[BUG] Unable to install pyradiomics with Python 3.10

[marek-lechowicz]

Hi, I have a followitg problem with pyradiomics installation.

when I specify the version I get such output: Requested pyradiomics==3.1.0 from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz has inconsistent version: expected '3.1.0', but metadata has '3.0.1a1' ERROR: Could not find a version that satisfies the requirement pyradiomics==3.1.0 (from versions: 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 3.0, 3.0.1a3, 3.0.1, 3.1.0) ERROR: No matching distribution found for pyradiomics==3.1.0

If I run general command it switches to install other version but fails in a weird way (I have numpy installed)

pip install pyradiomics
Collecting pyradiomics
  Using cached pyradiomics-3.1.0.tar.gz (34.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Discarding https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz (from https://pypi.org/simple/pyradiomics/): Requested pyradiomics from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz has inconsistent version: expected '3.1.0', but metadata has '3.0.1a1'
  Using cached pyradiomics-3.0.1.tar.gz (34.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [17 lines of output]
      Traceback (most recent call last):
        File "D:\studia_zadania\Others\AIImageDetection\venv\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 353, in <module>
          main()
        File "D:\studia_zadania\Others\AIImageDetection\venv\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "D:\studia_zadania\Others\AIImageDetection\venv\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
          return self._get_build_requires(config_settings, requirements=['wheel'])
        File "C:\Users\mlech\AppData\Local\Temp\pip-build-env-zvyo7zaq\overlay\Lib\site-packages\setuptools\build_meta.py", line 295, in _get_build_requires
          self.run_setup()
        File "C:\Users\mlech\AppData\Local\Temp\pip-build-env-zvyo7zaq\overlay\Lib\site-packages\setuptools\build_meta.py", line 480, in run_setup
          super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
        File "C:\Users\mlech\AppData\Local\Temp\pip-build-env-zvyo7zaq\overlay\Lib\site-packages\setuptools\build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 7, in <module>
      ModuleNotFoundError: No module named 'numpy'
      [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.

Version (please complete the following information):

• OS: Windows 10
• Python version: 3.10.11
• PyRadiomics version: 3.1.0

Additional context Using python virtual environment

[marek-lechowicz]

Running pip install pyradiomics inside Windows Terminal with Admin priviliges helped

[jim-bo]

I too have this problem. On OsX same error.

[jim-bo]

For what it's worth, I was able to gitclone the repo, build the dependencies and install it manually (including compilation). I think there might be something wrong with the wheels/conda packages that are built. I'm no expert though so I don't have a recommendation... just an FYI

[strixy16]

I'm having this problem as well on macOS. Trying to install in a conda environment after pip installing numpy, I try to install pyradiomics 3.1.0 and get this output

pip install pyradiomics
Collecting pyradiomics
  Using cached pyradiomics-3.1.0.tar.gz (34.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Discarding https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz (from https://pypi.org/simple/pyradiomics/): Requested pyradiomics from https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz has inconsistent version: expected '3.1.0', but metadata has '3.0.1a1'
  Using cached pyradiomics-3.0.1-cp39-cp39-macosx_10_9_x86_64.whl
Requirement already satisfied: numpy>=1.9.2 in /Users/katyscott/opt/miniconda3/envs/temp/lib/python3.9/site-packages (from pyradiomics) (1.26.3)
Collecting SimpleITK>=0.9.1 (from pyradiomics)
  Using cached SimpleITK-2.3.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (7.9 kB)
Collecting PyWavelets>=0.4.0 (from pyradiomics)
  Using cached pywavelets-1.5.0-cp39-cp39-macosx_10_13_x86_64.whl.metadata (9.0 kB)
Collecting pykwalify>=1.6.0 (from pyradiomics)
  Using cached pykwalify-1.8.0-py2.py3-none-any.whl (24 kB)
Collecting six>=1.10.0 (from pyradiomics)
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting docopt>=0.6.2 (from pykwalify>=1.6.0->pyradiomics)
  Using cached docopt-0.6.2-py2.py3-none-any.whl
Collecting python-dateutil>=2.8.0 (from pykwalify>=1.6.0->pyradiomics)
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting ruamel.yaml>=0.16.0 (from pykwalify>=1.6.0->pyradiomics)
  Using cached ruamel.yaml-0.18.5-py3-none-any.whl.metadata (23 kB)
Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml>=0.16.0->pykwalify>=1.6.0->pyradiomics)
  Using cached ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.2 kB)
Using cached pywavelets-1.5.0-cp39-cp39-macosx_10_13_x86_64.whl (4.4 MB)
Using cached SimpleITK-2.3.1-cp39-cp39-macosx_10_9_x86_64.whl (44.9 MB)
Using cached ruamel.yaml-0.18.5-py3-none-any.whl (116 kB)
Using cached ruamel.yaml.clib-0.2.8-cp39-cp39-macosx_10_9_x86_64.whl (148 kB)
Installing collected packages: SimpleITK, docopt, six, ruamel.yaml.clib, PyWavelets, ruamel.yaml, python-dateutil, pykwalify, pyradiomics
Successfully installed PyWavelets-1.5.0 SimpleITK-2.3.1 docopt-0.6.2 pykwalify-1.8.0 pyradiomics-3.0.1 python-dateutil-2.8.2 ruamel.yaml-0.18.5 ruamel.yaml.clib-0.2.8 six-1.16.0

So it manages to install pyradiomics 3.0.1, but not the latest version. This happens with both Python 3.10.13 and 3.9.0

[dsantiago]

Like @strixy16 said, the error that it doesn't install the 3.1.0 appear to be in meta data. I am getting this error also...

...
Discarding https://files.pythonhosted.org/packages/03/c1/20fc2c50ab1e3304da36d866042
a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz (from https://pypi.org/simple/pyradiomics/): 

Requested pyradiomics from https://files.pythonhosted.org/packages/03/c1/
20fc2c50ab1e3304da36d866042a1905a2b05a1431ece35448ab6b4578f2/pyradiomics-3.1.0.tar.gz 
has inconsistent version: expected '3.1.0', but metadata has '3.0.1a1'

[kirbyju]

I just learned that if you setup an environment with Python 3.9 it will work, but there are no wheels for later versions yet.

[kirbyju]

Update: I finally got around to trying with Python 3.9 in a fresh virtual environment and it still didn't work. However, I did have success installing it inside of 3D Slicer's Python environment (which apparently runs 3.9 so I'm not sure why it worked there but not in my other testing).

[mluerig]

it did install fine for me under python 3.10, but I had to remove the version in my pipeline (was "pyradiomics==3.1.0"). @JoostJM would you mind looking into this? I think it's just a matter of updating the meta-data...