I have a panel app utilizing Matplotlib panes.
It works fine in one environment but not in another.
It throws an AttributeError as get_ipython() returns None instead of an IPython instance - as if the IPython is not launched correctly.
Here is a minimum example:
import panel as pn
from matplotlib import pyplot as plt
fig, ax = plt.subplots()
ax.plot([0,1,2], [2,2,4])
pn.pane.plot.Matplotlib(fig, interactive=True).show()
I have created the conda environment via requirements:
matplotlib
holoviz
ipympl
ipywidgets-bokeh
Any suggestions?
My conda list:
# Name Version Build Channel
argon2-cffi 20.1.0 py38h294d835_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 21.2.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
bokeh 2.4.0 py38haa244fe_0 conda-forge
brotlipy 0.7.0 py38h294d835_1001 conda-forge
bzip2 1.0.8 h8ffe710_4 conda-forge
ca-certificates 2021.5.30 h5b45459_0 conda-forge
certifi 2021.5.30 py38haa244fe_0 conda-forge
cffi 1.14.6 py38hd8c33c5_1 conda-forge
cftime 1.5.1 py38h6f4d8f0_0 conda-forge
chardet 4.0.0 py38haa244fe_1 conda-forge
charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge
click 8.0.1 py38haa244fe_0 conda-forge
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
colorcet 2.0.6 py_0 pyviz
cryptography 3.4.7 py38hd7da0ea_0 conda-forge
curl 7.79.1 h789b8ee_1 conda-forge
cycler 0.10.0 py_2 conda-forge
cytoolz 0.11.0 py38h294d835_3 conda-forge
dask 2021.9.1 pyhd8ed1ab_0 conda-forge
dask-core 2021.9.1 pyhd8ed1ab_0 conda-forge
datashader 0.13.0 py_0 pyviz
datashape 0.5.4 py_1 conda-forge
debugpy 1.4.1 py38h885f38d_0 conda-forge
decorator 5.1.0 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
distributed 2021.9.1 py38haa244fe_0 conda-forge
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
fastparquet 0.4.0 py38h40bdaab_0 pyviz
freetype 2.10.4 h546665d_1 conda-forge
fsspec 2021.10.0 pyhd8ed1ab_0 conda-forge
hdf4 4.2.15 h0e5069d_3 conda-forge
hdf5 1.12.1 nompi_h2a0e4a3_101 conda-forge
heapdict 1.0.1 py_0 conda-forge
holoviews 1.14.6 py_0 pyviz
holoviz 0.13.0 py_0 pyviz
hvplot 0.7.3 py_0 pyviz
icu 68.1 h0e60522_0 conda-forge
idna 3.1 pyhd3deb0d_0 conda-forge
importlib-metadata 4.8.1 py38haa244fe_0 conda-forge
intel-openmp 2021.3.0 h57928b3_3372 conda-forge
ipykernel 6.4.1 py38h595d716_0 conda-forge
ipympl 0.8.0 pyhd8ed1ab_0 conda-forge
ipython 7.28.0 py38h595d716_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.5 pyhd8ed1ab_0 conda-forge
ipywidgets-bokeh 1.2.1 pypi_0 pypi
jbig 2.1 h8d14728_2003 conda-forge
jedi 0.18.0 py38haa244fe_2 conda-forge
jinja2 3.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9d h8ffe710_0 conda-forge
jsonschema 4.0.1 pyhd8ed1ab_0 conda-forge
jupyter_client 7.0.6 pyhd8ed1ab_0 conda-forge
jupyter_core 4.8.1 py38haa244fe_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_widgets 1.0.2 pyhd8ed1ab_0 conda-forge
kiwisolver 1.3.2 py38hbd9d945_0 conda-forge
krb5 1.19.2 hbae68bd_2 conda-forge
lcms2 2.12 h2a16943_0 conda-forge
lerc 2.2.1 h0e60522_0 conda-forge
libblas 3.9.0 11_win64_mkl conda-forge
libcblas 3.9.0 11_win64_mkl conda-forge
libclang 11.1.0 default_h5c34c98_1 conda-forge
libcurl 7.79.1 h789b8ee_1 conda-forge
libdeflate 1.7 h8ffe710_5 conda-forge
liblapack 3.9.0 11_win64_mkl conda-forge
libnetcdf 4.8.1 nompi_h1cc8e9d_101 conda-forge
libpng 1.6.37 h1d00b33_2 conda-forge
libsodium 1.0.18 h8d14728_1 conda-forge
libssh2 1.10.0 h680486a_2 conda-forge
libtiff 4.3.0 h0c97f57_1 conda-forge
libzip 1.8.0 hfed4ece_1 conda-forge
libzlib 1.2.11 h8ffe710_1013 conda-forge
llvmlite 0.37.0 py38h57a6900_0 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.9.3 h8ffe710_1 conda-forge
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
markdown 3.3.4 pyhd8ed1ab_0 conda-forge
markupsafe 2.0.1 py38h294d835_0 conda-forge
matplotlib 3.4.3 py38haa244fe_1 conda-forge
matplotlib-base 3.4.3 py38h1f000d6_1 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mistune 0.8.4 py38h294d835_1004 conda-forge
mkl 2021.3.0 hb70f87d_564 conda-forge
msgpack-python 1.0.2 py38hbd9d945_1 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
nbclient 0.5.4 pyhd8ed1ab_0 conda-forge
