Merge pull request #487 from hakonanes/prepare-for-0.12.0-release

Prepare for 0.12.0 release

.github/pull_request_template.md

@@ -2,9 +2,9 @@
 
 
 #### Progress of the PR
-- [ ] [Docstrings for all functions](https://github.com/numpy/numpy/blob/master/doc/example.py)
+- [ ] [Docstrings for all functions](https://numpydoc.readthedocs.io/en/latest/example.html)
 - [ ] Unit tests with pytest for all lines
-- [ ] Clean code style by [running black via pre-commit](https://orix.readthedocs.io/en/latest/contributing.html#code-style)
+- [ ] Clean code style by [running black via pre-commit](https://orix.readthedocs.io/en/latest/dev/code_style.html)
 
 #### Minimal example of the bug fix or new feature
 ```python

.github/workflows/build.yml

@@ -10,9 +10,6 @@ on:
   workflow_dispatch:
     workflow: '*'
 
-env:
-  MPLBACKEND: agg
-
 jobs:
   code:
     name: code style
@@ -24,7 +21,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.11'
 
       - uses: isort/isort-action@master
         with:
@@ -59,16 +56,17 @@ jobs:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
+    env:
+      MPLBACKEND: agg
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.9, "3.10"]
+        python-version: ['3.10', '3.11']
         include:
           - os: ubuntu-latest
-            python-version: 3.7
-            OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: diffpy.structure==3  matplotlib==3.3
+            python-version: 3.8
+            DEPENDENCIES: diffpy.structure==3.0.2  matplotlib==3.5
             LABEL: -oldest
     steps:
       - uses: actions/checkout@v3
@@ -84,7 +82,7 @@ jobs:
           pip install -U -e .'[doc, tests]'
 
       - name: Install oldest supported version
-        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
+        if: ${{ contains(matrix.LABEL, 'oldest') }}
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 
@@ -102,7 +100,7 @@ jobs:
 
       - name: Run tests
         run: |
-          pytest -n 2 --cov=orix --pyargs orix
+          pytest --pyargs orix --reruns 2 -n 2 --cov=orix
 
       - name: Generate line coverage
         if: ${{ matrix.os == 'ubuntu-latest' }}

.github/workflows/perhaps_make_a_tagged_release_draft.yml

@@ -15,12 +15,12 @@ jobs:
   make-tagged-release:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
-    - uses: r-lib/actions/setup-pandoc@v1
+    - uses: r-lib/actions/setup-pandoc@v2
 
     - name: Set up Python ${{ runner.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
 

.github/workflows/python-publish.yml

@@ -20,8 +20,11 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python
       uses: actions/setup-python@v2
@@ -37,15 +40,10 @@ jobs:
       run: |
         python -m build
 
-    - name: Publish package to TestPyPI
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+    - name: Publish package distribution to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
-        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
 
-    - name: Publish package to PyPI
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+    - name: Publish package distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test_documentation_notebooks.yml

@@ -18,22 +18,25 @@ jobs:
     env:
       MPLBACKEND: agg
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
-
-      - name: Display versions
-        run: python -V; pip -V
+          python-version: '3.11'
 
       - name: Install dependencies and package
         shell: bash
         run: |
           pip install -U -e .'[tests, doc]'
           pip install nbval
 
+      - name: Display versions
+        run: |
+          python -V
+          pip -V
+          pip list
+
       - name: Test documentation notebooks
         run: |
           pytest -v --nbval doc

.gitignore

@@ -67,6 +67,7 @@ doc/build/
 doc/examples/
 doc/reference/generated/
 doc/source/_autosummary/
+doc/sg_execution_times.rst
 
 # PyBuilder
 target/

.pre-commit-config.yaml

@@ -1,15 +1,19 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 24.3.0
     hooks:
       - id: black
       - id: black-jupyter
         files: \.ipynb
         args: [--line-length=77]
