Plots don't display in Jupyter with WebIO v0.8.1 #278

halleysfifthinc · 2019-04-15T22:18:01Z

Upon updating WebIO to v0.8.1 from v0.7.0, plots no longer display/mount in Jupyter. This is reproducible (for me) in a clean environment with only IJulia and PlotlyJS added.

With ] st of

(v1.1) pkg> st
    Status `~/.julia/environments/v1.1/Project.toml`
  [7073ff75] IJulia v1.18.1
  [f0f68f2c] PlotlyJS v0.12.3
  [0f1e0344] WebIO v0.8.1

running using IJulia and plot(scatter(;y=rand(50))) doesn't show any plot. (In the Firefox developer console, running the plot cell produces a "Jupyter WebIO extension detected, not mounting.")

After pinning Webio to v0.7.0, running those same commands in jupyter does produce a plot. (And I can see several XHR requests for JS files being made which don't happen with WebIO at v0.8.1.)

I also tried this with on PlotlyJS master with WebIO v0.8.1 which didn't work (no plot).

julia> versioninfo()
Julia Version 1.1.0
Commit 80516ca202 (2019-01-21 21:24 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, skylake)

The text was updated successfully, but these errors were encountered:

sglyon · 2019-04-16T00:35:24Z

Thanks @halleysfifthinc for letting us know and for doing some homework on it.

Very helpful.

perhaps @travigd or @shashi know why recent WebIO changes would have broken things?

twavv · 2019-04-16T01:17:48Z

Few diagnostic questions.

Is this using Jupyter notebook or Jupyter lab?
How are you launching Jupyter (e.g. jupyter notebook command or from within Julia running using IJulia; notebook() or something else)? Have you tried restarting?
Can you produce the output of jupyter --data-dir? That directory (for me it's /home/travigd/.local/share/jupyter) should contain an nbextensions directory and that directory should contain a webio directory.

$ ls $(jupyter --data-dir)/nbextensions/webio
main.js

Thanks!

halleysfifthinc · 2019-04-16T15:29:19Z

This is in Jupyter notebook, launched from terminal with jupyter notebook. Do you mean restarting my whole computer or Jupyter? I restarted Jupyter in between the environment changes.

I have the same contents of the webio nbextension as above:

$ ls $(jupyter --data-dir)/nbextensions/webio
main.js

twavv · 2019-04-16T15:32:46Z

Hmmm... and there are no errors in the console? Can you (in the browser console) run localStorage.debug = "*" and refresh and see if there's any other output there? It should look something like this.

halleysfifthinc · 2019-04-16T16:25:26Z

I don't see anything like that. This is all I see, but this is before anything is run:

WebIO:jupyter-notebook Registering WebIO node MIME type (application/vnd.webio.node+json). +0ms main.js:1:6001
WebIO:jupyter-notebook OutputArea display order: +1ms 
Array(11) [ "application/vnd.webio.node+json", "application/javascript", "text/html", "text/markdown", "text/latex", "image/svg+xml", "image/png", "image/jpeg", "image/gif", "application/pdf", … ]
main.js:1:6001
WebIO:jupyter-notebook Rerendering all WebIO cells. +1ms main.js:1:6001

sglyon · 2019-04-19T11:42:48Z

Hi @halleysfifthinc Are you running this in jupyterlab or the notebook?

if you are running in jupyterlab try installing the jupyterlab plotly extension as noted in the just published update to the readme of this repo.

That still doesn't quite fix the WebIO in jupyter problem (so you won't be able to do cool WebIO dependent things like update a chart was already displayed or assign julia callbacks to plot events), but at least you'll be able to see your plots

shashi · 2019-04-19T19:26:52Z

Hi @halleysfifthinc

I know this should have run on its own, but could you try again after running ]build WebIO and restarting the Jupyter server?

halleysfifthinc · 2019-04-19T20:47:25Z

@sglyon, this is in Jupyter notebook, not jupyterlab. For the moment, everything is working fine for me with WebIO pinned at v0.7.0; plots show up fine with that version.

@shashi I said in the first comment that I switched between the two mentioned environments (the difference between the two being WebIO v0.7.0 and WebIO v0.8.1) and built everything (WebIO included) before starting the Jupyter server.

JobJob · 2019-05-03T18:53:10Z

I have the same problem as the OP (in jupyter notebook) in v0.8.1, and working in v0.7.0.

