Merge pull request #678 from hakonanes/prepare-for-0.10.0-release

Prepare for 0.10.0 release

.github/workflows/perhaps_make_tagged_release_draft.py

@@ -1,4 +1,4 @@
-# Copyright 2019-2023 The kikuchipy developers
+# Copyright 2019-2024 The kikuchipy developers
 #
 # This file is part of kikuchipy.
 #
@@ -19,7 +19,6 @@
 
 from outdated import check_outdated
 
-
 with open("../../kikuchipy/release.py") as fid:
     for line in fid:
         if line.startswith("version"):

.github/workflows/tests.yml

@@ -8,17 +8,24 @@ on:
     branches:
       - '*'
   workflow_dispatch:
-    workflow: '*'
 
 jobs:
   code:
     name: code style
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: psf/black@stable
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - uses: isort/isort-action@master
+        with:
+          configuration: --profile black --filter-files --force-sort-within-sections --check-only --diff
+
       - name: Install Black with Jupyter extension
         run: |
           pip install black[jupyter]
@@ -32,9 +39,9 @@ jobs:
     name: check manifest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -60,17 +67,17 @@ jobs:
         python-version: ['3.10', '3.11']
         include:
           - os: ubuntu-latest
-            python-version: 3.7
-            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.1 hyperspy==1.7.3 matplotlib==3.5 numba==0.55 numpy==1.21.6 orix==0.11.1 pooch==1.3.0 pyebsdindex==0.2 scikit-image==0.16.2
+            python-version: 3.8
+            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.2 hyperspy==1.7.3 matplotlib==3.5 numba==0.57 numpy==1.23.0 orix==0.12.1 pooch==1.3.0 pyebsdindex==0.2.0 scikit-image==0.21.0
             LABEL: -oldest
           - os: ubuntu-latest
             python-version: 3.11
             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 }}
 
@@ -85,13 +92,20 @@ jobs:
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 
-      - name: Install optional dependencies
-        if: ${{ contains(matrix.LABEL, 'minimum_requirement') == false }}
+      - name: Install optional dependencies on Linux and Windows
+        if: ${{ contains(matrix.LABEL, 'minimum_requirement') == false && matrix.os != 'macos-latest' }}
         shell: bash
         run: |
           pip install -e .'[all]'
           pip install pyopencl
 
+      - name: Install optional dependencies on macOS (without nlopt)
+        if: ${{ contains(matrix.LABEL, 'minimum_requirement') == false && matrix.os == 'macos-latest' }}
+        shell: bash
+        run: |
+          pip install -e .
+          pip install 'pyebsdindex[gpu]' pyvista
+
       - name: Display Python, pip and package versions
         run: |
           python -V

.gitignore

@@ -65,6 +65,7 @@ instance/
 doc/build/
 doc/reference/generated/
 doc/examples/
+sg_execution_times.rst
 
 # PyBuilder
 target/

.pre-commit-config.yaml

@@ -1,5 +1,18 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
+    # https://black.readthedocs.io/en/stable/index.html
+    - repo: https://github.com/psf/black-pre-commit-mirror
+      rev: 24.4.2
+      hooks:
       - id: black
+        language_version: python3.11
+      - id: black-jupyter
+        files: \.ipynb
+        args: [--line-length=77]
+    # https://pycqa.github.io/isort/
+    - repo: https://github.com/pycqa/isort
+      rev: 5.13.2
+      hooks:
+        - id: isort
+          name: isort (python)
+          args:
+            [--profile=black, --filter-files, --force-sort-within-sections]

CHANGELOG.rst

@@ -13,6 +13,36 @@ its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>
 List entries are sorted in descending chronological order. Contributors to each release
 were listed in alphabetical order by first name until version 0.7.0.
 
+0.10.0 (2024-06-02)
+===================
+
+Changed
+-------
+- Minimum Python version is now 3.8.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+- Minimum NumPy version is now 1.23.0.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+- Minimum Numba version is now 0.57.0.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+- Minimum scikit-image version is now 0.22.0.
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+- Upon creation of an ``EBSDDetector``, the following attributes are forced to be
+  floats: sample tilt, tilt, azimuthal angle, binning, pixel size, and the projection
+  centers (PCs). (`#677 <https://github.com/pyxem/kikuchipy/pull/677>`_)
+- Simpler string representation of an ``EBSDDetector``, also showing the sample tilt.
+  (`#677 <https://github.com/pyxem/kikuchipy/pull/677>`_)
+- Exclude PyEBSDIndex versions 0.3.0 and 0.3.1 since these versions cannot perform Hough
+  indexing with Dask arrays. This was previously unintentionally supported due to a
+  side-effect. It should now be supported going forward.
+  (`#678 <https://github.com/pyxem/kikuchipy/pull/678>`_)
+
+Fixed
+-----
+- The order of the new shape of the detector of a downsampled EBSD signal, returned from
+  ``downsample()``, was previously previously incorrect, (n columns, n rows). This is
+  now correct, (n rows, n columns).
+  (`#674 <https://github.com/pyxem/kikuchipy/pull/674>`_)
+
 0.9.0 (2023-11-03)
 ==================
 
@@ -513,8 +543,8 @@ Deprecated
   removed in version 0.7. Use the ``kikuchipy.simulations.KikuchiPatternSimulator``
   class instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
 - The ``kikuchipy.crystallography.matrices`` module is deprecated and will be removed in
-  version 0.7, access the matrices via :class:`diffpy.structure.lattice.Lattice`
-  attributes instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
+  version 0.7, access the matrices via ``diffpy.structure.lattice.Lattice`` attributes
+  instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
 - The following functions for processing of pattern chunks in the
   ``kikuchipy.pattern.chunk`` module are deprecated and will be removed in version 0.7:
   ``get_image_quality()``, ``remove_dynamic_background()`` and

RELEASE.rst

@@ -14,37 +14,37 @@ Preparation
 - Locally, create a minor release branch from the ``develop`` branch when making a minor
   release, or create a patch release branch from the ``main`` branch when making a patch
   release. Ideally, a patch release is published immediately after a bug fix is merged
-  in ``main``. Therefore, it might be best to do the release updates directly on the bug
-  fix branch, so that no separate patch release branch has to be made.
+  on ``main``. Therefore, it might be best to do the release updates directly on the bug
+  fix branch. This way, we do not have to create a separate patch release branch.
 
-- Run tutorial notebooks and examples in the documentation locally and confirm that they
-  produce the expected results.
-  From time to time, check the documentation links (``make linkcheck``) and fix any
-  broken ones.
+- Run tutorial notebooks and examples in the documentation locally.
+  Confirm that they produce the expected results.
+  From time to time, check the documentation links (``make linkcheck``).
+  Fix broken links.
 
-- Review the contributor list ``__credits__`` in ``kikuchipy/release.py`` to ensure all
-  contributors are included and sorted correctly.
+- Ensure all contributors are included and sorted correctly by reviewing the contributor
+  list ``__credits__`` in ``kikuchipy/release.py``.
   Do the same for the Zenodo contributors file ``.zenodo.json``.
   Review ``.all-contributorsrc`` and regenerate the table if necessary.
 
 - Increment the version number in ``kikuchipy/release.py``.
   Review and clean up ``CHANGELOG.rst`` as per Keep a Changelog.
 
 - Make a PR of the release branch to ``main``.
-  Discuss the changelog with others, and make any changes *directly* to the release
+  Discuss the changelog with others and make any changes *directly* to the release
   branch.
-  Merge the branch into ``main``.
+  Merge the branch onto ``main``.
 
 Tag and release
 ---------------
 - If the ``__version__`` in ``kikuchipy/release.py`` on ``main`` has changed in a new
   commit, a tagged, annotated release *draft* is automatically created.
-  If ``__version__`` is now "0.42.0", the release name is "kikuchipy 0.42.0", and the
+  If ``__version__`` is now "0.42.0", the release name is "kikuchipy 0.42.0" and the
   tag name is "v0.42.0".
   The tag target will be the ``main`` branch.
   The release body contains a static description and a link to the changelog.
-  This release draft can be published as is, or changes to the release body can be made
-  before publishing.
+  This release draft can be published as is.
+  Or, changes to the release body can be made before publishing.
 
 - Monitor the publish workflow to ensure the release is successfully published to PyPI.
 
@@ -56,21 +56,22 @@ Post-release action
 - Ensure that `Zenodo <https://doi.org/10.5281/zenodo.3597646>`__ displays the new
   release.
 
-- Ensure that Binder can run the user guide notebooks by clicking the Binder badges in
-  the top banner of one of the tutorials via `Read The Docs
+- Ensure that Binder can run the tutorial notebooks by clicking the Binder badge in the
+  top banner of one of the tutorials in the `online documentation
   <https://kikuchipy.org/en/stable>`__.
 
