AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data

https://allensdk.readthedocs.io/en/latest/

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Use pynwb NWBGroupSpec and NWBNamespaceBuilder to programatically create yaml definition files for extensions #1528

Open pickles-bread-and-butter opened 4 years ago

pickles-bread-and-butter commented 4 years ago

Overview:

We currently hand edit the yaml files for the extensions in NWB files, this is not usable long term as eventually the yaml format will change. We need to implement the use of NWBGroupSpec and NWBNamespaceBuilder to have pynwb generate these files for us agnostic to version.

Tasks

[ ] Create namespace builder for ophys behavior nwb
[ ] Each module needs to specify custom objects (extensions) as NWBGroupSpec Objects
[ ] Add each GroupSpec to the extension yaml writer
[ ] include and export namespace for extension

Information

https://pynwb.readthedocs.io/en/stable/extensions.html#extending-nwb https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html

rly commented 4 years ago

You can also use the ndx-template rather than hand-editing the YAML files.