@travigd @shashi try find me on the Julia slack if you want to more interactively debug this.

DhruvaSambrani · 2019-06-01T12:10:11Z

This was supposed to be solved after WebIO updated to 0.8.2. Look at this. But PlotlyJS 0.12.4 has a dependency of WebIO 0.8.1, and this needs to be updated.

sglyon · 2019-06-01T14:49:14Z

@DhruvaSambrani in the Project.toml for PlotlyJS 0.12.4 it looks like the requirement is WebIO version at least 0.8.0. I don't see a 0.8.1 anywhere, could I be missing it?

If I'm not missing anything, then I suppose an up command from pkg mode should get the latest WebIO (perhaps 0.8.2 -- I'm not following release there super closely) and we can test if the latest fixes PlotlyJS?

DhruvaSambrani · 2019-06-02T08:21:50Z

Yes sorry, it's not a problem with PlotlyJS but instead with WebIO. They haven't released the 0.8.2 and 0.8.3 packages publicly yet. I'm opening an issue there. Let's see how it goes!

DhruvaSambrani · 2019-06-07T17:26:00Z

I've updated WebIO to the latest version (v0.8.4),
I see

Warning: Accessing scope.id is deprecated; use scopeid(scope) instead.
caller = ip:0x0
@ Core :-1

and

WebIO not detected

with no plot. Are we absolutely sure its a WebIO issue? Because other WebIO objects are rendering perfectly

sglyon · 2019-06-07T17:44:57Z

might be an issue with how we use WebIO here. @travigd any idea?

twavv · 2019-06-07T20:03:00Z

The WebIO not detected method implies that nothing WebIO related is getting rendered.

twavv · 2019-06-07T20:25:40Z

If you get WebIO not detected, please...

Update to latest WebIO (especially important for Windows - there was a fix about installing the extensions to the wrong place on Windows due to not correctly expanding path macros like %APPDATA%)
Rebuild WebIO
Check output of jupyter nbextension list and see whether or not WebIO is listed there (and whether or not there's an error)

twavv · 2019-06-07T20:34:06Z

Ah - there is an issue here.

There needs to be a display method for

Base.show(::IO, ::WebIO.WEBIO_NODE_MIME, ::SyncPlot)

I thought we had some logic to try to do this automatically in WebIO (basically define a method for show(::IO, ::WEBIO_NODE_MIME, ::T) that then checks if a relevant WebIO.render(::T) method is defined) but I'm not sure. @sglyon can we chat in Slack?

DhruvaSambrani · 2019-06-08T04:44:35Z

If you get WebIO not detected, please...

Update to latest WebIO (especially important for Windows - there was a fix about installing the extensions to the wrong place on Windows due to not correctly expanding path macros like %APPDATA%)

Rebuild WebIO

Check output of jupyter nbextension list and see whether or not WebIO is listed there (and whether or not there's an error)

The result of jupyter nbextension list

Known nbextensions:
config dir: C:\Users\Dhruva Sambrani.jupyter\nbconfig
notebook section
codefolding/main enabled
- Validating: ok
printview/main disabled
skill/main enabled
- Validating: ok
hinterland/hinterland enabled
- Validating: ok
scratchpad/main enabled
- Validating: ok
autosavetime/main enabled
- Validating: ok
skip-traceback/main disabled
webio/main enabled
- Validating: ok
splitcell/splitcell enabled
- Validating: ok
collapsible_headings/main enabled
- Validating: ok
execute_time/ExecuteTime enabled
- Validating: ok
toc2/main enabled
- Validating: ok
notify/notify enabled
- Validating: ok
edit section
codefolding/edit enabled
- Validating: ok
config dir: c:\program files\python37\etc\jupyter\nbconfig
notebook section
jupyter-js-widgets/extension enabled
- Validating: ok
config dir: C:\ProgramData\jupyter\nbconfig
notebook section
nbextensions_configurator/config_menu/main enabled
- Validating: problems found:
- require? X nbextensions_configurator/config_menu/main
contrib_nbextensions_help_item/main enabled
- Validating: ok
tree section
nbextensions_configurator/tree_tab/main enabled
- Validating: problems found:
- require? X nbextensions_configurator/tree_tab/main

xiuliren · 2019-06-19T20:20:23Z

thanks for working on this issue!

