Problem with Holoviews

[boweiliu0428]

When running w2_majorana/nanowire.md, I ran into problems when using Holoviews. Basically, whenever there is a graph with a bar to tune the parameters, I get ModuleNotFoundError: No module named 'bokeh.models.arrow_heads', see, for example, the section in the notebook attached called "The need for spin."

I know this is because my bokeh version is 3.1.1, which is too high (bokeh.models.arrow_heads' only exists for bokeh<3), but changing it to version 2.4.3 introduces additional errors concerning the package panel. A complete list of packages and their versions in my Python 3.9.16 conda environment created from environment.yml is:

---

accessible-pygments 0.0.4
alabaster 0.7.13
anyio 3.7.0
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.2.1
attrs 23.1.0
Babel 2.12.1
backcall 0.2.0
backports.functools-lru-cache 1.6.4
beautifulsoup4 4.12.2
bleach 6.0.0
bokeh 3.1.1
certifi 2023.5.7
cffi 1.15.1
charset-normalizer 3.1.0
click 8.1.3
colorama 0.4.6
colorcet 3.0.1
comm 0.1.3
contourpy 1.1.0
crossrefapi 1.5.0
cycler 0.11.0
debugpy 1.6.7
decorator 5.1.1
defusedxml 0.7.1
docutils 0.18.1
entrypoints 0.4
exceptiongroup 1.1.1
executing 1.2.0
fastcache 1.1.0
fastjsonschema 2.17.1
feedparser 6.0.10
flit_core 3.9.0
gmpy2 2.1.2
greenlet 2.0.2
holoviews 1.13.1
idna 3.4
imagesize 1.4.1
importlib-metadata 6.6.0
importlib-resources 5.12.0
iniconfig 2.0.0
ipykernel 6.23.1
ipython 8.14.0
ipython-genutils 0.2.0
jedi 0.18.2
Jinja2 3.1.2
jsonschema 4.17.3
jupyter-book 0.15.1
jupyter-cache 0.6.1
jupyter_client 8.2.0
jupyter_core 5.3.1
jupyter-events 0.6.3
jupyter_server 2.6.0
jupyter_server_terminals 0.4.4
jupyterlab-pygments 0.2.2
jupytext 1.14.6
kiwisolver 1.4.4
kwant 1.4.3
latexcodec 2.0.1
linkify-it-py 2.0.0
Markdown 3.4.3
markdown-it-py 2.2.0
MarkupSafe 2.1.3
matplotlib 3.3.4
matplotlib-inline 0.1.6
mdit-py-plugins 0.3.5
mdurl 0.1.0
mistune 2.0.5
mpmath 1.3.0
myst-nb 0.17.2
myst-parser 0.18.1
nbclassic 1.0.0
nbclient 0.7.4
nbconvert 7.5.0
nbformat 5.9.0
nest-asyncio 1.5.6
notebook 6.5.4
notebook_shim 0.2.3
numpy 1.22.4
overrides 7.3.1
packaging 23.1
pandas 2.0.2
pandocfilters 1.5.0
panel 1.1.0
param 1.13.0
parso 0.8.3
pexpect 4.8.0
pfapack 0.3.1
pickleshare 0.7.5
Pillow 9.5.0
pip 23.1.2
pkgutil_resolve_name 1.3.10
platformdirs 3.5.3
pluggy 1.0.0
prometheus-client 0.17.0
prompt-toolkit 3.0.38
psutil 5.9.5
ptyprocess 0.7.0
publist 0.1.2.dev9+g1c02a37
pure-eval 0.2.2
pybtex 0.24.0
pybtex-docutils 1.0.2
pycparser 2.21
pyct 0.4.6
pydata-sphinx-theme 0.13.3
Pygments 2.15.1
pyobjc-core 9.2
pyobjc-framework-Cocoa 9.2
pyparsing 3.0.9
pyrsistent 0.19.3
PySocks 1.7.1
pytest 7.3.2
python-dateutil 2.8.2
python-json-logger 2.0.7
pytz 2023.3
pyviz-comms 2.3.2
PyYAML 6.0
pyzmq 25.1.0
qsymm 1.3.0
requests 2.31.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
ruamel.yaml 0.17.32
ruamel.yaml.clib 0.2.7
SciPy 1.7.3
Send2Trash 1.8.2
setuptools 67.7.2
sgmllib3k 1.0.0
six 1.16.0
sniffio 1.3.0
snowballstemmer 2.2.0
soupsieve 2.3.2.post1
Sphinx 5.0.2
sphinx-book-theme 1.0.1
sphinx-comments 0.0.3
sphinx-copybutton 0.5.2
sphinx_design 0.3.0
sphinx_external_toc 0.3.1
sphinx-jupyterbook-latex 0.5.2
sphinx-multitoc-numbering 0.1.3
sphinx-thebe 0.2.1
sphinx-togglebutton 0.3.2
sphinxcontrib-applehelp 1.0.4
sphinxcontrib-bibtex 2.5.0
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.1
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
sphinxext-opengraph 0.8.2
SQLAlchemy 2.0.16
stack-data 0.6.2
sympy 1.6.2
tabulate 0.9.0
terminado 0.17.1
tinyarray 1.2.4
tinycss2 1.2.1
toml 0.10.2
tomli 2.0.1
tornado 6.3.2
tqdm 4.65.0
traitlets 5.9.0
typing_extensions 4.6.3
typing-utils 0.1.0
tzdata 2023.3
uc-micro-py 1.0.1
urllib3 2.0.3
wcwidth 0.2.6
webencodings 0.5.1
websocket-client 1.5.3
wheel 0.40.0
xyzservices 2023.5.0
zipp 3.15.0

I believe the error is a result of incompatibility with `Holoviews', 'panel', and 'bokeh'. I can't simply upgrade everything to the newest version because the code is incompatible. I hope you can give me the complete list of packages and versions that this project can run successfully without errors.

[boweiliu0428]

nanowire.ipynb.zip

This is an example notebook with the error output.