Merge pull request #652 from hakonanes/support-pyebsdindex-0-2

Make kikuchipy compatible with PyEBSDIndex 0.2

.all-contributorsrc

@@ -106,6 +106,15 @@
       "contributions": [
         "doc"
       ]
+    },
+    {
+      "login": "CSSFrancis",
+      "name": "Carter Francis",
+      "avatar_url": "https://avatars.githubusercontent.com/u/41125831?v=4",
+      "profile": "https://github.com/CSSFrancis",
+      "contributions": [
+        "doc"
+      ]
     }
   ]
 }

.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

.github/workflows/tests.yml

@@ -10,9 +10,6 @@ on:
   workflow_dispatch:
     workflow: '*'
 
-env:
-  MPLBACKEND: agg
-
 jobs:
   code:
     name: code style
@@ -53,6 +50,9 @@ 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:
@@ -61,7 +61,7 @@ jobs:
         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 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: 3.11
@@ -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: |

.zenodo.json

@@ -32,6 +32,11 @@
       "orcid": "0000-0003-0311-8584",
       "affiliation": "Norwegian University of Science and Technology"
     },
+    {
+      "name": "Carter Francis",
+      "orcid": "0000-0003-2564-1851",
+      "affiliation": "University of Wisconsin Madison"
+    },
     {
       "name": "Magnus Nord",
       "orcid": "0000-0001-7981-5293",

CHANGELOG.rst

@@ -19,7 +19,19 @@ Unreleased
 Added
 -----
 - Explicit support for Python 3.11.
-  (`#645 <https://github.com/pyxem/kikuchipy/pull/645>`_)
+  (`#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()`` when obtaining the
+  ``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
+  particle swarm optimization (PSO). These are passed on to the new PSO 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
 -------
@@ -28,8 +40,13 @@ Changed
   internally to set the default color to white anymore, but uses ``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, and Matplotlib to 0.5.1, 1.21.6, and
-  3.5 respectively. (`#645 <https://github.com/pyxem/kikuchipy/pull/645>`_)
+- 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 interactive 3D
+  visualization of master patterns in the documentation (the hope is to reintroduce it
+  with trame at some point). (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
 
 Deprecated
 ----------
@@ -43,9 +60,9 @@ Removed
 
 Fixed
 -----
-
-Security
---------
+- Conversion from EDAX TSL projection center (PC) convention for (PCy, PCz) for
+  rectangular detectors is corrected.
+  (`#652 <https://github.com/pyxem/kikuchipy/pull/652>`_)
 
 0.8.7 (2023-07-24)
 ==================

CODE_OF_CONDUCT.rst

@@ -5,134 +5,141 @@ kikuchipy Code of Conduct
 Introduction
 ============
 
-This code of conduct applies to all spaces managed by the kikuchipy project,
-including all public and private mailing lists, issue trackers, wikis, blogs,
-Twitter, and any other communication channel used by our community. The
-kikuchipy project does not organise in-person events, however events related to
-our community should have a code of conduct similar in spirit to this one.
-
-This code of conduct should be honoured by everyone who participates in the
-kikuchipy community formally or informally, or claims any affiliation with the
-project, in any project-related activities and especially when representing the
-project, in any role.
-
-This code is not exhaustive or complete. It serves to distill our common
-understanding of a collaborative, shared environment and goals. Please try to
-follow this code in spirit as much as in letter, to create a friendly and
+This code of conduct applies to all spaces managed by the kikuchipy project, including
+all public and private mailing lists, issue trackers, wikis, blogs, and any other
+communication channel used by our community.
+The kikuchipy project does not organise in-person events, however events related to our
+community should have a code of conduct similar in spirit to this one.
+
+This code of conduct should be honoured by everyone who participates in the kikuchipy
+community formally or informally, or claims any affiliation with the project, in any
+project-related activities and especially when representing the project, in any role.
+
+This code is not exhaustive or complete. It serves to distill our common understanding
+of a collaborative, shared environment and goals.
+Please try to follow this code in spirit as much as in letter, to create a friendly and
 productive environment that enriches the surrounding community.
 
