HTML view not working with py3Dmol

Psirving commented 3 years ago

Nobody has reported an issue with py3Dmol, but there was one about a performance issue with NGLview, which is a similar package for viewing molecular models. However, I think the backends of these two packages are different, and the issue I am having is different.

Py3Dmol is a python implementation of 3Dmol.js. The output displays in browser implementations of a Jupyter Notebook (using Chrome), and it was working around a month ago in VS Code, but now it creates an empty output cell of roughly the correct size.

Environment data

VS Code version: 1.57.1
Jupyter Extension version (available under the Extensions sidebar): v2021.6.999662501
Python Extension version (available under the Extensions sidebar): v2021.6.944021595
OS (Windows | Mac | Linux distro) and version: Windows 10.0.19043 build 19043
Python and/or Anaconda version: Anaconda 2020.11 Python 3.7.9
Type of virtual environment used (N/A | venv | virtualenv | conda | ...): conda, but using 'base'
Jupyter server running: Local

Expected behaviour

An interactive plot should display in the output cell.

Actual behaviour

A blank output of roughly the correct size displays in the output cell.

Steps to reproduce:

Run the following in a code cell:

!pip install py3Dmol
import py3Dmol
p = py3Dmol.view(query='mmtf:1ycr')
p.setStyle({'cartoon': {'color':'spectrum'}})
p

