pyxem · hakonanes · Nov 3, 2023 · Feb 11, 2023 · Feb 11, 2023 · Feb 11, 2023
diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -65,7 +65,8 @@
       "profile": "https://github.com/ericpre",
       "contributions": [
         "code",
-        "maintenance"
+        "maintenance",
+        "bug"
       ]
     },
     {
@@ -97,6 +98,24 @@
       "contributions": [
         "bug"
       ]
+    },
+    {
+      "login": "AndreasBugten",
+      "name": "AndreasBugten",
+      "avatar_url": "https://avatars.githubusercontent.com/u/106192446?v=4",
+      "profile": "https://github.com/AndreasBugten",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "CSSFrancis",
+      "name": "Carter Francis",
+      "avatar_url": "https://avatars.githubusercontent.com/u/41125831?v=4",
+      "profile": "https://github.com/CSSFrancis",
+      "contributions": [
+        "doc"
+      ]
     }
   ]
 }
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -3,9 +3,9 @@
 
 
 #### 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://kikuchipy.org/en/latest/contributing.html#code-style)
+- [ ] Clean code style by [running black via pre-commit](https://kikuchipy.org/en/latest/dev/code_style.html)
 
 #### Minimal example of the bug fix or new feature
 ```python

diff --git a/.github/workflows/perhaps_make_tagged_release_draft.py b/.github/workflows/perhaps_make_tagged_release_draft.py
@@ -47,7 +47,7 @@
                 changelog_end = i - 1
     with open("release_part_in_changelog.rst", mode="w") as f:
         f.write(
-            "kikuchipy is an open-source Python library for processing and analysis of electron backscatter diffraction (EBSD) patterns.\n\n"
+            "kikuchipy is an open-source Python library for processing, simulating and indexing of electron backscatter diffraction (EBSD) patterns.\n\n"
             f"See below, the `changelog <https://kikuchipy.org/en/stable/changelog.html>`_ or the `GitHub changelog <https://github.com/pyxem/kikuchipy/compare/v{pypi_version}...v{branch_version}>`_ for all updates from the previous release.\n\n"
         )
         for line in content[changelog_start:changelog_end]:

diff --git a/.github/workflows/perhaps_make_tagged_release_draft.yml b/.github/workflows/perhaps_make_tagged_release_draft.yml
@@ -14,35 +14,42 @@ jobs:
   make-tagged-release:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: r-lib/actions/setup-pandoc@v1
+    - uses: actions/checkout@v3
+
+    - uses: r-lib/actions/setup-pandoc@v2
+
     - name: Set up Python ${{ runner.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install outdated
+
     - name: Check whether a tagged release draft should be made
       run: |
         cd .github/workflows
         eval x=($(python perhaps_make_tagged_release_draft.py))
         echo "MAKE_RELEASE=${x[0]}" >> $GITHUB_ENV
         echo "PYPI_VERSION=${x[1]}" >> $GITHUB_ENV
         echo "BRANCH_VERSION=${x[2]}" >> $GITHUB_ENV
+
     - name: Make tagged release draft body from changelog
       if: ${{ env.MAKE_RELEASE == 'true' }}
-      run: pandoc .github/workflows/release_part_in_changelog.rst -f rst -t markdown -o release_part_in_changelog.md --wrap=none
+      run: |
+        pandoc .github/workflows/release_part_in_changelog.rst -f rst -t markdown -o release_part_in_changelog.md --wrap=none
+
     - name: Make tagged release draft
       if: ${{ env.MAKE_RELEASE == 'true' }}
-      uses: actions/create-release@v1
+      uses: softprops/action-gh-release@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       with:
-        draft: true
-        tag_name: v${{ env.BRANCH_VERSION }}
-        release_name: kikuchipy ${{ env.BRANCH_VERSION }}
-        commitish: main
         body_path: release_part_in_changelog.md
+        draft: true
         prerelease: false
+        name: kikuchipy ${{ env.BRANCH_VERSION }}
+        tag_name: v${{ env.BRANCH_VERSION }}
+        target_commitish: main
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -20,11 +20,14 @@ on:
 jobs:
   upload:
