module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'? still occuring with pip install

[julesmorata]

please reopen if this issue still exists in the latest master branch.

Originally posted by @hjmjohnson in #886

I am trying to install pyradiomics on a new virtual environment and the issue with ConfigParser mentionned in the quoted thread still occurs so I reopen an issue as mentionned in yesterday post. I also tried the patch as used before by cloning the repo, changing the SafeConfigParser stuff and installing from source but as the setup.py no longer exists it wasn't possible

[hjmjohnson]

@julesmorata Can you provide details so that we can try to replicate the issue? Or can you provide a PR that resolves the issue?

[helderc]

Hi @hjmjohnson. I'm having the same issue with Python 3.12.

Below is the log after running pip install pyradiomics.
Feel free to let me know if you require any additional information.

(py312) C:\Projects\cancer-detection>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
  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)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [30 lines of output]
      C:\Users\helde\AppData\Local\Temp\pip-install-1sf0bagf\pyradiomics_6c8485f470f5436b8e8844009eec4037\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
      C:\Users\helde\AppData\Local\Temp\pip-install-1sf0bagf\pyradiomics_6c8485f470f5436b8e8844009eec4037\versioneer.py:418: SyntaxWarning: invalid escape sequence '\s'      
        LONG_VERSION_PY['git'] = '''
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 35, in <module>
        File "C:\Users\helde\AppData\Local\Temp\pip-install-1sf0bagf\pyradiomics_6c8485f470f5436b8e8844009eec4037\setup.py", line 79, in <module>
          version=versioneer.get_version(),
                  ^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\helde\AppData\Local\Temp\pip-install-1sf0bagf\pyradiomics_6c8485f470f5436b8e8844009eec4037\versioneer.py", line 1476, in get_version
          return get_versions()["version"]
                 ^^^^^^^^^^^^^^
        File "C:\Users\helde\AppData\Local\Temp\pip-install-1sf0bagf\pyradiomics_6c8485f470f5436b8e8844009eec4037\versioneer.py", line 1408, in get_versions
          cfg = get_config_from_root(root)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\helde\AppData\Local\Temp\pip-install-1sf0bagf\pyradiomics_6c8485f470f5436b8e8844009eec4037\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]

[shoeffner]

This is because the last release on PyPI is 3.1.0 from 2023 and it uses an old version of versioneer.
The current master branch no longer uses versioneer (and instead relies on setuptools_scm) since cb87a3e (May 13, 2025).

You could still make it work by checking out the source code of version 3.1.0:

$ git clone --branch v3.1.0 https://github.com/AIM-Harvard/pyradiomics

and applying the following to versioneer.py in lines 342ff:

-    parser = configparser.SafeConfigParser()
-    with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+    parser = configparser.ConfigParser()
+    parser.read(setup_cfg)

After that, install from your checkout pip install ./pyradiomics rather than from PyPI.

Update: The relevant docs are here (readfp had been deprecated since 3.2):
https://docs.python.org/3.9/library/configparser.html#configparser.ConfigParser.readfp
(Alternatively, instead of parser.read, you can use parser.read_file(f))