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Merge branch 'fix-mypy-no-implicit-optional' into 'development' 

PEP 484 compatibility (no-implicit-optional in mypy)

See merge request damask/DAMASK!664
This commit is contained in:
Martin Diehl 2022-11-25 21:25:33 +00:00
parent 8993b5caac 6315f97f4a
commit 92ae86b636
12 changed files with 141 additions and 138 deletions
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16
python/damask/_colormap.py
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@ -2,7 +2,7 @@ import os
import json import json
import functools import functools
import colorsys import colorsys
from typing import Union, TextIO from typing import Optional, Union, TextIO
from itertools import chain from itertools import chain
import numpy as np import numpy as np
@ -275,8 +275,8 @@ class Colormap(mpl.colors.ListedColormap):
def shade(self, def shade(self,
field: np.ndarray, field: np.ndarray,
bounds: FloatSequence = None, bounds: Optional[FloatSequence] = None,
gap: float = None) -> Image: gap: Optional[float] = None) -> Image:
""" """
Generate PIL image of 2D field using colormap. Generate PIL image of 2D field using colormap.
@ -315,7 +315,7 @@ class Colormap(mpl.colors.ListedColormap):
def reversed(self, def reversed(self,
name: str = None) -> 'Colormap': name: Optional[str] = None) -> 'Colormap':
""" """
Reverse. Reverse.
@ -364,7 +364,7 @@ class Colormap(mpl.colors.ListedColormap):
def save_paraview(self, def save_paraview(self,
fname: FileHandle = None): fname: Optional[FileHandle] = None):
""" """
Save as JSON file for use in Paraview. Save as JSON file for use in Paraview.
@ -388,7 +388,7 @@ class Colormap(mpl.colors.ListedColormap):
def save_ASCII(self, def save_ASCII(self,
fname: FileHandle = None): fname: Optional[FileHandle] = None):
""" """
Save as ASCII file. Save as ASCII file.
@ -403,7 +403,7 @@ class Colormap(mpl.colors.ListedColormap):
t.save(self._get_file_handle(fname,'.txt')) t.save(self._get_file_handle(fname,'.txt'))
def save_GOM(self, fname: FileHandle = None): def save_GOM(self, fname: Optional[FileHandle] = None):
""" """
Save as ASCII file for use in GOM Aramis. Save as ASCII file for use in GOM Aramis.
@ -424,7 +424,7 @@ class Colormap(mpl.colors.ListedColormap):
def save_gmsh(self, def save_gmsh(self,
fname: FileHandle = None): fname: Optional[FileHandle] = None):
""" """
Save as ASCII file for use in gmsh. Save as ASCII file for use in gmsh.

6
python/damask/_config.py
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@ -2,7 +2,7 @@ import copy
from io import StringIO from io import StringIO
from collections.abc import Iterable from collections.abc import Iterable
import abc import abc
from typing import Union, Dict, Any, Type, TypeVar from typing import Optional, Union, Dict, Any, Type, TypeVar
import numpy as np import numpy as np
import yaml import yaml
@ -21,7 +21,7 @@ class NiceDumper(yaml.SafeDumper):
"""Make YAML readable for humans.""" """Make YAML readable for humans."""
def write_line_break(self, def write_line_break(self,
data: str = None): data: Optional[str] = None):
super().write_line_break(data) super().write_line_break(data)
if len(self.indents) == 1: if len(self.indents) == 1:
@ -53,7 +53,7 @@ class Config(dict):
"""YAML-based configuration.""" """YAML-based configuration."""
def __init__(self, def __init__(self,
yml: Union[str, Dict[str, Any]] = None, yml: Union[None, str, Dict[str, Any]] = None,
**kwargs): **kwargs):
"""Initialize from YAML, dict, or key=value pairs.""" """Initialize from YAML, dict, or key=value pairs."""
if isinstance(yml,str): if isinstance(yml,str):

16
python/damask/_configmaterial.py
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@ -1,6 +1,6 @@
import numpy as np import numpy as np
import h5py import h5py
from typing import Union, Sequence, Dict, Any, Collection from typing import Optional, Union, Sequence, Dict, Any, Collection
from ._typehints import FileHandle from ._typehints import FileHandle
from . import Config from . import Config
@ -22,7 +22,7 @@ class ConfigMaterial(Config):
""" """
def __init__(self, def __init__(self,
d: Dict[str, Any] = None, d: Optional[Dict[str, Any]] = None,
**kwargs): **kwargs):
""" """
New material configuration. New material configuration.
@ -83,13 +83,13 @@ class ConfigMaterial(Config):
@staticmethod @staticmethod
def load_DREAM3D(fname: str, def load_DREAM3D(fname: str,
grain_data: str = None, grain_data: Optional[str] = None,
cell_data: str = None, cell_data: Optional[str] = None,
cell_ensemble_data: str = 'CellEnsembleData', cell_ensemble_data: str = 'CellEnsembleData',
phases: str = 'Phases', phases: str = 'Phases',
Euler_angles: str = 'EulerAngles', Euler_angles: str = 'EulerAngles',
phase_names: str = 'PhaseName', phase_names: str = 'PhaseName',
base_group: str = None) -> 'ConfigMaterial': base_group: Optional[str] = None) -> 'ConfigMaterial':
""" """
Load DREAM.3D (HDF5) file. Load DREAM.3D (HDF5) file.
@ -354,8 +354,8 @@ class ConfigMaterial(Config):
def material_rename_phase(self, def material_rename_phase(self,
mapping: Dict[str, str], mapping: Dict[str, str],
ID: Sequence[int] = None, ID: Optional[Sequence[int]] = None,
constituent: Sequence[int] = None) -> 'ConfigMaterial': constituent: Optional[Sequence[int]] = None) -> 'ConfigMaterial':
""" """
Change phase name in material. Change phase name in material.
@ -388,7 +388,7 @@ class ConfigMaterial(Config):
def material_rename_homogenization(self, def material_rename_homogenization(self,
mapping: Dict[str, str], mapping: Dict[str, str],
ID: Sequence[int] = None) -> 'ConfigMaterial': ID: Optional[Sequence[int]] = None) -> 'ConfigMaterial':
""" """
Change homogenization name in material. Change homogenization name in material.

18
python/damask/_crystal.py
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@ -1,4 +1,4 @@
from typing import Union, Dict, List, Tuple from typing import Optional, Union, Dict, List, Tuple
import numpy as np import numpy as np
@ -324,10 +324,10 @@ class Crystal():
""" """
def __init__(self, *, def __init__(self, *,
family: CrystalFamily = None, family: Optional[CrystalFamily] = None,
lattice: CrystalLattice = None, lattice: Optional[CrystalLattice] = None,
a: float = None, b: float = None, c: float = None, a: Optional[float] = None, b: Optional[float] = None, c: Optional[float] = None,
alpha: float = None, beta: float = None, gamma: float = None, alpha: Optional[float] = None, beta: Optional[float] = None, gamma: Optional[float] = None,
degrees: bool = False): degrees: bool = False):
""" """
New representation of a crystal. New representation of a crystal.
@ -690,8 +690,8 @@ class Crystal():
self.lattice[-1],None),dtype=float) self.lattice[-1],None),dtype=float)
def to_lattice(self, *, def to_lattice(self, *,
direction: FloatSequence = None, direction: Optional[FloatSequence] = None,
plane: FloatSequence = None) -> np.ndarray: plane: Optional[FloatSequence] = None) -> np.ndarray:
""" """
Calculate lattice vector corresponding to crystal frame direction or plane normal. Calculate lattice vector corresponding to crystal frame direction or plane normal.
@ -717,8 +717,8 @@ class Crystal():
def to_frame(self, *, def to_frame(self, *,
uvw: FloatSequence = None, uvw: Optional[FloatSequence] = None,
hkl: FloatSequence = None) -> np.ndarray: hkl: Optional[FloatSequence] = None) -> np.ndarray:
""" """
Calculate crystal frame vector corresponding to lattice direction [uvw] or plane normal (hkl). Calculate crystal frame vector corresponding to lattice direction [uvw] or plane normal (hkl).