I tried to switch to @travigd 's WebIO branch
https://github.com/JuliaGizmos/WebIO.jl/tree/td/add-register-renderable-macro

Unfortunately, I still can not see any plot, I got this message in the browser console:

Jupyter WebIO nbextension detected; not loading ad-hoc.
VM1369:3 Jupyter WebIO extension detected, not mounting.

(v1.0) pkg> st
    Status `/usr/opt/julia-1.0.4/local/share/julia/environments/v1.0/Project.toml`
  [c7e460c6] ArgParse v0.6.2
  [c2a8506f] BigArrays v0.8.0+ [`/usr/opt/julia-1.0.4/local/share/julia/dev/BigArrays`]
  [336ed68f] CSV v0.5.5
  [aaaa29a8] Clustering v0.13.1
  [35d6a980] ColorSchemes v3.3.0
  [3da002f7] ColorTypes v0.8.0
  [5ae59095] Colors v0.9.5
  [d58978e5] Dagger v0.8.0
  [a93c6f00] DataFrames v0.18.3
  [7806a523] DecisionTree v0.8.1
  [b4f34e82] Distances v0.8.0
  [5789e2e9] FileIO v1.0.7
  [53c48c17] FixedPointNumbers v0.6.1
  [4d00f742] GeometryTypes v0.7.5
  [f67ccb44] HDF5 v0.11.1
  [7073ff75] IJulia v1.18.1
  [6218d12a] ImageMagick v0.7.4
  [033835bb] JLD2 v0.1.2
  [682c06a0] JSON v0.20.0
  [a93385a2] JuliaDB v0.12.0
  [6f286f6a] MultivariateStats v0.6.0
  [b8a86587] NearestNeighbors v0.4.3
  [9b87118b] PackageCompiler v0.6.4+ [`/usr/opt/julia-1.0.4/local/share/julia/dev/PackageCompiler`]
  [58dd65bb] Plotly v0.2.0
  [f0f68f2c] PlotlyJS v0.12.4
  [91a5bcdd] Plots v0.25.1
  [92933f4c] ProgressMeter v1.0.0
  [438e738f] PyCall v1.91.2
  [d330b81b] PyPlot v2.8.1
  [a8468747] QHull v0.1.0
  [1a8c2f83] Query v0.11.0
  [6f49c342] RCall v0.13.2
  [4491297b] RealNeuralNetworks v0.8.0+ [`/usr/opt/julia-1.0.4/local/share/julia/dev/RealNeuralNetworks`]
  [295af30f] Revise v2.1.6
  [3646fa90] ScikitLearn v0.5.0
  [2913bbd2] StatsBase v0.30.0
  [0796e94c] Tokenize v0.5.4
  **[0f1e0344] WebIO v0.8.5 [`/usr/opt/julia-1.0.4/local/share/julia/dev/WebIO`]**
  [8ba89e20] Distributed 
  [37e2e46d] LinearAlgebra 
  [10745b16] Statistics

ghuba · 2019-06-27T22:26:09Z

I am having a similar issue. No plot shows up in my Jupyter notebooks. Any advice on what to do?

[f0f68f2c] PlotlyJS v0.12.4

jupyter nbextension list
Known nbextensions:
  config dir: /Users/.../.jupyter/nbconfig
    notebook section
      webio/main  enabled 
      - Validating: OK
  config dir: /Users/.../anaconda3/etc/jupyter/nbconfig
    notebook section
      jupyter-js-widgets/extension  enabled 
      - Validating: OK

julia> versioninfo()
Julia Version 1.1.1
Commit 55e36cc (2019-05-16 04:10 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin15.6.0)
  CPU: Intel(R) Core(TM) i7-7567U CPU @ 3.50GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, skylake)

Command to start notebook:

using IJulia; notebook(dir=".")

In the Chrome developer console:

Screenshot of notebook:

sglyon · 2019-06-28T19:06:14Z

#285 addresses this problem and has been merged. Would people here be willing to test out the latest master?

I could not reproduce the issue, so having another test would be helpful (Thanks @travigd for the fix and @DhruvaSambrani for testing already)!

Either when I get another positive report or a day or two has passed I'll release a new version, whichever happens first

Thanks!

ghuba · 2019-06-28T22:00:27Z

Let me give it a try!

ghuba · 2019-06-28T22:10:46Z

Happy to report this is working now! Problem fixed. Here are some screenshots. There are still a couple of minor warnings but it looks benign.

