from libc.math cimport exp, log, sqrt, pow, fabs
      cimport numpy as np
      from numpy.math cimport INFINITY
      ^
      ------------------------------------------------------------
      
      sklearn_extra/robust/_robust_weighted_estimator_helper.pyx:18:0: 'numpy/math/INFINITY.pxd' not found
      performance hint: sklearn_extra/robust/_robust_weighted_estimator_helper.pyx:24:0: Exception check on '_euclidean_dense_dense' will always require the GIL to be acquired. Declare '_euclidean_dense_dense' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
      Compiling sklearn_extra/utils/_cyfht.pyx because it changed.
      Compiling sklearn_extra/cluster/_k_medoids_helper.pyx because it changed.
      Compiling sklearn_extra/robust/_robust_weighted_estimator_helper.pyx because it changed.
      Compiling sklearn_extra/cluster/_commonnn_inner.pyx because it changed.
      [1/4] Cythonizing sklearn_extra/cluster/_commonnn_inner.pyx
      [2/4] Cythonizing sklearn_extra/cluster/_k_medoids_helper.pyx
      [3/4] Cythonizing sklearn_extra/robust/_robust_weighted_estimator_helper.pyx
      Traceback (most recent call last):
        File "/home/user/.local/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
        File "/home/user/.local/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/user/.local/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 143, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-1oc1tedk/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 331, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-1oc1tedk/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 301, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-1oc1tedk/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 512, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-1oc1tedk/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
        File "<string>", line 58, in <module>
        File "/tmp/pip-build-env-1oc1tedk/overlay/local/lib/python3.12/dist-packages/Cython/Build/Dependencies.py", line 1145, in cythonize
          cythonize_one(*args)
        File "/tmp/pip-build-env-1oc1tedk/overlay/local/lib/python3.12/dist-packages/Cython/Build/Dependencies.py", line 1289, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: sklearn_extra/robust/_robust_weighted_estimator_helper.pyx
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

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

[LaurieGale10]

Getting the same problem on a Windows machine with Python 3.13.0. Tried installing cython and reinstalling numpy but neither helped - perhaps related to #180?

[TimotheeMathieu]

Hello.
Apparently, there is a deprecated cython call in there that is messing with the install. I think I fixed it in my fork (or at least I was able to install with Python 3.13 on my laptop) you can find the fork here: https://github.com/TimotheeMathieu/scikit-learn-extra and install it with pip install git+https://github.com/TimotheeMathieu/scikit-learn-extra, if you do not use eigenpro then you can use this fork.
As explained in issue #177 there is some outdated code in scikit-learn-extra that does not work any more and we are waiting for it to be fixed before making a new release so for now my fork is all you got to fix it, sorry.

[snav9795]

Encountered the same issue with Python 3.13. I resolved it by switching to Python 3.10 and downgrading NumPy to version 1.26.4, which allowed scikit-learn-extra to install successfully