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trying to fix circular imports in typing constructs
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Sadly, the register function of singledispatch does
not handle the ForwardRefs very elegantly
as the objects references *needs* to be available
in the global space.
This is rather unfortunate as this is exactly what
we are trying to avoid using __future__ annotations.

I'll have to see later if this causes issues in the
documentation build.

Signed-off-by: Nick Papior <[email protected]>
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@zerothi
zerothi committed Jan 18, 2024
1 parent fa21085 commit 201298e
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Showing 10 changed files with 103 additions and 107 deletions.
12 changes: 12 additions & 0 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,12 +55,14 @@
extensions = [
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"sphinx.ext.coverage",
"sphinx.ext.intersphinx",
"sphinx.ext.extlinks",
"sphinx.ext.mathjax",
"sphinx.ext.napoleon",
"sphinx.ext.todo",
"sphinx.ext.viewcode",
"sphinx_copybutton",
"sphinx_autodoc_typehints",
"sphinxcontrib.jquery", # a bug in 4.1.0 means search didn't work without explicit extension
"sphinx_inline_tabs",
Expand Down Expand Up @@ -240,6 +242,16 @@
# If this is false we do not have double method sections
# numpydoc_show_class_members = False

# Attributes section will be formatted as methods
numpydoc_attributes_as_param_list = False

# Plot directives for matplotlib
plot_include_source = True
plot_formats = [("png", 90)]
plot_pre_code = """\
import numpy as np
import sisl as si"""

# -----------------------------------------------------------------------------
# Intersphinx configuration
# -----------------------------------------------------------------------------
Expand Down
38 changes: 16 additions & 22 deletions src/sisl/_core/_ufuncs_geometry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,32 +5,26 @@

from functools import reduce
from numbers import Integral
from typing import TYPE_CHECKING, Optional, Union
from typing import Optional, Union

import numpy as np

import sisl._array as _a
from sisl._ufuncs import register_sisl_dispatch
from sisl.messages import deprecate_argument, warn
from sisl.typing import AtomsArgument, Coord, CoordOrScalar, LatticeOrGeometryLike
from sisl.utils import direction
from sisl.utils.mathematics import fnorm

from .geometry import Geometry
from .lattice import Lattice
from .quaternion import Quaternion

AtomsArgument = "AtomsArgument"
LatticeOrGeometryLike = "LatticeOrGeometryLike"
Coord = "Coord"
CoordOrScalar = "CoordOrScalar"
if TYPE_CHECKING:
from sisl.typing import AtomsArgument, Coord, CoordOrScalar, LatticeOrGeometryLike

# Nothing gets exposed here
__all__ = []


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def copy(geometry: Geometry) -> Geometry:
"""Create a new object with the same content (a copy)."""
g = geometry.__class__(
Expand All @@ -42,7 +36,7 @@ def copy(geometry: Geometry) -> Geometry:
return g


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def tile(geometry: Geometry, reps: int, axis: int) -> Geometry:
"""Tile the geometry to create a bigger one
Expand Down Expand Up @@ -109,7 +103,7 @@ def tile(geometry: Geometry, reps: int, axis: int) -> Geometry:
return geometry.__class__(xyz, atoms=geometry.atoms.tile(reps), lattice=lattice)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def untile(
geometry: Geometry,
reps: int,
Expand Down Expand Up @@ -187,7 +181,7 @@ def untile(
return new


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def repeat(geometry: Geometry, reps: int, axis: int) -> Geometry:
"""Create a repeated geometry
Expand Down Expand Up @@ -266,7 +260,7 @@ def repeat(geometry: Geometry, reps: int, axis: int) -> Geometry:
return geometry.__class__(xyz, atoms=geometry.atoms.repeat(reps), lattice=lattice)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def unrepeat(geometry: Geometry, reps: int, axis: int, *args, **kwargs) -> Geometry:
"""Unrepeats the geometry similarly as `untile`
Expand All @@ -284,7 +278,7 @@ def unrepeat(geometry: Geometry, reps: int, axis: int, *args, **kwargs) -> Geome
return geometry.sub(atoms).untile(reps, axis, *args, **kwargs)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def translate(
geometry: Geometry,
v: CoordOrScalar,
Expand Down Expand Up @@ -322,7 +316,7 @@ def translate(
Geometry.move = Geometry.translate


