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Implement Dynamictable #6

Merged
merged 61 commits into from
Aug 15, 2024
Merged

Implement Dynamictable #6

merged 61 commits into from
Aug 15, 2024

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sneakers-the-rat
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@sneakers-the-rat sneakers-the-rat commented Aug 6, 2024 •
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  • Simple dynamictable with reference - eg. ElectrodeSeries
  • Dynamictable with index
  • AlignedDynamicTable
  • DynamicTableRegion

@sneakers-the-rat
add dynamictable, vectordata, vectorindex mixins
d118477
@sneakers-the-rat
update hdmf models/schema
abf1b0e
@sneakers-the-rat
lint
38e8a6f
@sneakers-the-rat
add pandas
776078a
@sneakers-the-rat
fix hdmf forwardrefs, remove numpy types temporarily
1d527d8
@sneakers-the-rat
regenerate models, lint
0d10ba9
@sneakers-the-rat
fix attr access in linkml provider result
2fef717
@sneakers-the-rat
no op to update github cache?
66369c7
@sneakers-the-rat
update numpydantic version and relock
b2d7b12
@sneakers-the-rat
make names less lengthy by only contatenating one layer of nesting wi…
9bfee35 
…th __
@sneakers-the-rat
update models with shorter names
e72c860
@sneakers-the-rat
unify naming of derived child groups, arrays, and values as just all …
b3b5b9d 
…being named "value". Add link building. Fix erroneously collapsing anonymous and named container groups.
@sneakers-the-rat
update models
0a150d6
@sneakers-the-rat
fix name array -> value in hdmf mixins
374bd89
@sneakers-the-rat
update hdmf common table
652ddb3
@sneakers-the-rat
correctly handle attributes
da6d0d8
@sneakers-the-rat
regenerate models
e5d1cc5
@sneakers-the-rat
first impl of dynamictable working!
c06859a
@sneakers-the-rat
regenerate models
51ceb14
@sneakers-the-rat
lint!
83dd59d
@sneakers-the-rat
update tests
6431afa
@sneakers-the-rat
fuckin LINT
c2e663e
@sneakers-the-rat
use coveralls action
fbb06da
@sneakers-the-rat
working ragged array indexing before rebuilding models
a11d3d0
@sneakers-the-rat
regenerate model, lint
a309c25
@sneakers-the-rat
remove dask, nptyping
edea802
@sneakers-the-rat
fix array casting for dtypes that have a shape attr but nothing in it
3ee7c68
@sneakers-the-rat
continue removing nptyping, actually fix indexing
a993ee1
@sneakers-the-rat
my god it works but what have i done
a990948
@sneakers-the-rat
oop
9e7c533
@sneakers-the-rat
add logging. less janky adapter instantiation using model validators.…
0452a43 
… correctly propagate properties from ancestor classes when building
@sneakers-the-rat
actually no that's stupid, linkml handles inheritance except for the …
994b79e 
…one special case of compound dtypes which aren't a thing in linkml and are here used exclusively for 1d vectors.
@sneakers-the-rat
regenerate models
dd99ac2
@sneakers-the-rat
working aligned dynamic table and TimeSeriesReferenceVectorData
06a18c2
@sneakers-the-rat
regenerate models
6c07b87
@sneakers-the-rat
lint
0a93195
@sneakers-the-rat
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This will be good to go after writing tests and fixing the schema provider - which is broken because i tried to make the resolution of imports a little less implicit but that broke the delayed resolution that was already in place. just need to clean up the providers a bit so that NWB core schema never gets provided without the correct and matching version of hdmf schema.

then it'll be time to

  • refactor out the models into a separate package so they can be included elsewhere, and
  • do some major tidying bc i am feeling the weight of being halfway between implementations, need to cut out some crust and do some renaming... "adapters" "generators," "providers," and "maps" are not even close to intuitive lol

@sneakers-the-rat
eager resolution of hdmf namespace when loaded from yaml
9bd3634
@sneakers-the-rat
lint
1715043
@sneakers-the-rat
fuckin codespell.
50005d3 
also don't double run tests
@sneakers-the-rat
Make VectorData and VectorIndex generics to ensure coercion to Vector…
01e46f7 
…Data for declared columns
@sneakers-the-rat
regenerate models
980db25
@sneakers-the-rat
more texts. Fix coercion with ndarrays and vectordata, incl numpydant…
43ff350 
…ic 1.3.3 making ndarray types callable
@sneakers-the-rat
regenerate models
d61d1ec
@sneakers-the-rat
indexing tests, fix for pytest 8, logging tests
5780947
@sneakers-the-rat
vectordata indexing tests
b610f32
@sneakers-the-rat
lint
7cb8eea
@sneakers-the-rat
region tests
36add1a
@sneakers-the-rat
lint
b601027
@sneakers-the-rat
codespell istg
54409c7
@sneakers-the-rat
fix setattr for index and data
7e7cbc1
@sneakers-the-rat
aligned dynamictable tests
ce096db
@sneakers-the-rat
regenerate models
1096574
@sneakers-the-rat
reference vector series tests, fix model tests
24494b8
@sneakers-the-rat
update models
f5a4173
@sneakers-the-rat
lint
3cda6c3
@sneakers-the-rat
fix tsrv test
ec7a825
@sneakers-the-rat
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and with that we call it implemented

@sneakers-the-rat sneakers-the-rat marked this pull request as ready for review August 15, 2024 08:57
@sneakers-the-rat sneakers-the-rat merged commit ff77f0a into main Aug 15, 2024
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