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

@@ -5,12 +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

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

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