Merge pull request #538 from hakonanes/prepare-0.13.3-release

Prepare 0.13.3 release

.github/workflows/build.yml

@@ -48,7 +48,8 @@ jobs:
         include:
           - os: ubuntu-latest
             python-version: '3.10'
-            DEPENDENCIES: diffpy.structure==3.0.2 matplotlib==3.6.1
+            # Matplotlib 3.6.1 is not compatible with NumPy v2
+            DEPENDENCIES: diffpy.structure==3.0.2 matplotlib==3.6.1 "numpy<2"
             LABEL: -oldest
           - os: ubuntu-latest
             python-version: '3.12'

.license.tmpl

@@ -0,0 +1,16 @@
+Copyright 2019-${years} the ${projectname} developers
+
+This file is part of ${projectname}.
+
+${projectname} is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+${projectname} is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with ${projectname}. If not, see <http://www.gnu.org/licenses/>.

.pre-commit-config.yaml

@@ -1,6 +1,24 @@
+##
+## Copyright 2019-2025 the orix developers
+##
+## This file is part of orix.
+##
+## orix is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 3 of the License, or
+## (at your option) any later version.
+##
+## orix is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with orix. If not, see <http://www.gnu.org/licenses/>.
+##
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
       - id: black-jupyter
@@ -13,7 +31,15 @@ repos:
         name: isort (python)
         args:
           [--profile=black, --filter-files, --force-sort-within-sections]
+  - repo: https://github.com/johann-petrak/licenseheaders.git
+    rev: 'v0.8.8'
+    hooks:
+        - id: licenseheaders
+          args: ["-t", ".license.tmpl", "-cy", "-n", "orix", "-f"]
+# https://pre-commit.ci/#configuration
 ci:
   # Don't run automatically on PRs, instead add the comment
   # "pre-commit.ci autofix" on a pull request to manually trigger auto-fixing
-  autofix_prs: false
+  autofix_prs: false
+  # TODO: Remove skip once (nearly) all files are formatted with the license template
+  skip: [licenseheaders]

CHANGELOG.rst

@@ -6,6 +6,13 @@ All user facing changes to this project are documented in this file. The format
 on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`__, and this project tries
 its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`__.
 
+2025-01-01 - version 0.13.3
+==========
+
+Fixed
+-----
+- Handle all EDAX TSL point group aliases.
+
 2024-09-25 - version 0.13.2
 ===========================
 
@@ -234,7 +241,7 @@ Added
 - Seven methods for sampling unit vectors from regular grids on *S2* via
   ``orix.sampling.sample_S2()``.
 - Calculation of the Inverse Pole Density Function (IPDF), ie. pole density in the
-  crystal point group fundamental sector, through 
+  crystal point group fundamental sector, through
   ``InversePoleFigurePlot.pole_density_function()``.
 - The ``orix.measure`` module has been introduced. The ``measure`` module is related to
   quantification of orientation and vector data.
@@ -422,7 +429,7 @@ Deprecated
 - Setting (Mis)Orientation symmetry via ``set_symmetry()`` is deprecated in 0.8, in
   favour of setting it directly via a ``symmetry.setter``, and will be removed in 0.9.
   Use ``map_into_symmetry_reduced_zone()`` instead.
- 
+
 Removed
 -------
 - ``StereographicPlot`` methods ``azimuth_grid()`` and ``polar_grid()``.

README.rst

@@ -23,7 +23,7 @@ orix is released under the GPL v3 license.
 .. |build_status| image:: https://github.com/pyxem/orix/workflows/build/badge.svg
    :target: https://github.com/pyxem/orix/actions/workflows/build.yml
 
-.. |python| image:: https://img.shields.io/badge/python-3.8+-blue.svg
+.. |python| image:: https://img.shields.io/badge/python-3.10+-blue.svg
    :target: https://www.python.org/downloads/
 
 .. |Coveralls| image:: https://coveralls.io/repos/github/pyxem/orix/badge.svg?branch=develop

doc/dev/setting_up_development_installation.rst

@@ -30,3 +30,6 @@ globally (in the ``conda`` environment)::
 
 This installs all necessary development dependencies, including those for running tests
 and building documentation.
+
+Finally, please insteall the pre-commit hooks as described in the :doc:`/dev/code_style`
+guide.

orix/__init__.py

@@ -1,4 +1,21 @@
-__version__ = "0.13.2"
+#
+# Copyright 2018-2024 the orix developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.#
+__version__ = "0.13.3"
 # Sorted by line contributions (ideally excluding lines in notebook files)
 __credits__ = [
     "Håkon Wiik Ånes",

orix/crystal_map/phase_list.py

@@ -31,10 +31,10 @@
 import numpy as np
 
 from orix.quaternion.symmetry import (
+    _EDAX_POINT_GROUP_ALIASES,
     Symmetry,
     _groups,
     get_point_group,
-    point_group_aliases,
 )
 from orix.vector import Miller, Vector3d
 
@@ -229,9 +229,9 @@ def point_group(self, value: int | str | Symmetry | None) -> None:
         if isinstance(value, int):
             value = str(value)
         if isinstance(value, str):
-            for correct, aliases in point_group_aliases.items():
+            for key, aliases in _EDAX_POINT_GROUP_ALIASES.items():
                 if value in aliases:
-                    value = correct
+                    value = key
                     break
             for point_group in _groups:
                 if value == point_group.name:

orix/io/plugins/ang.py

@@ -30,7 +30,7 @@
 from orix import __version__
 from orix.crystal_map import CrystalMap, PhaseList, create_coordinate_arrays
 from orix.quaternion import Rotation
-from orix.quaternion.symmetry import point_group_aliases
+from orix.quaternion.symmetry import _EDAX_POINT_GROUP_ALIASES
 
