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Vectorization of xrd_simulator #9

Merged
merged 321 commits into from
Jun 13, 2024
Merged

Vectorization of xrd_simulator #9

merged 321 commits into from
Jun 13, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jan 5, 2022

  1. trying macos build

    Axel Henningsson committed Jan 5, 2022
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  2. macos workflow work

    Axel Henningsson committed Jan 5, 2022
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  3. trying macos build

    Axel Henningsson committed Jan 5, 2022
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  4. macos ci sudo priviledge

    Axel Henningsson committed Jan 5, 2022
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  5. logo added

    Axel Henningsson committed Jan 5, 2022
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  6. logo tweak

    Axel Henningsson committed Jan 5, 2022
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  7. repair the docs

    Axel Henningsson committed Jan 5, 2022
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  8. remove image target

    Axel Henningsson committed Jan 5, 2022
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  9. fixing docs

    Axel Henningsson committed Jan 5, 2022
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  10. rolback to Weilzl algorithm as implemented in miniball

    Axel Henningsson committed Jan 5, 2022
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  11. Work on docs

    Axel Henningsson committed Jan 5, 2022
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  12. bumping version to 0.1.6 and distributing

    Axel Henningsson committed Jan 5, 2022
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  13. igonre release file

    Axel Henningsson committed Jan 5, 2022
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  14. remove autoreleae

    Axel Henningsson committed Jan 5, 2022
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  15. bumping version to 0.1.7 and distributing

    Axel Henningsson committed Jan 5, 2022
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  16. bumping version to 0.1.8 and distributing

    Axel Henningsson committed Jan 5, 2022
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  17. bumping version to 0.1.9 and distributing

    Axel Henningsson committed Jan 5, 2022
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  18. bumping version to 0.2.0 and distributing

    Axel Henningsson committed Jan 5, 2022
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  19. bumping version to 0.2.1 and distributing

    Axel Henningsson committed Jan 5, 2022
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  20. bumping version to 0.2.2 and distributing

    Axel Henningsson committed Jan 5, 2022
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  21. bumping version to 0.2.3 and distributing

    Axel Henningsson committed Jan 5, 2022
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  22. bumping version to 0.2.4 and distributing

    Axel Henningsson committed Jan 5, 2022
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  23. bumping version to 0.2.5 and distributing

    Axel Henningsson committed Jan 5, 2022
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  24. bumping version to 0.2.6 and distributing

    Axel Henningsson committed Jan 5, 2022
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  25. bumping version to 0.2.7 and distributing

    Axel Henningsson committed Jan 5, 2022
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Commits on Jan 7, 2022

  1. Readme

    Axel Henningsson committed Jan 7, 2022
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  2. readme changes

    Axel Henningsson committed Jan 7, 2022
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  3. README update

    Axel Henningsson committed Jan 7, 2022
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  4. README updates

    Axel Henningsson committed Jan 7, 2022
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  5. readme

    Axel Henningsson committed Jan 7, 2022
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  6. Bumped version to 0.2.9 and released to pypi.org

    Axel Henningsson committed Jan 7, 2022
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  7. Bumped version to 0.3.0 and released to pypi.org

    Axel Henningsson committed Jan 7, 2022
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  8. Released pypi version 0.3.0 to anaconda.org

    Axel Henningsson committed Jan 7, 2022
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  9. README credits added

    Axel Henningsson committed Jan 7, 2022
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Commits on Jan 8, 2022

  1. automating code inclusion in README.rst

    Axel Henningsson committed Jan 8, 2022
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  2. Refactoring detector and examples

    Axel Henningsson committed Jan 8, 2022
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  3. fix docs logo rendering

    Axel Henningsson committed Jan 8, 2022
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  4. Alpha release tag added

    Axel Henningsson committed Jan 8, 2022
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  5. Work on basic walkthrough examples

    Axel Henningsson committed Jan 8, 2022
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  6. Allow for strain representation of polycrystal

    Axel Henningsson committed Jan 8, 2022
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Commits on Jan 9, 2022

  1. test polycrystal and add mesh saving

    Axel Henningsson committed Jan 9, 2022
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  2. Adding a motion example

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  3. some pep8 comforming

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  4. Running flake8 and cleaning up

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  5. work on end to end example and example parameter tuning

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  6. remove mesh saving in example

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  7. remove ignored files from git cache

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  8. impleent :lines: in serve doc

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  9. Added diffraction pattern example image

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  10. Align example image

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  11. updates to README

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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  12. README updates

    @AxelHenningsson
    AxelHenningsson committed Jan 9, 2022
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Commits on Jan 10, 2022

