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Handle skeleton encoding internally #1970

Merged
merged 40 commits into from
Sep 25, 2024
Merged

Handle skeleton encoding internally #1970

merged 40 commits into from
Sep 25, 2024

Commits on Sep 20, 2024

  1. start class SkeletonEncoder

    @eberrigan
    eberrigan committed Sep 20, 2024
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Commits on Sep 21, 2024

  1. start class SkeletonEncoder

    @eberrigan
    eberrigan committed Sep 21, 2024
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  2. _encoded_objects need to be a dict to add to

    @eberrigan
    eberrigan committed Sep 21, 2024
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Commits on Sep 23, 2024

  1. add notebook for testing

    @eberrigan
    eberrigan committed Sep 23, 2024
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  2. format

    @eberrigan
    eberrigan committed Sep 23, 2024
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  3. fix type in docstring

    @eberrigan
    eberrigan committed Sep 23, 2024
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  4. finish classmethod for encoding Skeleton as a json string

    @eberrigan
    eberrigan committed Sep 23, 2024
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  5. test encoded Skeleton as json string by decoding it

    @eberrigan
    eberrigan committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. add test for decoded encoded skeleton

    @eberrigan
    eberrigan committed Sep 24, 2024
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  2. update jupyter notebook for easy testing

    @eberrigan
    eberrigan committed Sep 24, 2024
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  3. constraining attrs in dev environment to make sure decode format is a… 

    …lways the same locally
    @eberrigan
    eberrigan committed Sep 24, 2024
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  4. encode links first then encode source then target then type

    @eberrigan
    eberrigan committed Sep 24, 2024
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  5. save first enconding statically as an input to _get_or_assign_id so t… 

    …hat we do not always get py/id
    @eberrigan
    eberrigan committed Sep 24, 2024
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  6. save first encoding statically

    @eberrigan
    eberrigan committed Sep 24, 2024
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  7. first encoding is passed to _get_or_assign_id

    @eberrigan
    eberrigan committed Sep 24, 2024
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  8. use first_encoding variable to determine if we should assign a py/id

    @eberrigan
    eberrigan committed Sep 24, 2024
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  9. add print statements for debugging

    @eberrigan
    eberrigan committed Sep 24, 2024
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  10. update notebook for easy testing

    @eberrigan
    eberrigan committed Sep 24, 2024
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  11. black

    @eberrigan
    eberrigan committed Sep 24, 2024
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  12. remove comment

    @eberrigan
    eberrigan committed Sep 24, 2024
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  13. adding attrs constraint to show this passes for certain attrs version… 

    … only
    @eberrigan
    eberrigan committed Sep 24, 2024
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  14. add import

    @eberrigan
    eberrigan committed Sep 24, 2024
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  15. switch out jsonpickle.encode

    @eberrigan
    eberrigan committed Sep 24, 2024
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  16. oops remove import

    @eberrigan
    eberrigan committed Sep 24, 2024
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  17. can attrs be unconstrained?

    @eberrigan
    eberrigan committed Sep 24, 2024
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  18. forgot comma

    @eberrigan
    eberrigan committed Sep 24, 2024
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  19. pin attrs for testing

    @eberrigan
    eberrigan committed Sep 24, 2024
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  20. test Skeleton from json, template, with symmetries, and template

    @eberrigan
    eberrigan committed Sep 24, 2024
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  21. use SkeletonEncoder.encode

    @eberrigan
    eberrigan committed Sep 24, 2024
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  22. black

    @eberrigan
    eberrigan committed Sep 24, 2024
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  23. try removing None values in EdgeType reduced

    @eberrigan
    eberrigan committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. Handle case when nodes are replaced by integer indices from caller

    @eberrigan
    eberrigan committed Sep 25, 2024
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  2. Remove prototyping notebook

    @talmo
    talmo committed Sep 25, 2024
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  3. Merge branch 'develop' into elizabeth/handle-skeleton-encoding-intern… 

    …ally
    @talmo
    talmo committed Sep 25, 2024
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  4. Remove attrs pins

    @talmo
    talmo committed Sep 25, 2024
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  5. Remove sort keys (which flips the neccessary ordering of our py/ids)

    @roomrys
    roomrys committed Sep 25, 2024
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  6. Do not add extra indents to encoded file

    @roomrys
    roomrys committed Sep 25, 2024
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  7. Only append links after fully encoded (fat-finger)

    @roomrys
    roomrys committed Sep 25, 2024
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  8. Remove outdated comment

    @roomrys
    roomrys authored Sep 25, 2024
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  9. Lint

    @roomrys
    roomrys committed Sep 25, 2024
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