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Prepare for 0.12.0 release #487

Merged
merged 199 commits into from
Apr 12, 2024
Merged

Prepare for 0.12.0 release #487

merged 199 commits into from
Apr 12, 2024

Commits on Feb 27, 2023

  1. Merge pull request pyxem#432 from hakonanes/main-into-develop-post-0.… 

    …11-release

Main into develop post 0.11 release
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Commits on Mar 14, 2023

  1. Merge branch 'develop' into main-into-develop-post-0.11.1-release

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  2. Revert release version to 0.12.dev0 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Add Unreleased section to changelog 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Merge pull request pyxem#436 from hakonanes/main-into-develop-post-0.… 

    …11.1-release

Bring changes in main into develop after 0.11.1 release
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  5. Fixed failing example in from_matrix docs of quaternion

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  6. Merge pull request pyxem#438 from anderscmathisen/quat_matrix_example… 

    …_fix

Fixed failing example in from_matrix docs of quaternion
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Commits on Apr 22, 2023

  1. Add method to create vectors along a 'path' on the sphere 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Make polar stereograhic grid use Matplotlib's 'grid.alpha' 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Add example showing how to combine rotations (from left to right) 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Simplify code in docs, use (e1, e2) labels in crystal stereo. 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  5. Remove broken doc link, mention another related project 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  6. Correct statement about combining transformations in example 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  7. Expedite removal of 'convention' in some Quaternion methods to 0.13 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Apr 23, 2023

  1. Merge pyxem#446 from hakonanes/expediate-removal-convention-parameter 

    Expedite removal convention parameter in from/to_euler() methods
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Commits on May 2, 2023

  1. Merge pull request pyxem#445 from hakonanes/create-vectors-from-path-… 

    …ends

Create vectors from path ends
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  2. Add convenience function to get nice vector labels for plotting 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Add parameter for coordinate offset in StereographicPlot.text() 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Improve parameter description of vector_labels in Vector3d.scatter() 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  5. Update changelog 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  6. Rename format_vector_labels() -> format_labels() 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  7. Increase zorder of border of stereographic plot 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  8. Use vector label formatting function in examples 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  9. Use vector label formatting in tutorials 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  10. Return array of labels instead of list from format_labels() 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  11. Fix getting labels of (hkil) or [UVTW] vectors 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  12. Simplify getting an array of one color per family of vectors 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  13. add label offset

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  14. Merge pull request pyxem#443 from hakonanes/improve-vector-label-plac… 

    …ement

Improve plotting of vector labels
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Commits on May 3, 2023

  1. history-retaining copy of orientations.py

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  2. duplicate orientation history: ori to temp

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  3. Merge commit '68eae3a12da2db6e4ae5f7450682485fcea798f6' into Class_In… 

    …heritance_Cleanup
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  4. duplicate orientation history: rename temp to ori

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  5. duplicate orientation history: remove duplicate classes

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Commits on May 5, 2023

  1. seperating mis and ori: cleanup

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Commits on May 21, 2023

  1. Merge pull request pyxem#449 from argerlt/Class_Inheritance_Cleanup 

    Splitting Misorientation and Orientation into seperate files
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Commits on Jul 23, 2023

  1. Add explicit support for Python 3.11 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Replace Python 3.9 test job with 3.11 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. List explicit support for Python 3.11 in changelog 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Replace API token with 'trusted publisher' approach for PyPI upload 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  5. Update versions of some GitHub actions 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  6. Make readthedocs build docs with Python 3.11 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Jul 26, 2023

  1. Merge pull request pyxem#455 from hakonanes/python-3-11-support 

    List explicit support for Python 3.11
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Commits on Nov 2, 2023

  1. Install pandoc version compatible with nbconvert (nbsphinx) 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Fix PR template links 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Specify that also docstring lines should be capped at 72 characters 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Add *.yml files from doc/ directory to source distribution 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  5. Silence some warnings related to Sphinx-Gallery in the docs 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Nov 3, 2023

  1. Add clean-up command to Makefile, remove Windows make.bat file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Remove Sphinx last-updated-by-git in doc footer 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Remove htmlzip build of docs to reduce build time 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Explicitly remove Class.set() methods from API 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  5. Describe exclusion of set() methods in dev guide for writing docs 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  6. Re-run clustering notebooks 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  7. Re-introduce ipykernel dependency required by nbsphinx 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Nov 4, 2023

  1. Merge pull request pyxem#462 from hakonanes/fix-doc-nbconvert-pandoc 

    Fix doc build
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Commits on Nov 7, 2023

  1. Remove_Neo_Eulerian: replacing quat_from functions

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  2. Remove_Neo_Eulerian: Removed from quaternion

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  3. Including changes suggested by @hakonanes 

    Does not pass build or formatting tests
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  4. edits to make black and unittests pass

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  5. Update orix/quaternion/quaternion.py 

    Co-authored-by: Håkon Wiik Ånes <[email protected]>
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  6. Update orix/quaternion/quaternion.py 

    Co-authored-by: Håkon Wiik Ånes <[email protected]>
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  7. Update orix/quaternion/quaternion.py 

