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ME-ICA / tedana

TE-dependent analysis of multi-echo fMRI
https://tedana.readthedocs.io
GNU Lesser General Public License v2.1
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dynamics reports crashing with bokeh 3.4.0 #1063

Closed handwerkerd closed 2 months ago

handwerkerd commented 3 months ago

Summary

A user just sent me a crashed run and I think the issue is that they are using bokeh=3.4.0, which was released in March 2024.

Additional Detail

The log contains

INFO.   tedana:tedana_workflow:903 Generating dynamic report
BokehDeprecationWarning: 'circle() method with size value' was deprecated in Bokeh 3.4.0 and will be removed, use 'scatter(size=...) instead' instead.

The trackback crashes here: https://github.com/ME-ICA/tedana/blob/a21d65ec5b1682a52cb8fe0eee1689d5eb3154a3/tedana/reporting/dynamic_figures.py#L350

The bokeh 3.4.0 version release includes Deprecated figure.circle(size=10) in favour of figure.scatter(size=10) API (pull request 13283)

Next Steps

gottss commented 3 months ago

Summary

A user just sent me a crashed run and I think the issue is that they are using bokeh=3.4.0, which was released in March 2024.

Additional Detail

The log contains

INFO.   tedana:tedana_workflow:903 Generating dynamic report
BokehDeprecationWarning: 'circle() method with size value' was deprecated in Bokeh 3.4.0 and will be removed, use 'scatter(size=...) instead' instead.

The trackback crashes here:

https://github.com/ME-ICA/tedana/blob/a21d65ec5b1682a52cb8fe0eee1689d5eb3154a3/tedana/reporting/dynamic_figures.py#L350

The bokeh 3.4.0 version release includes Deprecated figure.circle(size=10) in favour of figure.scatter(size=10) API (pull request 13283)

Next Steps

  • Confirm this really is causing a full crash with the newest version of Bokeh
  • Figure out, if we switch from circle to scatter if that affects our visualizations or if we'll need to update the minimum acceptable version of bokeh

A follow-up: Uninstalling Bokeh 3.4.0 and installing Bokeh 3.3.0 fixed this issue.

eurunuela commented 3 months ago

I would say let's limit the version of Bokeh to a maximum of <3.4.0. We can update this later in the future if necessary.