Add support for NWB schema 2.3.0 #1245
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@@ Coverage Diff @@
## dev #1245 +/- ##
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- Coverage 73.41% 73.41% -0.01%
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Files 37 37
Lines 2310 2328 +18
Branches 354 357 +3
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+ Hits 1696 1709 +13
- Misses 553 557 +4
- Partials 61 62 +1
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Only validation errors remain before this is ready to merge. (This is not tested on per-PR CI, but nightly CI.) The main error is: hdmf-experimental is cached within the file but NWB objects should not be validated against it. |
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* remove validate_core_schema. You can check the core schema with e.g. * Update Subject unit test * Fix Subject unit test, add check for date_of_birth Co-authored-by: Ryan Ly <[email protected]>
* add option to include source_channels for DecompositionSeries and include round trip test * Use latest schema * Add unit test
* Add optional link to Device in ImageSeries * Add support for device in ImageSeries subclasses * Update ImageMaskSeries docstring * Update schema
* add continuity optional arg to TimeSeries.__init__ * use new enum feature of hdmf to check against controlled vocabulary * Fix flake8 * Add integration test * Fix flake8 * Add correct mapping for data.continuity Co-authored-by: Ryan Ly <[email protected]>
oruebel
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src/pynwb/file.py
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| @@ -55,7 +56,8 @@ class Subject(NWBContainer): | |||
| {'name': 'subject_id', 'type': str, 'doc': 'a unique identifier for the subject', 'default': None}, | |||
| {'name': 'weight', 'type': str, 'doc': 'the weight of the subject', 'default': None}, | |||
| {'name': 'date_of_birth', 'type': datetime, 'default': None, | |||
| 'doc': 'datetime of date of birth. May be supplied instead of age.'}) | |||
| 'doc': 'datetime of date of birth. May be supplied instead of age.'}, | |||
| {'name': 'strain', 'type': str, 'doc': 'the strain of the subject', 'default': None}) | |||
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Do we have a recommendation for how the strain should be specified. If so, it would be nice to add an example in the 'doc' .
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I updated this. Please review.
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oruebel
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The current release of PyNWB, version 1.3.2, supports nwb-schema version 2.2.5. This PR adds support for nwb-schema minor version 2.3.0.
This PR tracks the dev branch of nwb-schema to ensure that changes in nwb-schema are compatible with PyNWB or are accompanied with corresponding changes in PyNWB. Those changes in PyNWB should be merged into this branch.
waveformscolumn to theUnitstable.strainfield toSubject.DecompositionSeriesan optionalDynamicTableRegioncalledsource_channels.ImageSeriesan optional link toDevice.continuityfield toTimeSeries.filteringattribute toElectricalSeries.stimulus_descriptionforIZeroCurrentClampto have the fixed valueN/A.ExternalResourcesandEnumDatadata types. Schema in the HDMF-experimental namespace are experimental and subject to breaking changes at any time.
ExternalResourcesfor storing ontology information / external resource references.EnumDatato store data from a set of fixed values.CSRMatrixfrom 'int' to 'uint' and added missingdata_type_inc: Containerto the
CSRMatrixtype.SimpleMultiContainer, a Container for storing other Container and Data objects together.AlignedDynamicTable, a DynamicTable type with support for categories (or sub-headings) each described by a separate DynamicTable.VectorIndex.VectorIndexnow extendsVectorDatainstead ofIndex.Indexdata type.cd src/pynwb/nwb-schema/,git checkout dev,git pull origin dev,git fetch --tags,git checkout dev,cd ../../..,git add .,git commit -m "Update nwb-schema submodule to [new_release], andgit pushAfter merging: