Import types only in if TYPE_CHECKING blocks (#3064)

* Import types only in `if TYPE_CHECKING` blocks

* Fixes

* one more get_args fix

* Fix mpl link

* undo more

benchmarks/benchmarks/_utils.py

@@ -2,7 +2,7 @@
 
 import warnings
 from functools import cache
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 import numpy as np
 import pooch
@@ -11,6 +11,8 @@
 import scanpy as sc
 
 if TYPE_CHECKING:
+    from typing import Literal
+
     from anndata import AnnData
 
     Dataset = Literal["pbmc68k_reduced", "pbmc3k", "bmmc", "lung93k"]

docs/extensions/function_images.py

@@ -3,9 +3,11 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
+    from typing import Any
+
     from sphinx.application import Sphinx
     from sphinx.ext.autodoc import Options
 

pyproject.toml

@@ -253,3 +253,6 @@ required-imports = ["from __future__ import annotations"]
 "pytest.importorskip".msg = "Use the “@needs” decorator/mark instead"
 "pandas.api.types.is_categorical_dtype".msg = "Use isinstance(s.dtype, CategoricalDtype) instead"
 "pandas.value_counts".msg = "Use pd.Series(a).value_counts() instead"
+[tool.ruff.lint.flake8-type-checking]
+exempt-modules = []
+strict = true

scanpy/_settings.py

@@ -7,14 +7,22 @@
 from logging import getLevelName
 from pathlib import Path
 from time import time
-from typing import TYPE_CHECKING, Any, Literal, TextIO, Union
+from typing import TYPE_CHECKING
 
 from . import logging
 from ._compat import old_positionals
 from .logging import _RootLogger, _set_log_file, _set_log_level
 
 if TYPE_CHECKING:
     from collections.abc import Generator, Iterable
+    from typing import Any, Literal, TextIO, Union
+
+    # Collected from the print_* functions in matplotlib.backends
+    _Format = Union[
+        Literal["png", "jpg", "tif", "tiff"],
+        Literal["pdf", "ps", "eps", "svg", "svgz", "pgf"],
+        Literal["raw", "rgba"],
+    ]
 
 _VERBOSITY_TO_LOGLEVEL = {
     "error": "ERROR",
@@ -28,14 +36,6 @@
     _VERBOSITY_TO_LOGLEVEL[v] = level
 
 
-# Collected from the print_* functions in matplotlib.backends
-_Format = Union[
-    Literal["png", "jpg", "tif", "tiff"],
-    Literal["pdf", "ps", "eps", "svg", "svgz", "pgf"],
-    Literal["raw", "rgba"],
-]
-
-
 class Verbosity(IntEnum):
     """Logging verbosity levels."""
 

scanpy/_utils/__init__.py

@@ -19,21 +19,11 @@
 from operator import mul, truediv
 from textwrap import dedent
 from types import MethodType, ModuleType
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Callable,
-    Literal,
-    TypeVar,
-    Union,
-    overload,
-)
+from typing import TYPE_CHECKING, overload
 from weakref import WeakSet
 
 import numpy as np
-from anndata import AnnData
 from anndata import __version__ as anndata_version
-from numpy.typing import NDArray
 from packaging.version import Version
 from scipy import sparse
 from sklearn.utils import check_random_state
@@ -46,8 +36,14 @@
 if TYPE_CHECKING:
     from collections.abc import Mapping
     from pathlib import Path
+    from typing import Any, Callable, Literal, TypeVar, Union
 
-    from numpy.typing import DTypeLike
+    from anndata import AnnData
+    from numpy.typing import DTypeLike, NDArray
+
+    # e.g. https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html
+    # maybe in the future random.Generator
+    AnyRandom = Union[int, np.random.RandomState, None]
 
 
 class Empty(Enum):
@@ -59,10 +55,6 @@ def __repr__(self) -> str:
 
 _empty = Empty.token
 
-# e.g. https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html
-# maybe in the future random.Generator
-AnyRandom = Union[int, np.random.RandomState, None]
-
 
 class RNGIgraph:
     """
@@ -535,9 +527,10 @@ def update_params(
 # --------------------------------------------------------------------------------
 
 
-_SparseMatrix = Union[sparse.csr_matrix, sparse.csc_matrix]
-_MemoryArray = Union[NDArray, _SparseMatrix]
-_SupportedArray = Union[_MemoryArray, DaskArray]
+if TYPE_CHECKING:
+    _SparseMatrix = Union[sparse.csr_matrix, sparse.csc_matrix]
+    _MemoryArray = Union[NDArray, _SparseMatrix]
+    _SupportedArray = Union[_MemoryArray, DaskArray]
 
 
 @singledispatch
@@ -561,7 +554,8 @@ def _elem_mul_dask(x: DaskArray, y: DaskArray) -> DaskArray:
     return da.map_blocks(elem_mul, x, y)
 
