Bug Report

The pykdtree package has a Cython module with a single class definition. Recently a stub was added for this class in a separate kdtree.pyi file (see below). Starting with mypy 1.18.x the stubtest has started failing because mypy considers it a disjoint base, but I'm not sure how that is possible since it is a single class. I have very little knowledge of how mypy investigates a C-level class like this so we could easily be doing something wrong.

To Reproduce

I have a Cython class that you can find the full source for at:

https://github.com/storpipfugl/pykdtree/blob/master/pykdtree/kdtree.pyx

And stub file:

https://github.com/storpipfugl/pykdtree/blob/master/pykdtree/kdtree.pyi

Here's the init-level part of the Cython class:

cdef class KDTree: def __cinit__(KDTree self): ... def __init__(KDTree self, np.ndarray data_pts not None, int leafsize=16): ...

And the relevant portion of the stub file:

class KDTree: def __init__(self, data_pts: np.ndarray, leafsize: int = 16): ...

Since __cinit__ is a C-level only method it is not in the stub file.

Expected Behavior

Testing the stub with "stubtest" should report no issues. This is true for mypy 1.17.x.

Actual Behavior

error: pykdtree.kdtree.KDTree is a disjoint base at runtime, but isn't marked with @disjoint_base in the stub Stub: in file /home/davidh/repos/git/pykdtree/pykdtree/kdtree.pyi:21 <TypeInfo pykdtree.kdtree.KDTree> Runtime: <class 'pykdtree.kdtree.KDTree'> 

Note: I did not write the stub file for this, but am one of the maintainers of pykdtree. I don't fully understand the best way to stub a Cython file, but it used to work so I'm surprised by this.

Possibly Related: #19877 #19887 #19740

Your Environment

• Mypy version used: 1.18.2 (and 1.18.1)
• Mypy command-line flags: stubtest pykdtree
• Mypy configuration options from mypy.ini (and other config files): None
• Python version used: 3.12