    Co-authored-by: Håkon Wiik Ånes <[email protected]>
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  8. Update orix/quaternion/quaternion.py 

    Co-authored-by: Håkon Wiik Ånes <[email protected]>
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  9. Additional edits suggested by @hakonanes

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  10. move quaternion.to_* functions to _conversions.py

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  11. Pass existing unit tests 

    still requires additional tests to satisfy coveralls
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  12. partial addressing of PR pyxem#450 review 

    still need to complete coverage and add examples to new to/from function descriptions.
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  13. add qu2ax, fix warnings, update tests 

    Part of pyxem#450, but still not ready for final merging
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  14. Remove_Neo_Eulerian: replacing quat_from functions

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  15. Remove_Neo_Eulerian: Removed from quaternion

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  16. Including changes suggested by @hakonanes 

    Does not pass build or formatting tests
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  17. Additional edits suggested by @hakonanes

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  18. move quaternion.to_* functions to _conversions.py

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  19. partial addressing of PR review 

    still need to complete coverage and add examples to new to/from function descriptions.
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  20. add rodrigues_frank to/from plus tests

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  21. isort fix

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  22. missed suggestions from previous PR review 

    replaced previous #TODO with real examples, changed the wording of the warnings for rodrigues, and changed raised UserWarnings to warnings.warn

Co-Authored-By: Håkon Wiik Ånes <[email protected]>
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  23. Update quaternion.py

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  24. roll back test_orientations to include neo_euler tests

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  25. Add paper by Frank (1988) to bibliography 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  26. Add quaternion->homochoric and improve readability 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  27. Move fixtures to conftest and increase readability of tests 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  28. Remove unused imports in misorientation file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  29. Remove unused imports and increase readability in orientation file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  30. Remove unused imporst and simplify orientation region methods 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  31. Add from/to homochoric class methods, improve readability 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  32. Remove reference to deprecated neo_euler, simplify empty check 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  33. Remove unused import in symmetry file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  34. Catch some deprecation warnings for neo_euler in orientation tests 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  35. Remove unnecessary 'return None' from orientation region tests 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  36. Move quaternion tests to quaternion test file, test homochoric 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  37. Add a few tests of unique rotations 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  38. Simplify docs of NeoEuler 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  39. Remove unused import in vector file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  40. Fix quaternion docstring tests 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  41. Refer to related methods in docstrings 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  42. Add deprecation of from_neo_euler() and new methods to changelog 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  43. clarify from_rodrigues description.

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  44. Repair error from code rebase

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  45. Remove_Neo_Eulerian: Removed from quaternion

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  46. Including changes suggested by @hakonanes 

    Does not pass build or formatting tests
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  47. edits to make black and unittests pass

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  48. Additional edits suggested by @hakonanes

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  49. move quaternion.to_* functions to _conversions.py

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  50. partial addressing of PR pyxem#450 review 

    still need to complete coverage and add examples to new to/from function descriptions.
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  51. add qu2ax, fix warnings, update tests 

    Part of pyxem#450, but still not ready for final merging
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  52. Remove_Neo_Eulerian: Removed from quaternion

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  53. Including changes suggested by @hakonanes 

    Does not pass build or formatting tests
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  54. Additional edits suggested by @hakonanes

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  55. move quaternion.to_* functions to _conversions.py

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  56. add rodrigues_frank to/from plus tests

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  57. missed suggestions from previous PR review 

    replaced previous #TODO with real examples, changed the wording of the warnings for rodrigues, and changed raised UserWarnings to warnings.warn

Co-Authored-By: Håkon Wiik Ånes <[email protected]>
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  58. Update quaternion.py

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  59. Add quaternion->homochoric and improve readability 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  60. Move fixtures to conftest and increase readability of tests 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  61. Remove unused imports and increase readability in orientation file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  62. Remove unused imporst and simplify orientation region methods 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  63. Add from/to homochoric class methods, improve readability 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  64. Remove unused import in vector file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  65. Repair duplication mistakes from force push

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Commits on Nov 8, 2023

  1. Merge pull request pyxem#450 from argerlt/Remove_Neo_Eulerian 

    Adding Jit-accelerated to/from functions to quaternion class
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Commits on Nov 10, 2023

  1. Make it clearer that Object3d is private, rename _conversions file 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Improve mathematical description of quaternions 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Nov 11, 2023

  1. Allow reshaping 3D objects with a tuple of integers 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Nov 19, 2023

  1. Fix example showing combination of rotations, better describe rotatio… 

    …n convention

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  2. Start to use consistent notation of variable names 

    Uppercase for rotations: Q, R, O, M, S
Lowercase for vectors: v, m (t, g)

Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Add inv() method replicating ~, convenient if chaining operations 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Add examples to Rotation docstring 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  5. Make new Vector3d.scatter figures layout tight by default 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  6. Add random() method to all classes inheriting from Object3d 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  7. Slightly improve mathematical notation description 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  8. Update use of random() methods in tests 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  9. Add to changelog: not allowed passing list as shape ident. to random() 

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  10. Use Vector3d.random() in PDF tutorial 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  11. Increase minimal version of Matplotlib to 3.5 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Nov 20, 2023

  1. Fix typos in docs 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Use consistent mathematical notation in tutorial notebooks 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Nov 21, 2023

  1. Update notation in examples 

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Commits on Nov 23, 2023

  1. Improve control over members listed in API reference 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Dec 4, 2023

  1. Merge pull request pyxem#464 from hakonanes/complete-convention-descr… 

    …iption

Mathematical notation, more convenient random(), inv() equal to "~"
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Commits on Mar 20, 2024

  1. Ensure atom positions are expressed in the new basis

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  1. Test for proper atom positions in Phase

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  1. CI: Add pre-commit CI

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  2. Black: Formatting change 2023->2024

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  3. Black: Update CI version

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  4. Merge pyxem#472 from CSSFrancis/add_precommit_ci 

    CI: Add pre-commit CI
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  5. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  6. New Feature: Add get_sample_reduced_fundamental

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  7. Testing: Add Tests for get_sample_reduced_fundamental

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  8. New Feature: Add sampling for ZoneAxis patterns

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  9. Refactor: Removed transform3d dependency

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  10. Refactor: Cleaned up doc strings and unused code

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  11. BugFix: Fixed Quotes around error

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  12. Formatting: Run isort

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  13. Documentation: Add orcid ID

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  14. Documentation: copyright from 2023-->2024

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  15. Documentation: Added CHANGELOG.rst

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  16. Coverage: Update coverage

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  17. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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Commits on Mar 27, 2024

  1. testing refactor: making test_atom_position a little clearer

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  2. Changelog: PR pyxem#469

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  4. Merge pyxem#469, bugfixing. 

    Ensure atom positions are expressed in the new basis when initializing Phase with structure
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  5. Merge pyxem#473 from CSSFrancis/update_copyright 

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  1. Add @viljarjf to contributors

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  2. Documentation: Update CHANGELOG.rst

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  3. Merge pull request pyxem#476 from viljarjf/update-contributors 

    Add @viljarjf to contributors
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  4. Merge pyxem#460 which adds new sampling approaches

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Commits on Apr 1, 2024

  1. [pre-commit.ci] pre-commit autoupdate 

    updates:
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Commits on Apr 2, 2024

  1. Merge pull request pyxem#477 from pyxem/pre-commit-ci-update-config 

    [pre-commit.ci] pre-commit autoupdate
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  2. Simplify test failing on macOS with Python 3.11 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Add test dependency on pytest-rerunfailures 

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  4. Rerun flaky tests using pytest-rerunfailures on GitHub CI 

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  5. Clarify change of atom positions in Phase when enforcing axes alignment 

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  6. Add Carter Francis to package credits (not just Zenodo) 

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Commits on Apr 4, 2024

  1. Remove PDF build of docs for now so that "latest" build passes 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Apr 7, 2024

  1. Move example of creation of empty crystal map to examples gallery 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Pass "c" to Matplotlib for setting facecolor instead of "fc" 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  3. Encapsulate PyPI selectors in string, ".[dev]", so it works on Mac wi… 

    …th zsh

Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Update list of applications paper with the one from @maclariz on Ti 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  5. Add links to DREAM.3D and pymicro docs to our related projects docs 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  6. Replace deprecated use of inset axes in Matplotlib 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  7. Add new example showing the use of get_sample_reduced_fundamental() 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  8. Make git ignore doc file with Sphinx-Gallery execution times 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Apr 9, 2024

  1. Remove get_sample_zone_axis() 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Add example showing how to get rotations mapping Z-vector to crystal … 

    …directions

Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Apr 10, 2024

  1. Improve test of sampling rotations taking Z-vector to fundamental sector 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  2. Rephrase addition of new sampling function in changelog, remove non-u… 

    …ser facing change

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  3. Improve wording based on review by @CSSFrancis 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Bugfix: numpy.infty to np.inf

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Commits on Apr 11, 2024

  1. Merge pull request pyxem#483 from CSSFrancis/fix_numpy2 

    Numpy 2.0.0 Fixes
    @CSSFrancis
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  2. Merge pull request pyxem#478 from hakonanes/prepare-for-0.12 

    Minor maintenance updates before 0.12.0 release
    @hakonanes
    hakonanes authored Apr 11, 2024
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  3. Remove support for Python 3.7 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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  4. Merge pull request pyxem#485 from hakonanes/drop-python-3.7-support 

    Remove support for Python 3.7
    @hakonanes
    hakonanes authored Apr 11, 2024
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  5. Update README to use status badge table, rephrase reference to MTEX 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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Commits on Apr 12, 2024

  1. Merge pull request pyxem#486 from hakonanes/update-readme

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  2. Update order of contributors according to line additions on GitHub 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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    hakonanes-xn committed Apr 12, 2024
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  3. Set version to 0.12.0, update title in changelog 

    Signed-off-by: Håkon Wiik Ånes <[email protected]>
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    hakonanes-xn committed Apr 12, 2024
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