alphaplinkpython installation fails under Linux Mint/Python 3.10

[Npaffen]

When I try to install alphaplinkpython via pip I recieve the follwoing error message. I was unable to fix this. Reproducible under Python 3.10 with Linux Kernel 5.15.0-56-generic by running:

pip install alphaplinkpython
Stacktrace of the error:

Collecting alphaplinkpython
  Using cached alphaplinkpython-0.0.5.tar.gz (283 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [12 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-i9uppgw3/alphaplinkpython_09e8cea2ebda43a1a92c62826bed8a6d/setup.py", line 96, in <module>
          ext_modules=cythonize(ext_modules, gdb_debug=True),
        File "/home/oem/.local/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 970, in cythonize
          module_list, module_metadata = create_extension_list(
        File "/home/oem/.local/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 816, in create_extension_list
          for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
        File "/home/oem/.local/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 114, in nonempty
          raise ValueError(error_msg)
      ValueError: 'alphaplinkpython/cpp_src/PlinkWriter.pyx' doesn't match any files
      [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.

[gregorgorjanc]

I think this should be sorted as part of #2, but will leave this open so we can test this at some point

[sergiogonmoll]

I have the same issue, although some of the lines where the installation fails are different. Here is the message I get:

(first_env) [p309374@login2 AlphaImpute2]$ python3 -m pip install alphaplinkpython
Collecting alphaplinkpython
Using cached alphaplinkpython-0.0.5.tar.gz (283 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [12 lines of output]
Traceback (most recent call last):
File "", line 2, in
File "", line 34, in
File "/tmp/pip-install-2dzuldj0/alphaplinkpython_ea57a8b38aa24aa3a3aa29125aa31a79/setup.py", line 96, in
ext_modules=cythonize(ext_modules, gdb_debug=True),
File "/scratch/p309374/venvs/first_env/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 990, in cythonize
module_list, module_metadata = create_extension_list(
File "/scratch/p309374/venvs/first_env/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 825, in create_extension_list
for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
File "/scratch/p309374/venvs/first_env/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 119, in nonempty
raise ValueError(error_msg)
ValueError: 'alphaplinkpython/cpp_src/PlinkWriter.pyx' doesn't match any files
[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.

[gregorgorjanc]

@sergiogonmoll we are aware of this issue and have looked at how to support this going onwards - see above links. It will not happen soon because we don't have dedicated funding just now for AlphaFamImpute so it's low on our priority. You can of course use other file format too!