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Add support for creation of box object from non-triangular matrices #1769

Merged
merged 37 commits into from
May 16, 2024
Merged

Add support for creation of box object from non-triangular matrices #1769

merged 37 commits into from
May 16, 2024

Commits on Apr 23, 2024

  1. from_box accepts general cell matrices now

    @DomFijan
    DomFijan committed Apr 23, 2024
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  2. add tests for non upper triangular matrices for box from_matrix

    @DomFijan
    DomFijan committed Apr 23, 2024
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  3. remove dimensions argument

    @DomFijan
    DomFijan committed Apr 23, 2024
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  4. linters

    @DomFijan
    DomFijan committed Apr 23, 2024
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  5. change box matrix for the test

    @DomFijan
    DomFijan committed Apr 23, 2024
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  6. add tolerance for box test and add test for 2D boxes

    @DomFijan
    DomFijan committed Apr 23, 2024
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  7. flake8 function name ignore

    @DomFijan
    DomFijan committed Apr 23, 2024
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Commits on Apr 25, 2024

  1. Change test function name 

    Co-authored-by: Joshua A. Anderson <joaander@umich.edu>
    @DomFijan @joaander
    DomFijan and joaander committed Apr 25, 2024
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Commits on Apr 30, 2024

  1. update docstring to reflect differences wrt to_matrix

    @DomFijan
    DomFijan committed Apr 30, 2024
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  2. add from matrix back

    @DomFijan
    DomFijan committed Apr 30, 2024
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  3. return quaternion alongside box object

    @DomFijan
    DomFijan committed Apr 30, 2024
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  4. change tests for new api

    @DomFijan
    DomFijan committed Apr 30, 2024
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  5. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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    pre-commit-ci[bot] committed Apr 30, 2024
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  6. Merge branch 'trunk-patch' into feat/non_triangular_box_matrices_for_… 

    …box_from_matrix
    @DomFijan
    DomFijan committed Apr 30, 2024
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  7. Revert "Merge branch 'trunk-patch' into feat/non_triangular_box_matri… 

    …ces_for_box_from_matrix"

This reverts commit 0d08f36, reversing
changes made to 487359e.
    @DomFijan
    DomFijan committed Apr 30, 2024
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  8. linting

    @DomFijan
    DomFijan committed Apr 30, 2024
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  9. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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    pre-commit-ci[bot] committed Apr 30, 2024
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  10. support 2D lattice vectors

    @DomFijan
    DomFijan committed Apr 30, 2024
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  11. swap matrices for rotation determination

    @DomFijan
    DomFijan committed Apr 30, 2024
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  12. add valueerror when 2d box is not properly set

    @DomFijan
    DomFijan committed Apr 30, 2024
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  13. return rotation matrix instead of quaternion

    @DomFijan
    DomFijan committed Apr 30, 2024
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  14. change and add more tests

    @DomFijan
    DomFijan committed Apr 30, 2024
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  15. update docstrings

    @DomFijan
    DomFijan committed Apr 30, 2024
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  16. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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    pre-commit-ci[bot] committed Apr 30, 2024
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  17. fix lines too long

    @DomFijan
    DomFijan committed Apr 30, 2024
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  18. small update to docstring

    @DomFijan
    DomFijan committed Apr 30, 2024
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Commits on May 3, 2024

  1. fix 2D incorrect numpy function

    @DomFijan
    DomFijan committed May 3, 2024
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  2. fix 2d box logic

    @DomFijan
    DomFijan committed May 3, 2024
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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Commits on May 15, 2024

  1. Merge branch 'trunk-minor' into feat/non_triangular_box_matrices_for_… 

    …box_from_matrix
    @joaander
    joaander committed May 15, 2024
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  2. Restore dependabot.yaml and .pre-commit-config.yaml

    @joaander
    joaander committed May 15, 2024
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  3. Retore more files.

    @joaander
    joaander committed May 15, 2024
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  4. Update hoomd/box.py

    @joaander
    joaander committed May 15, 2024
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  5. Merge branch 'trunk-minor' into feat/non_triangular_box_matrices_for_… 

    …box_from_matrix
    @janbridley
    janbridley committed May 15, 2024
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  6. Switch box_matrix initialization to explicitly use default (np.float64)

    @janbridley
    janbridley committed May 15, 2024
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  7. Switch to more explicit variable naming of box matrix

    @janbridley
    janbridley committed May 15, 2024
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  8. Parametrize test_from_basis_vectors_non_triangular tests

    @janbridley
    janbridley committed May 15, 2024
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