Trouble installing pyradiomics from pip in notebook environment

[CelinaHallal]

I've been using pyradiomics in a google colab notebook without problems until 2 or 3 days ago. Today I tried to install it on a new notebook and got the following:

Requirement already satisfied: pip in /usr/local/lib/python3.12/dist-packages (24.1.2)
Collecting pip
Downloading pip-25.2-py3-none-any.whl.metadata (4.7 kB)
Requirement already satisfied: setuptools in /usr/local/lib/python3.12/dist-packages (75.2.0)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Requirement already satisfied: wheel in /usr/local/lib/python3.12/dist-packages (0.45.1)
Requirement already satisfied: numpy in /usr/local/lib/python3.12/dist-packages (2.0.2)
Collecting numpy
Using cached numpy-2.3.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
Downloading pip-25.2-py3-none-any.whl (1.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 31.3 MB/s eta 0:00:00
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Using cached numpy-2.3.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)
Installing collected packages: setuptools, pip, numpy
Attempting uninstall: setuptools
Found existing installation: setuptools 75.2.0
Uninstalling setuptools-75.2.0:
Successfully uninstalled setuptools-75.2.0
Attempting uninstall: pip
Found existing installation: pip 24.1.2
Uninstalling pip-24.1.2:
Successfully uninstalled pip-24.1.2
Attempting uninstall: numpy
Found existing installation: numpy 2.0.2
Uninstalling numpy-2.0.2:
Successfully uninstalled numpy-2.0.2
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
ipython 7.34.0 requires jedi>=0.16, which is not installed.
opencv-python-headless 4.12.0.88 requires numpy<2.3.0,>=2; python_version >= "3.9", but you have numpy 2.3.2 which is incompatible.
numba 0.60.0 requires numpy<2.1,>=1.22, but you have numpy 2.3.2 which is incompatible.
opencv-python 4.12.0.88 requires numpy<2.3.0,>=2; python_version >= "3.9", but you have numpy 2.3.2 which is incompatible.
tensorflow 2.19.0 requires numpy<2.2.0,>=1.26.0, but you have numpy 2.3.2 which is incompatible.
opencv-contrib-python 4.12.0.88 requires numpy<2.3.0,>=2; python_version >= "3.9", but you have numpy 2.3.2 which is incompatible.
cupy-cuda12x 13.3.0 requires numpy<2.3,>=1.22, but you have numpy 2.3.2 which is incompatible.
Successfully installed numpy-2.3.2 pip-25.2 setuptools-80.9.0
WARNING: The following packages were previously imported in this runtime:
[_distutils_hack,numpy]
You must restart the runtime in order to use newly installed versions.
Collecting pyradiomics==3.0.1
Using cached pyradiomics-3.0.1.tar.gz (34.5 MB)
error: subprocess-exited-with-error

× python setup.py egg_info 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.
Preparing metadata (setup.py) ... error
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.

[Trion129]

Facing same issue here is the log that I get when trying to pip install it on google colab notebook

Collecting pyradiomics
  Downloading pyradiomics-3.1.0.tar.gz (34.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 5.9 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... 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'
  Downloading pyradiomics-3.0.1.tar.gz (34.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.5/34.5 MB 3.6 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [38 lines of output]
      /tmp/pip-install-resoo47y/pyradiomics_1f9cdf7c4d284157b9f3cd40be890444/setup.py:9: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
      !!
      
              ********************************************************************************
              Please remove any references to `setuptools.command.test` in all supported versions of the affected package.
      
              This deprecation is overdue, please update your project and remove deprecated
              calls to avoid build errors in the future.
              ********************************************************************************
      
      !!
        from setuptools.command.test import test as TestCommand
      /tmp/pip-install-resoo47y/pyradiomics_1f9cdf7c4d284157b9f3cd40be890444/versioneer.py:418: SyntaxWarning: invalid escape sequence '\s'
        LONG_VERSION_PY['git'] = '''
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
          exec(compile('''
          ~~~~^^^^^^^^^^^^
          # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          ...<32 lines>...
          exec(compile(setup_py_code, filename, "exec"))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          ''' % ('/tmp/pip-install-resoo47y/pyradiomics_1f9cdf7c4d284157b9f3cd40be890444/setup.py',), "<pip-setuptools-caller>", "exec"))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<pip-setuptools-caller>", line 35, in <module>
        File "/tmp/pip-install-resoo47y/pyradiomics_1f9cdf7c4d284157b9f3cd40be890444/setup.py", line 79, in <module>
          version=versioneer.get_version(),
                  ~~~~~~~~~~~~~~~~~~~~~~^^
        File "/tmp/pip-install-resoo47y/pyradiomics_1f9cdf7c4d284157b9f3cd40be890444/versioneer.py", line 1476, in get_version
          return get_versions()["version"]
                 ~~~~~~~~~~~~^^
        File "/tmp/pip-install-resoo47y/pyradiomics_1f9cdf7c4d284157b9f3cd40be890444/versioneer.py", line 1408, in get_versions
          cfg = get_config_from_root(root)
        File "/tmp/pip-install-resoo47y/pyradiomics_1f9cdf7c4d284157b9f3cd40be890444/versioneer.py", line 342, in get_config_from_root
          parser = configparser.SafeConfigParser()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?
      [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.

[nucli-vicky]

Same issue here. This happens because of versioneer. You can bypass versioneer by using pip install git+https://github.com/AIM-Harvard/pyradiomics instead of pip install pyradiomics. Another option is to downgrade your Python version, which may not be ideal.

[soumyasahu]

Hi,
I am facing an installation issue. I am using Python 3.13. I have used pip install git+https://github.com/AIM-Harvard/pyradiomics but I am facing the following issue. Can you give me any suggestions?

Error:

Running command git clone --filter=blob:none --quiet https://github.com/AIM-Harvard/pyradiomics 'C:\Users\SSahu3\AppData\Local\Temp\pip-req-build-wearsv_z'
error: subprocess-exited-with-error

Building wheel for pyradiomics (pyproject.toml) did not run successfully.
exit code: 1

[18 lines of output]
*** scikit-build-core 0.11.6 using CMake 4.2.1 (wheel)
*** Configuring CMake...
loading initial cache file build\cp313-cp313-win_amd64\CMakeInit.txt
-- Building for: NMake Makefiles
CMake Error at CMakeLists.txt:3 (project):
Running

 'nmake' '-?'

failed with:

 no such file or directory

CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
-- Configuring incomplete, errors occurred!

*** CMake configuration failed
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pyradiomics
ERROR: Failed to build installable wheels for some pyproject.toml based projects (pyradiomics)