remove numpy 1 support (#119)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: flying-sheep

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
       - id: trailing-whitespace
       - id: no-commit-to-branch
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.12
+    rev: v0.13.0
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]

docs/conf.py

@@ -85,7 +85,6 @@
     source_directory="docs/",
 )
 
-_np_aliases = {"bool_": "bool"}
 _np_nocls = {"float64": "attr"}
 _optional_types = {
     "CupyArray": "cupy.ndarray",
@@ -111,7 +110,7 @@ def find_type_alias(name: str) -> tuple[str, str, str | None] | tuple[None, None
             return "class", path, None
         return "data", f"fast_array_utils.{name}", None
     if name.startswith("np."):
-        name = _np_aliases.get(name[3:], name[3:])
+        name = name.removeprefix("np.")
         return _np_nocls.get(name, "class"), f"numpy.{name}", f"np.{name}"
     if name in npt.__all__:
         return "data", f"numpy.typing.{name}", None

pyproject.toml

@@ -24,8 +24,9 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dynamic = [ "description", "readme", "version" ]
-dependencies = [ "numpy>=1.25.2" ]
+dependencies = [ "numpy>=2" ]
 optional-dependencies.accel = [ "numba>=0.57" ]
+optional-dependencies.dask = [ "dask>=2023.6.1" ]
 optional-dependencies.doc = [
   "furo>=2024.8.6",
   "pytest>=8.4",
@@ -34,7 +35,7 @@ optional-dependencies.doc = [
   "sphinx-autodoc-typehints>=3.2",
   "sphinx-autofixture>=0.4.1",
 ]
-optional-dependencies.full = [ "dask", "fast-array-utils[accel,sparse]", "h5py", "zarr" ]
+optional-dependencies.full = [ "fast-array-utils[accel,dask,sparse]", "h5py", "zarr" ]
 optional-dependencies.sparse = [ "scipy>=1.11" ]
 optional-dependencies.test = [
   "anndata",
@@ -99,7 +100,7 @@ overrides.matrix.resolution.features = [
 ]
 overrides.matrix.resolution.dependencies = [
   # TODO: move to min dep once this is fixed: https://github.com/tlambert03/hatch-min-requirements/issues/5
-  { if = [ "lowest" ], value = "dask==2023.5.1" },
+  { if = [ "lowest" ], value = "dask==2023.6.1" },
 ]
 
 [[tool.hatch.envs.hatch-test.matrix]]
@@ -144,13 +145,12 @@ lint.per-file-ignores."typings/**/*.pyi" = [ "A002", "F403", "F405", "N801" ] #
 lint.allowed-confusables = [ "×", "’" ]
 lint.flake8-bugbear.extend-immutable-calls = [ "testing.fast_array_utils.Flags" ]
 lint.flake8-copyright.notice-rgx = "SPDX-License-Identifier: MPL-2\\.0"
-lint.flake8-tidy-imports.banned-api."numpy.bool".msg = "Use `np.bool_` instead for numpy>=1.24<2 compatibility"
 lint.flake8-type-checking.exempt-modules = [  ]
 lint.flake8-type-checking.strict = true
 lint.isort.known-first-party = [ "fast_array_utils" ]
 lint.isort.lines-after-imports = 2
-lint.isort.required-imports = [ "from __future__ import annotations" ]
 lint.pydocstyle.convention = "numpy"
+lint.future-annotations = true
 
 [tool.pytest.ini_options]
 addopts = [

src/fast_array_utils/stats/__init__.py

@@ -29,19 +29,19 @@
 @overload
 def is_constant(x: NDArray[Any] | types.CSBase | types.CupyArray, /, *, axis: None = None) -> bool: ...
 @overload
-def is_constant(x: NDArray[Any] | types.CSBase, /, *, axis: Literal[0, 1]) -> NDArray[np.bool_]: ...
+def is_constant(x: NDArray[Any] | types.CSBase, /, *, axis: Literal[0, 1]) -> NDArray[np.bool]: ...
 @overload
 def is_constant(x: types.CupyArray, /, *, axis: Literal[0, 1]) -> types.CupyArray: ...
 @overload
-def is_constant(x: types.DaskArray, /, *, axis: Literal[0, 1, None] = None) -> types.DaskArray: ...
+def is_constant(x: types.DaskArray, /, *, axis: Literal[0, 1] | None = None) -> types.DaskArray: ...
 
 
 def is_constant(
     x: NDArray[Any] | types.CSBase | types.CupyArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
-) -> bool | NDArray[np.bool_] | types.CupyArray | types.DaskArray:
+    axis: Literal[0, 1] | None = None,
+) -> bool | NDArray[np.bool] | types.CupyArray | types.DaskArray:
     """Check whether values in array are constant.
 
     Parameters
@@ -80,7 +80,7 @@ def is_constant(
 # TODO(flying-sheep): support CSDataset (TODO)
 # https://github.com/scverse/fast-array-utils/issues/52
 @overload
-def mean(x: CpuArray | GpuArray | DiskArray, /, *, axis: Literal[None] = None, dtype: DTypeLike | None = None) -> np.number[Any]: ...
+def mean(x: CpuArray | GpuArray | DiskArray, /, *, axis: None = None, dtype: DTypeLike | None = None) -> np.number[Any]: ...
 @overload
 def mean(x: CpuArray | DiskArray, /, *, axis: Literal[0, 1], dtype: DTypeLike | None = None) -> NDArray[np.number[Any]]: ...
 @overload
@@ -93,7 +93,7 @@ def mean(
     x: CpuArray | GpuArray | DiskArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     dtype: DTypeLike | None = None,
 ) -> NDArray[np.number[Any]] | types.CupyArray | np.number[Any] | types.DaskArray:
     """Mean over both or one axis.
@@ -131,24 +131,24 @@ def mean(
     from ._mean import mean_
 
     validate_axis(x.ndim, axis)
-    return mean_(x, axis=axis, dtype=dtype)  # type: ignore[no-any-return]  # literally the same type, wtf mypy
+    return mean_(x, axis=axis, dtype=dtype)
 
 
 @overload
-def mean_var(x: CpuArray | GpuArray, /, *, axis: Literal[None] = None, correction: int = 0) -> tuple[np.float64, np.float64]: ...
+def mean_var(x: CpuArray | GpuArray, /, *, axis: None = None, correction: int = 0) -> tuple[np.float64, np.float64]: ...
 @overload
 def mean_var(x: CpuArray, /, *, axis: Literal[0, 1], correction: int = 0) -> tuple[NDArray[np.float64], NDArray[np.float64]]: ...
 @overload
 def mean_var(x: GpuArray, /, *, axis: Literal[0, 1], correction: int = 0) -> tuple[types.CupyArray, types.CupyArray]: ...
 @overload
-def mean_var(x: types.DaskArray, /, *, axis: Literal[0, 1, None] = None, correction: int = 0) -> tuple[types.DaskArray, types.DaskArray]: ...
+def mean_var(x: types.DaskArray, /, *, axis: Literal[0, 1] | None = None, correction: int = 0) -> tuple[types.DaskArray, types.DaskArray]: ...
 
 
 def mean_var(
     x: CpuArray | GpuArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     correction: int = 0,
 ) -> (
     tuple[np.float64, np.float64]
@@ -218,14 +218,14 @@ def sum(x: GpuArray, /, *, axis: Literal[0, 1], dtype: DTypeLike | None = None,
 
 
 @overload
-def sum(x: types.DaskArray, /, *, axis: Literal[0, 1, None] = None, dtype: DTypeLike | None = None, keep_cupy_as_array: bool = False) -> types.DaskArray: ...
+def sum(x: types.DaskArray, /, *, axis: Literal[0, 1] | None = None, dtype: DTypeLike | None = None, keep_cupy_as_array: bool = False) -> types.DaskArray: ...
 
 
 def sum(
     x: CpuArray | GpuArray | DiskArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     dtype: DTypeLike | None = None,
     keep_cupy_as_array: bool = False,
 ) -> NDArray[Any] | types.CupyArray | np.number[Any] | types.DaskArray:

src/fast_array_utils/stats/_is_constant.py

@@ -24,13 +24,13 @@ def is_constant_(
     a: NDArray[Any] | types.CSBase | types.CupyArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
-) -> bool | NDArray[np.bool_] | types.CupyArray | types.DaskArray:  # pragma: no cover
+    axis: Literal[0, 1] | None = None,
+) -> bool | NDArray[np.bool] | types.CupyArray | types.DaskArray:  # pragma: no cover
     raise NotImplementedError
 
 
 @is_constant_.register(np.ndarray | types.CupyArray)
-def _is_constant_ndarray(a: NDArray[Any] | types.CupyArray, /, *, axis: Literal[0, 1, None] = None) -> bool | NDArray[np.bool_] | types.CupyArray:
+def _is_constant_ndarray(a: NDArray[Any] | types.CupyArray, /, *, axis: Literal[0, 1] | None = None) -> bool | NDArray[np.bool] | types.CupyArray:
     # Should eventually support nd, not now.
     match axis:
         case None:
@@ -41,13 +41,13 @@ def _is_constant_ndarray(a: NDArray[Any] | types.CupyArray, /, *, axis: Literal[
             return _is_constant_rows(a)
 
 
-def _is_constant_rows(a: NDArray[Any] | types.CupyArray) -> NDArray[np.bool_] | types.CupyArray:
+def _is_constant_rows(a: NDArray[Any] | types.CupyArray) -> NDArray[np.bool] | types.CupyArray:
     b = np.broadcast_to(a[:, 0][:, np.newaxis], a.shape)
-    return cast("NDArray[np.bool_]", (a == b).all(axis=1))
+    return cast("NDArray[np.bool]", (a == b).all(axis=1))
 
 
 @is_constant_.register(types.CSBase)
-def _is_constant_cs(a: types.CSBase, /, *, axis: Literal[0, 1, None] = None) -> bool | NDArray[np.bool_]:
+def _is_constant_cs(a: types.CSBase, /, *, axis: Literal[0, 1] | None = None) -> bool | NDArray[np.bool]:
     from . import is_constant
 
     if len(a.shape) == 1:  # pragma: no cover
@@ -68,9 +68,9 @@ def _is_constant_cs(a: types.CSBase, /, *, axis: Literal[0, 1, None] = None) ->
 
 
 @numba.njit(cache=True)
-def _is_constant_cs_major(a: types.CSBase, shape: tuple[int, int]) -> NDArray[np.bool_]:
+def _is_constant_cs_major(a: types.CSBase, shape: tuple[int, int]) -> NDArray[np.bool]:
     n = len(a.indptr) - 1
-    result = np.ones(n, dtype=np.bool_)
+    result = np.ones(n, dtype=np.bool)
     for i in numba.prange(n):
         start = a.indptr[i]
         stop = a.indptr[i + 1]
@@ -83,13 +83,13 @@ def _is_constant_cs_major(a: types.CSBase, shape: tuple[int, int]) -> NDArray[np
 
 
 @is_constant_.register(types.DaskArray)
-def _is_constant_dask(a: types.DaskArray, /, *, axis: Literal[0, 1, None] = None) -> types.DaskArray:
+def _is_constant_dask(a: types.DaskArray, /, *, axis: Literal[0, 1] | None = None) -> types.DaskArray:
     import dask.array as da
 
     from . import is_constant
 
     if axis is not None:
-        return da.map_blocks(partial(is_constant, axis=axis), a, drop_axis=axis, meta=np.array([], dtype=np.bool_))
+        return da.map_blocks(partial(is_constant, axis=axis), a, drop_axis=axis, meta=np.array([], dtype=np.bool))
 
     rv = (
         (a == a[0, 0].compute()).all()

src/fast_array_utils/stats/_mean.py

@@ -1,7 +1,7 @@
 # SPDX-License-Identifier: MPL-2.0
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, no_type_check
+from typing import TYPE_CHECKING
 
 import numpy as np
 
@@ -17,14 +17,13 @@
     from ..typing import CpuArray, DiskArray, GpuArray
 
 
-@no_type_check  # mypy is very confused
 def mean_(
     x: CpuArray | GpuArray | DiskArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     dtype: DTypeLike | None = None,
 ) -> NDArray[np.number[Any]] | np.number[Any] | types.DaskArray:
     total = sum_(x, axis=axis, dtype=dtype)
     n = np.prod(x.shape) if axis is None else x.shape[axis]
-    return total / n
+    return total / n  # type: ignore[call-overload,operator,return-value]

src/fast_array_utils/stats/_mean_var.py

@@ -23,7 +23,7 @@ def mean_var_(
     x: CpuArray | GpuArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     correction: int = 0,
 ) -> (
     tuple[NDArray[np.float64], NDArray[np.float64]]

src/fast_array_utils/stats/_sum.py

@@ -17,15 +17,15 @@
 
     from ..typing import CpuArray, DiskArray, GpuArray
 
-    ComplexAxis: TypeAlias = tuple[Literal[0], Literal[1]] | tuple[Literal[0, 1]] | Literal[0, 1, None]
+    ComplexAxis: TypeAlias = tuple[Literal[0], Literal[1]] | tuple[Literal[0, 1]] | Literal[0, 1] | None
 
 
 @singledispatch
 def sum_(
     x: CpuArray | GpuArray | DiskArray | types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     dtype: DTypeLike | None = None,
     keep_cupy_as_array: bool = False,
 ) -> NDArray[Any] | np.number[Any] | types.CupyArray | types.DaskArray:
@@ -43,7 +43,7 @@ def _sum_cupy(
     x: GpuArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     dtype: DTypeLike | None = None,
     keep_cupy_as_array: bool = False,
 ) -> types.CupyArray | np.number[Any]:
@@ -56,7 +56,7 @@ def _sum_cs(
     x: types.CSBase,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     dtype: DTypeLike | None = None,
     keep_cupy_as_array: bool = False,
 ) -> NDArray[Any] | np.number[Any]:
@@ -76,7 +76,7 @@ def _sum_dask(
     x: types.DaskArray,
     /,
     *,
-    axis: Literal[0, 1, None] = None,
+    axis: Literal[0, 1] | None = None,
     dtype: DTypeLike | None = None,
     keep_cupy_as_array: bool = False,
 ) -> types.DaskArray:
@@ -129,7 +129,7 @@ def sum_dask_inner(
     return cast("NDArray[Any] | types.CupyArray", rv.reshape(shape))
 
 
-def normalize_axis(axis: ComplexAxis, ndim: int) -> Literal[0, 1, None]:
+def normalize_axis(axis: ComplexAxis, ndim: int) -> Literal[0, 1] | None:
     """Adapt `axis` parameter passed by Dask to what we support."""
     match axis:
         case int() | None:
@@ -145,7 +145,7 @@ def normalize_axis(axis: ComplexAxis, ndim: int) -> Literal[0, 1, None]:
     return axis
 
 
-def get_shape(a: NDArray[Any] | np.number[Any] | types.CupyArray, *, axis: Literal[0, 1, None], keepdims: bool) -> tuple[int] | tuple[int, int]:
+def get_shape(a: NDArray[Any] | np.number[Any] | types.CupyArray, *, axis: Literal[0, 1] | None, keepdims: bool) -> tuple[int] | tuple[int, int]:
     """Get the output shape of an axis-flattening operation."""
     match keepdims, a.ndim:
         case False, 0: