Documentation Bug for Calcium Imaging Data Tutorial

MarikeReimer commented 4 years ago

Description

I tried viewing the file created in the pynwb Calcium Imaging Data tutorial in a Jupyter notebook with NWB2Widgets. When viewing the the image segmentation group, I got an error message.

Steps to Reproduce

1) Go to: https://pynwb.readthedocs.io/en/stable/tutorials/domain/ophys.html#sphx-glr-tutorials-domain-ophys-py

2) At the bottom of the page, select Download Jupyter notebook: Ophys.ipynb

3) Open notebook and paste the following code at the bottom:

from nwbwidgets import nwb2widget io = NWBHDF5IO('ophys_example.nwb', mode='r') nwb = io.read() nwb2widget(nwb)

4) Select the processing module >ophys>ImageSegmentation.

5) After waiting a while for rendering, I got the following error:

Notebook validation failed: {'version_major': 2, 'version_minor': 0, 'model_id': '87c09359c2074c13891ca080691a0f53'} is not valid under any of the given schemas: { "version_major": 2, "version_minor": 0, "model_id": "87c09359c2074c13891ca080691a0f53" }

Environment

Python Executable: Conda
Python Version: 3.7
Operating System: Windows
HDMF Version: pynwb 1.3.0

Checklist

[x ] Have you ensured the feature or change was not already [reported] It may be related to https://github.com/NeurodataWithoutBorders/pynwb/issues/1192, but since I am using the latest release, I wanted to raise the issue.

(https://github.com/NeurodataWithoutBorders/pynwb/issues)?

[ x] Have you included a brief and descriptive title?
[ x] Have you included a clear description of the problem you are trying to solve?
[x ] Have you included a minimal code snippet that reproduces the issue you are encountering?
[ x] Have you checked our Contributing document?

bendichter commented 4 years ago

@MarikeReimer Thanks for the report. I'm not quite sure what to make of this, but it looks like it may be an error with nwbwidgets, not pynwb. I'm going to move this over there until we can figure out what the root cause is.

oruebel commented 4 years ago

Just a thought, maybe Sphinx Gallery needs to be updated to create the notebooks in a new version of the notebook schema to work with nwb-widgets?

NeurodataWithoutBorders / nwbwidgets