Merge #523 which prepares us for a 0.13.1 release

.github/workflows/build.yml

@@ -14,13 +14,13 @@ jobs:
     name: code style
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: psf/black@stable
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - uses: isort/isort-action@master
         with:
@@ -34,23 +34,6 @@ jobs:
         run: |
           black --diff --line-length 77 doc/tutorials/*.ipynb
 
-  # Make sure all necessary files will be included in a release
-  manifest:
-    name: check manifest
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-
-      - name: Install dependencies
-        run: |
-          pip install manifix
-
-      - name: Check MANIFEST.in file
-        run: |
-          python setup.py manifix
-
   build-with-pip:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
@@ -61,24 +44,33 @@ 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: '3.12'
+            LABEL: -minimum_requirement
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install depedencies and package
+      - name: Install core depedencies and package
+        shell: bash
+        run: |
+          pip install -U -e .'[tests,coverage]'
+
+      - name: Install optional dependencies
+        if: ${{ !contains(matrix.LABEL, 'minimum_requirement') }}
         shell: bash
         run: |
-          pip install -U -e .'[doc, tests]'
+          pip install -e .'[all]'
 
       - name: Install oldest supported version
         if: ${{ contains(matrix.LABEL, 'oldest') }}

.gitignore

@@ -63,7 +63,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-doc/build/
+_build/
 doc/examples/
 doc/reference/generated/
 doc/source/_autosummary/

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
       - id: black-jupyter

.zenodo.json

@@ -3,7 +3,7 @@
     {
       "name": "Håkon Wiik Ånes",
       "orcid": "0000-0002-1213-2911",
-      "affiliation": "Norwegian University of Science and Technology"
+      "affiliation": "Xnovo Technology ApS"
     },
     {
       "name": "Ben Martineau"

CHANGELOG.rst

@@ -6,6 +6,27 @@ 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>`__.
 
+2024-09-20 - version 0.13.1
+===========================
+
+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.
+
+Removed
+-------
+- Support for Python 3.8 and 3.9.
+
+Fixed
+-----
+- ``Phase.from_cif()`` still gives a valid phase even though the space group could not
+  be read.
+
 2024-09-03 - version 0.13.0
 ===========================
 

README.rst

@@ -1,15 +1,8 @@
-.. raw:: html
-
-    <p>
-      <h1>
-        <a href="https://orix.readthedocs.io"><img valign="middle" src="https://raw.githubusercontent.com/pyxem/orix/develop/doc/_static/img/orix_logo.png" width="50" alt="orix logo"/></a>
-        orix
-      </h1>
-    </p>
-
-.. Content above here until EXCLUDE plus one line is excluded from the long description
-.. in the source distributions uploaded to PyPI
-.. EXCLUDE
+|logo| orix
+===========
+
+.. |logo| image:: https://raw.githubusercontent.com/pyxem/orix/develop/doc/_static/img/orix_logo.png
+  :width: 50
 
 orix is an open-source Python library for analysing orientations and crystal symmetry.
 

RELEASE.rst

@@ -1,7 +1,7 @@
 How to make a new release of ``orix``
 =====================================
 
-After version 0.9.0, orix' branching model changed to one similar to the Gitflow
+After version 0.9.0, orix's branching model changed to one similar to the Gitflow
 Workflow (`original blog post
 <https://nvie.com/posts/a-successful-git-branching-model/>`__).
 

doc/Makefile

@@ -6,7 +6,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = PYDEVD_DISABLE_FILE_VALIDATION=1 python -Xfrozen_modules=off -m sphinx
 SOURCEDIR     = .
-BUILDDIR      = build
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

doc/conf.py

@@ -21,8 +21,8 @@
 sys.path.append("../")
 
 project = "orix"
-copyright = f"2018-{str(datetime.now().year)}, {orix.__author__}"
-author = orix.__author__
+author = "orix developers"
+copyright = f"2018-{str(datetime.now().year)}, {author}"
 release = orix.__version__
 
 # Add any Sphinx extension module names here, as strings. They can be
@@ -59,8 +59,10 @@
     "matplotlib": ("https://matplotlib.org/stable", None),
     "nbsphinx": ("https://nbsphinx.readthedocs.io/en/latest", None),
     "nbval": ("https://nbval.readthedocs.io/en/latest", None),
+    "numba": ("https://numba.readthedocs.io/en/latest", None),
     "numpy": ("https://numpy.org/doc/stable", None),
     "numpydoc": ("https://numpydoc.readthedocs.io/en/latest", None),
+    "pooch": ("https://www.fatiando.org/pooch/latest", None),
     "pytest": ("https://docs.pytest.org/en/stable", None),
     "python": ("https://docs.python.org/3", None),
     "pyxem": ("https://pyxem.readthedocs.io/en/latest", None),
@@ -78,7 +80,7 @@
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
-    "build",
+    "_build",
     "Thumbs.db",
     ".DS_Store",
     # Suppress warnings from Sphinx regarding "duplicate source files":
@@ -120,10 +122,10 @@
 # modifications to point nbviewer and Binder to the GitHub develop
 # branch links when the documentation is launched from a kikuchipy
 # version with "dev" in the version
-if "dev" in orix.__version__:
+if "dev" in release:
     release_version = "develop"
 else:
-    release_version = "v" + orix.__version__
+    release_version = "v" + release
 # This is processed by Jinja2 and inserted before each notebook
 nbsphinx_prolog = (
     r"""
@@ -234,14 +236,14 @@ def linkcode_resolve(domain, info):
     fn = relpath(fn, start=startdir).replace(os.path.sep, "/")
 
     if fn.startswith("orix/"):
-        m = re.match(r"^.*dev0\+([a-f\d]+)$", orix.__version__)
+        m = re.match(r"^.*dev0\+([a-f\d]+)$", release)
         pre_link = "https://github.com/pyxem/orix/blob/"
         if m:
             return pre_link + "%s/%s%s" % (m.group(1), fn, linespec)
-        elif "dev" in orix.__version__:
+        elif "dev" in release:
             return pre_link + "develop/%s%s" % (fn, linespec)
         else:
-            return pre_link + "v%s/%s%s" % (orix.__version__, fn, linespec)
+            return pre_link + "v%s/%s%s" % (release, fn, linespec)
     else:
         return None
 
@@ -329,7 +331,7 @@ def _str_examples(self):
     "filename_pattern": "^((?!sgskip).)*$",
     "gallery_dirs": "examples",
     "reference_url": {"orix": None},
-    "run_stale_examples": True,
+    "run_stale_examples": False,
     "show_memory": True,
 }
 autosummary_generate = True

doc/dev/building_writing_documentation.rst

@@ -112,7 +112,7 @@ We use :doc:`nbval <nbval:index>` for this.
 The tutorial notebooks can be run interactively in the browser with the help of Binder.
 When creating a server from the orix source code, Binder installs the packages listed in
 the ``environment.yml`` configuration file, which must include all ``doc`` dependencies
-in ``setup.py`` necessary to run the notebooks.
+in ``pyproject.toml`` necessary to run the notebooks.
 
 Writing API reference
 ---------------------

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::

doc/tutorials/crystal_map.ipynb

@@ -1330,7 +1330,7 @@
     "    vmax=angles.max() - 10,\n",
     "    overlay=xmap.iq,\n",
     "    colorbar=True,\n",
-    "    colorbar_label=\"Rotation angle, $\\omega$ [$^{\\circ}$]\",\n",
+    "    colorbar_label=r\"Rotation angle, $\\omega$ [$\\degree$]\",\n",
     ")"
    ]
   },
@@ -1492,7 +1492,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,

doc/tutorials/pole_density_function.ipynb

@@ -236,19 +236,19 @@
     "v = Vector3d.random(1_000_000)\n",
     "\n",
     "ax[0].pole_density_function(v, log=False, resolution=1)\n",
-    "ax[0].set(title=\"Sampling resolution: 1$\\degree$\")\n",
+    "ax[0].set(title=r\"Sampling resolution: 1$\\degree$\")\n",
     "\n",
     "# change sampling resolution on S2\n",
     "ax[1].pole_density_function(v, log=False, resolution=5)\n",
-    "ax[1].set(title=\"Sampling resolution: 5$\\degree$\")\n",
+    "ax[1].set(title=r\"Sampling resolution: 5$\\degree$\")\n",
     "\n",
     "# increase peak broadening\n",
     "ax[2].pole_density_function(v, log=False, resolution=1, sigma=15)\n",
-    "ax[2].set(title=\"Sampling resolution: 1$\\degree$\\n$\\sigma$: 15$\\degree$\")\n",
+    "ax[2].set(title=\"Sampling resolution: 1$\\\\degree$\\n$\\\\sigma$: 15$\\\\degree$\")\n",
     "\n",
     "# change colormap\n",
     "ax[3].pole_density_function(v, log=False, resolution=1, cmap=\"gray_r\")\n",
-    "ax[3].set(title='Sampling resolution: 1$\\degree$\\ncmap: \"gray_r\"')\n",
+    "ax[3].set(title=\"Sampling resolution: 1$\\\\degree$\\ncmap: 'gray_r'\")\n",
     "\n",
     "for a in ax:\n",
     "    a.set_labels(\"X\", \"Y\", None)"
@@ -352,7 +352,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,