36
python/damask/_grid.py
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@ -4,7 +4,7 @@ import warnings
import multiprocessing as mp import multiprocessing as mp
from functools import partial from functools import partial
import typing import typing
from typing import Union, Optional, TextIO, List, Sequence, Dict from typing import Optional, Union, TextIO, List, Sequence, Dict
from pathlib import Path from pathlib import Path
import numpy as np import numpy as np
@ -34,8 +34,8 @@ class Grid:
material: np.ndarray, material: np.ndarray,
size: FloatSequence, size: FloatSequence,
origin: FloatSequence = np.zeros(3), origin: FloatSequence = np.zeros(3),
initial_conditions: Dict[str,np.ndarray] = None, initial_conditions: Optional[Dict[str,np.ndarray]] = None,
comments: Union[str, Sequence[str]] = None): comments: Union[None, str, Sequence[str]] = None):
""" """
New geometry definition for grid solvers. New geometry definition for grid solvers.
@ -348,9 +348,11 @@ class Grid:
@staticmethod @staticmethod
def load_DREAM3D(fname: Union[str, Path], def load_DREAM3D(fname: Union[str, Path],
feature_IDs: str = None, cell_data: str = None, feature_IDs: Optional[str] = None,
phases: str = 'Phases', Euler_angles: str = 'EulerAngles', cell_data: Optional[str] = None,
base_group: str = None) -> 'Grid': phases: str = 'Phases',
Euler_angles: str = 'EulerAngles',
base_group: Optional[str] = None) -> 'Grid':
""" """
Load DREAM.3D (HDF5) file. Load DREAM.3D (HDF5) file.
@ -463,7 +465,7 @@ class Grid:
size: FloatSequence, size: FloatSequence,
seeds: np.ndarray, seeds: np.ndarray,
weights: FloatSequence, weights: FloatSequence,
material: IntSequence = None, material: Optional[IntSequence] = None,
periodic: bool = True): periodic: bool = True):
""" """
Create grid from Laguerre tessellation. Create grid from Laguerre tessellation.
@ -520,7 +522,7 @@ class Grid:
def from_Voronoi_tessellation(cells: IntSequence, def from_Voronoi_tessellation(cells: IntSequence,
size: FloatSequence, size: FloatSequence,
seeds: np.ndarray, seeds: np.ndarray,
material: IntSequence = None, material: Optional[IntSequence] = None,
periodic: bool = True) -> 'Grid': periodic: bool = True) -> 'Grid':
""" """
Create grid from Voronoi tessellation. Create grid from Voronoi tessellation.
@ -763,9 +765,9 @@ class Grid:
def canvas(self, def canvas(self,
cells: IntSequence = None, cells: Optional[IntSequence] = None,
offset: IntSequence = None, offset: Optional[IntSequence] = None,
fill: int = None) -> 'Grid': fill: Optional[int] = None) -> 'Grid':
""" """
Crop or enlarge/pad grid. Crop or enlarge/pad grid.
@ -901,7 +903,7 @@ class Grid:
def rotate(self, def rotate(self,
R: Rotation, R: Rotation,
fill: int = None) -> 'Grid': fill: Optional[int] = None) -> 'Grid':
""" """
Rotate grid (and pad if required). Rotate grid (and pad if required).
@ -1093,10 +1095,10 @@ class Grid:
def clean(self, def clean(self,
distance: float = np.sqrt(3), distance: float = np.sqrt(3),
selection: IntCollection = None, selection: Optional[IntCollection] = None,
invert_selection: bool = False, invert_selection: bool = False,
periodic: bool = True, periodic: bool = True,
rng_seed: NumpyRngSeed = None) -> 'Grid': rng_seed: Optional[NumpyRngSeed] = None) -> 'Grid':
""" """
Smooth grid by selecting most frequent material ID within given stencil at each location. Smooth grid by selecting most frequent material ID within given stencil at each location.
@ -1163,7 +1165,7 @@ class Grid:
dimension: Union[FloatSequence, IntSequence], dimension: Union[FloatSequence, IntSequence],
center: Union[FloatSequence, IntSequence], center: Union[FloatSequence, IntSequence],
exponent: Union[FloatSequence, float], exponent: Union[FloatSequence, float],
fill: int = None, fill: Optional[int] = None,
R: Rotation = Rotation(), R: Rotation = Rotation(),
inverse: bool = False, inverse: bool = False,
periodic: bool = True) -> 'Grid': periodic: bool = True) -> 'Grid':
@ -1254,8 +1256,8 @@ class Grid:
def vicinity_offset(self, def vicinity_offset(self,
distance: float = np.sqrt(3), distance: float = np.sqrt(3),
offset: int = None, offset: Optional[int] = None,
selection: IntCollection = None, selection: Optional[IntCollection] = None,
invert_selection: bool = False, invert_selection: bool = False,
periodic: bool = True) -> 'Grid': periodic: bool = True) -> 'Grid':
""" """

22
python/damask/_orientation.py
View File

@ -1,6 +1,6 @@
import inspect import inspect
import copy import copy
from typing import Union, Callable, Dict, Any, Tuple, TypeVar from typing import Optional, Union, Callable, Dict, Any, Tuple, TypeVar
import numpy as np import numpy as np
@ -98,10 +98,10 @@ class Orientation(Rotation,Crystal):
def __init__(self, def __init__(self,
rotation: Union[FloatSequence, Rotation] = np.array([1.,0.,0.,0.]), rotation: Union[FloatSequence, Rotation] = np.array([1.,0.,0.,0.]),
*, *,
family: CrystalFamily = None, family: Optional[CrystalFamily] = None,
lattice: CrystalLattice = None, lattice: Optional[CrystalLattice] = None,
a: float = None, b: float = None, c: float = None, a: Optional[float] = None, b: Optional[float] = None, c: Optional[float] = None,
alpha: float = None, beta: float = None, gamma: float = None, alpha: Optional[float] = None, beta: Optional[float] = None, gamma: Optional[float] = None,
degrees: bool = False): degrees: bool = False):
""" """
New orientation. New orientation.
@ -131,7 +131,7 @@ class Orientation(Rotation,Crystal):
def __copy__(self: MyType, def __copy__(self: MyType,
rotation: Union[FloatSequence, Rotation] = None) -> MyType: rotation: Union[None, FloatSequence, Rotation] = None) -> MyType:
""" """
Return deepcopy(self). Return deepcopy(self).
@ -617,7 +617,7 @@ class Orientation(Rotation,Crystal):
def average(self, def average(self,
weights: FloatSequence = None, weights: Optional[FloatSequence] = None,
return_cloud: bool = False): return_cloud: bool = False):
""" """
Return orientation average over last dimension. Return orientation average over last dimension.
@ -819,8 +819,8 @@ class Orientation(Rotation,Crystal):
# functions that require lattice, not just family # functions that require lattice, not just family
def to_pole(self, *, def to_pole(self, *,
uvw: FloatSequence = None, uvw: Optional[FloatSequence] = None,
hkl: FloatSequence = None, hkl: Optional[FloatSequence] = None,
with_symmetry: bool = False, with_symmetry: bool = False,
normalize: bool = True) -> np.ndarray: normalize: bool = True) -> np.ndarray:
""" """
@ -861,8 +861,8 @@ class Orientation(Rotation,Crystal):
def Schmid(self, *, def Schmid(self, *,
N_slip: IntSequence = None, N_slip: Optional[IntSequence] = None,
N_twin: IntSequence = None) -> np.ndarray: N_twin: Optional[IntSequence] = None) -> np.ndarray:
u""" u"""
Calculate Schmid matrix P = d ⨂ n in the lab frame for selected deformation systems. Calculate Schmid matrix P = d ⨂ n in the lab frame for selected deformation systems.

