meta00 / vital_sqi

A package for physiological signal quality control
MIT License
31 stars 11 forks source link

Python 3.10 support #98

Closed tiagofrepereira2012 closed 1 year ago

tiagofrepereira2012 commented 1 year ago

It is not possible to pip install this package using python 3.10 (Ubuntu 22.04 with conda).

There is an issue with numba, as you can see on the log below

     error: Command "gcc -pthread -B /home/miniconda3/envs/vital_exploratory/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/miniconda3/envs/vital_exploratory/include -fPIC -O2 -isystem /home/miniconda3/envs/vital_exploratory/include -fPIC -I/home/miniconda3/envs/vital_exploratory/lib/python3.10/site-packages/numpy/core/include -I/home/miniconda3/envs/vital_exploratory/include/python3.10 -c numba/_dispatcher.c -o build/temp.linux-x86_64-cpython-310/numba/_dispatcher.o" failed with exit status 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for numba
  Running setup.py clean for numba
  Building wheel for llvmlite (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [15 lines of output]
      running bdist_wheel
      /home/miniconda3/envs/vital_exploratory/bin/python /tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py
      LLVM version... 14.0.0

      Traceback (most recent call last):
        File "/tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py", line 191, in <module>
          main()
        File "/tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py", line 181, in main
          main_posix('linux', '.so')
        File "/tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py", line 143, in main_posix
          raise RuntimeError(msg)
      RuntimeError: Building llvmlite requires LLVM 10.0.x or 9.0.x, got '14.0.0'. Be sure to set LLVM_CONFIG to the right executable path.
      Read the documentation at http://llvmlite.pydata.org/ for more information about building llvmlite.

      error: command '/home/miniconda3/envs/vital_exploratory/bin/python' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for llvmlite
  Running setup.py clean for llvmlite
Failed to build numba llvmlite
Installing collected packages: llvmlite, lazy-loader, joblib, future, et-xmlfile, Cython, chardet, audioread, astunparse, tzlocal, soundfile, scikit-learn, pyflowchart, py-ecg-detectors, pooch, openpyxl, numba, nolds, mbstrdecoder, astropy, wfdb, typepy, statsmodels, pycwt, librosa, hrv-analysis, heartpy, dateparser, pmdarima, datetimerange, vital-sqi
  Running setup.py install for llvmlite ... error
  error: subprocess-exited-with-error

  × Running setup.py install for llvmlite did not run successfully.
  │ exit code: 1
  ╰─> [31 lines of output]
      running install
      /home/miniconda3/envs/vital_exploratory/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
      !!

              ********************************************************************************
              Please avoid running ``setup.py`` directly.
              Instead, use pypa/build, pypa/installer, pypa/build or
              other standards-based tools.

              See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
              ********************************************************************************

      !!
        self.initialize_options()
      running build
      got version from file /tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/llvmlite/_version.py {'version': '0.34.0', 'full': 'c5889c9e98c6b19d5d85ebdd982d64a03931f8e2'}
      running build_ext
      /home/miniconda3/envs/vital_exploratory/bin/python /tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py
      LLVM version... 14.0.0

      Traceback (most recent call last):
        File "/tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py", line 191, in <module>
          main()
        File "/tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py", line 181, in main
          main_posix('linux', '.so')
        File "/tmp/pip-install-h8sz9tgi/llvmlite_913a0b1a0397448cbb8db46c559ed13d/ffi/build.py", line 143, in main_posix
          raise RuntimeError(msg)
      RuntimeError: Building llvmlite requires LLVM 10.0.x or 9.0.x, got '14.0.0'. Be sure to set LLVM_CONFIG to the right executable path.
      Read the documentation at http://llvmlite.pydata.org/ for more information about building llvmlite.

      error: command '/home/miniconda3/envs/vital_exploratory/bin/python' failed with exit code 1
      [end of output]

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

× Encountered error while trying to install package.
╰─> llvmlite

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
tiagofrepereira2012 commented 1 year ago

Fixed with https://github.com/meta00/vital_sqi/pull/99