-- Bring changes on ``main`` into ``develop`` by branching from ``main``, merge
-  ``develop`` into the new branch and fix potential conflicts.
-  After these conflicts are fixed, update or revert ``__version__`` and make any updates
+- Bring changes on ``main`` onto ``develop`` by branching from ``main``, merging
+  ``develop`` onto the new branch, and fixing potential conflicts.
+  After any conflicts are fixed, update or revert ``__version__`` and make any updates
   to this guide if necessary.
   Make a PR to ``develop`` and merge.
 
 - Tidy up GitHub issues and close the corresponding milestone.
 
-- A PR to the conda-forge feedstock will be created by the conda-forge bot.
-  Follow the relevant instructions from the conda-forge documentation on updating
-  packages, as well as the instructions in the PR.
-  Merge after checks pass.
-  Monitor the Azure pipeline CI to ensure the release is successfully published to
+- A PR to the conda-forge feedstock will automatically be created by the conda-forge
+  bot.
+  Follow the instructions in the PR and any relevant instructions in the conda-forge
+  documentation on updating packages.
+  Merge the PR after checks pass.
+  Monitor the Azure pipeline CI to ensure that the release is successfully published to
   conda-forge.

benchmarks/indexing/test_dictionary_indexing.py

@@ -1,4 +1,4 @@
-# Copyright 2019-2023 The kikuchipy developers
+# Copyright 2019-2024 The kikuchipy developers
 #
 # This file is part of kikuchipy.
 #

benchmarks/indexing/test_refinement.py

@@ -1,4 +1,4 @@
-# Copyright 2019-2023 The kikuchipy developers
+# Copyright 2019-2024 The kikuchipy developers
 #
 # This file is part of kikuchipy.
 #

doc/_static/image/reference_frames/doc_reference_frames.py

@@ -1,4 +1,4 @@
-# Copyright 2019-2023 The kikuchipy developers
+# Copyright 2019-2024 The kikuchipy developers
 #
 # This file is part of kikuchipy.
 #
@@ -19,9 +19,8 @@
 
 import matplotlib.pyplot as plt
 
-from kikuchipy.detectors import EBSDDetector
 from kikuchipy import load
-
+from kikuchipy.detectors import EBSDDetector
 
 data = "/home/hakon/kode/kikuchipy/kikuchipy/data/kikuchipy_h5ebsd/patterns.h5"
 outdir = "/home/hakon/kode/kikuchipy/doc/_static/image"

doc/conf.py

@@ -5,16 +5,15 @@
 from datetime import datetime
 import inspect
 import os
-from os.path import relpath, dirname
+from os.path import dirname, relpath
 import re
 import sys
 
-import pyvista as pv
 from numpydoc.docscrape_sphinx import SphinxDocString
+import pyvista as pv
 
 import kikuchipy as kp
 
-
 # If extensions (or modules to document with autodoc) are in another
 # directory, add these directories to sys.path here. If the directory
 # is relative to the documentation root, use os.path.abspath to make it

doc/tutorials/feature_maps.ipynb

@@ -404,7 +404,7 @@
     "    colorbar=True,\n",
     "    colorbar_label=\"Average dot product\",\n",
     "    remove_padding=True,\n",
-    "    return_figure=True\n",
+    "    return_figure=True,\n",
     ")\n",
     "fig.axes[0].scatter(x, y, c=\"r\");"
    ]

doc/tutorials/hough_indexing.ipynb

@@ -339,7 +339,7 @@
     "    [[1, 1, 1], [2, 0, 0], [2, 2, 0], [3, 1, 1]],\n",
     "    nBands=10,\n",
     "    tSigma=2,\n",
-    "    rSigma=2\n",
+    "    rSigma=2,\n",
     ")\n",
     "\n",
     "print(indexer.vendor)\n",
@@ -475,7 +475,7 @@
     "    [[1, 1, 1], [2, 0, 0], [2, 2, 0], [3, 1, 1]],\n",
     "    nBands=10,\n",
     "    tSigma=2,\n",
-    "    rSigma=2\n",
+    "    rSigma=2,\n",
     ")\n",
     "indexer.PC"
    ]
@@ -527,14 +527,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#io.save(\"xmap_ni.h5\", xmap)\n",
-    "#io.save(\n",
+    "# io.save(\"xmap_ni.h5\", xmap)\n",
+    "# io.save(\n",
     "#    \"xmap_ni.ang\",\n",
     "#    xmap,\n",
     "#    image_quality_prop=\"pq\",\n",
     "#    confidence_index_prop=\"cm\",\n",
     "#    extra_prop=\"nmatch\",\n",
-    "#)"
+    "# )"
    ]
   },
   {