72
python/damask/_result.py
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@ -11,7 +11,7 @@ from pathlib import Path
from functools import partial from functools import partial
from collections import defaultdict from collections import defaultdict
from collections.abc import Iterable from collections.abc import Iterable
from typing import Union, Callable, Any, Sequence, Literal, Dict, List, Tuple, Optional from typing import Optional, Union, Callable, Any, Sequence, Literal, Dict, List, Tuple
import h5py import h5py
import numpy as np import numpy as np
@ -189,11 +189,11 @@ class Result:
def _manage_view(self, def _manage_view(self,
action: Literal['set', 'add', 'del'], action: Literal['set', 'add', 'del'],
increments: Union[int, Sequence[int], str, Sequence[str], bool] = None, increments: Union[None, int, Sequence[int], str, Sequence[str], bool] = None,
times: Union[float, Sequence[float], str, Sequence[str], bool] = None, times: Union[None, float, Sequence[float], str, Sequence[str], bool] = None,
phases: Union[str, Sequence[str], bool] = None, phases: Union[None, str, Sequence[str], bool] = None,
homogenizations: Union[str, Sequence[str], bool] = None, homogenizations: Union[None, str, Sequence[str], bool] = None,
fields: Union[str, Sequence[str], bool] = None) -> "Result": fields: Union[None, str, Sequence[str], bool] = None) -> "Result":
""" """
Manages the visibility of the groups. Manages the visibility of the groups.
@ -256,8 +256,8 @@ class Result:
def increments_in_range(self, def increments_in_range(self,
start: Union[str, int] = None, start: Union[None, str, int] = None,
end: Union[str, int] = None) -> Sequence[int]: end: Union[None, str, int] = None) -> Sequence[int]:
""" """
Get all increments within a given range. Get all increments within a given range.
@ -280,8 +280,8 @@ class Result:
return [i for i in self.incs if s <= i <= e] return [i for i in self.incs if s <= i <= e]
def times_in_range(self, def times_in_range(self,
start: float = None, start: Optional[float] = None,
end: float = None) -> Sequence[float]: end: Optional[float] = None) -> Sequence[float]:
""" """
Get times of all increments within a given time range. Get times of all increments within a given time range.
@ -304,12 +304,12 @@ class Result:
def view(self,*, def view(self,*,
increments: Union[int, Sequence[int], str, Sequence[str], bool] = None, increments: Union[None, int, Sequence[int], str, Sequence[str], bool] = None,
times: Union[float, Sequence[float], str, Sequence[str], bool] = None, times: Union[None, float, Sequence[float], str, Sequence[str], bool] = None,
phases: Union[str, Sequence[str], bool] = None, phases: Union[None, str, Sequence[str], bool] = None,
homogenizations: Union[str, Sequence[str], bool] = None, homogenizations: Union[None, str, Sequence[str], bool] = None,
fields: Union[str, Sequence[str], bool] = None, fields: Union[None, str, Sequence[str], bool] = None,
protected: bool = None) -> "Result": protected: Optional[bool] = None) -> "Result":
""" """
Set view. Set view.
@ -361,11 +361,11 @@ class Result:
def view_more(self,*, def view_more(self,*,
increments: Union[int, Sequence[int], str, Sequence[str], bool] = None, increments: Union[None, int, Sequence[int], str, Sequence[str], bool] = None,
times: Union[float, Sequence[float], str, Sequence[str], bool] = None, times: Union[None, float, Sequence[float], str, Sequence[str], bool] = None,
phases: Union[str, Sequence[str], bool] = None, phases: Union[None, str, Sequence[str], bool] = None,
homogenizations: Union[str, Sequence[str], bool] = None, homogenizations: Union[None, str, Sequence[str], bool] = None,
fields: Union[str, Sequence[str], bool] = None) -> "Result": fields: Union[None, str, Sequence[str], bool] = None) -> "Result":
""" """
Add to view. Add to view.
@ -404,11 +404,11 @@ class Result:
def view_less(self,*, def view_less(self,*,
increments: Union[int, Sequence[int], str, Sequence[str], bool] = None, increments: Union[None, int, Sequence[int], str, Sequence[str], bool] = None,
times: Union[float, Sequence[float], str, Sequence[str], bool] = None, times: Union[None, float, Sequence[float], str, Sequence[str], bool] = None,
phases: Union[str, Sequence[str], bool] = None, phases: Union[None, str, Sequence[str], bool] = None,
homogenizations: Union[str, Sequence[str], bool] = None, homogenizations: Union[None, str, Sequence[str], bool] = None,
fields: Union[str, Sequence[str], bool] = None) -> "Result": fields: Union[None, str, Sequence[str], bool] = None) -> "Result":
""" """
Remove from view. Remove from view.
@ -650,7 +650,7 @@ class Result:
formula: str, formula: str,
name: str, name: str,
unit: str = 'n/a', unit: str = 'n/a',
description: str = None): description: Optional[str] = None):
""" """
Add result of a general formula. Add result of a general formula.
@ -966,7 +966,7 @@ class Result:
} }
def add_equivalent_Mises(self, def add_equivalent_Mises(self,
T_sym: str, T_sym: str,
kind: str = None): kind: Optional[str] = None):
""" """
Add the equivalent Mises stress or strain of a symmetric tensor. Add the equivalent Mises stress or strain of a symmetric tensor.
@ -1021,7 +1021,7 @@ class Result:
} }
def add_norm(self, def add_norm(self,
x: str, x: str,
ord: Union[int, float, Literal['fro', 'nuc']] = None): ord: Union[None, int, float, Literal['fro', 'nuc']] = None):
""" """
Add the norm of vector or tensor. Add the norm of vector or tensor.
@ -1101,8 +1101,8 @@ class Result:
def add_pole(self, def add_pole(self,
q: str = 'O', q: str = 'O',
*, *,
uvw: FloatSequence = None, uvw: Optional[FloatSequence] = None,
hkl: FloatSequence = None, hkl: Optional[FloatSequence] = None,
with_symmetry: bool = False, with_symmetry: bool = False,
normalize: bool = True): normalize: bool = True):
""" """
@ -1593,7 +1593,7 @@ class Result:
output: Union[str, List[str]] = '*', output: Union[str, List[str]] = '*',
flatten: bool = True, flatten: bool = True,
prune: bool = True, prune: bool = True,
constituents: IntSequence = None, constituents: Optional[IntSequence] = None,
fill_float: float = np.nan, fill_float: float = np.nan,
fill_int: int = 0) -> Optional[Dict[str,Any]]: fill_int: int = 0) -> Optional[Dict[str,Any]]:
""" """
@ -1683,7 +1683,7 @@ class Result:
def export_XDMF(self, def export_XDMF(self,
output: Union[str, List[str]] = '*', output: Union[str, List[str]] = '*',
target_dir: Union[str, Path] = None, target_dir: Union[None, str, Path] = None,
absolute_path: bool = False): absolute_path: bool = False):
""" """
Write XDMF file to directly visualize data from DADF5 file. Write XDMF file to directly visualize data from DADF5 file.
@ -1811,8 +1811,8 @@ class Result:
def export_VTK(self, def export_VTK(self,
output: Union[str,List[str]] = '*', output: Union[str,List[str]] = '*',
mode: str = 'cell', mode: str = 'cell',
constituents: IntSequence = None, constituents: Optional[IntSequence] = None,
target_dir: Union[str, Path] = None, target_dir: Union[None, str, Path] = None,
fill_float: float = np.nan, fill_float: float = np.nan,
fill_int: int = 0, fill_int: int = 0,
parallel: bool = True): parallel: bool = True):
@ -1958,7 +1958,7 @@ class Result:
def export_simulation_setup(self, def export_simulation_setup(self,
output: Union[str, List[str]] = '*', output: Union[str, List[str]] = '*',
target_dir: Union[str, Path] = None, target_dir: Union[None, str, Path] = None,
overwrite: bool = False, overwrite: bool = False,
): ):
""" """

