Merge pull request #429 from hakonanes/v0.5.0

Prepare for release of v0.5.0

.all-contributorsrc

@@ -6,7 +6,7 @@
   "commit": false,
   "contributorsPerLine": 7,
   "contributorsSortAlphabetically": true,
-  "badgeTemplate": "[![All Contributors](https://img.shields.io/badge/all_contributors-<%= contributors.length %>-yellow.svg)](#contributors)",
+  "badgeTemplate": "[![All Contributors](https://img.shields.io/badge/all_contributors-<%= contributors.length %>-yellow.svg)](#contributors-)",
   "projectName": "kikuchipy",
   "projectOwner": "pyxem",
   "repoType": "github",
@@ -57,6 +57,16 @@
         "code",
         "review"
       ]
+    },
+    {
+      "login": "ericpre",
+      "name": "Eric Prestat",
+      "avatar_url": "https://avatars.githubusercontent.com/u/11851990?v=4",
+      "profile": "https://github.com/ericpre",
+      "contributions": [
+        "code",
+        "maintenance"
+      ]
     }
   ]
-}
+}

.github/pull_request_template.md

@@ -1,4 +1,5 @@
 #### Description of the change
+<!-- Remember to branch off the develop branch for new features and the main branch for patches. -->
 
 
 #### Progress of the PR

.github/workflows/build.yml

@@ -40,7 +40,7 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.7
             OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: dask==2.18 diffsims==0.4.0 hyperspy==1.5.2 matplotlib==3.3 numpy==1.19 orix==0.6.0 scikit-image==0.16.2
+            DEPENDENCIES: dask==2021.8.1 diffsims==0.4.0 hyperspy==1.6.4 matplotlib==3.3 numba==0.48 numpy==1.19 orix==0.6.0 scikit-image==0.16.2
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -49,12 +49,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Display versions
         run: python -V; pip -V
-      - name: Install depedencies and package
-        shell: bash
-        run: pip install -U -e .'[tests]'
       - name: Install oldest supported version
         if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
         run: pip install ${{ matrix.DEPENDENCIES }}
+      - name: Install depedencies and package
+        shell: bash
+        run: pip install -U -e .'[tests]'
       - name: Run docstring tests
         if: ${{ matrix.os == 'ubuntu-latest' }}
         run: pytest --doctest-modules --ignore-glob=kikuchipy/*/tests

.github/workflows/test_documentation_notebooks.yml

@@ -0,0 +1,28 @@
+name: Test documentation notebooks
+
+on:
+  schedule:
+    - cron: '15 6 * * 1'
+
+jobs:
+  test-documentation-notebooks:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    env:
+      MPLBACKEND: agg
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+      - name: Display versions
+        run: python -V; pip -V
+      - name: Install dependencies and package
+        shell: bash
+        run: |
+          pip install -U -e .'[tests]'
+          pip install nbval
+      - name: Test documentation notebooks
+        run: |
+          pytest -v --nbval doc/user_guide doc/examples

README.md

@@ -1,6 +1,8 @@
-<img align="right" width="200px" src="https://kikuchipy.org/en/stable/_static/plasma_logo.svg">
-
-## kikuchipy
+<div align="center">
+  <a href="https://kikuchipy.org">
+    <img width="60%" src="doc/_static/logo/plasma_banner.png">
+  </a>
+</div>
 
 kikuchipy is an open-source Python library for processing and analysis of electron
 backscatter diffraction (EBSD) patterns. The library builds on the tools for
@@ -10,11 +12,11 @@ multi-dimensional data analysis provided by the HyperSpy library.
 [![Gitter chat](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/pyxem/kikuchipy)
 [![Documentation status](https://readthedocs.org/projects/kikuchipy/badge/?version=latest)](https://kikuchipy.org/en/latest/)
 [![Build status](https://github.com/pyxem/kikuchipy/workflows/build/badge.svg)](https://github.com/pyxem/kikuchipy/actions)
-[![Coverage status](https://coveralls.io/repos/github/pyxem/kikuchipy/badge.svg?branch=master)](https://coveralls.io/github/pyxem/kikuchipy?branch=master)
+[![Coverage status](https://coveralls.io/repos/github/pyxem/kikuchipy/badge.svg?branch=develop)](https://coveralls.io/github/pyxem/kikuchipy?branch=develop)
 [![PyPI version](https://img.shields.io/pypi/v/kikuchipy.svg)](https://pypi.python.org/pypi/kikuchipy)
 [![Downloads per month](https://pepy.tech/badge/kikuchipy/month)](https://pepy.tech/project/kikuchipy)
 [![Zenodo DOI](https://zenodo.org/badge/doi/10.5281/zenodo.3597646.svg)](https://doi.org/10.5281/zenodo.3597646)
-[![All Contributors](https://img.shields.io/badge/all_contributors-4-yellow.svg)](#contributors)
+[![All Contributors](https://img.shields.io/badge/contributors-5-b1aee3.svg)](#contributors-)
 