 
-Scaling_T = TypeVar("Scaling_T", DaskArray, np.ndarray)
+if TYPE_CHECKING:
+    Scaling_T = TypeVar("Scaling_T", DaskArray, np.ndarray)
 
 
 def broadcast_axis(divisor: Scaling_T, axis: Literal[0, 1]) -> Scaling_T:

scanpy/_utils/compute/is_constant.py

@@ -3,7 +3,7 @@
 from collections.abc import Callable
 from functools import partial, singledispatch, wraps
 from numbers import Integral
-from typing import TYPE_CHECKING, Literal, TypeVar, overload
+from typing import TYPE_CHECKING, TypeVar, overload
 
 import numpy as np
 from numba import njit
@@ -12,6 +12,8 @@
 from ..._compat import DaskArray
 
 if TYPE_CHECKING:
+    from typing import Literal
+
     from numpy.typing import NDArray
 
 C = TypeVar("C", bound=Callable)

scanpy/cli.py

@@ -7,11 +7,13 @@
 from functools import lru_cache, partial
 from pathlib import Path
 from shutil import which
-from subprocess import CompletedProcess, run
-from typing import TYPE_CHECKING, Any
+from subprocess import run
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from collections.abc import Generator, Mapping, Sequence
+    from subprocess import CompletedProcess
+    from typing import Any
 
 
 class _DelegatingSubparsersAction(_SubParsersAction):

scanpy/datasets/_datasets.py

@@ -2,7 +2,7 @@
 
 import warnings
 from pathlib import Path
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 import anndata as ad
 import numpy as np
@@ -16,6 +16,8 @@
 from ._utils import check_datasetdir_exists, filter_oldformatwarning
 
 if TYPE_CHECKING:
+    from typing import Literal
+
     from .._utils import AnyRandom
 
 HERE = Path(__file__).parent

scanpy/datasets/_ebi_expression_atlas.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import BinaryIO
+from typing import TYPE_CHECKING
 from urllib.error import HTTPError
 from urllib.request import urlopen
 from zipfile import ZipFile
@@ -15,6 +15,9 @@
 from ..readwrite import _download
 from ._utils import check_datasetdir_exists
 
+if TYPE_CHECKING:
+    from typing import BinaryIO
+
 
 def _filter_boring(dataframe: pd.DataFrame) -> pd.DataFrame:
     unique_vals = dataframe.apply(lambda x: len(x.unique()))

scanpy/experimental/pp/_highly_variable_genes.py

@@ -3,7 +3,7 @@
 import warnings
 from functools import partial
 from math import sqrt
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 import numba as nb
 import numpy as np
@@ -27,6 +27,8 @@
 from scanpy.preprocessing._utils import _get_mean_var
 
 if TYPE_CHECKING:
+    from typing import Literal
+
     from numpy.typing import NDArray
 
 

scanpy/experimental/pp/_normalization.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 from warnings import warn
 
 import numpy as np
@@ -10,7 +10,6 @@
 
 from ... import logging as logg
 from ..._utils import (
-    Empty,
     _doc_params,
     _empty,
     check_nonnegative_integers,
@@ -31,6 +30,9 @@
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
+    from typing import Any
+
+    from ..._utils import Empty
 
 
 def _pearson_residuals(X, theta, clip, check_values, copy: bool = False):

scanpy/external/pl.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -23,6 +23,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Collection
+    from typing import Any
 
 
 __all__ = [

scanpy/external/pp/_bbknn.py

@@ -1,11 +1,13 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
 
 from ..._compat import old_positionals
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
+    from typing import Callable
+
     from anndata import AnnData
     from sklearn.metrics import DistanceMetric
 

scanpy/external/pp/_dca.py

@@ -1,18 +1,19 @@
 from __future__ import annotations
 
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING
 
 from ..._compat import old_positionals
 
 if TYPE_CHECKING:
     from collections.abc import Mapping, Sequence
+    from typing import Any, Literal
 
     from anndata import AnnData
 
     from ..._utils import AnyRandom
 
-_AEType = Literal["zinb-conddisp", "zinb", "nb-conddisp", "nb"]
+    _AEType = Literal["zinb-conddisp", "zinb", "nb-conddisp", "nb"]
 
 
 @old_positionals(

scanpy/external/pp/_magic.py

@@ -4,7 +4,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 from packaging.version import Version
 
@@ -14,6 +14,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Literal
 
     from anndata import AnnData
 

scanpy/external/pp/_mnn_correct.py

@@ -1,11 +1,12 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING
 
 from ..._settings import settings
 
 if TYPE_CHECKING:
     from collections.abc import Collection, Sequence
+    from typing import Any, Literal
 
     import numpy as np
     import pandas as pd

scanpy/external/tl/_phate.py

@@ -4,14 +4,16 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Literal
+from typing import TYPE_CHECKING
 
 from ... import logging as logg
 from ..._compat import old_positionals
 from ..._settings import settings
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
+    from typing import Literal
+
     from anndata import AnnData
 
     from ..._utils import AnyRandom

scanpy/external/tl/_phenograph.py

@@ -4,7 +4,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING
 
 import pandas as pd
 from anndata import AnnData
@@ -15,6 +15,8 @@
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
+    from typing import Any, Literal
+
     import numpy as np
     from scipy.sparse import spmatrix