22
python/damask/_rotation.py
View File

@ -1,5 +1,5 @@
import copy import copy
from typing import Union, Sequence, Tuple, Literal, List, TypeVar from typing import Optional, Union, Sequence, Tuple, Literal, List, TypeVar
import numpy as np import numpy as np
@ -99,7 +99,7 @@ class Rotation:
def __copy__(self: MyType, def __copy__(self: MyType,
rotation: Union[FloatSequence, 'Rotation'] = None) -> MyType: rotation: Union[None, FloatSequence, 'Rotation'] = None) -> MyType:
""" """
Return deepcopy(self). Return deepcopy(self).
@ -514,7 +514,7 @@ class Rotation:
def average(self: MyType, def average(self: MyType,
weights: FloatSequence = None) -> MyType: weights: Optional[FloatSequence] = None) -> MyType:
""" """
Average along last array dimension. Average along last array dimension.
@ -1044,8 +1044,8 @@ class Rotation:
@staticmethod @staticmethod
def from_random(shape: Union[int, IntSequence] = None, def from_random(shape: Union[None, int, IntSequence] = None,
rng_seed: NumpyRngSeed = None) -> 'Rotation': rng_seed: Optional[NumpyRngSeed] = None) -> 'Rotation':
""" """
Initialize with samples from a uniform distribution. Initialize with samples from a uniform distribution.
@ -1078,10 +1078,10 @@ class Rotation:
@staticmethod @staticmethod
def from_ODF(weights: np.ndarray, def from_ODF(weights: np.ndarray,
phi: np.ndarray, phi: np.ndarray,
shape: Union[int, IntSequence] = None, shape: Union[None, int, IntSequence] = None,
degrees: bool = False, degrees: bool = False,
fractions: bool = True, fractions: bool = True,
rng_seed: NumpyRngSeed = None) -> 'Rotation': rng_seed: Optional[NumpyRngSeed] = None) -> 'Rotation':
""" """
Initialize with samples from a binned orientation distribution function (ODF). Initialize with samples from a binned orientation distribution function (ODF).
@ -1135,9 +1135,9 @@ class Rotation:
@staticmethod @staticmethod
def from_spherical_component(center: 'Rotation', def from_spherical_component(center: 'Rotation',
sigma: float, sigma: float,
shape: Union[int, IntSequence] = None, shape: Union[None, int, IntSequence] = None,
degrees: bool = False, degrees: bool = False,
rng_seed: NumpyRngSeed = None) -> 'Rotation': rng_seed: Optional[NumpyRngSeed] = None) -> 'Rotation':
""" """
Initialize with samples from a Gaussian distribution around a given center. Initialize with samples from a Gaussian distribution around a given center.
@ -1188,9 +1188,9 @@ class Rotation:
def from_fiber_component(crystal: IntSequence, def from_fiber_component(crystal: IntSequence,
sample: IntSequence, sample: IntSequence,
sigma: float = 0., sigma: float = 0.,
shape: Union[int, IntSequence] = None, shape: Union[None, int, IntSequence] = None,
degrees: bool = False, degrees: bool = False,
rng_seed: NumpyRngSeed = None) -> 'Rotation': rng_seed: Optional[NumpyRngSeed] = None) -> 'Rotation':
""" """
Initialize with samples from a Gaussian distribution around a given direction. Initialize with samples from a Gaussian distribution around a given direction.

12
python/damask/_table.py
View File

@ -1,6 +1,6 @@
import re import re
import copy import copy
from typing import Union, Tuple, List, Iterable from typing import Optional, Union, Tuple, List, Iterable
import pandas as pd import pandas as pd
import numpy as np import numpy as np
@ -13,8 +13,8 @@ class Table:
def __init__(self, def __init__(self,
shapes: dict = {}, shapes: dict = {},
data: np.ndarray = None, data: Optional[np.ndarray] = None,
comments: Union[str, Iterable[str]] = None): comments: Union[None, str, Iterable[str]] = None):
""" """
New spreadsheet. New spreadsheet.
@ -188,7 +188,7 @@ class Table:
def _add_comment(self, def _add_comment(self,
label: str, label: str,
shape: Tuple[int, ...], shape: Tuple[int, ...],
info: str = None): info: Optional[str] = None):
if info is not None: if info is not None:
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=np.int64) > 1 else ""}: {info}' specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=np.int64) > 1 else ""}: {info}'
general = util.execution_stamp('Table') general = util.execution_stamp('Table')
@ -383,7 +383,7 @@ class Table:
def set(self, def set(self,
label: str, label: str,
data: np.ndarray, data: np.ndarray,
info: str = None) -> 'Table': info: Optional[str] = None) -> 'Table':
""" """
Add new or replace existing column data. Add new or replace existing column data.
@ -458,7 +458,7 @@ class Table:
def rename(self, def rename(self,
old: Union[str, Iterable[str]], old: Union[str, Iterable[str]],
new: Union[str, Iterable[str]], new: Union[str, Iterable[str]],
info: str = None) -> 'Table': info: Optional[str] = None) -> 'Table':
""" """
Rename column data. Rename column data.

14
python/damask/_vtk.py
View File

@ -1,7 +1,7 @@
import os import os
import multiprocessing as mp import multiprocessing as mp
from pathlib import Path from pathlib import Path
from typing import Union, Literal, List, Sequence from typing import Optional, Union, Literal, List, Sequence
import numpy as np import numpy as np
import vtk import vtk
@ -286,7 +286,7 @@ class VTK:
@staticmethod @staticmethod
def load(fname: Union[str, Path], def load(fname: Union[str, Path],
dataset_type: Literal['ImageData', 'UnstructuredGrid', 'PolyData', 'RectilinearGrid'] = None) -> 'VTK': dataset_type: Literal[None, 'ImageData', 'UnstructuredGrid', 'PolyData', 'RectilinearGrid'] = None) -> 'VTK':
""" """
Load from VTK file. Load from VTK file.
@ -409,11 +409,11 @@ class VTK:
# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data # Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
def set(self, def set(self,
label: str = None, label: Optional[str] = None,
data: Union[np.ndarray, np.ma.MaskedArray] = None, data: Union[None, np.ndarray, np.ma.MaskedArray] = None,
info: str = None, info: Optional[str] = None,
*, *,
table: 'Table' = None): table: Optional['Table'] = None):
""" """
Add new or replace existing point or cell data. Add new or replace existing point or cell data.
@ -533,7 +533,7 @@ class VTK:
def show(self, def show(self,
label: str = None, label: Optional[str] = None,
colormap: Union[Colormap, str] = 'cividis'): colormap: Union[Colormap, str] = 'cividis'):
""" """
Render. Render.

10
python/damask/seeds.py
View File

@ -1,6 +1,6 @@
"""Functionality for generation of seed points for Voronoi or Laguerre tessellation.""" """Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
from typing import Tuple as _Tuple from typing import Optional as _Optional, Tuple as _Tuple
from scipy import spatial as _spatial from scipy import spatial as _spatial
import numpy as _np import numpy as _np
@ -13,8 +13,8 @@ from . import grid_filters as _grid_filters
def from_random(size: _FloatSequence, def from_random(size: _FloatSequence,
N_seeds: int, N_seeds: int,
cells: _IntSequence = None, cells: _Optional[_IntSequence] = None,
rng_seed: _NumpyRngSeed = None) -> _np.ndarray: rng_seed: _Optional[_NumpyRngSeed] = None) -> _np.ndarray:
""" """
Place seeds randomly in space. Place seeds randomly in space.
@ -54,7 +54,7 @@ def from_Poisson_disc(size: _FloatSequence,
N_candidates: int, N_candidates: int,
distance: float, distance: float,
periodic: bool = True, periodic: bool = True,
rng_seed: _NumpyRngSeed = None) -> _np.ndarray: rng_seed: _Optional[_NumpyRngSeed] = None) -> _np.ndarray:
""" """
Place seeds according to a Poisson disc distribution. Place seeds according to a Poisson disc distribution.
@ -106,7 +106,7 @@ def from_Poisson_disc(size: _FloatSequence,
def from_grid(grid, def from_grid(grid,
selection: _IntCollection = None, selection: _Optional[_IntCollection] = None,
invert_selection: bool = False, invert_selection: bool = False,
average: bool = False, average: bool = False,
periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]: periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:

35
python/damask/util.py
View File

@ -10,8 +10,9 @@ import signal as _signal
import fractions as _fractions import fractions as _fractions
from collections import abc as _abc from collections import abc as _abc
from functools import reduce as _reduce, partial as _partial from functools import reduce as _reduce, partial as _partial
from typing import Callable as _Callable, Union as _Union, Iterable as _Iterable, Sequence as _Sequence, Dict as _Dict, \ from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \
List as _List, Tuple as _Tuple, Literal as _Literal, Any as _Any, Collection as _Collection, TextIO as _TextIO Sequence as _Sequence, Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
Any as _Any, Collection as _Collection, TextIO as _TextIO
from pathlib import Path as _Path from pathlib import Path as _Path
import numpy as _np import numpy as _np
@ -140,8 +141,8 @@ def strikeout(msg) -> str:
def run(cmd: str, def run(cmd: str,
wd: str = './', wd: str = './',
env: _Dict[str, str] = None, env: _Optional[_Dict[str, str]] = None,
timeout: int = None) -> _Tuple[str, str]: timeout: _Optional[int] = None) -> _Tuple[str, str]:
""" """
Run a command. Run a command.
@ -215,7 +216,7 @@ def open_text(fname: _FileHandle,
def execution_stamp(class_name: str, def execution_stamp(class_name: str,
function_name: str = None) -> str: function_name: _Optional[str] = None) -> str:
"""Timestamp the execution of a (function within a) class.""" """Timestamp the execution of a (function within a) class."""
now = _datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z') now = _datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
_function_name = '' if function_name is None else f'.{function_name}' _function_name = '' if function_name is None else f'.{function_name}'
@ -238,7 +239,7 @@ def natural_sort(key: str) -> _List[_Union[int, str]]:
def show_progress(iterable: _Iterable, def show_progress(iterable: _Iterable,
N_iter: int = None, N_iter: _Optional[int] = None,
prefix: str = '', prefix: str = '',
bar_length: int = 50) -> _Any: bar_length: int = 50) -> _Any:
""" """
@ -418,7 +419,7 @@ def project_equal_area(vector: _np.ndarray,
def hybrid_IA(dist: _FloatSequence, def hybrid_IA(dist: _FloatSequence,
N: int, N: int,
rng_seed: _NumpyRngSeed = None) -> _np.ndarray: rng_seed: _Optional[_NumpyRngSeed] = None) -> _np.ndarray:
""" """
Hybrid integer approximation. Hybrid integer approximation.
@ -540,10 +541,10 @@ def shapeblender(a: _Tuple[int, ...],
def _docstringer(docstring: _Union[str, _Callable], def _docstringer(docstring: _Union[str, _Callable],
extra_parameters: str = None, extra_parameters: _Optional[str] = None,
# extra_examples: str = None, # extra_examples: _Optional[str] = None,
# extra_notes: str = None, # extra_notes: _Optional[str] = None,
return_type: _Union[str, _Callable] = None) -> str: return_type: _Union[None, str, _Callable] = None) -> str:
""" """
Extend a docstring. Extend a docstring.
@ -593,8 +594,8 @@ def _docstringer(docstring: _Union[str, _Callable],
fr'\1{return_type_}\n', fr'\1{return_type_}\n',
docstring_,flags=_re.MULTILINE) docstring_,flags=_re.MULTILINE)
def extend_docstring(docstring: _Union[str, _Callable] = None, def extend_docstring(docstring: _Union[None, str, _Callable] = None,
extra_parameters: str = None) -> _Callable: extra_parameters: _Optional[str] = None) -> _Callable:
""" """
Decorator: Extend the function's docstring. Decorator: Extend the function's docstring.
@ -678,8 +679,8 @@ def DREAM3D_cell_data_group(fname: _Union[str, _Path]) -> str:
def Bravais_to_Miller(*, def Bravais_to_Miller(*,
uvtw: _np.ndarray = None, uvtw: _Optional[_np.ndarray] = None,
hkil: _np.ndarray = None) -> _np.ndarray: hkil: _Optional[_np.ndarray] = None) -> _np.ndarray:
""" """
Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl). Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
@ -706,8 +707,8 @@ def Bravais_to_Miller(*,
return _np.einsum('il,...l',basis,axis) return _np.einsum('il,...l',basis,axis)
def Miller_to_Bravais(*, def Miller_to_Bravais(*,
uvw: _np.ndarray = None, uvw: _Optional[_np.ndarray] = None,
hkl: _np.ndarray = None) -> _np.ndarray: hkl: _Optional[_np.ndarray] = None) -> _np.ndarray:
""" """
Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil). Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).