missing dependency
TidyData opened this issue · comments
created environment file using the repo's environment.yml and was getting the below error quite frequently.
[E 22:54:05.375 NotebookApp] Notebook JSON is invalid: 'application/vnd.bokehjs_load.v0+json' does not match any of the regexes: '^(?!application/json$)[a-zA-Z0-9]+/[a-zA-Z0-9\\-\\+\\.]+$'
Failed validating 'additionalProperties' in display_data['properties']['data']:
On instance['cells'][5]['outputs'][1]['data']:
{'application/javascript': '\n'
'(function(root) {\n'
' function now() {\n'
' return new Date();\n'
' }...',
'application/vnd.bokehjs_load.v0+json': '\n'
'(function(root) {\n'
' function now() {\n'
' return new Date();\n'
' }...'}
some searching indicated to install conda install -n bokeh nbformat
and problem seems to have gone away
i proposed a pull request TidyData:missing-dependency-72 which I believe resolves the error
@TidyData AFAIK that message indicates that you do not have the bokeh jupyterlab extension installed. nbformat is definitely not required for basic usage of Bokeh in either the classic notebook or jupyterlab. More details about package versions in your environment would be helpful here.
RHEL 8.1 4.18.0-147.3.1.el8_1.x86_64
Error occurs with multiple browsers.
I initially created the environment file using conda 4.8.0 but it still occurring after making another environment file using conda 4.8.1.
The 1st conda list has the error.
The 2nd conda list is after I installed nbformat and the error hasn't occurred for 30 minutes, when it took <2 seconds after starting a notebook
(bokeh_with_error) [<redacted> bokeh-notebooks]$ conda list
# packages in environment at <redacted>/miniconda3/envs/bokeh_with_error:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
attrs 19.3.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bleach 3.1.0 py_0 conda-forge
bokeh 1.4.0 py_0 bokeh
ca-certificates 2019.11.28 hecc5488_0 conda-forge
certifi 2019.11.28 py37_0 conda-forge
cffi 1.13.2 py37h8022711_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
click 7.0 py_0 conda-forge
cloudpickle 1.2.2 py_1 conda-forge
colorcet 2.0.1 py_0 conda-forge
cryptography 2.8 py37h72c5cf5_1 conda-forge
cycler 0.10.0 py_2 conda-forge
cytoolz 0.10.1 py37h516909a_0 conda-forge
dask 2.9.1 py_0 conda-forge
dask-core 2.9.1 py_0 conda-forge
datashader 0.9.0 py_0 conda-forge
datashape 0.5.4 py_1 conda-forge
decorator 4.4.1 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
distributed 2.9.1 py_0 conda-forge
entrypoints 0.3 py37_1000 conda-forge
flask 1.1.1 py_1 conda-forge
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.0 he983fc9_1 conda-forge
fsspec 0.6.2 py_0 conda-forge
futures-compat 1.0 py3_0 conda-forge
heapdict 1.0.1 py_0 conda-forge
holoviews 1.12.7 py_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 py37_1000 conda-forge
imageio 2.6.1 py37_0 conda-forge
importlib_metadata 1.4.0 py37_0 conda-forge
ipykernel 5.1.3 py37h5ca1d4c_0 conda-forge
ipython 7.11.1 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
itsdangerous 1.1.0 py_0 conda-forge
jedi 0.15.2 py37_0 conda-forge
jinja2 2.10.3 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 3.2.0 py37_0 conda-forge
jupyter_client 5.3.4 py37_0 conda-forge
jupyter_core 4.6.1 py37_0 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_7 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_4 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libllvm8 8.0.1 hc9558a2_0 conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libtiff 4.1.0 hc3755c2_3 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
llvmlite 0.31.0 py37h8b12597_0 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
markupsafe 1.1.1 py37h516909a_0 conda-forge
matplotlib-base 3.1.2 py37h250f245_1 conda-forge
mistune 0.8.4 py37h516909a_1000 conda-forge
more-itertools 8.0.2 py_0 conda-forge
msgpack-python 0.6.2 py37hc9558a2_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
nbconvert 5.6.1 py37_0 conda-forge
nbformat 5.0.3 py_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.4 py_0 conda-forge
notebook 6.0.1 py37_0 conda-forge
numba 0.47.0 py37hb3f55d8_0 conda-forge
numpy 1.17.3 py37h95a1406_0 conda-forge
olefile 0.46 py_0 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
packaging 20.0 py_0 conda-forge
pandas 0.25.3 py37hb3f55d8_0 conda-forge
pandoc 2.9.1.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
param 1.9.2 py_0 conda-forge
parso 0.5.2 py_0 conda-forge
partd 1.1.0 py_0 conda-forge
pexpect 4.7.0 py37_0 conda-forge
phantomjs 2.1.1 1 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 7.0.0 py37hefe7db6_0 conda-forge
pip 19.3.1 py37_0 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt_toolkit 3.0.2 py_0 conda-forge
psutil 5.6.7 py37h516909a_0 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pycparser 2.19 py37_1 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pygments 2.5.2 py_0 conda-forge
pyopenssl 19.1.0 py37_0 conda-forge
pyparsing 2.4.6 py_0 conda-forge
pyrsistent 0.15.7 py37h516909a_0 conda-forge