nbconvert 6.2.0 py38haa244fe_0 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge
netcdf4 1.5.7 nompi_py38h0500770_103 conda-forge
notebook 6.4.4 pyha770c72_0 conda-forge
numba 0.54.0 py38h5858985_0 conda-forge
numpy 1.20.3 py38h09042cb_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjpeg 2.4.0 hb211442_1 conda-forge
openssl 1.1.1l h8ffe710_0 conda-forge
packaging 21.0 pyhd8ed1ab_0 conda-forge
pandas 1.3.3 py38h5d928e2_0 conda-forge
pandoc 2.14.2 h8ffe710_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panel 0.12.4 py_0 pyviz
param 1.11.1 py_0 pyviz
parso 0.8.2 pyhd8ed1ab_0 conda-forge
partd 1.2.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 8.3.2 py38h794f750_0 conda-forge
pip 21.2.4 pyhd8ed1ab_0 conda-forge
prometheus_client 0.11.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.20 pyha770c72_0 conda-forge
psutil 5.8.0 py38h294d835_1 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pyct 0.4.8 py_0 pyviz
pyct-core 0.4.8 py_0 pyviz
pygments 2.10.0 pyhd8ed1ab_0 conda-forge
pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.12.3 py38haa244fe_7 conda-forge
pyqt-impl 5.12.3 py38h885f38d_7 conda-forge
pyqt5-sip 4.19.18 py38h885f38d_7 conda-forge
pyqtchart 5.12 py38h885f38d_7 conda-forge
pyqtwebengine 5.12.1 py38h885f38d_7 conda-forge
pyrsistent 0.17.3 py38h294d835_2 conda-forge
pysocks 1.7.1 py38haa244fe_3 conda-forge
python 3.8.12 h7840368_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-snappy 0.6.0 py38h8566a25_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
pyviz_comms 2.1.0 py_0 pyviz
pywin32 301 py38h294d835_0 conda-forge
pywinpty 1.1.4 py38hd3f51b4_0 conda-forge
pyyaml 5.4.1 py38h294d835_1 conda-forge
pyzmq 22.3.0 py38h09162b1_0 conda-forge
qt 5.12.9 h5909a2a_4 conda-forge
requests 2.26.0 pyhd8ed1ab_0 conda-forge
rise 5.7.1 py38haa244fe_0 conda-forge
scipy 1.7.1 py38ha1292f7_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 58.2.0 py38haa244fe_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.8 ha925a31_3 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
sqlite 3.36.0 h8ffe710_2 conda-forge
tbb 2021.3.0 h2d74725_0 conda-forge
tblib 1.7.0 pyhd8ed1ab_0 conda-forge
terminado 0.12.1 py38haa244fe_0 conda-forge
testpath 0.5.0 pyhd8ed1ab_0 conda-forge
thrift 0.11.0 py38h6538335_1001 conda-forge
tk 8.6.11 h8ffe710_1 conda-forge
toolz 0.11.1 py_0 conda-forge
tornado 6.1 py38h294d835_1 conda-forge
tqdm 4.62.3 pyhd8ed1ab_0 conda-forge
traitlets 5.1.0 pyhd8ed1ab_0 conda-forge
typing_extensions 3.10.0.2 pyha770c72_0 conda-forge
ucrt 10.0.20348.0 h57928b3_0 conda-forge
urllib3 1.26.7 pyhd8ed1ab_0 conda-forge
vc 14.2 hb210afc_5 conda-forge
vs2015_runtime 14.29.30037 h902a5da_5 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.37.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 3.5.1 py38haa244fe_4 conda-forge
win_inet_pton 1.1.0 py38haa244fe_2 conda-forge
winpty 0.4.3 4 conda-forge
xarray 0.19.0 pyhd8ed1ab_1 conda-forge
xz 5.2.5 h62dcd97_1 conda-forge
yaml 0.2.5 he774522_0 conda-forge
zeromq 4.3.4 h0e60522_1 conda-forge
zict 2.0.0 py_0 conda-forge
zipp 3.6.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h8ffe710_1013 conda-forge
zstd 1.5.0 h6255e5f_0 conda-forge
This is the error I get
Traceback (most recent call last):
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/tornado/web.py", line 1704, in _execute
result = await result
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/io/server.py", line 214, in get
session = await self.get_session()
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/bokeh/server/views/session_handler.py", line 144, in get_session
session = await self.application_context.create_session_if_needed(session_id, self.request, token)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/bokeh/server/contexts.py", line 243, in create_session_if_needed
self._application.initialize_document(doc)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/io/server.py", line 173, in initialize_document
super().initialize_document(doc)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/bokeh/application/application.py", line 195, in initialize_document
h.modify_document(doc)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/bokeh/application/handlers/function.py", line 143, in modify_document
self._func(doc)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/io/server.py", line 82, in _eval_panel
doc = as_panel(panel)._modify_doc(server_id, title, doc, location)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/viewable.py", line 244, in _modify_doc
return self.server_doc(doc, title, location)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/viewable.py", line 794, in server_doc
model = self.get_root(doc)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/pane/base.py", line 267, in get_root
root = self._get_model(doc, comm=comm)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/pane/plot.py", line 192, in _get_model
manager = self._get_widget(self.object)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/panel/pane/plot.py", line 170, in _get_widget
from ipympl.backend_nbagg import FigureManager, Canvas, is_interactive
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/ipympl/__init__.py", line 27, in <module>
matplotlib.use('module://ipympl.backend_nbagg')
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/matplotlib/__init__.py", line 1080, in use
plt.switch_backend(name)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/matplotlib/pyplot.py", line 277, in switch_backend
class backend_mod(matplotlib.backend_bases._Backend):
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/matplotlib/pyplot.py", line 278, in backend_mod
locals().update(vars(importlib.import_module(backend_name)))
File "/home/jovyan/conda-envs/pmat/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/jovyan/conda-envs/pmat/lib/python3.9/site-packages/ipympl/backend_nbagg.py", line 431, in <module>
ip.events.register('post_execute', flush_figures)
AttributeError: 'NoneType' object has no attribute 'events'
When running python script.py in a new environment created using
conda create --name=pmat -c conda-forge -c bokeh -c pyviz matplotlib holoviz ipympl ipywidgets_bokeh
I’ve tried to downgrade to Ipykernel<6.0 (6.0 is known to not work with ipywidgets_bokeh yet. There should be a bug fix in the master branch already) and panel 0.12.1 and bokeh 2.3.3.
I would recommend reporting it as a bug.
Honestly dislike the fact that you register events on the global get_ipython() object a lot. That said it looks like this has already been addressed in ipympl here: https://github.com/matplotlib/ipympl/pull/364
But do file an issue in ipywidgets_bokeh to see if we can somehow provide a shim for the get_ipython global and register events like this.
Thanks Phillip. I agree that the registering the global get_ipython() is not optimal. If there are more MatplotlibPanes in a Panel app, events generated in one of them will be broadcast to all of them, so the user needs to implement a custom filter to only process the events that are relevant for a given MatplotlibPane.
I tried applying the few lines of code changed in the pull request you mentioned. It does indeed fix the first attribute error, but then the next exception arises:
ERROR:fake:Invalid Message
Traceback (most recent call last):
File "C:\Users\nchvg\Miniconda3\envs\optisoil-engineering-tools\lib\site-packages\ipykernel\kernelbase.py", line 312, in dispatch_shell
msg = self.session.deserialize(msg, content=True, copy=False)
File "C:\Users\nchvg\Miniconda3\envs\optisoil-engineering-tools\lib\site-packages\jupyter_client\session.py", line 1048, in deserialize
raise ValueError("Duplicate Signature: %r" % signature)
ValueError: Duplicate Signature: b'9b25b08aacbdc8c77ef9f91368742482787dd5afe83a7a6872bb7f3e1366b335'
In addition the ipywidgets_bokeh source doesn’t mention get_ipython() in the source code, so I wonder if it is indeed the right place to file the issue? (If it is, I will happily do it)
I have narrowed down the problematic versions, ie this is the highest combination of requirements where neither the Attribute error or duplicate signature are raised:
- pip:
- ipykernel<6
- ipympl==0.7.0
- panel<=0.12.1
If any of these three packages are upgraded, the minimal example fails…