  1. more readme updates

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  2. fix some readme bugs

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  3. Add transform() example to readme

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  4. fix readme typo

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  5. update filename readme

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  6. readme language

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  7. Bumped version to 0.3.1 and released to pypi.org

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  8. Released pypi version 0.3.1 to anaconda.org

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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  9. replace Welzl miniball by a simplified iterative method

    @AxelHenningsson
    AxelHenningsson committed Jan 10, 2022
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Commits on Jan 11, 2022

  1. Trying to add -conda-forge to .condarc

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  2. Bumped version to 0.3.2 and released to pypi.org

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  3. removed build in meat.yaml

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  4. solving python version issues

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  5. Bumped version to 0.3.3 and released to pypi.org

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  6. removing redundant build.sh

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    AxelHenningsson committed Jan 11, 2022
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  7. Bumped version to 0.3.4 and released to pypi.org

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    AxelHenningsson committed Jan 11, 2022
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  8. Released pypi version 0.3.4 to anaconda.org

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  9. try to specify conda-forge dependecy

    @AxelHenningsson
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  10. Bumped version to 0.3.5 and released to pypi.org

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  11. temporary rollback conda forge manual adding

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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  12. Released pypi version 0.3.5 to anaconda.org

    @AxelHenningsson
    AxelHenningsson committed Jan 11, 2022
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Commits on Jan 13, 2022

  1. serve docs and try meta.yaml updates

    @AxelHenningsson
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  2. try to specify channel in meta.yaml

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  3. try some more channel dependecy stuff

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  4. make conda respect python in meta.yaml

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  5. Bumped version to 0.3.6 and released to pypi.org

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  6. change python specs

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  7. messing about with the conda recipie

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  8. Bumped version to 0.3.7 and released to pypi.org

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  9. Released pypi version 0.3.7 to anaconda.org

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  10. add forge back to build scripts

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  11. updates to .yaml and urls

    @AxelHenningsson
    AxelHenningsson committed Jan 13, 2022
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  12. trying noarch distribution for conda

    @AxelHenningsson
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  13. Bumped version to 0.3.8 and released to pypi.org

    @AxelHenningsson
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  14. Released pypi version 0.3.8 to anaconda.org

    @AxelHenningsson
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  15. Allow for arbitrary matplotlib versions, trying to extend python vers… 

    …ion dependecy
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  16. Bumped version to 0.3.9 and released to pypi.org

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  17. try to get python verison in there

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  18. Bumped version to 0.3.10 and released to pypi.org

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  19. Released pypi version 0.3.10 to anaconda.org

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  20. update actions

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    AxelHenningsson committed Jan 13, 2022
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Commits on Jan 14, 2022

  1. conda install from conda-forge updated

    @AxelHenningsson
    AxelHenningsson committed Jan 14, 2022
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  2. reserve the docs

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Commits on Jan 16, 2022

  1. add beam unittest for setting vertices

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    AxelHenningsson committed Jan 16, 2022
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  2. update readme

    @AxelHenningsson
    AxelHenningsson committed Jan 16, 2022
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  3. Initiating owork on documentation and refactoring cleanup

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    AxelHenningsson committed Jan 16, 2022
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Commits on Jan 19, 2022

  1. end to end test changes

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    AxelHenningsson committed Jan 19, 2022
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Commits on Jan 20, 2022

  1. fix lorentz factor normalisation

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  2. notes

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    AxelHenningsson committed Jan 20, 2022
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Commits on Jan 25, 2022

  1. cleanup polycrystal __init__ and some minor unittest changes

    @AxelHenningsson
    AxelHenningsson committed Jan 25, 2022
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  2. Support save via pickle for class RigidBodyMotion

    @AxelHenningsson
    AxelHenningsson committed Jan 25, 2022
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Commits on Jan 29, 2022

  1. Change to print from sys

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    AxelHenningsson committed Jan 29, 2022
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Commits on Feb 3, 2022

  1. fail at renderig when structure_factors are true but .cif is lacking

    @AxelHenningsson
    AxelHenningsson committed Feb 3, 2022
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Commits on Feb 6, 2022

  1. Add xfab mod missing LICENSE.txt file

    @AxelHenningsson
    AxelHenningsson committed Feb 6, 2022
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Commits on Mar 16, 2022

  1. work on air scattering

    @AxelHenningsson
    AxelHenningsson committed Mar 16, 2022
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  2. fix passing cif path in test_templates.py

    @AxelHenningsson
    AxelHenningsson committed Mar 16, 2022
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  3. updates to lorentz

    @AxelHenningsson
    AxelHenningsson committed Mar 16, 2022
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Commits on Mar 18, 2022

  1. Add point spread function to detector class.

    @AxelHenningsson
    AxelHenningsson committed Mar 18, 2022
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  2. Transition pickling to dill allowing mutating psf

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  3. removing dependecy version pinns.

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  4. Bumped version to 0.3.11 and released to pypi.org

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  5. latest conda build

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Commits on Apr 2, 2022

  1. Remove bundled xfab version in favor of external version (now on cond… 

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  2. Seperate conda build and pytest by using semi-manual build actions

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  3. Remove last-updated badge from README

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  4. make release scripts local

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  5. Remove extra scripts

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  6. Bumped version to 0.3.12 and released to pypi.org

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Commits on Apr 6, 2022

  1. README updates

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Commits on Apr 9, 2022

  1. updates to docs

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  2. Updates to beam.py docs

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  3. Make save and load custom and module level

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  4. Re-rendered docs

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Commits on Apr 10, 2022

  1. Improve polycrystal.py docs

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  2. Refactor scatterer.py

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  3. Fix example

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  4. Bumped version to 0.3.13 and released to pypi.org

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  5. Update detector.py docs

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  6. Updates to motion.py docs

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  7. Update laue.py docs

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  8. Refactor parametric laue

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  9. Updates to mesh.py docs

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  10. update mesh image

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  11. updates to mesh docs

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  12. Removed unused code in mesh.py

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  13. updates to phase.py docs

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  14. updates to phase.py docs

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  15. Updates to scattering_unit.py

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  16. updates to templates.py docs

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  17. re-serve docs

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  18. cleanup tests

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  19. Minimal unittests for mesh.py

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  20. docs fixes for mesh.py

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  21. Bumped version to 0.3.14 and released to pypi.org

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  22. GitHub Action updates

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  23. fix windows build

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  24. fix windows build yml

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  25. updates to README

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Commits on Jun 8, 2022

  1. updates and render to README

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  2. add h5py and netcdf4 to setup.py

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  3. Bumped version to 0.3.15 and released to pypi.org

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Commits on Jun 10, 2022

  1. readme docs updates

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  2. New titles for .xdmf fields in polycrystal.save()

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  3. README typo correction

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Commits on Jul 31, 2022

  1. Bug fix to polycrystal save

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  2. Fix Detector frame size bug

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  3. Vectorize pixel coordinate creation for speed

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Commits on Aug 2, 2022

  1. Throttle diffraction progress bar update rate

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  2. prepping for faster proximity checks

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  3. .gitignore updates

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  4. Performance boosts to Polycrystal.transform

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  5. Added approximate collision detection as default for speed

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  6. Diffraction loop optimisation

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Commits on Aug 29, 2022

  1. optimization

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  2. optimization to beam

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  3. Adding parallel runs for diffraction computation

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Commits on Aug 30, 2022

  1. optimization

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Commits on Aug 31, 2022

  1. work on optimisation of proximity intervalls

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Commits on Sep 1, 2022

  1. Heavy optimisation and fixed rotation axis frame splitting implemented

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  2. optimize frame splitting

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Commits on Sep 2, 2022

  1. OPtimisation and paralellisation to rendering

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Commits on Sep 6, 2022

  1. ODF docs example

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  2. fix import in example docs

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  3. Fix np.nan bug in detector and add unit test

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  4. Remove debug leftovers

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Commits on Sep 16, 2022

  1. docs for templates

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  2. doc fixes

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  3. Bumped version to 0.4.0 and released to pypi.org

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Commits on Sep 20, 2022

  1. theta eta computation utility added to detector

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Commits on Sep 24, 2022

  1. Handle corner case feasible points with zeros in slack

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Commits on Oct 4, 2022

  1. Added centroid rendering with better scintilator models

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Commits on Oct 5, 2022

  1. Docs and fixes for new optional rendering method

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Commits on Oct 13, 2022

  1. handle non-orthogonal detector sides

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Commits on Oct 24, 2022

  1. add translate and rotate funcs on mesh

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Commits on Oct 26, 2022

  1. Default to Green-Lagrange large strain tensor interpretation

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  2. Fixes for workflow tests on linux

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  3. Investigating Linux build errors

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  4. Investigating Linux build errors

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  5. Investigating Linux build errors

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  6. README updates

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Commits on Nov 14, 2022

  1. packaging for more python version

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  2. packaging for more python version

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  3. Bumped version to 0.4.1 and released to pypi.org

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Commits on Nov 17, 2022

  1. adding optional origin argument to RigidBodyMotion

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Commits on Nov 18, 2022

  1. Making RigidBodyMotion.rotate detached from the origin for vector rot… 

    …ation
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Commits on Apr 7, 2023

  1. Added package citation links

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  2. patching github actions

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Commits on Jun 15, 2023

  1. Update README.rst

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Commits on Oct 27, 2023

  1. Allow new python versions

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Commits on Dec 4, 2023

  1. tighten bounds on possible scattering angles

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  2. Merge pull request FABLE-3DXRD#5 from AxelHenningsson/main 

    tighten bounds on possible scattering angles
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Commits on Mar 5, 2024

  1. Modifications in mesh polycrystal and utils for performance (Tensor o… 

    …perations)
    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 5, 2024
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Commits on Mar 6, 2024

  1. Modified files to proceed with vectorization

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  2. reflections_df summarizes all relevant data in _diffract

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 6, 2024
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Commits on Mar 8, 2024

  1. Diffraction method almost fully vectorized

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 8, 2024
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Commits on Mar 11, 2024

  1. Sample generation and diffraction vectorized. Missing euler angles wh… 

    …ile saving and convex hull computation
    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 11, 2024
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Commits on Mar 12, 2024

  1. All working, but sample creation slow. Starting _eB optimization

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 12, 2024
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  2. Vectorized the eB calculation in polycrystal.py

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 12, 2024
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  3. tests adapted to file structure

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. Gitignore updated

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 13, 2024
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Commits on Mar 14, 2024

  1. Vectorization in progress for tomographic runs"

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 14, 2024
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  2. Further optimized for tomography

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 14, 2024
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Commits on Mar 18, 2024

  1. Added breakpoints

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  2. Breakpoint

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  3. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  4. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  5. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  6. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  7. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  8. changed stuff in get_G

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  9. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  10. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  11. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  12. debug

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  13. The issue is probably in the BB filtering due to too many reflections… 

    … being filtered
    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  14. Added radius of mean ecentroid to BB

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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  15. Found out that BB was failing for confusing xyz

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 18, 2024
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Commits on Mar 19, 2024

  1. BB_intersection updated to use the radius of each grain

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Mar 19, 2024
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Commits on Apr 8, 2024

  1. Removed original files

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Apr 8, 2024
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Commits on Apr 10, 2024

  1. makefile added to gitignore

    Marc Raventos Tato - Tel 4563 [P1 office45/seat104] committed Apr 10, 2024
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Commits on Apr 11, 2024

  1. Merge branch 'vectorization'

    @Marcraven
    Marcraven committed Apr 11, 2024
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  2. Some comments added

    @Marcraven
    Marcraven committed Apr 11, 2024
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  3. Bug fixed in polycrystal.py

    @Marcraven
    Marcraven committed Apr 11, 2024
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Commits on Apr 30, 2024

  1. Pandas added to the required packages to install in setup.py

    @Marcraven
    Marcraven committed Apr 30, 2024
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  2. Corrected minor bugs

    @Marcraven
    Marcraven committed Apr 30, 2024
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Commits on May 31, 2024

  1. Tests verified to pass with the vectorized implementation.

    @Marcraven
    Marcraven committed May 31, 2024
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  2. Removed unnecesary imports

    @Marcraven
    Marcraven committed May 31, 2024
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Commits on Jun 12, 2024

  1. "Strange docstring fixed in render"

    @Marcraven
    Marcraven committed Jun 12, 2024
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  2. minor docstring fix

    @Marcraven
    Marcraven committed Jun 12, 2024
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  3. Fixed the docstring of lab_strain_to_B_matrix

    @Marcraven
    Marcraven committed Jun 12, 2024
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  4. Docstring added. Som internal functions hidden to the user

    @Marcraven
    Marcraven committed Jun 12, 2024
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  5. Docstring modified.

    @Marcraven
    Marcraven committed Jun 12, 2024
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  6. Hidden functions modified wherever they were called

    @Marcraven
    Marcraven committed Jun 12, 2024
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  7. Added by Axel

    @Marcraven
    Marcraven committed Jun 12, 2024
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  8. Changes with respect to radii

    @Marcraven
    Marcraven committed Jun 12, 2024
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  9. Added some docstrings

    @Marcraven
    Marcraven committed Jun 12, 2024
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  10. ConvexHull added back to polycrystal

    @Marcraven
    Marcraven committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. Minor bug in new test_compute_mesh_spheres

    @Marcraven
    Marcraven committed Jun 13, 2024
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