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def sub(geometry: Geometry, atoms: AtomsArgument) -> Geometry:
"""Create a new `Geometry` with a subset of this `Geometry`
Expand All @@ -348,7 +342,7 @@ def sub(geometry: Geometry, atoms: AtomsArgument) -> Geometry:
)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def remove(geometry: Geometry, atoms: AtomsArgument) -> Geometry:
"""Remove atoms from the geometry.
Expand All @@ -372,7 +366,7 @@ def remove(geometry: Geometry, atoms: AtomsArgument) -> Geometry:
return geometry.sub(atoms)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
@deprecate_argument(
"only",
"what",
Expand Down Expand Up @@ -490,7 +484,7 @@ def rotate(
return geometry.__class__(xyz, atoms=geometry.atoms.copy(), lattice=lattice)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def swapaxes(
geometry: Geometry,
axes_a: Union[int, str],
Expand Down Expand Up @@ -571,7 +565,7 @@ def swapaxes(
)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def center(
geometry: Geometry, atoms: Optional[AtomsArgument] = None, what: str = "xyz"
) -> np.ndarray:
Expand Down Expand Up @@ -631,7 +625,7 @@ def center(
)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def append(
geometry: Geometry,
other: LatticeOrGeometryLike,
Expand Down Expand Up @@ -719,7 +713,7 @@ def append(
return geometry.__class__(xyz, atoms=atoms, lattice=lattice, names=names)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def prepend(
geometry: Geometry,
other: LatticeOrGeometryLike,
Expand Down Expand Up @@ -807,7 +801,7 @@ def prepend(
return geometry.__class__(xyz, atoms=atoms, lattice=lattice, names=names)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Geometry, module="sisl")
def add(
geometry: Geometry,
other: LatticeOrGeometryLike,
Expand Down
19 changes: 8 additions & 11 deletions src/sisl/_core/_ufuncs_grid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,25 +3,22 @@
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from __future__ import annotations

from typing import TYPE_CHECKING, Optional, Sequence, Union
from typing import Optional, Sequence, 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 GridLike

from .grid import Grid

GridLike = "GridLike"
if TYPE_CHECKING:
from sisl.typing import GridLike

# Nothing gets exposed here
__all__ = []


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Grid, module="sisl")
def copy(grid: Grid, dtype=None):
"""Copy the object, possibly changing the data-type"""
d = grid._sc_geometry_dict()
Expand All @@ -35,7 +32,7 @@ def copy(grid: Grid, dtype=None):
return out


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Grid, module="sisl")
def swapaxes(grid: Grid, axis_a: int, axis_b: int):
"""Swap two axes in the grid (also swaps axes in the lattice)
Expand All @@ -60,7 +57,7 @@ def swapaxes(grid: Grid, axis_a: int, axis_b: int):
return out


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Grid, module="sisl")
def sub(grid: Grid, idx: Union[int, Sequence[int]], axis: int):
"""Retains certain indices from a specified axis.
Expand Down Expand Up @@ -101,7 +98,7 @@ def sub(grid: Grid, idx: Union[int, Sequence[int]], axis: int):
return out


