finalized documentation issues and PEP 585

Signed-off-by: Nick Papior <[email protected]>

docs/api/typing.rst

@@ -13,6 +13,7 @@ The typing types are shown below:
 .. autosummary::
    :toctree: generated/
 
+   AxisIntLiteral
    CellAxisStrLiteral
    CellAxisLiteral
    CartesianAxisStrLiteral
@@ -34,7 +35,9 @@ The typing types are shown below:
 .. autosummary::
    :toctree: generated/
 
+   AtomLike
    AtomsLike
+   CellLike
    Coord
    CoordOrScalar
    FuncType

src/sisl/_core/_ufuncs_geometry.py

@@ -3,9 +3,10 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
+from collections.abc import Callable
 from functools import reduce
 from numbers import Integral
-from typing import Callable, Literal, Optional, Union
+from typing import Literal, Optional, Union
 
 import numpy as np
 

src/sisl/_core/geometry.py

@@ -184,8 +184,8 @@ class Geometry(
     def __init__(
         self,
         xyz: npt.ArrayLike,
-        atoms: AtomsLike = None,
-        lattice: LatticeLike = None,
+        atoms: Optional[AtomsLike] = None,
+        lattice: Optional[LatticeLike] = None,
         names=None,
     ):
         # Create the geometry coordinate, be aware that we do not copy!
@@ -206,7 +206,7 @@ def __init__(
 
         self._init_lattice(lattice)
 
-    def _init_lattice(self, lattice: LatticeLike) -> None:
+    def _init_lattice(self, lattice: Optional[LatticeLike]) -> None:
         """Initializes the supercell by *calculating* the size if not supplied
 
         If the supercell has not been passed we estimate the unit cell size

src/sisl/_environ.py

@@ -4,10 +4,11 @@
 from __future__ import annotations
 
 import os
+from collections.abc import Callable
 from contextlib import contextmanager
 from pathlib import Path
 from textwrap import dedent
-from typing import Any, Callable
+from typing import Any
 
 __all__ = ["register_environ_variable", "get_environ_variable", "sisl_environ"]
 

src/sisl/io/_exceptions.py

@@ -4,8 +4,9 @@
 from __future__ import annotations
 
 import warnings
+from collections.abc import Callable
 from functools import wraps
-from typing import Callable, Optional, Union
+from typing import Optional, Union
 
 from sisl._internal import set_module
 from sisl.messages import SislError, SislException, SislInfo, SislWarning, info, warn

src/sisl/io/_multiple.py

@@ -3,11 +3,12 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
+from collections.abc import Callable
 from functools import reduce, update_wrapper
 from itertools import zip_longest
 from numbers import Integral
 from textwrap import dedent
-from typing import Any, Callable, Optional
+from typing import Any, Optional
 
 Func = Callable[..., Optional[Any]]
 

src/sisl/io/sile.py

@@ -6,14 +6,15 @@
 import gzip
 import logging
 import re
+from collections.abc import Callable
 from functools import wraps
 from io import TextIOBase
 from itertools import product
 from operator import contains
 from os.path import basename, splitext
 from pathlib import Path
 from textwrap import dedent, indent
-from typing import Any, Callable, Optional, Union
+from typing import Any, Optional, Union
 
 import sisl.io._exceptions as _exceptions
 from sisl._environ import get_environ_variable

src/sisl/mixing/base.py

@@ -6,9 +6,9 @@
 import operator as op
 from abc import abstractmethod
 from collections import deque
-from collections.abc import Iterator, Sequence
+from collections.abc import Callable, Iterator, Sequence
 from numbers import Integral
-from typing import Any, Callable, Optional, TypeVar, Union
+from typing import Any, Optional, TypeVar, Union
 
 from sisl._internal import set_module
 

src/sisl/physics/electron.py

@@ -44,8 +44,9 @@
 """
 from __future__ import annotations
 
+from collections.abc import Callable
 from functools import reduce
-from typing import TYPE_CHECKING, Callable, Literal, Optional, Union
+from typing import TYPE_CHECKING, Literal, Optional, Union
 
 import numpy as np
 import numpy.typing as npt

src/sisl/physics/state.py

@@ -3,8 +3,9 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
+from collections.abc import Callable
 from functools import singledispatchmethod
-from typing import Callable, Literal, Optional
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt

src/sisl/typing/_common.py

@@ -3,8 +3,8 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-from collections.abc import Sequence
-from typing import TYPE_CHECKING, Any, Callable, Union
+from collections.abc import Callable, Sequence
+from typing import TYPE_CHECKING, Any, Union
 
 import scipy.sparse as sps
 
@@ -19,7 +19,6 @@
     "CoordOrScalar",
     "FuncType",
     "KPoint",
-    "LatticeOrGeometry",
     "SeqFloat",
     "SeqOrScalarFloat",
     "SparseMatrix",
@@ -38,11 +37,6 @@
 # Short for *any* function
 FuncType = Callable[..., Any]
 
-LatticeOrGeometry = Union[
-    "Lattice",
-    "Geometry",
-]
-
 if hasattr(sps, "sparray"):
     SparseMatrixExt = Union[
         sps.spmatrix,

src/sisl/typing/_core.py

@@ -19,6 +19,7 @@
     "CellLike",
     "GeometryLike",
     "LatticeLike",
+    "LatticeOrGeometry",
     "LatticeOrGeometryLike",
     "GridLike",
 ]
@@ -50,6 +51,11 @@
 """Data-types that can be converted to a `Grid`"""
 
 
+LatticeOrGeometry = Union[
+    "Lattice",
+    "Geometry",
+]
+
 LatticeOrGeometryLike = Union[
     LatticeLike,
     GeometryLike,

src/sisl/viz/plots/geometry.py

@@ -3,8 +3,8 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-from collections.abc import Sequence
-from typing import Callable, Literal, Optional, TypeVar, Union
+from collections.abc import Callable, Sequence
+from typing import Literal, Optional, TypeVar, Union
 
 import numpy as np
 

src/sisl/viz/plots/grid.py

@@ -4,8 +4,8 @@
 from __future__ import annotations
 
 from collections import ChainMap
-from collections.abc import Sequence
-from typing import Callable, Literal, Optional, Union
+from collections.abc import Callable, Sequence
+from typing import Literal, Optional, Union
 
 from sisl._core import Geometry, Grid
 

src/sisl/viz/processors/atom.py

@@ -3,8 +3,8 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-from collections.abc import Sequence
-from typing import Any, Callable, Optional, Union
+from collections.abc import Callable, Sequence
+from typing import Any, Optional, Union
 
 import numpy as np
 from xarray import DataArray, Dataset

src/sisl/viz/processors/axes.py

@@ -4,8 +4,8 @@
 from __future__ import annotations
 
 import re
-from collections.abc import Sequence
-from typing import Callable, Optional, Union
+from collections.abc import Callable, Sequence
+from typing import Optional, Union
 
 import numpy as np
 

src/sisl/viz/processors/coords.py

@@ -3,7 +3,8 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-from typing import Callable, Optional, Union
+from collections.abc import Callable
+from typing import Optional, Union
 
 import numpy as np
 import numpy.typing as npt

src/sisl/viz/processors/grid.py

@@ -3,8 +3,8 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from __future__ import annotations
 
-from collections.abc import Sequence
-from typing import Callable, Literal, Optional, Union
+from collections.abc import Callable, Sequence
+from typing import Literal, Optional, Union
 
 import numpy as np
 import numpy.typing as npt

src/sisl/viz/processors/orbital.py

@@ -5,10 +5,10 @@
 # from __future__ import annotations
 
 from collections import ChainMap, defaultdict
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from dataclasses import asdict, is_dataclass
 from pathlib import Path
-from typing import Any, Callable, Optional, TypedDict, Union
+from typing import Any, Optional, TypedDict, Union
 
 import numpy as np
 import xarray

src/sisl/viz/processors/xarray.py

@@ -5,9 +5,9 @@
 # from __future__ import annotations
 
 from collections import defaultdict
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from functools import singledispatchmethod
-from typing import Any, Callable, Optional, TypedDict, Union
+from typing import Any, Optional, TypedDict, Union
 
 import numpy as np
 import xarray as xr

src/sisl_toolbox/cli/_cli.py

@@ -11,8 +11,8 @@
 
 import argparse
 import sys
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable
 
 
 class SToolBoxCLI: