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NWB Loader #10

Merged
merged 22 commits into from
Sep 12, 2024
Merged

NWB Loader #10

merged 22 commits into from
Sep 12, 2024

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sneakers-the-rat
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@sneakers-the-rat sneakers-the-rat commented Sep 2, 2024 •
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(working PR for NWB reading, going to work on that separately than dumping/loading to/from the yaml representation)

  • Make nwb_file fixture that creates nwb file with all the special data types we want to handle
  • Load from the nwb_file into nwb_linkml models
  • Test that all data is preserved :)

Then we'll work on saving in other PRs

@sneakers-the-rat
testing nwb file, and experimenting with yaml format
b555ccb
@sneakers-the-rat
working on grpah loading of nwb files
49585e4
@sneakers-the-rat
split up fixtures and nwb fixture in particular, add --clean pytest o…
3641d33 
…ption
@sneakers-the-rat
lint
53c415d
@sneakers-the-rat
codespell
a693427
@sneakers-the-rat
update models to correctly handle ElementIdentifiers
97135c1
@sneakers-the-rat
exclude metadata vars from column and category checks
ee35e59
@sneakers-the-rat
instantiate ValidationError according to pydantic/pydantic#6734
676d42d
@sneakers-the-rat
model update
cd3d7ca
@sneakers-the-rat
checkpointing working on model loading. it's a sloggggggggg
d1498a3
@sneakers-the-rat
CHECKPOINT WITH IT WORKING before cleanup and model regeneration
8078492
@sneakers-the-rat
updating model generation methods, still some models being converted …
27b5ddd 
…to str instead of being inlined, but almost there
@sneakers-the-rat
Updating model generation methods to make both loader tests and hdmf …
000ddde 
…include unit tests pass (pending following model update commit)
@sneakers-the-rat
regenerate models
dfcb395
@sneakers-the-rat
use in-repo version of models
3f360c2
@sneakers-the-rat
bump nwb-models version
b76b0fd
@sneakers-the-rat
bump version of dependant nwb-models
1f1325e
@sneakers-the-rat
clean up old hdf5 reader methods, fix truncate_hdf5 method, make prop…
d31ac29 
…er'd test data files with working references
@sneakers-the-rat
remove unused code, nocover some debug arms
bb59c9d
@sneakers-the-rat
working thru tests for nwb file
91b2abf
@sneakers-the-rat
add id to index name on aligneddynamictable correctly
95fbce1
@sneakers-the-rat
lint
0eeea4c
@sneakers-the-rat sneakers-the-rat mentioned this pull request Sep 12, 2024
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Good good yes calling this here so i can get yaml dumping ready by lab meeting

@sneakers-the-rat sneakers-the-rat marked this pull request as ready for review September 12, 2024 04:24
@sneakers-the-rat sneakers-the-rat merged commit f94a144 into main Sep 12, 2024
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