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Implement viewer representations #373

Merged
merged 96 commits into from
Nov 6, 2023
Merged

Implement viewer representations #373

merged 96 commits into from
Nov 6, 2023

Commits on Oct 14, 2022

  1. draft

    @cpignedoli
    cpignedoli committed Oct 14, 2022
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Commits on Oct 15, 2022

  1. work in progress

    @cpignedoli
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  2. first working version, to-do: add/remove atoms in edit structure

    @cpignedoli
    cpignedoli committed Oct 15, 2022
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  3. comments

    @cpignedoli
    cpignedoli committed Oct 15, 2022
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Commits on Oct 16, 2022

  1. toward general formalism

    @cpignedoli
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  2. starting modifiying addition and rmeova of atoms

    @cpignedoli
    cpignedoli committed Oct 16, 2022
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Commits on Oct 17, 2022

  1. intermediate mess

    @cpignedoli
    cpignedoli committed Oct 17, 2022
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  2. used same concept of fragments for representations

    @cpignedoli
    cpignedoli committed Oct 17, 2022
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  3. reordering representation class

    @cpignedoli
    cpignedoli committed Oct 17, 2022
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  4. first draft working

    @cpignedoli
    cpignedoli committed Oct 17, 2022
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Commits on Oct 18, 2022

  1. redesigned, debug prints present

    @cpignedoli
    cpignedoli committed Oct 18, 2022
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  2. refinements

    @cpignedoli
    cpignedoli committed Oct 18, 2022
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Commits on Oct 19, 2022

  1. use dtratlet input_structure

    @cpignedoli
    cpignedoli committed Oct 19, 2022
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  2. version for first evaluation

    @cpignedoli
    cpignedoli committed Oct 19, 2022
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Commits on Oct 21, 2022

  1. problem of syncronization of arrays in structure traitlet

    @cpignedoli
    cpignedoli committed Oct 21, 2022
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  2. updated validate structure

    @cpignedoli
    cpignedoli committed Oct 21, 2022
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  3. Fixed bug of representrations not passed

    @cpignedoli
    cpignedoli committed Oct 21, 2022
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  4. default -1 for arrays['representations'] for atoms not included in a rep

    @cpignedoli
    cpignedoli committed Oct 21, 2022
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  5. added show of representations

    @cpignedoli
    cpignedoli committed Oct 21, 2022
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  6. modification

    @cpignedoli
    cpignedoli committed Oct 21, 2022
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  7. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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Commits on Oct 22, 2022

  1. simplifying to single component

    @cpignedoli
    cpignedoli committed Oct 22, 2022
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  2. bug fix

    @cpignedoli
    cpignedoli committed Oct 22, 2022
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  3. bug fix

    @cpignedoli
    cpignedoli committed Oct 22, 2022
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Commits on Oct 23, 2022

  1. strange ngl problme

    @cpignedoli
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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Commits on Oct 24, 2022

  1. first working version

    @cpignedoli
    cpignedoli committed Oct 24, 2022
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  2. exclude from adavnced selection atoms not shown

    @cpignedoli
    cpignedoli committed Oct 24, 2022
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  3. cleaning

    @cpignedoli
    cpignedoli committed Oct 24, 2022
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  4. cleaning, removed orient_z_up to be put in separate PR

    @cpignedoli
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Commits on Jan 12, 2023

  1. Merge branch 'master' into viewer-representations

    @yakutovicha
    yakutovicha committed Jan 12, 2023
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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Commits on Jan 16, 2023

  1. some flake fixes

    @cpignedoli
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Commits on Jan 17, 2023

  1. falke fix

    @cpignedoli
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Commits on Jan 23, 2023

  1. Small fixes, more compact representations styling.

    @yakutovicha
    yakutovicha committed Jan 23, 2023
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Commits on Jan 24, 2023

  1. Simplify the code.

    @yakutovicha
    yakutovicha committed Jan 24, 2023
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  2. Continue with changes.

    @yakutovicha
    yakutovicha committed Jan 24, 2023
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Commits on Jan 25, 2023

  1. Fix supercell appearance (old components were not removed).

    @yakutovicha
    yakutovicha committed Jan 25, 2023
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  2. Further simplify and improve the code.

    @yakutovicha
    yakutovicha committed Jan 25, 2023
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Commits on Jan 26, 2023

  1. Improve hightlight_atoms(), simplify the handling of representations.

    @yakutovicha
    yakutovicha committed Jan 26, 2023
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  2. small, non-important changes.

    @yakutovicha
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Commits on Jan 30, 2023

  1. Keep representations after editing the structure

    @yakutovicha
    yakutovicha committed Jan 30, 2023
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Commits on Feb 1, 2023

  1. Apply suggestions from the code review. 

    - Create a default representation that can't be deleted and remains in the very top.
- If new atoms are added, put the into the default representation.
- Check that only existing atoms can be put in the representation.
    @yakutovicha
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  2. Fix numpy array type problem.

    @yakutovicha
    yakutovicha committed Feb 1, 2023
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  3. Remove atoms selection from non-default representations when new stru… 

    …cture is imported.
    @yakutovicha
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  4. Small change to a comment.

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Commits on Sep 25, 2023

  1. Merge branch 'master' into viewer-representations

    @yakutovicha
    yakutovicha committed Sep 25, 2023
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Commits on Sep 27, 2023

  1. Fix bugs.

    @yakutovicha
    yakutovicha committed Sep 27, 2023
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  2. Merge branch 'master' into viewer-representations

    @yakutovicha
    yakutovicha committed Sep 27, 2023
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Commits on Sep 28, 2023

  1. Fix bug for the editor.

    @yakutovicha
    yakutovicha committed Sep 28, 2023
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Commits on Oct 6, 2023

  1. Merge branch 'viewer-representations' of https://github.com/cpignedol… 

    …i/aiidalab-widgets-base into viewer-representations
    @yakutovicha
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Commits on Oct 8, 2023

  1. Fix tests.

    @yakutovicha
    yakutovicha committed Oct 8, 2023
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  2. Merge branch 'master' into viewer-representations

    @yakutovicha
    yakutovicha committed Oct 8, 2023
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Commits on Oct 9, 2023

  1. Add tests for the viewer.

    @yakutovicha
    yakutovicha committed Oct 9, 2023
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  2. Merge branch 'viewer-representations' of https://github.com/cpignedol… 

    …i/aiidalab-widgets-base into viewer-representations
    @yakutovicha
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  3. Fix tests

    @yakutovicha
    yakutovicha committed Oct 9, 2023
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  4. Test 3 atoms selection.

    @yakutovicha
    yakutovicha committed Oct 9, 2023
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  5. More tests.

    @yakutovicha
    yakutovicha committed Oct 9, 2023
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  6. More tests.

    @yakutovicha
    yakutovicha committed Oct 9, 2023
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  7. More tests.

    @yakutovicha
    yakutovicha committed Oct 9, 2023
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  8. Add tests for the representations.

    @yakutovicha
    yakutovicha committed Oct 9, 2023
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  9. Slightly improve datatypes viewers notebook.

    @yakutovicha
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Commits on Oct 10, 2023

  1. More tests.

    @yakutovicha
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  2. More tests.

    @yakutovicha
    yakutovicha committed Oct 10, 2023
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  3. More tests.

    @yakutovicha
    yakutovicha committed Oct 10, 2023
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  4. More tests.

    @yakutovicha
    yakutovicha committed Oct 10, 2023
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  5. Review.

    @yakutovicha
    yakutovicha committed Oct 10, 2023
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  6. Remove unnecessary warning check.

    @yakutovicha
    yakutovicha committed Oct 10, 2023
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Commits on Oct 12, 2023

  1. Merge branch 'master' into viewer-representations

    @yakutovicha
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Commits on Oct 20, 2023

  1. review

    @yakutovicha
    yakutovicha committed Oct 20, 2023
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  2. Improve selection color.

    @yakutovicha
    yakutovicha committed Oct 20, 2023
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  3. Merge branch 'master' into viewer-representations

    @yakutovicha
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Commits on Oct 23, 2023

  1. Representation arrays: convert them to bool type.

    @yakutovicha
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  2. Fix pytests

    @yakutovicha
    yakutovicha committed Oct 23, 2023
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  3. Fix tests.

    @yakutovicha
    yakutovicha committed Oct 23, 2023
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Commits on Oct 24, 2023

  1. Remove list_to_nglview function as it is used only in one place.

    @yakutovicha
    yakutovicha committed Oct 24, 2023
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  2. NglViewerRepresentation - improve class docstring, add comment for th… 

    …e master_class.
    @yakutovicha
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  3. fix

    @yakutovicha
    yakutovicha committed Oct 24, 2023
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  4. update sync_myself_to_array_from_atoms_object

    @yakutovicha
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  5. Add type annotations.

    @yakutovicha
    yakutovicha committed Oct 24, 2023
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  6. Better name for the nglview parameters dictionary.

    @yakutovicha
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  7. natoms - make it a class property.

    @yakutovicha
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  8. Put representation name into a constant

    @yakutovicha
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Commits on Oct 25, 2023

  1. _StructureDataBaseViewer work on docstrings.

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  2. delete_representation: add type hint.

    @yakutovicha
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  3. Slightly improve _observe_structure method.

    @yakutovicha
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  4. try to fix docs build.

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Commits on Oct 30, 2023

  1. Representation arrays: move back to int to properly handle new atoms. 

    The issues with the bool array is that only shows whether the atoms was
in the representation or not. This is not enough, because one also needs
to consider the newly added atoms.
    @yakutovicha
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Commits on Oct 31, 2023

  1. Remove return statements from the 'add_myself_to_atoms_object' method.

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  2. Replace "_aiidalab_viewer_representation_" with REPRESENTATION_PREFIX… 

    … constant.
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Commits on Nov 2, 2023

  1. Fix issue with representation's name constant.

    @yakutovicha
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  2. Split tests for better code maintainability.

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  3. review.

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  4. Rename master_class with viewer_class

    @yakutovicha
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Commits on Nov 6, 2023

  1. Merge branch 'master' into viewer-representations

    @yakutovicha
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  2. Remove aiida_datatypes_viewers.ipynb

    @yakutovicha
    yakutovicha committed Nov 6, 2023
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