2023.9.6 duplicate "self" argument in rdfiltercatalog/__init__.pyi

[JHucker]

Describe the bug
Upgrading to 2023.9.6 fails mypy in my pre-commit when importing FilterCatalogParams:

/home/jacobhucker/miniforge3/envs/min_rep_issue/lib/python3.11/site-packages/rdkit-stubs/Chem/rdfiltercatalog/__init__.pyi:671: error: Duplicate argument "self" in function definition
Found 1 error in 1 file (errors prevented further checking)

Viewing this file, self appears untyped and again typed:

class PythonFilterMatcher(FilterMatcherBase):
    __instance_size__: typing.ClassVar[int] = 72
    @staticmethod
    def __reduce__(*args, **kwargs):
        ...
    def __init__(self, self: typing.Any) -> None:
        """
            C++ signature :
                void __init__(_object*,_object*)
        """

To Reproduce
Minimal conda environment yaml:

name: min_rep_issue
channels:
  - conda-forge
dependencies:
  - python=3.11.8
  - pip
  - pip:
    - rdkit==2023.9.6
    - mypy==1.10.0

Minimal main.py:

from rdkit.Chem.rdfiltercatalog import FilterCatalogParams

if __name__ == "__main__":
    _ = FilterCatalogParams()

Running mypy:

$ mypy  .
/home/jacobhucker/miniforge3/envs/min_rep_issue/lib/python3.11/site-packages/rdkit-stubs/Chem/rdfiltercatalog/__init__.pyi:671: error: Duplicate argument "self" in function definition
Found 1 error in 1 file (errors prevented further checking)

Expected behavior
There should be no errors detected by mypy when scanning the above main.py example.

Configuration (please complete the following information):

• RDKit version: 2023.9.6
• OS: Pop!_OS 22.04 LTS
• Python version (if relevant): 3.11.8
• Are you using conda? In the minimal example yes, but this firstly originated when installing rdkit via poetry
• If you are using conda, which channel did you install the rdkit from? as above
• If you are not using conda: how did you install the RDKit? Via poetry 1.8.2

[ptosco]

Thanks for reporting. Automated stub generation with C++ Python wrappers is tricky. I'll fix that.

[lukasturcani]

I have a similar issue with rdkit-stubs/Chem/rdMolDescriptors.pyi:185: error: Duplicate argument "self" in function definition

[mikemhenry]

I've been having the same issues, so far pinning to rdkit=2023.09.5 fixes it, which is okay since for now we only need to worry about this error when running mypy

[nishant-aionics]

@ptosco Any updates on this? I'm facing the same issue as @lukasturcani

[nishant-aionics]

FWIW I've changed mypy.ini to the following to keep using rdkit version 2023.9.6:

[mypy]
disallow_untyped_defs = True
; disallow_any_unimported = True
no_implicit_optional = True
check_untyped_defs = True
; warn_return_any = True
show_error_codes = True 
warn_unused_ignores = True
exclude = venv|.venv

[mypy-rdkit.*]
follow_imports = skip
follow_imports_for_stubs = True

[ptosco]

Apologies, I have had very little time for RDKit lately; I’ll try to get this fixed for the next patch release.

[nishant-aionics]

Thanks @ptosco! Appreciate the help! 💯

[ElricleNecro]

The same problem exist in RDKit 2024.3.5 but in the file rdkit-stubs/Chem/rdMolDescriptors.pyi. In this declaration:

    def __init__(self, self: typing.Any, name: str, version: str) -> None:
        """
            C++ signature :
                void __init__(_object*,_object*,std::string,std::string)
        """

there is 2 self where only one should be needed:

    def __init__(self: typing.Any, name: str, version: str) -> None:
        """
            C++ signature :
                void __init__(_object*,_object*,std::string,std::string)
        """

[UnixJunkie]

maybe related to this one: #7554

[ElricleNecro]

Yes, they are both showing the same problem, just in different files. I posted in both, because the incriminated file was mentionned ion both. And I'm not sure which one is really active.