 __all__ = ["file_reader", "file_writer"]
 
@@ -594,9 +594,9 @@ def _get_header_from_phases(xmap: CrystalMap) -> str:
         else:
             proper_point_group = phase.point_group.proper_subgroup
             point_group_name = proper_point_group.name
-            for key, alias in point_group_aliases.items():
+            for key, aliases in _EDAX_POINT_GROUP_ALIASES.items():
                 if point_group_name == key:
-                    point_group_name = alias[0]
+                    point_group_name = aliases[0]
                     break
         header += (
             f"Phase {phase_id}\n"

orix/plot/direction_color_keys/direction_color_key_tsl.py

@@ -1,3 +1,4 @@
+#
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.
@@ -13,9 +14,7 @@
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with orix.  If not, see <http://www.gnu.org/licenses/>.
-
-from typing import Optional, Tuple, Union
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.#
 
 from matplotlib.figure import Figure
 import numpy as np
@@ -33,42 +32,39 @@
 
 
 class DirectionColorKeyTSL(DirectionColorKey):
-    """Assign colors to (crystal) directions rotated by crystal
-    orientations and projected into an inverse pole figure, according to
-    the Laue symmetry of the crystal.
-
-    This is based on the TSL color key implemented in MTEX.
+    """Assign colors to crystal directions in a fundamental sector given
+    by one of the eleven Laue symmetries.
+
+    Parameters
+    ----------
+    symmetry
+        Crystal symmetry. If a non-Laue symmetry is given, the
+        corresponding Laue symmetry is used.
+
+    Notes
+    -----
+    Coloring is based on the EDAX TSL color key as implemented in MTEX.
     """
 
     def __init__(self, symmetry: Symmetry) -> None:
-        """Create an inverse pole figure (IPF) color key to color
-        crystal directions according to a Laue symmetry's fundamental
-        sector (IPF).
-
-        Parameters
-        ----------
-        symmetry
-            (Laue) symmetry of the crystal. If a non-Laue symmetry
-            is given, the Laue symmetry of that symmetry will be used.
-        """
         laue_symmetry = symmetry.laue
         super().__init__(laue_symmetry)
 
     def direction2color(self, direction: Vector3d) -> np.ndarray:
-        """Return an RGB color per orientation given a Laue symmetry
-        and a sample direction.
+        """Return an RGB color per (crystal) direction.
 
         Plot the inverse pole figure color key with :meth:`plot`.
 
         Parameters
         ----------
         direction
-            Directions to color.
+            Crystal directions to color. Each direction is rotated to
+            the fundamental sector of the Laue symmetry.
 
         Returns
         -------
         rgb
-            Color array of shape ``direction.shape + (3,)``.
+            Color array of shape direction.shape + (3,).
         """
         laue_group = self.symmetry
         h = direction.in_fundamental_sector(laue_group)
@@ -78,11 +74,10 @@ def direction2color(self, direction: Vector3d) -> np.ndarray:
 
     def _create_rgba_grid(
         self, alpha: float = 1.0, return_extent: bool = False
-    ) -> Union[
-        np.ndarray,
-        Tuple[np.ndarray, Tuple[Tuple[float, float], Tuple[float, float]]],
-    ]:
-        """Create the 2d colormap used to represent crystal directions.
+    ) -> (
+        np.ndarray | tuple[np.ndarray, tuple[tuple[float, float], tuple[float, float]]]
+    ):
+        """Return the 2D colormap used to represent crystal directions.
 
         Parameters
         ----------
@@ -107,7 +102,7 @@ def _create_rgba_grid(
         sector = laue_group.fundamental_sector
 
         v = sample_S2(2)
-        v2 = Vector3d(np.row_stack((v[v <= sector].data, sector.edges.data)))
+        v2 = Vector3d(np.vstack((v[v <= sector].data, sector.edges.data)))
 
         rgb = self.direction2color(v2)
         r, g, b = rgb.T
@@ -144,18 +139,18 @@ def _create_rgba_grid(
         else:
             return rgba_grid
 
-    def plot(self, return_figure: bool = False) -> Optional[Figure]:
+    def plot(self, return_figure: bool = False) -> Figure | None:
         """Plot the inverse pole figure color key.
 
         Parameters
         ----------
         return_figure
-            Whether to return the figure. Default is ``False``.
+            Whether to return the figure. Default is False.
 
         Returns
         -------
         figure
-            Color key figure, returned if ``return_figure=True``.
+            Color key figure, returned if *return_figure* is True.
         """
         from orix.plot.inverse_pole_figure_plot import _setup_inverse_pole_figure_plot
 

orix/quaternion/rotation.py

@@ -117,8 +117,9 @@ def __mul__(
             return Q
         if isinstance(other, Vector3d):
             v = Quaternion(self) * other
-            improper = (self.improper * np.ones(other.shape)).astype(bool)
-            v[improper] = -v[improper]
+            if np.any(self.improper):
+                improper = (self.improper * np.ones(other.shape)).astype(bool)
+                v[improper] = -v[improper]
             return v
         if isinstance(other, int) or isinstance(other, list):  # abs(1)
             other = np.atleast_1d(other).astype(int)