I'm trying to visualize Bokeh plots and panels with a Bokeh backend in a notebook in JupyterLab. Things were running fine until I updated.
Current packages and versions are below
I have tried the following:
conda install jupyter_bokeh
conda install -c pyviz panel holoviews
conda install -c pyviz bokeh panel holoviews`
jupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager`
jupyter lab clean
import bokeh.io
from bokeh.io import output_notebook
bokeh.io.output_notebook()
hv.extension('bokeh')
As well as the following from this question
from bokeh.resources import INLINE
import bokeh.io
from bokeh import *
bokeh.io.output_notebook(INLINE)
Here is a toy example from the post cited above. I do see BokehJS 2.2.3 successfully loaded, but the plot does not render. There is no other error. I've tried the toy example with various permutations of the above substituted for the first two lines with no effect.
from bokeh.io import output_notebook, show
from bokeh.plotting import figure
output_notebook()
p = figure(plot_width=400, plot_height=400)
p.circle([1, 2, 3, 4, 5], [6, 7, 2, 4, 5], size=15, line_color="navy",
fill_color="orange", fill_alpha=0.5)
show(p)
I'd really appreciate any insight - I'm still not great at upgrading Jupyter Labs and getting Bokeh/Panels to render properly in-line. Thank you
current installed packages:
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
anyio 3.2.1 py38h578d9bd_0 conda-forge
argon2-cffi 20.1.0 py38h497a2fe_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
babel 2.9.1 pyh44b312d_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
bibtexparser 1.1.0 py_0 conda-forge
binutils_impl_linux-64 2.35.1 h193b22a_2 conda-forge
binutils_linux-64 2.35 h67ddf6f_30 conda-forge
bioconductor-biobase 2.50.0 r40hd029910_1 bioconda
bioconductor-biocgenerics 0.36.0 r40hdfd78af_1 bioconda
bioconductor-biocparallel 1.24.1 r40h399db7b_0 bioconda
bioconductor-biostrings 2.58.0 r40hd029910_1 bioconda
bioconductor-dada2 1.18.0 r40h399db7b_1 bioconda
bioconductor-delayedarray 0.16.3 r40hd029910_0 bioconda
bioconductor-genomeinfodb 1.26.4 r40hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.4 r40hdfd78af_2 bioconda
bioconductor-genomicalignments 1.26.0 r40hd029910_1 bioconda
bioconductor-genomicranges 1.42.0 r40hd029910_1 bioconda
bioconductor-iranges 2.24.1 r40hd029910_0 bioconda
bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0 bioconda
bioconductor-rhtslib 1.22.0 r40hd029910_1 bioconda
bioconductor-rsamtools 2.6.0 r40h399db7b_1 bioconda
bioconductor-s4vectors 0.28.1 r40hd029910_0 bioconda
bioconductor-shortread 1.48.0 r40h399db7b_1 bioconda
bioconductor-summarizedexperiment 1.20.0 r40hdfd78af_1 bioconda
bioconductor-xvector 0.30.0 r40hd029910_1 bioconda
bioconductor-zlibbioc 1.36.0 r40hd029910_1 bioconda
biom-format 2.1.10 py38h0b5ebd8_0 conda-forge
blas 1.1 openblas conda-forge
blast 2.11.0 pl526he19e7b1_0 bioconda
bleach 3.3.0 pyh44b312d_0 conda-forge
bokeh 2.3.1 py38h578d9bd_0 conda-forge
bowtie2 2.4.2 py38hc2f83ea_2 bioconda
brotlipy 0.7.0 py38h497a2fe_1001 conda-forge
bwidget 1.9.14 ha770c72_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h7f98852_1 conda-forge
ca-certificates 2021.5.30 ha878542_0 conda-forge
cachecontrol 0.12.6 py_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
certifi 2021.5.30 py38h578d9bd_0 conda-forge
cffi 1.14.5 py38ha65f79e_0 conda-forge
chardet 4.0.0 py38h578d9bd_1 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
colorcet 2.0.6 py_0 pyviz
cryptography 3.4.7 py38ha5dfef3_0 conda-forge
curl 7.76.1 h979ede3_1 conda-forge
cutadapt 3.4 py38h4a8c8d9_1 bioconda
cycler 0.10.0 py_2 conda-forge
cython 0.29.23 py38h709712a_1 conda-forge
dbus 1.13.6 h48d8840_2 conda-forge
deblur 1.1.0 py_2 bioconda
decorator 4.4.2 py_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dendropy 4.5.2 pyh3252c3a_0 bioconda
dnaio 0.5.0 py38h4a8c8d9_1 bioconda
emperor 1.0.3 py38h578d9bd_0 conda-forge
entrez-direct 13.9 pl5262he881be0_2 bioconda
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.3.0 h9c3ff4c_0 conda-forge
fastcluster 1.1.26 py38hc5bc63f_2 conda-forge
fasttree 2.1.10 0 bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.1 hba837de_1005 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
future 0.18.2 py38h578d9bd_3 conda-forge
gcc_impl_linux-64 9.3.0 h70c0ae5_19 conda-forge
gcc_linux-64 9.3.0 hf25ea35_30 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
gfortran_impl_linux-64 9.3.0 hc4a2995_19 conda-forge
gfortran_linux-64 9.3.0 hdc58fab_30 conda-forge
glib 2.68.1 h9c3ff4c_0 conda-forge
glib-tools 2.68.1 h9c3ff4c_0 conda-forge
gneiss 0.4.6 py_0 bioconda
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.6 he838d99_2 conda-forge
gst-plugins-base 1.18.4 hf529b03_2 conda-forge
gstreamer 1.18.4 h76c114f_2 conda-forge
gxx_impl_linux-64 9.3.0 hd87eabc_19 conda-forge
gxx_linux-64 9.3.0 h3fbe746_30 conda-forge
h5py 3.2.1 nompi_py38h9915d05_100 conda-forge
harfbuzz 2.8.0 h83ec7ef_1 conda-forge
hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge
hdmedians 0.14.2 py38h5c078b8_0 conda-forge
hmmer 3.1b2 3 bioconda
holoviews 1.14.4 py_0 pyviz
htslib 1.12 h9093b5e_1 bioconda
icu 68.1 h58526e2_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
ijson 3.1.3 pyhd3deb0d_0 conda-forge
importlib-metadata 3.10.1 py38h578d9bd_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 5.5.3 py38hd0cf306_0 conda-forge
ipython 7.22.0 py38hd0cf306_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge
iqtree 2.1.2 h56fc30b_0 bioconda
isa-l 2.30.0 ha770c72_4 conda-forge
jedi 0.18.0 py38h578d9bd_2 conda-forge
jinja2 2.11.3 pyh44b312d_0 conda-forge
joblib 1.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge
jupyter_bokeh 3.0.2 pyhd8ed1ab_0 conda-forge
jupyter_client 6.1.12 pyhd8ed1ab_0 conda-forge
jupyter_core 4.7.1 py38h578d9bd_0 conda-forge
jupyter_server 1.9.0 pyhd8ed1ab_0 conda-forge
jupyterlab 3.0.16 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_server 2.6.1 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge
kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge
kiwisolver 1.3.1 py38h1fd1430_1 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge
libblas 3.9.0 8_openblas conda-forge
libcblas 3.9.0 8_openblas conda-forge
libclang 11.1.0 default_ha53f305_1 conda-forge
libcurl 7.76.1 hc4aaa36_1 conda-forge
libdeflate 1.7 h7f98852_5 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 hcdb4288_3 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 9.3.0 h7864c58_19 conda-forge
libgcc-ng 9.3.0 h2828fa1_19 conda-forge
libgfortran-ng 9.3.0 hff62375_19 conda-forge
libgfortran5 9.3.0 hff62375_19 conda-forge
libglib 2.68.1 h3e27bee_0 conda-forge
libgomp 9.3.0 h2828fa1_19 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 8_openblas conda-forge
libllvm11 11.1.0 hf817b99_2 conda-forge
libnghttp2 1.43.0 h812cca2_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
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libpng 1.6.37 h21135ba_2 conda-forge
libpq 13.1 hfd2b0eb_2 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.9.0 ha56f1ee_6 conda-forge
libstdcxx-devel_linux-64 9.3.0 hb016644_19 conda-forge
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libtiff 4.2.0 hbd63e13_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.41.0 h7f98852_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
libxcb 1.13 h7f98852_1003 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.10 h72842e0_4 conda-forge
libxslt 1.1.33 h15afd5d_2 conda-forge
lockfile 0.12.2 py_1 conda-forge
lxml 4.6.3 py38hf1fe3a4_0 conda-forge
lz4 3.1.3 py38hebdc3cf_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_0 conda-forge
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make 4.3 hd18ef5c_1 conda-forge
markdown 3.3.4 pyhd8ed1ab_0 conda-forge
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matplotlib 3.4.1 py38h578d9bd_0 conda-forge
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more-itertools 8.7.0 pyhd8ed1ab_1 conda-forge
msgpack-python 1.0.2 py38h1fd1430_1 conda-forge
mysql-common 8.0.23 ha770c72_2 conda-forge
mysql-libs 8.0.23 h935591d_2 conda-forge
natsort 7.1.1 pyhd8ed1ab_0 conda-forge
nbclassic 0.3.1 pyhd8ed1ab_1 conda-forge
nbclient 0.5.3 pyhd8ed1ab_0 conda-forge
nbconvert 6.0.7 py38h578d9bd_3 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge
networkx 2.5.1 pyhd8ed1ab_0 conda-forge
nodejs 15.14.0 h92b4a50_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.3.0 pyha770c72_1 conda-forge
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nss 3.64 hb5efdd6_0 conda-forge
numpy 1.20.2 py38h9894fe3_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openblas 0.3.12 pthreads_h04b7a96_1 conda-forge
openjdk 11.0.1 h516909a_1016 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1k h7f98852_0 conda-forge
packaging 20.9 pyh44b312d_0 conda-forge
pandas 1.2.4 py38h1abd341_0 conda-forge
pandoc 2.12 h7f98852_0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
panel 0.11.3 py_0 pyviz
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param 1.11.1 py_0 pyviz
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perl 5.26.2 h36c2ea0_1008 conda-forge
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-base 2.23 pl526_1 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-file-listing 6.04 pl526_1 bioconda
perl-file-path 2.16 pl526_0 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tree 5.07 pl526_1 bioconda
perl-http-cookies 6.04 pl526_0 bioconda
perl-http-daemon 6.01 pl526_1 bioconda
perl-http-date 6.02 pl526_3 bioconda
perl-http-message 6.18 pl526_0 bioconda
perl-http-negotiate 6.01 pl526_3 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-socket-ssl 2.066 pl526_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-libwww-perl 6.39 pl526_0 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-lwp-mediatypes 6.04 pl526_0 bioconda
perl-lwp-protocol-https 6.07 pl526_4 bioconda
perl-mime-base64 3.15 pl526_1 bioconda
perl-mozilla-ca 20180117 pl526_1 bioconda
perl-net-http 6.19 pl526_0 bioconda
perl-net-ssleay 1.88 pl526h90d6eec_0 bioconda
perl-ntlm 1.09 pl526_4 bioconda
perl-parent 0.236 pl526_1 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-socket 2.027 pl526_1 bioconda
perl-storable 3.15 pl526h14c3975_0 bioconda
perl-test-requiresinternet 0.05 pl526_0 bioconda
perl-time-local 1.28 pl526_1 bioconda
perl-try-tiny 0.30 pl526_1 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
perl-uri 1.76 pl526_0 bioconda
perl-www-robotrules 6.02 pl526_3 bioconda
perl-xml-namespacesupport 1.12 pl526_0 bioconda
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perl-xml-sax 1.02 pl526_0 bioconda
perl-xml-sax-base 1.09 pl526_0 bioconda
perl-xml-sax-expat 0.51 pl526_3 bioconda
perl-xml-simple 2.25 pl526_1 bioconda
perl-xsloader 0.24 pl526_0 bioconda
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pip 21.0.1 pyhd8ed1ab_0 conda-forge
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psutil 5.8.0 py38h497a2fe_1 conda-forge
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pysocks 1.7.1 py38h578d9bd_3 conda-forge
pytest 6.2.3 py38h578d9bd_0 conda-forge
python 3.8.8 hffdb5ce_0_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python-isal 0.10.0 py38h497a2fe_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytz 2021.1 pyhd8ed1ab_0 conda-forge
pyviz_comms 2.1.0 py_0 pyviz
pyyaml 5.4.1 py38h497a2fe_0 conda-forge
pyzmq 22.0.3 py38h2035c66_1 conda-forge
qiime2 2021.4.0 py38_0 qiime2/label/r2021.4
qt 5.12.9 hda022c4_4 conda-forge
raxml 8.2.12 h779adbc_3 bioconda
readline 8.1 h46c0cb4_0 conda-forge
requests 2.25.1 pyhd3deb0d_0 conda-forge
requests-unixsocket 0.2.0 py_0 conda-forge
samtools 1.12 h9aed4be_1 bioconda
scikit-bio 0.5.6 py38h0b5ebd8_4 conda-forge
scikit-learn 0.24.1 py38h658cfdd_0 conda-forge
scipy 1.6.2 py38h7b17777_0 conda-forge
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sed 4.8 he412f7d_0 conda-forge
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sortmerna 2.0 he860b03_4 bioconda
sqlite 3.35.4 h74cdb3f_0 conda-forge
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sysroot_linux-64 2.12 h77966d4_13 conda-forge
tbb 2020.2 h4bd325d_4 conda-forge
terminado 0.9.4 py38h578d9bd_0 conda-forge
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threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge
tk 8.6.10 h21135ba_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py38h497a2fe_1 conda-forge
tqdm 4.61.2 pyhd8ed1ab_1 conda-forge
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tzlocal 2.1 pyh9f0ad1d_0 conda-forge
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urllib3 1.26.4 pyhd8ed1ab_0 conda-forge
vsearch 2.7.0 1 bioconda
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 0.57.0 py38h578d9bd_4 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
widgetsnbextension 3.5.1 py38h578d9bd_4 conda-forge
xopen 1.1.0 py38h578d9bd_3 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.0 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
zeromq 4.3.4 h9c3ff4c_0 conda-forge
zipp 3.4.1 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.4.9 ha95c52a_0 conda-forge