┌ Info: Recompiling stale cache file /Users/.../.julia/compiled/v1.1/PlotlyJS/1r9Ld.ji for PlotlyJS [f0f68f2c-4968-5e81-91da-67840de0976a]
└ @ Base loading.jl:1184
WARNING: could not import Base.quit into AtomShell

Chrome Console messages

Julia Version 1.1.1
macOS (x86_64-apple-darwin15.6.0)

sglyon · 2019-06-28T22:13:46Z

Thanks!

cstjean · 2019-07-10T18:03:17Z

The example works for me too, but not for my more complex app 😞. The console shows this:

Use of Mutation Events is deprecated. Use MutationObserver instead. jquery.min.js:5
actions jupyter-notebook:find-and-replace does not exist, still binding it in case it will be defined later... menubar.js:304
accessing "actions" on the global IPython/Jupyter is not recommended. Pass it to your objects contructors at creation time main.js:208
Loaded moment locale en-ca bidi.js:19
load_extensions 
Arguments { 0: "jupyter-js-widgets/extension", 1: "webio/main", … }
utils.js:60
Session: kernel_created (857d86c7-b019-4b2d-8760-e1fb7a16e5b8) session.js:54
Starting WebSockets: ws://magneto:8897/api/kernels/165d228e-6e6b-42fc-9333-0f34d5017287 kernel.js:459
WebIO is registering SystemJS window global. main.js:1:39743
Loading extension: webio/main utils.js:37
Loading extension: jupyter-js-widgets/extension utils.js:37
setTimeout executed 0 main.js:1:125191
Kernel: kernel_connected (165d228e-6e6b-42fc-9333-0f34d5017287) kernel.js:103
Kernel: kernel_ready (165d228e-6e6b-42fc-9333-0f34d5017287) kernel.js:103
WebIO detected Jupyter notebook environment. main.min.js:14:17
Jupyter WebIO nbextension detected; not loading ad-hoc. main.min.js:23:21
WebIO detected Jupyter notebook environment. main.min.js:14:17
Jupyter WebIO nbextension detected; not loading ad-hoc. main.min.js:23:21
Jupyter WebIO extension detected, not mounting.
main.min.js:2:17
WebIO detected Jupyter notebook environment. main.min.js:14:17
Jupyter WebIO nbextension detected; not loading ad-hoc. main.min.js:23:21
Jupyter WebIO extension detected, not mounting.
main.min.js:2:17
Source map error: request failed with status 404
Resource URL: http://magneto:8897/static/components/proptypes/index.js?v=c40890eb04df9811fcc4d47e53a29604
Source Map URL: index.js.map

Source map error: request failed with status 404
Resource URL: http://magneto:8897/static/components/preact/index.js?v=00a2fac73c670ce39ac53d26640eb542
Source Map URL: preact.min.js.map

Source map error: request failed with status 404
Resource URL: http://magneto:8897/static/components/preact-compat/index.js?v=f865e990e65ad27e3a2601d8adb48db1
Source Map URL: preact-compat.min.js.map

The last three errors seem unrelated? When I paste the URLs in the browser it works fine.

I did the ritual: build WebIO PlotlyJS; restart notebook server; restart browser.

sglyon · 2019-07-10T21:18:40Z

Grr I thought we had solved this one.

Is there any way you can create a minimal example from your more complex app that we could look at?

It’s hard to diagnose without seeing code

DhruvaSambrani · 2019-07-11T09:54:23Z

@cstjean are you using it with Plots? That still doesn't work

cstjean · 2019-07-11T10:58:00Z

No, I'm using it directly, but it's fairly involved. I'll do a MWE when I get the time, which might be in September...

gurvesh · 2019-07-22T16:37:43Z

Hi - I still get the same error. This is a fresh install of Julia. I've tried upgrading Jupyterlab, building Webio - still nothing shows.

gurvesh · 2019-07-22T16:49:58Z

Actually - it works in Jupyter notebook, but not in Jupyterlab. Also, as Dhruva said - it works only if used directly, but not via Plots.