pysocks 1.7.1 py37_0 conda-forge
python 3.7.6 h357f687_2 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
pytz 2019.3 py_0 conda-forge
pyviz_comms 0.7.2 py_0 conda-forge
pywavelets 1.1.1 py37hc1659b7_0 conda-forge
pyyaml 5.1.2 py37h516909a_0 conda-forge
pyzmq 18.1.1 py37h1768529_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 py37_1 conda-forge
scikit-image 0.16.2 py37hb3f55d8_0 conda-forge
scipy 1.4.1 py37h921218d_0 conda-forge
selenium 3.141.0 py37h516909a_1000 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 44.0.0 py37_0 conda-forge
six 1.13.0 py37_0 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tblib 1.6.0 py_0 conda-forge
terminado 0.8.3 py37_0 conda-forge
testpath 0.4.4 py_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h516909a_0 conda-forge
traitlets 4.3.3 py37_0 conda-forge
urllib3 1.25.7 py37_0 conda-forge
wcwidth 0.1.8 py_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 0.16.0 py_0 conda-forge
wheel 0.33.6 py37_0 conda-forge
xarray 0.14.1 py_1 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 h14c3975_1001 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zict 1.0.0 py_0 conda-forge
zipp 0.6.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
zstd 1.4.4 h3b9ef0a_1 conda-forge
Below has the error resolved after installing nbformat
(bokeh) [<redacted> bokeh-notebooks]$ conda list
# packages in environment at <redacted> /miniconda3/envs/bokeh:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
attrs 19.3.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bleach 3.1.0 py_0 conda-forge
bokeh 1.4.0 py_0 bokeh
ca-certificates 2019.11.27 0
certifi 2019.11.28 py37_0
cffi 1.13.2 py37h8022711_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
click 7.0 py_0 conda-forge
cloudpickle 1.2.2 py_1 conda-forge
colorcet 2.0.1 py_0 conda-forge
cryptography 2.8 py37h72c5cf5_1 conda-forge
cycler 0.10.0 py_2 conda-forge
cytoolz 0.10.1 py37h516909a_0 conda-forge
dask 2.9.1 py_0 conda-forge
dask-core 2.9.1 py_0 conda-forge
datashader 0.9.0 py_0 conda-forge
datashape 0.5.4 py_1 conda-forge
decorator 4.4.1 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
distributed 2.9.1 py_0 conda-forge
entrypoints 0.3 py37_1000 conda-forge
flask 1.1.1 py_1 conda-forge
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.0 he983fc9_1 conda-forge
fsspec 0.6.2 py_0 conda-forge
futures-compat 1.0 py3_0 conda-forge
heapdict 1.0.1 py_0 conda-forge
holoviews 1.12.7 py_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 py37_1000 conda-forge
imageio 2.6.1 py37_0 conda-forge
importlib_metadata 1.4.0 py37_0 conda-forge
ipykernel 5.1.3 py37h5ca1d4c_0 conda-forge
ipython 7.11.1 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
itsdangerous 1.1.0 py_0 conda-forge
jedi 0.15.2 py37_0 conda-forge
jinja2 2.10.3 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 3.2.0 py37_0 conda-forge
jupyter_client 5.3.4 py37_0 conda-forge
jupyter_core 4.6.1 py37_0 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_7 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_4 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libllvm8 8.0.1 hc9558a2_0 conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libtiff 4.1.0 hc3755c2_3 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
llvmlite 0.31.0 py37h8b12597_0 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
markupsafe 1.1.1 py37h516909a_0 conda-forge
matplotlib-base 3.1.2 py37h250f245_1 conda-forge
mistune 0.8.4 py37h516909a_1000 conda-forge
more-itertools 8.0.2 py_0 conda-forge
msgpack-python 0.6.2 py37hc9558a2_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
nbconvert 5.6.1 py37_0 conda-forge
nbformat 4.4.0 py37_0
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.4 py_0 conda-forge
notebook 6.0.1 py37_0 conda-forge
numba 0.47.0 py37hb3f55d8_0 conda-forge
numpy 1.17.3 py37h95a1406_0 conda-forge
olefile 0.46 py_0 conda-forge
openssl 1.1.1d h7b6447c_3
packaging 20.0 py_0 conda-forge
pandas 0.25.3 py37hb3f55d8_0 conda-forge
pandoc 2.9.1.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
param 1.9.2 py_0 conda-forge
parso 0.5.2 py_0 conda-forge
partd 1.1.0 py_0 conda-forge
pexpect 4.7.0 py37_0 conda-forge
phantomjs 2.1.1 1 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 7.0.0 py37hefe7db6_0 conda-forge
pip 19.3.1 py37_0 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt_toolkit 3.0.2 py_0 conda-forge
psutil 5.6.7 py37h516909a_0 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pycparser 2.19 py37_1 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pygments 2.5.2 py_0 conda-forge
pyopenssl 19.1.0 py37_0 conda-forge
pyparsing 2.4.6 py_0 conda-forge
pyrsistent 0.15.7 py37h516909a_0 conda-forge
pysocks 1.7.1 py37_0 conda-forge
python 3.7.6 h357f687_2 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
pytz 2019.3 py_0 conda-forge
pyviz_comms 0.7.2 py_0 conda-forge
pywavelets 1.1.1 py37hc1659b7_0 conda-forge
pyyaml 5.1.2 py37h516909a_0 conda-forge
pyzmq 18.1.1 py37h1768529_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 py37_1 conda-forge