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Grid, module="sisl")
def remove(grid: Grid, idx: Union[int, Sequence[int]], axis: int):
"""Removes certain indices from a specified axis.
Expand All @@ -118,7 +115,7 @@ def remove(grid: Grid, idx: Union[int, Sequence[int]], axis: int):
return grid.sub(ret_idx, axis)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Grid, module="sisl")
def append(grid: Grid, other: GridLike, axis: int):
"""Appends other `Grid` to this grid along axis"""
shape = list(grid.shape)
Expand All @@ -135,7 +132,7 @@ def append(grid: Grid, other: GridLike, axis: int):
return grid.__class__(shape, **d)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Grid, module="sisl")
def tile(grid: Grid, reps: int, axis: int):
"""Tile grid to create a bigger one
Expand Down
27 changes: 12 additions & 15 deletions src/sisl/_core/_ufuncs_lattice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,28 +6,25 @@
import math
from functools import reduce
from numbers import Integral
from typing import TYPE_CHECKING, Optional, Union
from typing import Optional, Union

import numpy as np

import sisl._array as _a
from sisl._ufuncs import register_sisl_dispatch
from sisl.messages import deprecate_argument
from sisl.typing import Coord
from sisl.utils import direction
from sisl.utils.mathematics import fnorm

from .lattice import Lattice
from .quaternion import Quaternion

Coord = "Coord"
if TYPE_CHECKING:
from sisl.typing import Coord

# Nothing gets exposed here
__all__ = []


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def copy(lattice: Lattice, cell=None, origin: Optional[Coord] = None) -> Lattice:
"""A deepcopy of the object
Expand Down Expand Up @@ -57,7 +54,7 @@ def copy(lattice: Lattice, cell=None, origin: Optional[Coord] = None) -> Lattice
return copy


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def swapaxes(
lattice: Lattice,
axes_a: Union[int, str],
Expand Down Expand Up @@ -174,7 +171,7 @@ def swapaxes(
)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
@deprecate_argument(
"only",
"what",
Expand Down Expand Up @@ -228,7 +225,7 @@ def rotate(
return lattice.copy(cell)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def add(lattice: Lattice, other) -> Lattice:
"""Add two supercell lattice vectors to each other
Expand All @@ -245,7 +242,7 @@ def add(lattice: Lattice, other) -> Lattice:
return lattice.__class__(cell, nsc=nsc, origin=origin)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def tile(lattice: Lattice, reps: int, axis: int) -> Lattice:
"""Extend the unit-cell `reps` times along the `axis` lattice vector
Expand Down Expand Up @@ -273,7 +270,7 @@ def tile(lattice: Lattice, reps: int, axis: int) -> Lattice:
return lattice.__class__(cell, nsc=nsc, origin=origin)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def repeat(lattice: Lattice, reps: int, axis: int) -> Lattice:
"""Extend the unit-cell `reps` times along the `axis` lattice vector
Expand All @@ -291,7 +288,7 @@ def repeat(lattice: Lattice, reps: int, axis: int) -> Lattice:
return lattice.tile(reps, axis)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def untile(lattice: Lattice, reps: int, axis: int) -> Lattice:
"""Reverses a `Lattice.tile` and returns the segmented version
Expand All @@ -312,7 +309,7 @@ def untile(lattice: Lattice, reps: int, axis: int) -> Lattice:
Lattice.unrepeat = untile


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def append(lattice: Lattice, other, axis: int) -> Lattice:
"""Appends other `Lattice` to this grid along axis"""
cell = np.copy(lattice.cell)
Expand All @@ -321,7 +318,7 @@ def append(lattice: Lattice, other, axis: int) -> Lattice:
return lattice.copy(cell)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def prepend(lattice: Lattice, other, axis: int) -> Lattice:
"""Prepends other `Lattice` to this grid along axis
Expand All @@ -330,7 +327,7 @@ def prepend(lattice: Lattice, other, axis: int) -> Lattice:
return other.append(lattice, axis)


@register_sisl_dispatch(module="sisl")
@register_sisl_dispatch(Lattice, module="sisl")
def center(lattice: Lattice, axis: Optional[int] = None) -> np.ndarray:
"""Returns center of the `Lattice`, possibly with respect to an axis"""
if axis is None:
Expand Down
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