Masacroso · 2019-07-26T12:45:06Z

Actually - it works in Jupyter notebook, but not in Jupyterlab. Also, as Dhruva said - it works only if used directly, but not via Plots.

it doesn't work in classical jupyter notebook either. I tried now in a jupyter notebook this code

using PlotlyJS
function area1()
    trace1 = scatter(;x=1:4, y=[0, 2, 3, 5], fill="tozeroy")
    trace2 = scatter(;x=1:4, y=[3, 5, 1, 7], fill="tonexty")
    plot([trace1, trace2])
end

But when I executed area1() it just show an empty cell. Context: Julia 1.1.1, IJulia 1.18.1, PlotlyJS 0.12.4 and WebIO 0.8.5. In windows 10 64 bits.

DhruvaSambrani · 2019-07-26T14:29:46Z

But when I executed area1() it just show an empty cell. Context: Julia 1.1.1, IJulia 1.18.1, PlotlyJS 0.12.4 and WebIO 0.8.5. In windows 10 64 bits.

@Masacroso you need to update to PlotlyJS 0.12.5

xiaodaigh · 2020-10-06T02:47:11Z

getting the same issues now ungrade doesn't work

mananbordia · 2021-04-02T18:24:10Z

Executed plot in Jupyter Notebook but gives blank output. What to do ?

empet · 2021-04-02T18:52:46Z

What Julia and PlotlyJS.jl version are you working with?

mananbordia · 2021-04-02T19:08:09Z

PlotlyJS => v"0.14.1"
Julia => v"1.4.2"

empet · 2021-04-02T19:30:20Z

It works with Julia 1.6.0 and the same PlotlyJS version. I installed the last Julia version a few days before, and it worked with 1.5.2. too.

Have you plotted with the same configuration before or this is the first trial?

mananbordia · 2021-04-02T22:08:21Z

I have installed Julia 1.6.0 and reinstalled PlotlyJS but still face the same issue.

And Yes this is my first time.
I am using Jupyter Notebook on Safari (hope that is not the issue).

diegozea · 2021-09-13T14:37:22Z

Same issue on Julia 1.6.2, with IJulia v1.23.2, WebIO v0.8.15, and PlotlyJS v0.18.7

The webio extension is installed:

shell> /home/diego/.local/bin/jupyter nbextension list
Known nbextensions:
  config dir: /home/diego/.jupyter/nbconfig
    notebook section
      jupyter-js-widgets/extension  enabled 
      - Validating: OK
      webio-jupyter-notebook  enabled 
      - Validating: OK

twavv · 2021-09-14T15:41:20Z

@diegozea Can you try updating to the latest WebIO and installing the new Jupyter extension? https://juliagizmos.github.io/WebIO.jl/latest/providers/ijulia/

diegozea · 2021-09-15T22:46:49Z

I have updated it, and it works! Thanks! :)

diegozea mentioned this issue May 9, 2019

PlotlyJS backend to Plots not working in Jupyter notebook JuliaPlots/Plots.jl#2003

Closed

DhruvaSambrani mentioned this issue Jun 1, 2019

No Output in Notebook (Julia v1.0.2) #255

Closed

twavv mentioned this issue Jun 7, 2019

Add @register_renderable macro. JuliaGizmos/WebIO.jl#306

Merged

DhruvaSambrani mentioned this issue Jun 27, 2019

Accessing scope.id is deprecated #283

Open

twavv mentioned this issue Jun 27, 2019

Update to latest WebIO. #285

Merged

sglyon closed this as completed in #285 Jun 28, 2019

sglyon reopened this Jun 28, 2019

sglyon closed this as completed Jun 28, 2019

henselman-petrusek mentioned this issue May 30, 2021

No plots been plotted henselman-petrusek/Eirene.jl#39

Open

sglyon reopened this Sep 14, 2021

halleysfifthinc closed this as completed Dec 9, 2022

Plots don't display in Jupyter with WebIO v0.8.1 #278

Plots don't display in Jupyter with WebIO v0.8.1 #278

Comments

halleysfifthinc commented Apr 15, 2019

sglyon commented Apr 16, 2019

twavv commented Apr 16, 2019

halleysfifthinc commented Apr 16, 2019

twavv commented Apr 16, 2019

halleysfifthinc commented Apr 16, 2019

sglyon commented Apr 19, 2019

shashi commented Apr 19, 2019

halleysfifthinc commented Apr 19, 2019

JobJob commented May 3, 2019

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ghuba commented Jun 27, 2019

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ghuba commented Jun 28, 2019

ghuba commented Jun 28, 2019

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DhruvaSambrani commented Jul 11, 2019

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Masacroso commented Jul 26, 2019

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