 - **User guide and API reference**: https://kikuchipy.org. The guide consists of Jupyter
   Notebooks with many links to detailed explanations of the input parameters and output
@@ -37,6 +39,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 <!-- markdownlint-disable -->
 <table>
   <tr>
+    <td align="center"><a href="https://github.com/ericpre"><img src="https://avatars.githubusercontent.com/u/11851990?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Eric Prestat</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/commits?author=ericpre" title="Code">💻</a> <a href="#maintenance-ericpre" title="Maintenance">🚧</a></td>
     <td align="center"><a href="https://www.ntnu.edu/employees/hakon.w.anes"><img src="https://avatars.githubusercontent.com/u/12139781?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Håkon Wiik Ånes</b></sub></a><br /></td>
     <td align="center"><a href="https://github.com/friedkitteh"><img src="https://avatars.githubusercontent.com/u/11888052?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Lars Lervik</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/issues?q=author%3Afriedkitteh" title="Bug reports">🐛</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=friedkitteh" title="Code">💻</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=friedkitteh" title="Documentation">📖</a> <a href="#question-friedkitteh" title="Answering Questions">💬</a> <a href="https://github.com/pyxem/kikuchipy/pulls?q=is%3Apr+reviewed-by%3Afriedkitteh" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=friedkitteh" title="Tests">⚠️</a></td>
     <td align="center"><a href="https://github.com/onatlandsmyr"><img src="https://avatars.githubusercontent.com/u/34620114?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Ole Natlandsmyr</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/commits?author=onatlandsmyr" title="Code">💻</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=onatlandsmyr" title="Documentation">📖</a> <a href="#question-onatlandsmyr" title="Answering Questions">💬</a> <a href="https://github.com/pyxem/kikuchipy/pulls?q=is%3Apr+reviewed-by%3Aonatlandsmyr" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=onatlandsmyr" title="Tests">⚠️</a></td>

RELEASE.rst

@@ -1,34 +1,31 @@
 How to make a new release of ``kikuchipy``
 ==========================================
 
-- Create a release branch v<major>.<minor>.x. If a new minor release is to be
-  made, branch off of master via the GitHub repo, and pull this branch locally.
-  If a new patch release is to be made, pull the existing minor branch locally
-  and branch off of it.
-- Review and clean up `doc/changelog.rst` as per Keep a Changelog. Make sure all
-  contributors and reviewers are acknowledged. Increment the version number in
-  `release.py`. Make a PR to the release branch.
-- Create a PR from the release branch to master. Discuss the changelog with
-  others, and make any changes *directly* to the release branch.
-- On the master branch, increment the version number in `release.py` to the next
-  v<major>.<minor>.dev0.
-- If a release candidate (RC) is to be made, make a PR to the release branch
-  with `-rc.1` added to the version name, like v0.42.0-rc.1, merge the PR after
-  all checks pass, and publish an RC release off of the release branch. See that
-  it is made available via PyPI, download it with the `dev` dependencies, and
-  run the tests to make sure everything is as it should be. Also check that
-  Binder can build the repository successfully by going to the Read the Docs PR
-  check in the RC PR above after the RC release.
-- Create a release draft (tag) via the GitHub repo from the release branch with
-  the correct tag version name, e.g. v0.42.0, and release title
-  "kikuchipy 0.42.0". Add the new release notes from the changelog, and convert
-  any reStructuredText formatting to Markdown by hand. Publish the release.
-- Monitor the publish GitHub Action to ensure the release is successfully
-  published to PyPI.
+kikuchipy's branching model is similar to the Gitflow Workflow (`original blog post
+<https://nvie.com/posts/a-successful-git-branching-model/>`_).
+
+- If a minor release is to be made, create a release branch v<major>.<minor>.0 off of
+  the `develop` branch locally. If a patch release is to be made, create a release
+  branch v<major>.<minor>.<patch> off of the `main` branch locally instead. Ideally, a
+  patch release should be made immediately after a bug fix has been made. Therefore, it
+  might be best to do the release updates, listed in the following steps, directly on
+  the bug fix branch, so that no separate patch release branch has to be made. The bug
+  fix branch should of course be branched off of `main`.
+- Increment the version number in `release.py`. Review and clean up `doc/changelog.rst`
+  as per Keep a Changelog. Make sure all contributors and reviewers are acknowledged.
+- Make a PR of the release branch to `main`. Discuss the changelog with others, and
+  make any changes *directly* to the release branch. Merge the branch into `main`. Then
+  make a PR of `main` to `develop`, and merge this.
+- Create a release draft (tag) via the GitHub repo from main with the correct tag
+  version name, e.g. v0.42.0, and release title "kikuchipy 0.42.0". Add the new release
+  notes from the changelog, and convert any reStructuredText formatting to Markdown by
+  hand. Publish the release.
+- Monitor the publish GitHub Action to ensure the release is successfully published to
+  PyPI.
 - Download the new version from PyPI with the `dev` dependencies with
   `pip install kikuchipy[dev]==0.42.0` locally and run the tests with
   `pytest --pyargs kikuchipy` to make sure everything is as it should be.
-- Make a PR to master with any updates to this guide if necessary.
+- Make a PR to `develop` with any updates to this guide if necessary.
 
 conda-forge
 -----------

doc/_static/data/pattern_match_ni_large.py

@@ -1,31 +1,23 @@
 from orix import sampling, io
-
 import kikuchipy as kp
 
 
 s_large = kp.data.nickel_ebsd_large()
-
 s_large.remove_static_background()
 s_large.remove_dynamic_background()
 s_large.average_neighbour_patterns(window="gaussian", std=2)
 
 mp = kp.data.nickel_ebsd_master_pattern_small(projection="lambert")
-
 r = sampling.get_sample_fundamental(
-    resolution=5, space_group=mp.phase.space_group.number
+    resolution=4, space_group=mp.phase.space_group.number
 )
-
 detector = kp.detectors.EBSDDetector(
     shape=s_large.axes_manager.signal_shape[::-1],
     pc=[0.421, 0.7794, 0.5049],
     convention="tsl",
     sample_tilt=70,
 )
+sim = mp.get_patterns(rotations=r, detector=detector, energy=20, compute=False)
 
-sim = mp.get_patterns(
-    rotations=r, detector=detector, energy=20, dtype_out=np.uint8, compute=True
-)
-
-xmap = s_large.dictionary_indexing(sim, keep_n=1, n_slices=10, metric="ncc")
-
+xmap = s_large.dictionary_indexing(sim, keep_n=1, metric="ncc")
 io.save("/home/hakon/ni_large.h5", xmap)

doc/changelog.rst

@@ -6,22 +6,26 @@ kikuchipy is an open-source Python library for processing and analysis of electr
 backscatter diffraction patterns: https://kikuchipy.org.
 
 All notable changes to this project will be documented in this file. The format is based
-on `Keep a Changelog <https://keepachangelog.com/en/1.1.0>`_, and this project adheres
-to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
+on `Keep a Changelog <https://keepachangelog.com/en/1.1.0>`_, and this project tries its
+best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
 Contributors to each release are listed in alphabetical order by first name. List
 entries are sorted in descending chronological order.
 
-Unreleased
-==========
+0.5.0 (2021-08-31)
+==================
 
 Contributors
 ------------
+- Eric Prestat
 - Håkon Wiik Ånes
 - Lars Andreas Hastad Lervik
 
 Added
 -----
+- Possibility to specify whether to rechunk experimental and simulated data sets and
+  which data type to use for dictionary indexing.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
 - How to use the new orientation and/or projection center refinements to the pattern
   matching notebook. (`#405 <https://github.com/pyxem/kikuchipy/pull/405>`_)
 - Notebooks to the documentation as shorter or longer "Examples" that don't fit in the
@@ -32,15 +36,49 @@ Added
 
 Changed
 -------
+- If a custom metric is to be used for dictionary indexing, it must now be a class
+  inheriting from an abstract *SimilarityMetric* class. This replaces the previous
+  *SimilarityMetric* class and the *make_similarity_metric()* function.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
+- Dictionary indexing parameter *n_slices* to *n_per_iteration*.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
+- *merge_crystal_maps* parameter *metric* to *greater_is_better*.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
+- *orientation_similarity_map* parameter *normalized* is by default False.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
+- Dependency versions for dask >= 2021.8.1, fixing some memory issues encountered after
+  2021.3.1, and HyperSpy >= 1.6.4. Remove importlib_metadata from package dependencies.
+  (`#418 <https://github.com/pyxem/kikuchipy/pull/418>`_)
 - Performance improvements to EBSD dictionary generation, giving a substantial speed-up.
   (`#405 <https://github.com/pyxem/kikuchipy/pull/405>`_)
 - Rename projection methods from `project()`/`iproject()` to
   `vector2xy()`/`xy2vector()`. (`#405 <https://github.com/pyxem/kikuchipy/pull/405>`_)
 - URLs of user guide topics have an extra "/user_guide/<topic>" added to them.
   (`#403 <https://github.com/pyxem/kikuchipy/pull/403>`_)
 
