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Access and Stream Trajectories with MDAnalysis #287

Merged
merged 55 commits into from
Sep 24, 2023
Merged

Access and Stream Trajectories with MDAnalysis #287

merged 55 commits into from
Sep 24, 2023

Commits on Aug 10, 2023

  1. access and stream universe

    @yuxuanzhuang
    yuxuanzhuang committed Aug 10, 2023
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Commits on Aug 14, 2023

  1. refactor and reactivate universe during reloading

    @yuxuanzhuang
    yuxuanzhuang committed Aug 14, 2023
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  2. ignore log

    @yuxuanzhuang
    yuxuanzhuang committed Aug 14, 2023
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Commits on Aug 15, 2023

  1. remove mol_objects and access it directly

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    yuxuanzhuang committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. add unknown element X

    @yuxuanzhuang
    yuxuanzhuang committed Aug 16, 2023
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  2. add support for multiple universe, clean up code, add representation … 

    …syntax
    @yuxuanzhuang
    yuxuanzhuang committed Aug 16, 2023
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  3. check existing mda session

    @yuxuanzhuang
    yuxuanzhuang committed Aug 16, 2023
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  4. update trajectory

    @yuxuanzhuang
    yuxuanzhuang committed Aug 16, 2023
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  5. update deleted objects

    @yuxuanzhuang
    yuxuanzhuang committed Aug 16, 2023
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  6. fix ui and add in_memory

    @yuxuanzhuang
    yuxuanzhuang committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. add updating atomgroup

    @yuxuanzhuang
    yuxuanzhuang committed Aug 17, 2023
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Commits on Aug 19, 2023

  1. switch to depgraph update

    @yuxuanzhuang
    yuxuanzhuang committed Aug 19, 2023
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  2. update depgraph during loading

    @yuxuanzhuang
    yuxuanzhuang committed Aug 19, 2023
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  3. add option to move to memory

    @yuxuanzhuang
    yuxuanzhuang committed Aug 19, 2023
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  4. add old code

    @yuxuanzhuang
    yuxuanzhuang committed Aug 19, 2023
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  5. node bug

    @yuxuanzhuang
    yuxuanzhuang committed Aug 19, 2023
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Commits on Aug 21, 2023

  1. remove in_memory from gui

    @yuxuanzhuang
    yuxuanzhuang committed Aug 21, 2023
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  2. start representation

    @yuxuanzhuang
    yuxuanzhuang committed Aug 21, 2023
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  3. retrieve universe

    @yuxuanzhuang
    yuxuanzhuang committed Aug 21, 2023
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Commits on Sep 13, 2023

  1. remove during reg

    @yuxuanzhuang
    yuxuanzhuang committed Sep 13, 2023
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Commits on Sep 14, 2023

  1. merge to main

    @yuxuanzhuang
    yuxuanzhuang committed Sep 14, 2023
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  2. fix initial node creation

    @BradyAJohnston
    BradyAJohnston committed Sep 14, 2023
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Commits on Sep 19, 2023

  1. fix style

    @yuxuanzhuang
    yuxuanzhuang committed Sep 19, 2023
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  2. add test for mda

    @yuxuanzhuang
    yuxuanzhuang committed Sep 19, 2023
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  3. test updating atomgroup

    @yuxuanzhuang
    yuxuanzhuang committed Sep 19, 2023
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  4. Merge remote-tracking branch 'origin/main' into streaming

    @yuxuanzhuang
    yuxuanzhuang committed Sep 19, 2023
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  5. test persistance

    @yuxuanzhuang
    yuxuanzhuang committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. mock mda if not installed

    @yuxuanzhuang
    yuxuanzhuang committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. change style selection to enum 

    Changes the style selection in the UI to an enum,
which it should have been initially.
    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  2. bump MDAnalysis version

    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  3. remove superfluos operator

    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  4. add some initial operator tests

    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  5. update docs permissions 

    update permission

update permissions for workflow
    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  6. update docs

    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  7. rename 'legacy' to 'in_memory' 

    The method of loading all frames in to memory I don't _immediately_ have plans to remove, so renaming it to 'in_memory' instead of legacy for now.
    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  8. skip test if mda not installed

    @yuxuanzhuang
    yuxuanzhuang committed Sep 21, 2023
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  9. import mda

    @yuxuanzhuang
    yuxuanzhuang committed Sep 21, 2023
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  10. testmda class

    @yuxuanzhuang
    yuxuanzhuang committed Sep 21, 2023
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  11. fix import In Memory

    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  12. add initial docs for MD import

    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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  13. Merge branch 'streaming' of https://github.com/yuxuanzhuang/Molecular… 

    …Nodes into pr/287
    @BradyAJohnston
    BradyAJohnston committed Sep 21, 2023
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Commits on Sep 22, 2023

  1. maybe fix? 

    test new token

without token

set deployments to v1

revoke edits on docs.yml

tweak permissions

tweak persmissions

tweak PAT

tweak PAT

tweak PAT
    @BradyAJohnston
    BradyAJohnston committed Sep 22, 2023
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  2. adding some details to recreate an animation

    @BradyAJohnston
    BradyAJohnston committed Sep 22, 2023
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  3. add in_memory for show

    @yuxuanzhuang
    yuxuanzhuang committed Sep 22, 2023
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  4. add test for in_memory

    @yuxuanzhuang
    yuxuanzhuang committed Sep 22, 2023
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  5. add test for in_memory 2

    @yuxuanzhuang
    yuxuanzhuang committed Sep 22, 2023
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  6. use show with in_memory

    @yuxuanzhuang
    yuxuanzhuang committed Sep 22, 2023
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Commits on Sep 24, 2023

  1. rename representation to style 

    Aligns with the use of `Style` inside of Molecular Nodes nodegroups.
    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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  2. fix: importing uses default selected style

    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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  3. add atom_name to test

    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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  4. cleanup style nodes

    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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  5. add tests to compare operator and api usage

    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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  6. more details for MD tutorial

    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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  7. fix test floating point

    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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  8. update test to fix floating point error

    @BradyAJohnston
    BradyAJohnston committed Sep 24, 2023
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