flying-sheep/hatch-scanpy-typeshed

hatch-scanpy-typeshed

What does it do?

For functions using keyword-only arguments (*, copy: ...), it is able to clear up the function signature for copy, telling type checkers that a function returns None precisely when copy=False, and otherwise an AnnData instance.

E.g. when run on scanpy’s tl._score_genes module, it creates a .pyi file like this:

from collections.abc import Sequence
from typing import Literal, overload
from anndata import AnnData
from .._utils import AnyRandom

def score_genes(
    adata: AnnData, gene_list: Sequence[str], ctrl_size: int = ..., gene_pool: Sequence[str] | None = ...,
    n_bins: int = ..., score_name: str = ..., random_state: AnyRandom = ..., copy: bool = ..., use_raw: bool | None = ...,
) -> AnnData | None: ...
@overload
def score_genes_cell_cycle(adata: AnnData, s_genes: Sequence[str], g2m_genes: Sequence[str], copy: Literal[True], **kwargs) -> AnnData: ...
@overload
def score_genes_cell_cycle(adata: AnnData, s_genes: Sequence[str], g2m_genes: Sequence[str], copy: Literal[False] = False, **kwargs) -> None: ...

Together with (at the time of writing) a warning about a function that has not been converted to kw-only arguments yet:

UserWarning: Parameter 'copy' must be a keyword-only argument in scanpy.tools._score_genes function score_genes

Usage

The plan is to soon include it as a plugin to a scanpy-like API’s pyproject.toml:

[build-system]
requires = ["hatchling", "hatch-scanpy-typeshed"]
build-backend = "hatchling.build"

License

hatch-scanpy-typeshed is distributed under the terms of the GPL 3 (or later) license.