 Specific guidelines
 ===================
 
 We strive to:
 
-1. Be open. We invite anyone to participate in our community. We prefer to use
-   public methods of communication for project-related messages, unless
-   discussing something sensitive. This applies to messages for help or
-   project-related support, too; not only is a public-support request much more
-   likely to result in an answer to a question, it also ensures that any
-   inadvertent mistakes in answering are more easily detected and corrected.
-
-2. Be empathetic, welcoming, friendly, and patient. We work together to resolve
-   conflict, and assume good intentions. We may all experience some frustration
-   from time to time, but we do not allow frustration to turn into a personal
-   attack. A community where people feel uncomfortable or threatened is not a
-   productive one.
-
-3. Be collaborative. Our work will be used by other people, and in turn we will
-   depend on the work of others. When we make something for the benefit of the
-   project, we are willing to explain to others how it works, so that they can
-   build on the work to make it even better. Any decision we make will affect
-   users and colleagues, and we take those consequences seriously when making
-   decisions.
-
-4. Be inquisitive. Nobody knows everything! Asking questions early avoids many
-   problems later, so we encourage questions, although we may direct them to the
-   appropriate forum. We will try hard to be responsive and helpful.
-
-5. Be careful in the words that we choose. We are careful and respectful in our
-   communication and we take responsibility for our own speech. Be kind
-   others. Do not insult or put down other participants. We will not accept
-   harassment or other exclusionary behaviour, such as:
+1. Be open.
+   We invite anyone to participate in our community.
+   We prefer to use public methods of communication for project-related messages, unless
+   discussing something sensitive.
+   This applies to messages for help or project-related support, too; not only is a
+   public-support request much more likely to result in an answer to a question, it also
+   ensures that any inadvertent mistakes in answering are more easily detected and
+   corrected.
+
+2. Be empathetic, welcoming, friendly, and patient.
+   We work together to resolve conflict, and assume good intentions.
+   We may all experience some frustration from time to time, but we do not allow
+   frustration to turn into a personal attack.
+   A community where people feel uncomfortable or threatened is not a productive one.
+
+3. Be collaborative.
+   Our work will be used by other people, and in turn we will depend on the work of
+   others.
+   When we make something for the benefit of the project, we are willing to explain to
+   others how it works, so that they can build on the work to make it even better.
+   Any decision we make will affect users and colleagues, and we take those consequences
+   seriously when making decisions.
+
+4. Be inquisitive.
+   Nobody knows everything!
+   Asking questions early avoids many problems later, so we encourage questions,
+   although we may direct them to the appropriate forum.
+   We will try hard to be responsive and helpful.
+
+5. Be careful in the words that we choose.
+   We are careful and respectful in our communication and we take responsibility for our
+   own speech.
+   Be kind others.
+   Do not insult or put down other participants.
+   We will not accept harassment or other exclusionary behaviour, such as:
 
    - Violent threats or language directed against another person.
    - Sexist, racist, ableist, or otherwise discriminatory jokes and language.
    - Posting sexually explicit or violent material.
-   - Posting (or threatening to post) other people's personally identifying
-     information ("doxing").
-   - Sharing private content, such as emails sent privately or non-publicly, or
-     unlogged forums such as IRC channel history, without the sender's consent.
+   - Posting (or threatening to post) other people's personally identifying information
+     ("doxing").
+   - Sharing private content, such as emails sent privately or non-publicly, or unlogged
+     forums such as IRC channel history, without the sender's consent.
    - Personal insults, especially those using racist, sexist, or ableist terms.
-   - Intentional or repeated misgendering of participants who have explicitly
-     requested to be addressed by specific pronouns.
+   - Intentional or repeated misgendering of participants who have explicitly requested
+     to be addressed by specific pronouns.
    - Unwelcome sexual attention.
-   - Excessive profanity. Please avoid swearwords; people differ greatly in
-     their sensitivity to swearing.
-   - Repeated harassment of others. In general, if someone asks you to stop,
-     then stop.
+   - Excessive profanity.
+     Please avoid swearwords; people differ greatly in their sensitivity to swearing.
+   - Repeated harassment of others.
+     In general, if someone asks you to stop, then stop.
    - Advocating for, or encouraging, any of the above behaviour.
 
 Diversity statement
 ===================
 
-The kikuchipy project welcomes and encourages participation by everyone. We are
-committed to being a community that everyone enjoys being part of. Although we
-may not always be able to accommodate each individual's preferences, we try our
-best to treat everyone kindly.
+The kikuchipy project welcomes and encourages participation by everyone.
+We are committed to being a community that everyone enjoys being part of.
+Although we may not always be able to accommodate each individual's preferences, we try
+our best to treat everyone kindly.
 
 No matter how you identify yourself or how others perceive you: we welcome you.
-Though no list can hope to be comprehensive, we explicitly honour diversity in:
-age, culture, ethnicity, genotype, gender identity or expression, language,
-national origin, neurotype, phenotype, political beliefs, profession, race,
-religion, sexual orientation, socioeconomic status, subculture and technical
-ability, to the extent that these do not conflict with this code of conduct.
+Though no list can hope to be comprehensive, we explicitly honour diversity in: age,
+culture, ethnicity, genotype, gender identity or expression, language, national origin,
+neurotype, phenotype, political beliefs, profession, race, religion, sexual orientation,
+socioeconomic status, subculture and technical ability, to the extent that these do not
+conflict with this code of conduct.
 
-Though we welcome people fluent in all languages, kikuchipy development is
-conducted in English.
+Though we welcome people fluent in all languages, kikuchipy development is conducted in
+English.
 
-Standards for behaviour in the kikuchipy community are detailed in the Code of
-Conduct above. Participants in our community should uphold these standards in
-all their interactions and help others to do so as well (see next section).
+Standards for behaviour in the kikuchipy community are detailed in the Code of Conduct
+above.
+Participants in our community should uphold these standards in all their interactions
+and help others to do so as well (see next section).
 
 Reporting guidelines
 ====================
 
-We know that it is painfully common for internet communication to start at or
-devolve into obvious and flagrant abuse. We also recognize that sometimes people
-may have had a bad day, or be unaware of some of the guidelines in this Code of
-Conduct. Please keep this in mind when deciding how to respond to a breach of
-this Code.
+We know that it is painfully common for internet communication to start at or devolve
+into obvious and flagrant abuse.
+We also recognize that sometimes people may have had a bad day, or be unaware of some of
+the guidelines in this Code of Conduct.
+Please keep this in mind when deciding how to respond to a breach of this Code.
 
-For clearly intentional breaches, report those to the Code of Conduct Committee
-(see below). For possibly unintentional breaches, you may reply to the person
-and point out this Code of Conduct (either in public or in private, whatever is
-most appropriate). If you would prefer not to do that, please feel free to
-report to the code of conduct committee directly, or ask the committee for
-advice, in confidence.
+For clearly intentional breaches, report those to the Code of Conduct Committee (see
+below).
+For possibly unintentional breaches, you may reply to the person and point out this Code
+of Conduct (either in public or in private, whatever is most appropriate).
+If you would prefer not to do that, please feel free to report to the code of conduct
+committee directly, or ask the committee for advice, in confidence.
 
 You can report issues to the kikuchipy Code of Conduct Committee, at
-kikuchipy-conduct@googlegroups.com. Currently, the committee consists of:
+kikuchipy-conduct@googlegroups.com.
+Currently, the committee consists of:
 
 * `Håkon Wiik Ånes <https://github.com/hakonanes>`_ (chair)
 * `Tina Bergh <https://github.com/tinabe>`_
 
 Incident reporting resolution & Code of Conduct enforcement
 ===========================================================
 
-*This section summarizes the most important points, more details can be found
-in* :doc:`report_handling_manual`.
+*This section summarizes the most important points, more details can be found in*
+:doc:`report_handling_manual`.
 
-We will investigate and respond to all complaints. The kikuchipy Code of Conduct
-Committee will protect the identity of the reporter, and treat the content of
-complaints as confidential (unless the reporter agrees otherwise).
+We will investigate and respond to all complaints.
+The kikuchipy Code of Conduct Committee will protect the identity of the reporter, and
+treat the content of complaints as confidential (unless the reporter agrees otherwise).
 
-In case of severe and obvious breaches, e.g. personal threat or violent,
-sexist or racist language, we will immediately disconnect the originator from
-kikuchipy communication channels; please see the manual for details.
+In case of severe and obvious breaches, e.g. personal threat or violent, sexist or
+racist language, we will immediately disconnect the originator from kikuchipy
+communication channels; please see the manual for details.
 
-In cases not involving clear severe and obvious breaches of this code of
-conduct, the process for acting on any received code of conduct violation report
-will be:
+In cases not involving clear severe and obvious breaches of this code of conduct, the
+process for acting on any received code of conduct violation report will be:
 
 1. acknowledge report is received
 
@@ -144,14 +151,14 @@ will be:
 4. enforcement via transparent decision (see :ref:`resolutions`) by the Code of
    Conduct Committee
 
-The committee will respond to any report as soon as possible, and at most within
-72 hours.
+The committee will respond to any report as soon as possible, and at most within 72
+hours.
 
 Endnotes
 ========
 
-We are thankful to the groups behind the following documents, from which we drew
-content and inspiration:
+We are thankful to the groups behind the following documents, from which we drew content
+and inspiration:
 
 * `napari Code of Conduct <https://napari.org/community/code_of_conduct.html>`_
 * `NumPy Code of Conduct <https://numpy.org/code-of-conduct>`_