When attempting to install squidpy, I got the error: AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean 'RawConfigParser'?
This appears to be an issue with pygeos's versioneer file, but that project appears to be deprecated in favor of shapely. Attempting to install pygeos on its own produces the same error while shapely installs without issue.
Minimal reproducible example
In Windows command prompt, with administrator permissions:
py -m pip install squidpy
Traceback
```
...
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [35 lines of output]
:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
C:\Users\gegua\AppData\Local\Temp\pip-install-7gveaeps\pygeos_509fb143a42f4536b77e25e06ae78187\versioneer.py:421: SyntaxWarning: invalid escape sequence '\s'
LONG_VERSION_PY['git'] = '''
Could not find geos-config executable. Either append the path to geos-config to PATH or manually provide the include_dirs, library_dirs, libraries and other link args for compiling against a GEOS version >=3.5.
Compiling pygeos/_geometry.pyx because it changed.
Compiling pygeos/_geos.pyx because it changed.
[1/2] Cythonizing pygeos/_geometry.pyx
[2/2] Cythonizing pygeos/_geos.pyx
Traceback (most recent call last):
File "C:\Users\gegua\AppData\Local\Programs\Python\Python312\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 353, in
main()
File "C:\Users\gegua\AppData\Local\Programs\Python\Python312\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 "C:\Users\gegua\AppData\Local\Programs\Python\Python312\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\gegua\AppData\Local\Temp\pip-build-env-svo8upi_\overlay\Lib\site-packages\setuptools\build_meta.py", line 325, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\gegua\AppData\Local\Temp\pip-build-env-svo8upi_\overlay\Lib\site-packages\setuptools\build_meta.py", line 295, in _get_build_requires
self.run_setup()
File "C:\Users\gegua\AppData\Local\Temp\pip-build-env-svo8upi_\overlay\Lib\site-packages\setuptools\build_meta.py", line 311, in run_setup
exec(code, locals())
File "", line 214, in
File "C:\Users\gegua\AppData\Local\Temp\pip-install-7gveaeps\pygeos_509fb143a42f4536b77e25e06ae78187\versioneer.py", line 1480, in get_version
return get_versions()["version"]
^^^^^^^^^^^^^^
File "C:\Users\gegua\AppData\Local\Temp\pip-install-7gveaeps\pygeos_509fb143a42f4536b77e25e06ae78187\versioneer.py", line 1412, in get_versions
cfg = get_config_from_root(root)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\gegua\AppData\Local\Temp\pip-install-7gveaeps\pygeos_509fb143a42f4536b77e25e06ae78187\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: 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.
```
hi @azguan yes this is a known issue ith python 3.12 we will fix it soon but don't have an estimate now, easier it is to not use python3.12 with squidpy
Description
When attempting to install squidpy, I got the error:
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean 'RawConfigParser'?
This appears to be an issue with pygeos's versioneer file, but that project appears to be deprecated in favor of shapely. Attempting to install pygeos on its own produces the same error while shapely installs without issue.
Minimal reproducible example
In Windows command prompt, with administrator permissions:
py -m pip install squidpy
Traceback