scikit-image 0.16.2 py37hb3f55d8_0 conda-forge
scipy 1.4.1 py37h921218d_0 conda-forge
selenium 3.141.0 py37h516909a_1000 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 44.0.0 py37_0 conda-forge
six 1.13.0 py37_0 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tblib 1.6.0 py_0 conda-forge
terminado 0.8.3 py37_0 conda-forge
testpath 0.4.4 py_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h516909a_0 conda-forge
traitlets 4.3.3 py37_0 conda-forge
urllib3 1.25.7 py37_0 conda-forge
wcwidth 0.1.8 py_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 0.16.0 py_0 conda-forge
wheel 0.33.6 py37_0 conda-forge
xarray 0.14.1 py_1 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 h14c3975_1001 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zict 1.0.0 py_0 conda-forge
zipp 0.6.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
zstd 1.4.4 h3b9ef0a_1 conda-forge
I don't doubt that you are experiencing some issue, but I cannot see any way that nbformat could be related. It is used in precisely one place in the Bokeh codebase:
(base) ❯ grip nbformat
./application/handlers/notebook.py:
70 : nbformat = import_required('nbformat', 'The Bokeh notebook application handler requires Jupyter Notebook to be installed.')
114 : nb = nbformat.read(f, nbformat.NO_CONVERT)
This is the code path that is used when you run a notebook as a Bokeh server application, i.e. only when you execute bokeh serve foo.ipynb, and nowhere else. It has nothing at all to do with displaying things in a standard running notebook. And then also with notebooks, nbformat is only relevant when exporting notebooks as static html, not when actually running live notebooks connected to a kernel. Lastly, many people use Bokeh in notebooks without nbformat installed without issue.
So, being frank, I think the apparent fix is either a coincidence, or there is some separate connected cause. I'd encourage you to try and make more observations around this and maybe we can get to the root problem.
Frankness appreciated, feel free to close the issue. It can always be re-opened if others experience this issue.
RHEL 8 is new, possible source candidate for problem injections.
I'm running jupyter notebook (not fancy jupyter lab environment, but the old ipython version) and going through the bokeh-notebook tutorial lessons.
The difference between the two virtual environments is listed below. Possibly, another python module instead, maybe openssl, provides some functionality?
ca-certificates 2019.11.27 0
certifi 2019.11.28 py37_0
nbformat 4.4.0 py37_0
openssl 1.1.1d h7b6447c_3
thanks for supporting bokeh, it is wonderful
@TidyData I was considering merging the PR today, has there been an update on the situation on your end?
no update, was just trying to not leave issues hanging. Last I understood my fix wasn't the root of the problem and just didn't want things to linger if not relevant. Sorry to confuse. If I can provide additional testing I am happy to assist.
I couldn't tell if changes were applied to all branches due to some script when master gets committed too or if actual commits were applied to the merge request branch.
@TidyData Well, I still don't see how it can be the root of the problem, however:
- I could always be wrong, and
- adding it to the env is a pretty minimal and otherwise harmless change
So, on balance, in the interests of doing something that is not-harmful, possibly-useful I figured we could just merge it.
I don't understand the second question. There was a merge conflict with master on the branch which I just resolved in the GH UI a few minutes ago. Those changes appear on your branch to make the merge clean.
Actually @TidyData here is one more quick check you can do: You mention things work after installing nbformat. What happens if you now remove nbformat? Does it break again, or do things continue to still work? If not, I think this is a path, or else some secondary dependency, an installing nbformat is incidentally fixing that.
Also, thank you very much for the kind words earlier
I made various environments and think we can drop nbformat in environment.yml but retain package jupyter_contrib_nbextensions
without jupyter_contrib_nbextensions in less than 2 seconds was receiving below error
Interesting I don't know much about that package but it seems more likely to be relevant. Can you make a new PR for that package and we'll get it merged today!
Actually I guess it is already recently added on master:
https://github.com/bokeh/bokeh-notebooks/blob/master/environment.yml
So I don't think there is any further work?
agreed, closing this issue and the remaining pull request only has additional comments, which isn't that beneficial overall. Will be closing both with no need to merge.
- jupyter_contrib_nbextensions # resolves notebook validation failed
if for some reason you want to merge it, you're welcome to open the pull request and merge it in.
good work team, Go Bokeh!
@TidyData sounds good, thanks!