Merge pull request #818 from zerothi/pep-585-fixes

fixing many simple PEP-585 deprecations

CHANGELOG.md

@@ -66,6 +66,7 @@ we hit release version 1.0.0.
 - A new `AtomicMatrixPlot` to plot sparse matrices, #668
 
 ### Fixed
+- PEP-585 compliant
 - buildable for numpy>2, #791
 - `BrillouinZone.tocartesian()` now defaults to `k=self.k`
 - reading XV/STRUCT files from fdf siles could cause problems, #778

benchmarks/bz_parallel.py

@@ -19,7 +19,6 @@
 
 import os
 import sys
-import time
 
 import numpy as np
 

benchmarks/graphene_within.py

@@ -19,8 +19,6 @@
 
 import sys
 
-import numpy as np
-
 import sisl
 
 method = "cube"

benchmarks/sparse_matrices.py

@@ -17,7 +17,6 @@
 from __future__ import annotations
 
 import cProfile
-import io
 import pstats
 import sys
 

src/sisl/_core/_ufuncs_geometry.py

@@ -5,7 +5,7 @@
 
 from functools import reduce
 from numbers import Integral
-from typing import Callable, List, Literal, Optional, Tuple, Union
+from typing import Callable, Literal, Optional, Union
 
 import numpy as np
 
@@ -166,7 +166,7 @@ def apply(
 @register_sisl_dispatch(Geometry, module="sisl")
 def sort(
     geometry: Geometry, **kwargs
-) -> Union[Geometry, Tuple[Geometry, List[List[int]]]]:
+) -> Union[Geometry, tuple[Geometry, list[list[int]]]]:
     r"""Sort atoms in a nested fashion according to various criteria
 
     There are many ways to sort a `Geometry`.

src/sisl/_core/_ufuncs_grid.py

@@ -3,14 +3,15 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-from typing import Optional, Sequence, Union
+from collections.abc import Sequence
+from typing import Union
 
 import numpy as np
 
 import sisl._array as _a
 from sisl._ufuncs import register_sisl_dispatch
 from sisl.messages import SislError
-from sisl.typing import CellAxes, CellAxis, GridLike, SileLike
+from sisl.typing import CellAxis, GridLike, SileLike
 from sisl.utils import import_attr
 from sisl.utils.misc import direction
 

src/sisl/_core/_ufuncs_lattice.py

@@ -6,7 +6,7 @@
 import math
 from functools import reduce
 from numbers import Integral
-from typing import Optional, Union
+from typing import Union
 
 import numpy as np
 

src/sisl/_core/_ufuncs_orbital.py

@@ -3,8 +3,6 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-import numpy as np
-
 from sisl._ufuncs import register_sisl_dispatch
 
 from .orbital import (

src/sisl/_core/_ufuncs_sparse.py

@@ -3,13 +3,5 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-import numpy as np
-
-from sisl._indices import indices
-from sisl._ufuncs import register_sisl_dispatch
-from sisl.typing import SparseMatrixExt
-
-from .sparse import SparseCSR
-
 # Nothing gets exposed here
 __all__ = []

src/sisl/_core/_ufuncs_sparse_geometry.py

@@ -8,11 +8,10 @@
 import numpy as np
 
 from sisl import _array as _a
-from sisl._core.geometry import Geometry
 from sisl._ufuncs import register_sisl_dispatch
 from sisl.typing import AtomsIndex
 
-from .sparse import SparseCSR, _ncol_to_indptr, issparse
+from .sparse import SparseCSR, _ncol_to_indptr
 from .sparse_geometry import SparseAtom, SparseOrbital, _SparseGeometry
 
 # Nothing gets exposed here

src/sisl/_core/geometry.py

@@ -7,27 +7,25 @@
 import logging
 import warnings
 from collections import OrderedDict
+from collections.abc import Iterator, Sequence
 from functools import singledispatchmethod
 from itertools import product
 from math import acos
 from numbers import Integral, Real
 from pathlib import Path
-from typing import Iterator, List, Optional, Sequence, Tuple, Union
+from typing import Optional, Union
 
 import numpy as np
 import numpy.typing as npt
 from numpy import (
-    argsort,
     bool_,
     ceil,
     concatenate,
     diff,
     dot,
     floor,
     int32,
-    isin,
     ndarray,
-    split,
     sqrt,
     square,
     tile,
@@ -39,7 +37,7 @@
 from sisl._category import Category, GenericCategory
 from sisl._dispatch_class import _Dispatchs
 from sisl._dispatcher import AbstractDispatch, ClassDispatcher, TypeDispatcher
-from sisl._help import isndarray
+from sisl._help import has_module, isndarray
 from sisl._indices import (
     indices_gt_le,
     indices_in_sphere_with_dist,
@@ -310,7 +308,7 @@ def lasto(self) -> npt.NDArray[np.int32]:
         return self.atoms.lasto
 