+Deprecated
+----------
+- Custom EBSD metadata, meaning the *Acquisition_instrument.SEM.EBSD.Detector* and
+  *Sample.Phases* nodes, as well as the EBSD *set_experimental_parameters()* and
+  *set_phase_parameters()* methods. This will be removed in v0.6 The *static_background*
+  metadata array will become available as an EBSD property.
+  (`#428 <https://github.com/pyxem/kikuchipy/pull/428>`_)
+
+Removed
+-------
+- *make_similarity_metric()* function is replaced by the need to create a class inheriting
+  from a new abstract *SimilarityMetric* class, which provides more freedom over
+  preparations of arrays before dictionary indexing.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
+- *EBSD.match_patterns()* is removed, use *EBSD.dictionary_indexing()* instead.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
+- kikuchipy.pattern.correlate module.
+  (`#419 <https://github.com/pyxem/kikuchipy/pull/419>`_)
+
 Fixed
 -----
+- Allow static background in EBSD metadata to be a Dask array.
+  (`#413 <https://github.com/pyxem/kikuchipy/pull/413>`_)
 - Set newest supported version of Sphinx to 4.0.2 so that nbsphinx works.
   (`#403 <https://github.com/pyxem/kikuchipy/pull/403>`_)
 

doc/cite.rst

@@ -4,6 +4,4 @@ Cite
 
 If analysis using kikuchipy forms a part of published work please consider
 recognizing the code development by citing this DOI:
-
-.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.3597646.svg
-   :target: https://doi.org/10.5281/zenodo.3597646
+`https://doi.org/10.5281/zenodo.3597646 <https://doi.org/10.5281/zenodo.3597646>`_.

doc/conf.py

@@ -70,7 +70,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files. This image also
 # affects html_static_path and html_extra_path.
-exclude_patterns = ["build", "_static/icon/*.ipynb"]
+exclude_patterns = ["build", "_static/logo/*.ipynb"]
 
 # The theme to use for HTML and HTML Help pages. See the documentation
 # for a list of builtin themes.
@@ -86,16 +86,16 @@
 pygments_style = "friendly"
 
 # Logo
-html_logo = "_static/icon/plasma_logo.svg"
-html_favicon = "_static/icon/plasma_favicon.png"
+html_logo = "_static/logo/plasma_logo.svg"
+html_favicon = "_static/logo/plasma_favicon.png"
 
 # nbsphinx configuration
 # Taken from nbsphinx' own nbsphinx configuration file, with slight
-# modification to point nbviewer and Binder to the GitHub master links
-# when the documentation is launched from a kikuchipy version with
+# modification 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 version:
-    release_version = "master"
+    release_version = "develop"
 else:
     release_version = "v" + version
 # This is processed by Jinja2 and inserted before each notebook
@@ -148,11 +148,19 @@
 bibtex_bibfiles = ["bibliography.bib"]
 
 
+# Relevant for the PDF build with LaTeX
+latex_elements = {
+    # pdflatex doesn't like some Unicode characters, so a replacement
+    # for one of them is made here
+    "preamble": r"\DeclareUnicodeCharacter{2588}{-}"
+}
+
+
 def linkcode_resolve(domain, info):
     """Determine the URL corresponding to Python object.
 
     This is taken from SciPy's conf.py:
-    https://github.com/scipy/scipy/blob/master/doc/source/conf.py.
+    https://github.com/scipy/scipy/blob/develop/doc/source/conf.py.
     """
     if domain != "py":
         return None
@@ -202,7 +210,7 @@ def linkcode_resolve(domain, info):
         if m:
             return pre_link + "%s/%s%s" % (m.group(1), fn, linespec)
         elif "dev" in kikuchipy.__version__:
-            return pre_link + "master/%s%s" % (fn, linespec)
+            return pre_link + "develop/%s%s" % (fn, linespec)
         else:
             return pre_link + "v%s/%s%s" % (kikuchipy.__version__, fn, linespec)
     else: