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dynamics reports crashing with bokeh 3.4.0 #1063

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handwerkerd opened this issue Mar 20, 2024 · 2 comments · Fixed by #1068
Closed

dynamics reports crashing with bokeh 3.4.0 #1063

handwerkerd opened this issue Mar 20, 2024 · 2 comments · Fixed by #1068
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bug issues describing a bug or error found in the project good first issue issues that we think are good for new contributors. Equivalent to "very low" effort. reports issues related to boilerplate generation or visual reports

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@handwerkerd
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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:

tedana/tedana/reporting/dynamic_figures.py

Line 350 in a21d65e

circle = models.Circle(x=0, y=1, size=150, fill_color="white", line_color="white")

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
@handwerkerd handwerkerd added bug issues describing a bug or error found in the project good first issue issues that we think are good for new contributors. Equivalent to "very low" effort. reports issues related to boilerplate generation or visual reports labels Mar 20, 2024
@gottss
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gottss commented Mar 21, 2024

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:

tedana/tedana/reporting/dynamic_figures.py

Line 350 in a21d65e

circle = models.Circle(x=0, y=1, size=150, fill_color="white", line_color="white")

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
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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.

@handwerkerd handwerkerd mentioned this issue Apr 1, 2024
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bug issues describing a bug or error found in the project good first issue issues that we think are good for new contributors. Equivalent to "very low" effort. reports issues related to boilerplate generation or visual reports
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Fix dynamic reports with bokeh 3.4.0 problems handwerkerd/tedana
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@handwerkerd @eurunuela @gottss