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         args:
           [--profile=black, --filter-files, --force-sort-within-sections]
+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

.zenodo.json

@@ -34,9 +34,18 @@
       "name": "Anders Christian Mathisen",
       "affiliation": "Norwegian University of Science and Technology"
     },
+    {
+      "name": "Carter Francis",
+      "orcid": "0000-0003-2564-1851",
+      "affiliation": "University of Wisconsin Madison"
+    },
     {
       "name": "Simon Høgås"
     },
+    {
+      "name": "Viljar Johan Femoen",
+      "affiliation": "Norwegian University of Science and Technology"
+    },
     {
       "name": "Alexander Clausen",
       "orcid": "0000-0002-9555-7455",

CHANGELOG.rst

@@ -6,6 +6,61 @@ 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>`__.
 
+2024-04-13 - version 0.12.0
+===========================
+
+Added
+-----
+- ``Vector3d.from_path_ends()`` class method to get vectors between two vectors.
+- Convenience function ``plot.format_labels()`` to get nicely formatted vector labels to
+  use when plotting vectors.
+- Two offsets in the stereographic coordinates (X, Y) can be given to
+  ``StereographicPlot.text()`` to offset text coordinates.
+- Explicit support for Python 3.11.
+- Creating quaternions from neo-eulerian vectors via new class methods
+  ``from_rodrigues()`` and ``from_homochoric()``, replacing the now deprecated
+  ``from_neo_euler()``. ``from_rodrigues()`` accepts an angle parameter to allow passing
+  Rodrigues-Frank vectors.
+- Creating neo-eulerian vectors from quaternions via new methods ``to_axes_angles()``,
+  ``to_rodrigues()`` and ``to_homochoric()``. Rodrigues-Frank vectors can be returned
+  from ``to_rodrigues()`` by passing ``frank=True``.
+- ``inv()`` method for ``Quaternion``, ``Rotation``, ``Orientation``, and
+  ``Misorientation``. For the three first, its behavior is identical to the inversion
+  operator ``~``. For misorientations, it inverts the direction of the transformation.
+  Convenient for chaining operations.
+- The ``random()`` methods of ``Orientation`` and ``Misorientation`` now accept
+  ``symmetry``. A ``random()`` method is also added to ``Vector3d`` and ``Miller``, the
+  latter accepting a ``phase``.
+- Function ``orix.sampling.get_sample_reduced_fundamental()`` for sampling rotations
+  that rotate the Z-vector (0, 0, 1) onto the fundamental sector of the Laue group of a
+  given ``Symmetry``.
+
+Changed
+-------
+- The ``convention`` parameter in ``from_euler()`` and ``to_euler()`` will be removed in
+  the next minor release, 0.13, instead of release 1.0 as previously stated.
+- Allow passing a tuple of integers to ``reshape()`` methods of 3D objects.
+- ``random()`` methods no longer accept a list as a valid shape: pass a tuple instead.
+- Increase minimal version of Matplotlib to >= 3.5.
+
+Removed
+-------
+- Support for Python 3.7.
+
+Deprecated
+----------
+- Creating quaternions from neo-eulerian vectors via ``from_neo_euler()`` is deprecated
+  and will be removed in v0.13. Use the existing ``from_axes_angles()`` and the new
+  ``from_rodrigues()`` and ``from_homochoric()`` instead.
+
+Fixed
+-----
+- Transparency of polar stereographic grid lines can now be controlled by Matplotlib's
+  ``grid.alpha``, just like the azimuth grid lines.
+- Previously, ``Phase`` did not adjust atom positions when forcing
+  ``Phase.structure.lattice.base`` to use the crystal axes alignment ``e1 || a``,
+  ``e3 || c*``. This is now fixed.
+
 2023-03-14 - version 0.11.1
 ===========================
 

MANIFEST.in

@@ -2,14 +2,13 @@ include CHANGELOG.rst
 include CONTRIBUTING.rst
 include environment.yml
 include LICENSE
-include MANIFEST.in
 include README.rst
 include RELEASE.rst
 include readthedocs.yaml
 include setup.cfg
 include setup.py
 include tutorials/README.rst
 
-recursive-include doc Makefile make.bat *.rst *.py *.ipynb *.bib *.txt *.cfg *.sh
+recursive-include doc Makefile make.bat *.rst *.py *.ipynb *.bib *.txt *.cfg *.sh *.yml
 recursive-include doc/_static *.png *.jpb *.svg *.css *.sh
 recursive-include examples *.txt *.py