     @property
-    def orbitals(self) -> List[Orbital]:
+    def orbitals(self) -> list[Orbital]:
         """List of orbitals per atom"""
         return self.atoms.orbitals
 
@@ -505,7 +503,7 @@ def _(self, orbitals: bool) -> ndarray:
 
     def as_primary(
         self, na_primary: int, axes: Sequence[int] = (0, 1, 2), ret_super: bool = False
-    ) -> Union[Geometry, Tuple[Geometry, Lattice]]:
+    ) -> Union[Geometry, tuple[Geometry, Lattice]]:
         """Reduce the geometry to the primary unit-cell comprising `na_primary` atoms
 
         This will basically try and find the tiling/repetitions required for the geometry to only have
@@ -952,7 +950,7 @@ def iter_block_rand(
         iR: int = 20,
         R: Optional[float] = None,
         atoms: AtomsIndex = None,
-    ) -> Iterator[Tuple[ndarray, ndarray]]:
+    ) -> Iterator[tuple[ndarray, ndarray]]:
         """Perform the *random* block-iteration by randomly selecting the next center of block"""
 
         # We implement yields as we can then do nested iterators
@@ -1031,7 +1029,7 @@ def iter_block_rand(
 
     def iter_block_shape(
         self, shape=None, iR: int = 20, atoms: AtomsIndex = None
-    ) -> Iterator[Tuple[ndarray, ndarray]]:
+    ) -> Iterator[tuple[ndarray, ndarray]]:
         """Perform the *grid* block-iteration by looping a grid"""
 
         # We implement yields as we can then do nested iterators
@@ -1166,7 +1164,7 @@ def iter_block(
         R: Optional[float] = None,
         atoms: AtomsIndex = None,
         method: str = "rand",
-    ) -> Iterator[Tuple[ndarray, ndarray]]:
+    ) -> Iterator[tuple[ndarray, ndarray]]:
         """Iterator for performance critical loops
 
         NOTE: This requires that `R` has been set correctly as the maximum interaction range.
@@ -1244,7 +1242,7 @@ def overlap(
         atol: float = 0.1,
         offset: Sequence[float] = (0.0, 0.0, 0.0),
         offset_other: Sequence[float] = (0.0, 0.0, 0.0),
-    ) -> Tuple[ndarray, ndarray]:
+    ) -> tuple[ndarray, ndarray]:
         """Calculate the overlapping indices between two geometries
 
         Find equivalent atoms (in the primary unit-cell only) in two geometries.
@@ -2966,7 +2964,7 @@ def isc_tile(isc, n):
 
     def a2transpose(
         self, atoms1: AtomsIndex, atoms2: AtomsIndex = None
-    ) -> Tuple[ndarray, ndarray]:
+    ) -> tuple[ndarray, ndarray]:
         """Transposes connections from `atoms1` to `atoms2` such that supercell connections are transposed
 
         When handling supercell indices it is useful to get the *transposed* connection. I.e. if you have
@@ -3032,7 +3030,7 @@ def a2transpose(
 
     def o2transpose(
         self, orb1: OrbitalsIndex, orb2: Optional[OrbitalsIndex] = None
-    ) -> Tuple[ndarray, ndarray]:
+    ) -> tuple[ndarray, ndarray]:
         """Transposes connections from `orb1` to `orb2` such that supercell connections are transposed
 
         When handling supercell indices it is useful to get the *transposed* connection. I.e. if you have
@@ -3548,7 +3546,7 @@ def within_inf(
         periodic: Optional[Union[Sequence[bool], CellAxes]] = None,
         atol: float = 1e-5,
         origin: Sequence[float] = (0.0, 0.0, 0.0),
-    ) -> Tuple[ndarray, ndarray, ndarray]:
+    ) -> tuple[ndarray, ndarray, ndarray]:
         """Find all atoms within a provided supercell
 
         Note this function is rather different from `close` and `within`.
@@ -3683,7 +3681,7 @@ def within_inf(
         # infinite supercell indices
         return self.asc2uc(idx), xyz, isc
 
-    def _orbital_values(self, grid_shape: Tuple[int, int, int]):
+    def _orbital_values(self, grid_shape: tuple[int, int, int]):
         r"""Calculates orbital values for a given grid.
 
