Fix doc build by disallowing numpydoc v1.9.0

.github/workflows/build.yml

@@ -110,7 +110,7 @@ jobs:
 
       - name: Run tests
         run: |
-          pytest --pyargs orix --runslow --reruns 2 -n 2 --cov=orix
+          pytest --pyargs orix --slow --reruns 2 -n 2 --cov=orix
 
       - name: Generate line coverage
         if: ${{ matrix.os == 'ubuntu-latest' }}

doc/conf.py

@@ -1,3 +1,22 @@
+#
+# 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/>.
+#
+
 # Configuration file for the Sphinx documentation app.
 # See the documentation for a full list of configuration options:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -64,9 +83,10 @@
     "numpydoc": ("https://numpydoc.readthedocs.io/en/latest", None),
     "pooch": ("https://www.fatiando.org/pooch/latest", None),
     "pytest": ("https://docs.pytest.org/en/stable", None),
+    "pytest-xdist": ("https://pytest-xdist.readthedocs.io/en/stable/", None),
     "python": ("https://docs.python.org/3", None),
     "pyxem": ("https://pyxem.readthedocs.io/en/latest", None),
-    "readthedocs": ("https://docs.readthedocs.io/en/stable", None),
+    "readthedocs": ("https://docs.readthedocs.com/platform/stable/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy", None),
     "sklearn": ("https://scikit-learn.org/stable", None),
     "sphinx": ("https://www.sphinx-doc.org/en/master", None),

doc/dev/running_writing_tests.rst

@@ -3,11 +3,12 @@ Run and write tests
 
 All functionality in orix is tested with :doc:`pytest <pytest:index>`.
 The tests reside in a ``tests`` module.
-Tests are short methods that call functions in ``orix`` and compare resulting output
-values with known answers.
+Tests are short methods that call functions in orix and compare resulting output values
+with known answers.
+
 Install necessary dependencies to run the tests::
 
-   pip install --editable ".[tests]"
+    pip install -e ".[tests]"
 
 Some useful :doc:`fixtures <pytest:explanation/fixtures>` are available in the
 ``conftest.py`` file.
@@ -22,29 +23,28 @@ Some useful :doc:`fixtures <pytest:explanation/fixtures>` are available in the
 
 To run the tests::
 
-  pytest --cov --pyargs orix -n auto
+    pytest --cov --pyargs orix -n auto
 
-The ``-n auto`` is an optional flag to enable parallelized testing. 
-The ``--cov`` flag makes :doc:`coverage.py <coverage:index>` print a nice report.
-For an even nicer presentation, you can use ``coverage.py`` directly::
+The ``-n auto`` is an optional flag to enable parallelized testing with
+:doc:`pytest-xdist <pytest-xdist:index>`.
+We aim to cover all lines when all :ref:`dependencies` are installed.
+The ``--cov`` flag makes :doc:`coverage.py <coverage:index>` print a nice coverage
+report.
+For an even nicer presentation, you can use coverage.py directly::
 
-   coverage html
+    coverage html
 
 Coverage can then be inspected in the browser by opening ``htmlcov/index.html``.
 
-We strive for 100% test coverage of lines when all dependencies are installed.
-
-If you have a test that takes a long time to run, you can mark it to skip it from running by default
-
-.. code-block:: Python
+If a test takes a long time to run, you can mark it to skip it from running by default::
 
     @pytest.mark.slow
     def test_slow_function():
-        pass
+        ...
 
-Then you can run the tests with the ``--runslow`` option to skip slow tests::
+To run tests marked as slow, add the flag when running pytest::
 
-    pytest --runslow
+    pytest --slow
 
 Docstring examples are tested with :doc:`pytest <pytest:how-to/doctest>` as well.
 :mod:`numpy` and :mod:`matplotlib.pyplot` should not be imported in examples as they are

orix/crystal_map/phase_list.py

@@ -1,4 +1,5 @@
-# Copyright 2018-2024 the orix developers
+#
+# Copyright 2019-2025 the orix developers
 #
 # This file is part of orix.
 #
@@ -9,11 +10,12 @@
 #
 # 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
+# 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/>.
+# along with orix. If not, see <http://www.gnu.org/licenses/>.
+#
 
 from __future__ import annotations
 
@@ -37,7 +39,8 @@
     _groups,
     get_point_group,
 )
-from orix.vector import Miller, Vector3d
+from orix.vector.miller import Miller
+from orix.vector.vector3d import Vector3d
 
 # All named Matplotlib colors (tableau and xkcd already lower case hex)
 ALL_COLORS = mcolors.TABLEAU_COLORS
@@ -366,18 +369,26 @@ def deepcopy(self) -> Phase:
         return copy.deepcopy(self)
 
     def expand_asymmetric_unit(self) -> Phase:
-        """Return new instance with all symmetrically equivalent atoms.
+        """Return a new phase with all symmetrically equivalent atoms.
+
+        Returns
+        -------
+        expanded_phase
+            New phase with the a :attr:`structure` with the unit cell
+            filled with symmetrically equivalent atoms.
 
         Examples
         --------
+        >>> from diffpy.structure import Atom, Lattice, Structure
+        >>> import orix.crystal_map as ocm
         >>> atoms = [Atom("Si", xyz=(0, 0, 1))]
         >>> lattice = Lattice(4.04, 4.04, 4.04, 90, 90, 90)
         >>> structure = Structure(atoms = atoms,lattice=lattice)
-        >>> phase = Phase(structure=structure, space_group=227)
+        >>> phase = ocm.Phase(structure=structure, space_group=227)
         >>> phase.structure
         [Si   0.000000 0.000000 1.000000 1.0000]
-        >>> expanded = phase.expand_asymmetric_unit()
-        >>> expanded.structure
+        >>> expanded_phase = phase.expand_asymmetric_unit()
+        >>> expanded_phase.structure
         [Si   0.000000 0.000000 0.000000 1.0000,
          Si   0.000000 0.500000 0.500000 1.0000,
          Si   0.500000 0.500000 0.000000 1.0000,
@@ -411,9 +422,10 @@ def expand_asymmetric_unit(self) -> Phase:
                     diffpy_structure.append(new_atom)
 
         # This handles conversion back to correct alignment
-        out = Phase(self)
-        out.structure = diffpy_structure
-        return out
+        expanded_phase = self.__class__(self)
+        expanded_phase.structure = diffpy_structure
+
+        return expanded_phase
 
 
 class PhaseList: