Merge pull request #521 from hakonanes/remove-python38-39-compat

Update Python version compatibility to range 3.10-12
pyxem · Sep 18, 2024 · 3e31b35 · 3e31b35
2 parents 5367787 + 11a617b
commit 3e31b35
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -20,7 +20,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - uses: isort/isort-action@master
         with:
@@ -44,14 +44,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.10', '3.11']
+        python-version: ['3.11', '3.12']
         include:
           - os: ubuntu-latest
-            python-version: 3.8
-            DEPENDENCIES: diffpy.structure==3.0.2  matplotlib==3.5
+            python-version: '3.10'
+            DEPENDENCIES: diffpy.structure==3.0.2 matplotlib==3.6.1
             LABEL: -oldest
           - os: ubuntu-latest
-            python-version: 3.11
+            python-version: '3.12'
             LABEL: -minimum_requirement
     steps:
       - uses: actions/checkout@v4

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -11,15 +11,19 @@ Unreleased
 
 Added
 -----
+- Support for Python 3.12.
 
 Changed
 -------
+- numpy-quaternion is now an optional dependency and will not be installed with ``pip``
+  unless ``pip install orix[all]`` is used.
 
 Deprecated
 ----------
 
 Removed
 -------
+- Support for Python 3.8 and 3.9.
 
 Fixed
 -----

diff --git a/doc/dev/running_writing_tests.rst b/doc/dev/running_writing_tests.rst
@@ -4,7 +4,8 @@ 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. Install necessary dependencies to run the tests::
+values with known answers.
+Install necessary dependencies to run the tests::
 
    pip install --editable ".[tests]"
 
@@ -15,23 +16,24 @@ Some useful :doc:`fixtures <pytest:explanation/fixtures>` are available in the
 
     Some :mod:`orix.data` module tests check that data not part of the package
     distribution can be downloaded from the web, thus downloading some small datasets to
-    your local cache. See the section on the
-    :ref:`data module <adding-data-to-data-module>` for more details.
+    your local cache.
+    See the section on the :ref:`data module <adding-data-to-data-module>` for more
+    details.
 
 To run the tests::
 
    pytest --cov --pyargs orix
 
-The ``--cov`` flag makes :doc:`coverage.py <coverage:index>` prints a nice report in the
-terminal.
+The ``--cov`` flag makes :doc:`coverage.py <coverage:index>` print a nice report.
 For an even nicer presentation, you can use ``coverage.py`` directly::
 
    coverage html
 
-Then, you can open the created ``htmlcov/index.html`` in the browser and inspect the
-coverage in more detail.
+Coverage can then be inspected in the browser by opening ``htmlcov/index.html``.
 
-Docstring examples are tested :doc:`with pytest <pytest:how-to/doctest>` as well.
+We strive for 100% test coverage of lines when all dependencies are installed.
+
+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
 already available in the namespace as ``np`` and ``plt``, respectively.
 The docstring tests can be run from the top directory::

diff --git a/doc/user/installation.rst b/doc/user/installation.rst
@@ -4,7 +4,7 @@ Installation
 
 orix can be installed with `pip <https://pypi.org/project/orix/>`__,
 `conda <https://anaconda.org/conda-forge/orix>`__ or from source, and supports Python
->= 3.8.
+>= 3.10.
 All alternatives are available on Windows, macOS and Linux.
 
 .. _install-with-pip:
@@ -29,9 +29,9 @@ To update orix to the latest release::
 
     pip install --upgrade orix
 
-To install a specific version of orix (say version 0.8.1)::
+To install a specific version of orix (say version 0.12.1)::
 
-    pip install orix==0.8.1
+    pip install orix==0.12.1
 
 .. _install-with-anaconda:
 
@@ -43,7 +43,7 @@ To install with Anaconda, we recommend you install it in a `conda environment
 with the `Miniconda distribution <https://docs.conda.io/en/latest/miniconda.html>`__.
 To create an environment and activate it, run the following::
 
-   conda create --name orix-env python=3.11
+   conda create --name orix-env python=3.12
    conda activate orix-env
 
 If you prefer a graphical interface to manage packages and environments, you can install
@@ -64,9 +64,9 @@ To update orix to the latest release::
 
     conda update orix
 
-To install a specific version of orix (say version 0.8.1)::
+To install a specific version of orix (say version 0.12.1)::
 
-    conda install orix==0.8.1 -c conda-forge
+    conda install orix==0.12.1 -c conda-forge
 
 .. _install-from-source:
 

diff --git a/orix/_base.py b/orix/_base.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/_util.py b/orix/_util.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/constants.py b/orix/constants.py
@@ -26,7 +26,7 @@
     try:
         _ = version(pkg)
         installed[pkg] = True
-    except ImportError:
+    except ImportError:  # pragma: no cover
         installed[pkg] = False
 
 # Typical tolerances for comparisons in need of a precision. We

diff --git a/orix/crystal_map/__init__.py b/orix/crystal_map/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/crystal_map/crystal_map.py b/orix/crystal_map/crystal_map.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/crystal_map/crystal_map_properties.py b/orix/crystal_map/crystal_map_properties.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/crystal_map/phase_list.py b/orix/crystal_map/phase_list.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/data/__init__.py b/orix/data/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/data/_registry.py b/orix/data/_registry.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/io/__init__.py b/orix/io/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/io/plugins/__init__.py b/orix/io/plugins/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/io/plugins/_h5ebsd.py b/orix/io/plugins/_h5ebsd.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/io/plugins/ang.py b/orix/io/plugins/ang.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.
@@ -108,7 +107,7 @@ def file_reader(filename: str) -> CrystalMap:
     data_dict["phase_list"] = PhaseList(**phases)
 
     # Set which data points are not indexed
-    # TODO: Add not-indexed convention for INDEX ASTAR
+    # TODO: Add not-indexed convention for ASTAR INDEX
     if vendor in ["orix", "tsl"]:
         not_indexed = data_dict["prop"]["ci"] == -1
         data_dict["phase_id"][not_indexed] = -1

diff --git a/orix/io/plugins/bruker_h5ebsd.py b/orix/io/plugins/bruker_h5ebsd.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/io/plugins/ctf.py b/orix/io/plugins/ctf.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/io/plugins/emsoft_h5ebsd.py b/orix/io/plugins/emsoft_h5ebsd.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/io/plugins/orix_hdf5.py b/orix/io/plugins/orix_hdf5.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/measure/__init__.py b/orix/measure/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/measure/pole_density_function.py b/orix/measure/pole_density_function.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.
@@ -34,7 +33,7 @@ def pole_density_function(
     hemisphere: str = "upper",
     symmetry: Optional[Symmetry] = None,
     log: bool = False,
-    mrd: bool = True
+    mrd: bool = True,
 ) -> Tuple[np.ma.MaskedArray, Tuple[np.ndarray, np.ndarray]]:
     """Compute the Pole Density Function (PDF) of vectors in the
     stereographic projection. See :cite:`rohrer2004distribution`.

diff --git a/orix/plot/__init__.py b/orix/plot/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/_symmetry_marker.py b/orix/plot/_symmetry_marker.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/_util.py b/orix/plot/_util.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/crystal_map_plot.py b/orix/plot/crystal_map_plot.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.
@@ -428,8 +427,6 @@ def _override_status_bar(
         n_rows, n_cols = self._data_shape
 
         # Get rotations, ensuring correct masking
-        # TODO: Show orientations in Euler angles (computationally
-        #  intensive...)
         r = crystal_map.get_map_data("rotations", decimals=3)
 
         # Get image data, overwriting potentially masked regions set to 0.0

diff --git a/orix/plot/direction_color_keys/__init__.py b/orix/plot/direction_color_keys/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/direction_color_keys/_util.py b/orix/plot/direction_color_keys/_util.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/direction_color_keys/direction_color_key.py b/orix/plot/direction_color_keys/direction_color_key.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/direction_color_keys/direction_color_key_tsl.py b/orix/plot/direction_color_keys/direction_color_key_tsl.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/inverse_pole_figure_plot.py b/orix/plot/inverse_pole_figure_plot.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/orientation_color_keys/__init__.py b/orix/plot/orientation_color_keys/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/orientation_color_keys/euler_color_key.py b/orix/plot/orientation_color_keys/euler_color_key.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/orientation_color_keys/ipf_color_key.py b/orix/plot/orientation_color_keys/ipf_color_key.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/orientation_color_keys/ipf_color_key_tsl.py b/orix/plot/orientation_color_keys/ipf_color_key_tsl.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/rotation_plot.py b/orix/plot/rotation_plot.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/stereographic_plot.py b/orix/plot/stereographic_plot.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/plot/unit_cell_plot.py b/orix/plot/unit_cell_plot.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/projections/__init__.py b/orix/projections/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/projections/stereographic.py b/orix/projections/stereographic.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/quaternion/__init__.py b/orix/quaternion/__init__.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/quaternion/_conversions.py b/orix/quaternion/_conversions.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/quaternion/misorientation.py b/orix/quaternion/misorientation.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/quaternion/orientation.py b/orix/quaternion/orientation.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.

diff --git a/orix/quaternion/orientation_region.py b/orix/quaternion/orientation_region.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # Copyright 2018-2024 the orix developers
 #
 # This file is part of orix.