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Schema 2.3.0 #278

Merged
merged 20 commits into from
Jun 2, 2021
Merged

Schema 2.3.0 #278

merged 20 commits into from
Jun 2, 2021

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lawrence-mbf
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@lawrence-mbf lawrence-mbf commented May 12, 2021

Update NWB Schema to 2.3.0

  • Add Schema
  • Generate Schema and move default point
  • Pass tests
    • Pass PyNWB interop tests.
    • Pass MATLAB Tests
  • Update documentation
  • Update tutorials (if any)

@lawrence-mbf lawrence-mbf self-assigned this May 12, 2021
Lawrence added 11 commits May 12, 2021 15:55
Due to how VectorIndex is now a VectorData subtype, we now store
everything under the `vectordata` property in DynamicTable.

All references to the legacy `vectorindex` has been replaced.
remove reference to `vectorindex` property as that no longer exists.
- Given how the MATLAB table already requires data splitting
according to data type, adding a row by tableRow no longer requires
wrapping a cell.
- The mere existence of `tablepath` now forces the creation of a
Ragged Array regardless of whether or not the data fits to the
standard.
VectorIndex used to subclass the Index type which did not require
it to have a `description` property. It now automatically sets
it to prevent export errors.
- addRawData: reorganize redundant logic.
- checkDtype. Add error ID and reformat error message.
Due to quirks in the generation functions, DynamicTable utilities
may occur in vectordata OR vectorindex going forward.

All pre-2.3.0 Dynamic Tables only store their VectorIndex objects
into `vectorindex` while post-2.3.0 VectorIndex objects are stored
in `vectordata` along with VectorData.
@lawrence-mbf lawrence-mbf marked this pull request as ready for review May 27, 2021 17:28
@lawrence-mbf lawrence-mbf marked this pull request as draft May 27, 2021 17:29
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codecov bot commented May 27, 2021

Codecov Report

Merging #278 (392f72f) into master (8ddf90c) will decrease coverage by 0.17%.
The diff coverage is 83.33%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #278      +/-   ##
==========================================
- Coverage   47.82%   47.65%   -0.18%     
==========================================
  Files         124      124              
  Lines        5599     5634      +35     
==========================================
+ Hits         2678     2685       +7     
- Misses       2921     2949      +28     
Impacted Files Coverage Δ
+types/+util/+dynamictable/clear.m 0.00% <0.00%> (ø)
+types/+util/checkDtype.m 64.05% <ø> (ø)
tutorials/convertTrials.m 0.00% <ø> (ø)
tutorials/ecephys.m 0.00% <ø> (ø)
+types/+util/+dynamictable/addVecInd.m 75.00% <60.00%> (+12.50%) ⬆️
+types/+util/correctType.m 82.14% <87.50%> (+5.21%) ⬆️
+types/+util/+dynamictable/addRawData.m 86.11% <88.88%> (+9.18%) ⬆️
+types/+util/+dynamictable/getIndex.m 94.28% <88.88%> (+14.28%) ⬆️
+types/+util/+dynamictable/addTableRow.m 72.22% <100.00%> (+10.68%) ⬆️
+types/+util/+dynamictable/addVarargRow.m 91.30% <100.00%> (+4.34%) ⬆️
... and 16 more

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Lawrence added 6 commits May 27, 2021 14:17
- Actually treat the expected type as a minimum as is true in nwb-schema.
If the value type is larger than the expected type, then scale progressively to fit.

- Fix dynamic table indexing due to VectorIndex now being set to uint8 as an expected
type. The type should start at uint8 but scale upwards as the indices get larger.
- Fix logic error regarding intervals timeseries storage.
- Fix missing descriptor for the VectorIndex.
@lawrence-mbf lawrence-mbf marked this pull request as ready for review May 27, 2021 22:30
@lawrence-mbf lawrence-mbf requested a review from bendichter May 27, 2021 22:33
@lawrence-mbf lawrence-mbf merged commit 6d47856 into master Jun 2, 2021
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