         Parameters
@@ -4562,15 +4560,12 @@ def dispatch(self, **kwargs):
 
 
 to_dispatch.register("ase", GeometryToAseDispatch)
-try:
+if has_module("ase"):
     from ase import Atoms as ase_Atoms
 
     to_dispatch.register(ase_Atoms, GeometryToAseDispatch)
     del ase_Atoms
 
-except ImportError:
-    pass
-
 
 class GeometryTopymatgenDispatch(GeometryToDispatch):
     def dispatch(self, **kwargs):
@@ -4629,15 +4624,12 @@ def dispatch(self, *args, **kwargs):
 
 
 to_dispatch.register("dataframe", GeometryToDataframeDispatch)
-try:
+if has_module("pandas"):
     from pandas import DataFrame as pd_DataFrame
 
     to_dispatch.register(pd_DataFrame, GeometryToDataframeDispatch)
     del pd_DataFrame
 
-except ImportError:
-    pass
-
 
 # Clean up
 del new_dispatch, to_dispatch

src/sisl/_core/grid.py

@@ -1709,7 +1709,7 @@ def sgrid(grid=None, argv=None, ret_grid=False):
     import sys
     from pathlib import Path
 
-    from sisl.io import BaseSile, get_sile
+    from sisl.io import BaseSile
 
     # The file *MUST* be the first argument
     # (except --help|-h)
@@ -1757,7 +1757,6 @@ def sgrid(grid=None, argv=None, ret_grid=False):
     # First read the input "Sile"
     stdout_grid = True
     if grid is None:
-        from os.path import isfile
 
         argv, input_file = cmd.collect_input(argv)
 

src/sisl/_core/lattice.py

@@ -9,10 +9,11 @@
 
 import logging
 import math
+from collections.abc import Sequence
 from enum import IntEnum, auto
 from numbers import Integral
 from pathlib import Path
-from typing import Optional, Sequence, Tuple, Union
+from typing import Optional, Union
 
 import numpy as np
 from numpy import dot, ndarray
@@ -349,7 +350,7 @@ def conv(v):
 
     def parameters(
         self, rad: bool = False
-    ) -> Tuple[float, float, float, float, float, float]:
+    ) -> tuple[float, float, float, float, float, float]:
         r"""Cell parameters of this cell in 3 lengths and 3 angles
 
         Notes
@@ -609,7 +610,7 @@ def fit(self, xyz, axes: CellAxes = (0, 1, 2), atol: float = 0.05) -> Lattice:
 
     def plane(
         self, axis1: CellAxis, axis2: CellAxis, origin: bool = True
-    ) -> Tuple[ndarray, ndarray]:
+    ) -> tuple[ndarray, ndarray]:
         """Query point and plane-normal for the plane spanning `ax1` and `ax2`
 
         Parameters
@@ -755,7 +756,7 @@ def cell2length(self, length, axes: CellAxes = (0, 1, 2)) -> ndarray:
 
         return self.cell[axes] * (length / self.length[axes]).reshape(-1, 1)
 
-    def offset(self, isc=None) -> Tuple[float, float, float]:
+    def offset(self, isc=None) -> tuple[float, float, float]:
         """Returns the supercell offset of the supercell index"""
         if isc is None:
             return _a.arrayd([0, 0, 0])

src/sisl/_core/orbital.py

@@ -4,18 +4,16 @@
 from __future__ import annotations
 
 from collections import namedtuple
-from collections.abc import Iterable
 from functools import partial
 from math import factorial as fact
 from math import pi
 from math import sqrt as msqrt
 from numbers import Integral, Real
-from typing import Callable, Optional, Tuple
+from typing import Callable, Optional
 
 import numpy as np
 import numpy.typing as npt
-import scipy
-from numpy import cos, sin, sqrt, square, take
+from numpy import cos, sin, take
 from scipy.special import eval_genlaguerre, factorial, lpmv
 
 try:
@@ -341,7 +339,7 @@ def __setstate__(self, d):
 def radial_minimize_range(
     radial_func: Callable[[RadialFuncT], npt.NDArray],
     contains: float,
-    dr: Tuple[float, float] = (0.01, 0.0001),
+    dr: tuple[float, float] = (0.01, 0.0001),
     maxR: float = 100,
     func: Optional[Callable[[RadialFuncT, npt.ArrayLike], npt.NDArray]] = None,
 ) -> float:

src/sisl/_core/sparse_geometry.py

@@ -3,7 +3,6 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-import functools as ftool
 import warnings
 from collections import namedtuple
 from numbers import Integral

src/sisl/_core/tests/test_atom.py

@@ -3,8 +3,6 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-import math as m
-
 import numpy as np
 import pytest
 

src/sisl/_core/tests/test_atoms.py

@@ -3,8 +3,6 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-import math as m
-
 import numpy as np
 import pytest
 

src/sisl/_core/tests/test_geometry.py

@@ -4,8 +4,6 @@
 from __future__ import annotations
 
 import itertools
-import math as m
-import os.path as osp
 
 import numpy as np
 import pytest