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Make notebooks work with bokeh>=3 and remove bokeh<3 pin #3061

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merged 4 commits into from
Oct 2, 2024
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Make notebooks work with bokeh>=3 and remove bokeh<3 pin #3061

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c335844
Register `h.Vector` serialization function with Bokeh in notebooks
kbvw Aug 28, 2024
3b69a54
Unpin `bokeh<3` in documentation requirements and remove from main re…
kbvw Aug 29, 2024
9473753
Unpin `numpy<2` in documentation requirements
kbvw Aug 29, 2024
2d8ba03
Move serializer registration to `__init__.py`
kbvw Aug 29, 2024
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5 changes: 2 additions & 3 deletions docs/docs_requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,11 @@ jupyter
nbconvert
myst_parser
matplotlib
# bokeh 3 seems to break docs notebooks
bokeh<3
bokeh
# do not check import of next line
ipython
plotnine
numpy<2
numpy
plotly
nbsphinx
jinja2
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2 changes: 0 additions & 2 deletions nrn_requirements.txt
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Expand Up @@ -3,8 +3,6 @@ setuptools_scm
setuptools<=70.3.0
scikit-build
matplotlib
# bokeh 3 seems to break docs notebooks
bokeh<3
ipython
cython
packaging
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10 changes: 10 additions & 0 deletions share/lib/python/neuron/__init__.py
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Expand Up @@ -1835,3 +1835,13 @@
if _get_ipython() is not None:
html_formatter = _get_ipython().display_formatter.formatters["text/html"]
html_formatter.for_type(hoc.HocObject, _hocobj_html)

# in case Bokeh is installed, register a serialization function for hoc.Vector
try:
from bokeh.core.serialization import Serializer

Serializer.register(

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h.Vector, lambda obj, serializer: [serializer.encode(item) for item in obj]
)
except ImportError:
pass
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