     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
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
 
@@ -38,15 +41,10 @@ jobs:
         python -m build
 
     - name: Publish package to TestPyPI
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@release/v1
       continue-on-error: true
       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 }}
+      uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test_documentation_notebooks.yml b/.github/workflows/test_documentation_notebooks.yml
@@ -6,30 +6,32 @@ on:
   workflow_dispatch:
     workflow: "*"
 
+env:
+  MPLBACKEND: agg
+
 jobs:
   test-documentation-notebooks:
     runs-on: ubuntu-latest
     timeout-minutes: 30
-    env:
-      MPLBACKEND: agg
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
-
-      - name: Display versions
-        run: |
-          python -V
-          pip -V
+          python-version: '3.11'
 
       - name: Install package and dependencies
         shell: bash
         run: |
-          pip install -U -e .'[doc,tests,viz]'
-          pip install nbval
+          pip install -U -e .'[doc,tests,all]'
+          pip install -U nbval pyopencl
+
+      - name: Display Python, pip and package versions
+        run: |
+          python -V
+          pip -V
+          pip list
 
       - name: Test documentation notebooks
         run: |

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -10,9 +10,6 @@ on:
   workflow_dispatch:
     workflow: '*'
 
-env:
-  MPLBACKEND: agg
-
 jobs:
   code:
     name: code style
@@ -39,7 +36,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install dependencies
         run: |
@@ -53,18 +50,21 @@ jobs:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
+    env:
+      MPLBACKEND: agg
+      PYTEST_ARGS: --pyargs kikuchipy --reruns 2 -n 2 --cov=kikuchipy
     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
-            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.0 hyperspy==1.7.3 matplotlib==3.3 numba==0.55 numpy==1.19 orix==0.11.1 scikit-image==0.16.2
+            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
             LABEL: -oldest
           - os: ubuntu-latest
-            python-version: 3.10
+            python-version: 3.11
             LABEL: -minimum_requirement
     steps:
       - uses: actions/checkout@v3
@@ -120,12 +120,12 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install xvfb
-          xvfb-run pytest -n 2 --cov=kikuchipy --pyargs kikuchipy
+          xvfb-run pytest ${{ env.PYTEST_ARGS }}
 
-      - name: Run tests on Windows and macOS
+      - name: Run tests on Windows or macOS
         if: ${{ matrix.os != 'ubuntu-latest' }}
         run: |
-          pytest -n 2 --cov=kikuchipy --pyargs kikuchipy
+          pytest ${{ env.PYTEST_ARGS }}
 
       - name: Generate line coverage
         run: |

diff --git a/.zenodo.json b/.zenodo.json
@@ -6,7 +6,7 @@
       "affiliation": "Norwegian University of Science and Technology"
     },
     {
-      "name": "Lars Lervik"
+      "name": "Lars Andreas Hastad Lervik"
     },
     {
       "name": "Ole Natlandsmyr"
@@ -19,6 +19,11 @@
     {
       "name": "Eric Prestat"
     },
+    {
+      "name": "Andreas V. Bugten",
+      "orcid": "0000-0003-0311-8584",
+      "affiliation": "Norwegian University of Science and Technology"
+    },
     {
       "name": "Erlend Mikkelsen Østvold",
       "affiliation": "Norwegian University of Science and Technology"
@@ -27,6 +32,11 @@
       "name": "Zhou Xu",
       "affiliation": "Monash Centre for Electron Microscopy"
     },
+    {
+      "name": "Carter Francis",
+      "orcid": "0000-0003-2564-1851",
+      "affiliation": "University of Wisconsin Madison"
+    },
     {
       "name": "Magnus Nord",
       "orcid": "0000-0001-7981-5293",

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -13,6 +13,63 @@ 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.
 
+0.9.0 (2023-11-03)
+==================
+
+Added
+-----
+- Explicit support for Python 3.11.
+  (`#646 <https://github.com/pyxem/kikuchipy/pull/646>`_)
+- Allow Hough indexing of all Laue groups with PyEBSDIndex v0.2 (not just *m-3m*, i.e.
+  FCC and BCC). (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
+- Control of reflector lists in Hough indexing. One reflector list per phase in the
+  phase list can be passed to ``EBSDDetector.get_indexer()`` to obtain an
+  ``EBSDIndexer`` for use in ``EBSD.hough_indexing()``.
+  (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
+- Allow passing keyword arguments to ``EBSD.hough_indexing_optimize_pc()`` to control
+  the new particle swarm optimization algorithm in PyEBSDIndex v0.2.
+  (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
+- Allow getting one projection center (PC) per pattern when optimizing PCs using the new
+  particle swarm optimization in PyEBSDIndex v0.2 (passing ``batch=True``).
+  (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
+
+Changed
+-------
+- Parameter ``zone_axes_kwargs`` in
+  ``GeometricalKikuchiPatternSimulation.as_collections()`` does not accept ``color``
+  internally to set the default color to white anymore. It accepts ``fc`` (facecolor)
+  instead. This change was necessary to improve handling of other keyword arguments.
+  (`#643 <https://github.com/pyxem/kikuchipy/pull/643>`_)
+- Increase minimal versions of diffsims, NumPy, Matplotlib, and PyEBSDIndex to 0.5.1,
+  1.21.6, 3.5, and 0.2, respectively.
+  (`#646 <https://github.com/pyxem/kikuchipy/pull/646>`_,
+  `#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
+- Remove dependency on Panel for documentation, and with that the interactive 3D
+  visualization of master patterns in the documentation. The plan is to reintroduce the
+  interactive plots with trame later on.
+  (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
+- Restrict HyperSpy to below the forthcoming version 2. The plan is to remove this
+  restriction once kikuchipy is compatible with this version.
+  (`#657 <https://github.com/pyxem/kikuchipy/pull/657>`_)
+
+Removed
+-------
+- ``generators`` and ``projections`` modules which were deprecated in version 0.8.
+  (`#612 <https://github.com/pyxem/kikuchipy/pull/612>`_)
+- The deprecated PyPI selector ``viz`` is removed.
+  (`#643 <https://github.com/pyxem/kikuchipy/pull/643>`_)
+- The data module functions ``silicon_ebsd_moving_screen_x()``, where "x" is "in",
+  "out5mm" or "out10mm". They were deprecated in version 0.8.
+  (`#656 <https://github.com/pyxem/kikuchipy/pull/656>`_)
+
+Fixed
+-----
+- Conversion from EDAX TSL projection center (PC) convention for (PCy, PCz) for
+  rectangular detectors is corrected.
+  (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
+- Downloading files in the ``data`` module to the local cache on Windows.
+  (`#655 <https://github.com/pyxem/kikuchipy/pull/655>`_)
+
 0.8.7 (2023-07-24)
 ==================
 
@@ -187,7 +244,7 @@ Added
 
 Changed
 -------
-- Minimal version of orix set to >= 0.11 and of numba set to >= 0.55.
+- Minimal version of orix set to >= 0.11 and of Numba set to >= 0.55.
   (`#608 <https://github.com/pyxem/kikuchipy/pull/608>`_)
 - Added warnings when trying to perform adaptive histogram equalization on a signal with
   data in floating type or when some of the data is NaN.
@@ -206,8 +263,6 @@ Changed
   (`#588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
 - Minimal version of HyperSpy increased to >= 1.7.3.
   (`#585 <https://github.com/pyxem/kikuchipy/pull/585>`_)
-- Minimal version of Numba increased to >= 0.52.
-  (`#585 <https://github.com/pyxem/kikuchipy/pull/585>`_)
 - When binning the navigation dimension(s) with ``EBSD.rebin()``, the class attributes
   ``xmap`` and ``static_background`` are set to ``None`` and ``detector.pc`` is set to
   ``[0.5, 0.5, 0.5]`` in the appropriate navigation shape. If the signal dimension(s)