From 5b49b24f25afdea1ec751ba0be523bddde91ede1 Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <38299796+kbvw@users.noreply.github.com>
Date: Wed, 2 Oct 2024 20:58:00 +0200
Subject: [PATCH] Make notebooks work with `bokeh>=3` and remove `bokeh<3` pin
 (#3061)

* Register `h.Vector` serialization function with Bokeh in notebooks
* Unpin `bokeh<3` in documentation requirements and remove from main requirements
* Unpin `numpy<2` in documentation requirements
* Move serializer registration to `__init__.py`
---
 docs/docs_requirements.txt          |  5 ++---
 nrn_requirements.txt                |  2 --
 share/lib/python/neuron/__init__.py | 10 ++++++++++
 3 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt
index 6571d22ac2..cd4982ca08 100644
--- a/docs/docs_requirements.txt
+++ b/docs/docs_requirements.txt
@@ -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
diff --git a/nrn_requirements.txt b/nrn_requirements.txt
index f049602b4e..1de5573095 100644
--- a/nrn_requirements.txt
+++ b/nrn_requirements.txt
@@ -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
diff --git a/share/lib/python/neuron/__init__.py b/share/lib/python/neuron/__init__.py
index f84021c4da..7ea748288c 100644
--- a/share/lib/python/neuron/__init__.py
+++ b/share/lib/python/neuron/__init__.py
@@ -1835,3 +1835,13 @@ def _mview_html_tree(hlist, inside_mechanisms_in_use=0):
 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(
+        h.Vector, lambda obj, serializer: [serializer.encode(item) for item in obj]
+    )
+except ImportError:
+    pass