Logs

Output for Jupyter in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Jupyter)

``` Info 2021-07-08 11:32:41: restartKernel - finishing cells that are outstanding Info 2021-07-08 11:32:41: restartKernel - restarting kernel Info 2021-07-08 11:32:41: Restarting ea8fa227-96a8-4cc1-9268-13ca982d86f4 Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_onRestartKernel Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_kernelOptions Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Got new session 00e5c2cb-0f18-41aa-90ac-9f64a3c749ca Info 2021-07-08 11:32:41: Starting raw kernel Python 3.7.9 64-bit ('base': conda) Info 2021-07-08 11:32:41: installMissingDependencies C:\Users\psirv\Anaconda3\python.exe Info 2021-07-08 11:32:41: Started new restart session Info 2021-07-08 11:32:41: shutdownSession ea8fa227-96a8-4cc1-9268-13ca982d86f4, .jvsc74a57bd06c33f2e669c4252adcb6b35df72ed100d5670b3dff543db2a50ccff0137b1beb.C:\Users\psirv\Anaconda3\python.exe.C:\Users\psirv\Anaconda3\python.exe - start Info 2021-07-08 11:32:41: Session can be shutdown .jvsc74a57bd06c33f2e669c4252adcb6b35df72ed100d5670b3dff543db2a50ccff0137b1beb.C:\Users\psirv\Anaconda3\python.exe.C:\Users\psirv\Anaconda3\python.exe Info 2021-07-08 11:32:41: Dispose Kernel process Info 2021-07-08 11:32:41: kill daemon Info 2021-07-08 11:32:41: restartKernel - initialSetup Info 2021-07-08 11:32:41: Initial setup for untitled:Untitled-1.ipynb starting ... Info 2021-07-08 11:32:41: UpdateWorkingDirectoryAndPath Info 2021-07-08 11:32:41: Process Execution: > ~\Anaconda3\python.exe -c "import ipykernel" > ~\Anaconda3\python.exe -c "import ipykernel" Info 2021-07-08 11:32:41: KernelProcess output: Content-Length: 121 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"Execute rpc method kill_kernel in DS Daemon","pid":8940}} Info 2021-07-08 11:32:41: Python Daemon (pid: 8940): Execute rpc method kill_kernel in DS Daemon Info 2021-07-08 11:32:41: KernelProcess output: Content-Length: 153 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"Execute rpc method kill_kernel from C:\\Users\\psirv\\Anaconda3\\python.exe","pid":8940}}Content-Length: 118 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"Kill kernel in DS Kernel Launcher Daemon","pid":8940}}Content-Length: 129 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"Kill kernel in DS Kernel Launcher Daemon, pid 15236","pid":8940}}Content-Length: 38 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","id":2,"result":null} Info 2021-07-08 11:32:41: Python Daemon (pid: 8940): Execute rpc method kill_kernel from C:\Users\psirv\Anaconda3\python.exe Info 2021-07-08 11:32:41: Python Daemon (pid: 8940): Kill kernel in DS Kernel Launcher Daemon Info 2021-07-08 11:32:41: Python Daemon (pid: 8940): Kill kernel in DS Kernel Launcher Daemon, pid 15236 Info 2021-07-08 11:32:41: Dispose Kernel process Info 2021-07-08 11:32:41: shutdownSession ea8fa227-96a8-4cc1-9268-13ca982d86f4, .jvsc74a57bd06c33f2e669c4252adcb6b35df72ed100d5670b3dff543db2a50ccff0137b1beb.C:\Users\psirv\Anaconda3\python.exe.C:\Users\psirv\Anaconda3\python.exe - shutdown complete Info 2021-07-08 11:32:41: Dispose Kernel process Info 2021-07-08 11:32:41: KernelProcess Exit Exit - undefined Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_mirror_execute Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_registerCommTarget Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_registerCommTarget Info 2021-07-08 11:32:41: IPyWidgetMessageDispatcher.initialize Info 2021-07-08 11:32:41: IPyWidgetMessageDispatcher.initialize Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Kernel switching to busy Info 2021-07-08 11:32:41: Notebook Session status untitled:Untitled-1.ipynb # Busy Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_mirror_execute Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Kernel switching to idle Info 2021-07-08 11:32:41: Notebook Session status untitled:Untitled-1.ipynb # Idle Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Kernel switching to busy Info 2021-07-08 11:32:41: Notebook Session status untitled:Untitled-1.ipynb # Busy Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Kernel switching to idle Info 2021-07-08 11:32:41: Notebook Session status untitled:Untitled-1.ipynb # Idle Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Initial setup complete for untitled:Untitled-1.ipynb Info 2021-07-08 11:32:41: restartKernel - initialSetup completed Info 2021-07-08 11:32:41: Time to restart kernel is 0.152s Info 2021-07-08 11:32:41: Notebook Kernel restarted untitled:Untitled-1.ipynb Info 2021-07-08 11:32:41: Cancel all executions as Kernel was restarted Info 2021-07-08 11:32:41: Cancel pending cells Info 2021-07-08 11:32:41: Registering commtarget jupyter.widget Info 2021-07-08 11:32:41: UpdateWorkingDirectoryAndPath Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: changeDirectoryIfPossible Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_mirror_execute Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Kernel switching to busy Info 2021-07-08 11:32:41: Notebook Session status untitled:Untitled-1.ipynb # Busy Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:41: [32mPosting message to Notebook UI Info 2021-07-08 11:32:41: Kernel switching to idle Info 2021-07-08 11:32:41: Notebook Session status untitled:Untitled-1.ipynb # Idle Info 2021-07-08 11:32:41: Waiting for idle on (kernel): 00e5c2cb-0f18-41aa-90ac-9f64a3c749ca -> idle Info 2021-07-08 11:32:41: Finished waiting for idle on (kernel): 00e5c2cb-0f18-41aa-90ac-9f64a3c749ca -> idle Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:41: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:42: Install Missing Dependencies, Class name = w, completed in 942ms, has a falsy return value, Return Value: undefined Info 2021-07-08 11:32:42: Kernel launching with ports 9010,9011,9012,9013,9014. Start port is 9000 Info 2021-07-08 11:32:42: Launching kernel daemon for Python 3.7.9 64-bit ('base': conda) # C:\Users\psirv\Anaconda3\python.exe Info 2021-07-08 11:32:42: Fetching interpreter variables of Conda environment to be used as env vars of Kernel Info 2021-07-08 11:32:42: Creating daemon process for C:\Users\psirv\Anaconda3\python.exe with env variables count 67 Info 2021-07-08 11:32:42: Process Execution: > ~\Anaconda3\python.exe -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v > ~\Anaconda3\python.exe -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v Info 2021-07-08 11:32:42: Got custom variables for Kernel owned by a conda interpreter Info 2021-07-08 11:32:42: Python Daemon (pid: 17564): Execute rpc method exec_module in DS Daemon Info 2021-07-08 11:32:42: Python Daemon (pid: 17564): Execute rpc method exec_module from C:\Users\psirv\Anaconda3\python.exe Info 2021-07-08 11:32:42: Python Daemon (pid: 17564): Exec module in DS Kernel Launcher Daemon ipykernel_launcher with args ['--ip=127.0.0.1', '--stdin=9013', '--control=9011', '--hb=9010', '--Session.signature_scheme="hmac-sha256"', '--Session.key=b"7b65afe3-6949-453f-b9ca-6d4f1b0549d4"', '--shell=9012', '--transport="tcp"', '--iopub=9014', '--f=C:\\Users\\psirv\\AppData\\Local\\Temp\\tmp-40882I6r4f6j8YeC.json'] Info 2021-07-08 11:32:42: Python Daemon (pid: 17564): Exec in DS Kernel Launcher Daemon (observable) ipykernel_launcher with args ['--ip=127.0.0.1', '--stdin=9013', '--control=9011', '--hb=9010', '--Session.signature_scheme="hmac-sha256"', '--Session.key=b"7b65afe3-6949-453f-b9ca-6d4f1b0549d4"', '--shell=9012', '--transport="tcp"', '--iopub=9014', '--f=C:\\Users\\psirv\\AppData\\Local\\Temp\\tmp-40882I6r4f6j8YeC.json'] Info 2021-07-08 11:32:42: Python Daemon (pid: 17564): Exec in DS Kernel Launcher Daemon (observable) ['C:\\Users\\psirv\\Anaconda3\\python.exe', '-m', 'ipykernel_launcher', '--ip=127.0.0.1', '--stdin=9013', '--control=9011', '--hb=9010', '--Session.signature_scheme="hmac-sha256"', '--Session.key=b"7b65afe3-6949-453f-b9ca-6d4f1b0549d4"', '--shell=9012', '--transport="tcp"', '--iopub=9014', '--f=C:\\Users\\psirv\\AppData\\Local\\Temp\\tmp-40882I6r4f6j8YeC.json'] Info 2021-07-08 11:32:42: Python Daemon (pid: 17564): Exec in DS Kernel Launcher Daemon (observable) Info 2021-07-08 11:32:42: Python Daemon (pid: 17564): Kernel launched, with PID 9400 Warn 2021-07-08 11:32:42: Python Daemon (pid: 17564): Waiting for Kernel to die 9400 Info 2021-07-08 11:32:42: Launching kernel daemon, Class name = f, completed in 247ms, has a truthy return value, Arg 1: , Arg 2: "c:\\Users\\psirv\\OneDrive - University of North Carolina at Chapel Hill\\GitHub\\JNBTools", Arg 3: {"specFile":"C:\\Users\\psirv\\Anaconda3\\share\\jupyter\\kernels\\python3\\kernel.json","interpreterPath":"C:\\Users\\psirv\\Anaconda3\\python.exe","name":"python379jvsc74a57bd06c33f2e669c4252adcb6b35df72ed100d5670b3dff543db2a50ccff0137b1beb","argv":["C:/Users/psirv/Anaconda3\\python.exe","-m","ipykernel_launcher","--ip=127.0.0.1","--stdin=9013","--control=9011","--hb=9010","--Session.signature_scheme=\"hmac-sha256\"","--Session.key=b\"7b65afe3-6949-453f-b9ca-6d4f1b0549d4\"","--shell=9012","--transport=\"tcp\"","--iopub=9014","--f=C:\\Users\\psirv\\AppData\\Local\\Temp\\tmp-40882I6r4f6j8YeC.json"],"language":"python","path":"C:/Users/psirv/Anaconda3\\python.exe","display_name":"Python 3.7.9 64-bit ('base': conda)"}, Arg 4: {"sysPrefix":"C:\\Users\\psirv\\Anaconda3","envType":"Conda","envName":"base","envPath":"C:\\Users\\psirv\\Anaconda3","path":"C:\\Users\\psirv\\Anaconda3\\python.exe","architecture":3,"sysVersion":"3.7.9 (default, Aug 31 2020, 17:10:11) [MSC v.1916 64 bit (AMD64)]","version":{"raw":"3.7.9","major":3,"minor":7,"patch":9,"build":[],"prerelease":["final","0"]},"companyDisplayName":"ContinuumAnalytics","displayName":"Python 3.7.9 64-bit ('base': conda)"}, Return Value: Info 2021-07-08 11:32:42: Launching kernel in kernelProcess.ts, Class name = b, completed in 248ms, has a truthy return value, Arg 1: "c:\\Users\\psirv\\OneDrive - University of North Carolina at Chapel Hill\\GitHub\\JNBTools", Return Value: 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Info 2021-07-08 11:32:42: Execute Cells request 2 0, 1 Info 2021-07-08 11:32:42: Execute Cell 0 untitled:Untitled-1.ipynb Info 2021-07-08 11:32:42: Cell Index:0, state:1, exec: 1. User queued cell for execution Info 2021-07-08 11:32:42: Execute Cell 1 untitled:Untitled-1.ipynb Info 2021-07-08 11:32:42: Cell Index:1, state:undefined, exec: undefined. User queued cell for execution Info 2021-07-08 11:32:42: Cell Index:0, state:1, exec: 1. Ready to execute Info 2021-07-08 11:32:42: Cell Index:1, state:undefined, exec: undefined. Ready to execute Info 2021-07-08 11:32:42: Cell Index:0, state:1, exec: 1. Before Execute individual cell Info 2021-07-08 11:32:42: Cell Index:0, state:1, exec: 1. Start execution Info 2021-07-08 11:32:42: Cell Index:0, state:3, exec: undefined. Send code for execution Info 2021-07-08 11:32:42: Cell Index:0, state:3, exec: undefined. Wait for jupyter execution Info 2021-07-08 11:32:42: [32mWidget Coordinator sent IPyWidgets_mirror_execute Info 2021-07-08 11:32:42: [32mPosting message to Notebook UI Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:42: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:42: [32mPosting message to Notebook UI Info 2021-07-08 11:32:42: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:42: [32mPosting message to Notebook UI Info 2021-07-08 11:32:42: Cell Index:0, state:3, exec: undefined. Kernel switching to busy Info 2021-07-08 11:32:42: Notebook Session status untitled:Untitled-1.ipynb # Busy Info 2021-07-08 11:32:42: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:42: [32mPosting message to Notebook UI Info 2021-07-08 11:32:42: Cell Index:0, state:3, exec: 1. Update output Info 2021-07-08 11:32:42: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:42: [32mPosting message to Notebook UI Info 2021-07-08 11:32:42: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:42: [32mPosting message to Notebook UI Info 2021-07-08 11:32:42: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-08 11:32:42: [32mPosting message to Notebook UI Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-08 11:32:42: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-08 11:32:42: Cell Index:0, state:3, exec: 1. Update output Info 2021-07-08 11:32:43: Cell Index:0, state:3, exec: 1. Kernel switching to idle Info 2021-07-08 11:32:43: Notebook Session status untitled:Untitled-1.ipynb # Idle Info 2021-07-08 11:32:43: Cell Index:0, state:3, exec: 1. Jupyter execution completed Info 2021-07-08 11:32:43: Cell Index:0, state:3, exec: 1. Completed successfully Info 2021-07-08 11:32:43: Cell Index:0, state:3, exec: 1. Completed successfully & resolving Info 2021-07-08 11:32:43: Cell Index:0, state:3, exec: 1. After Execute individual cell 3 Info 2021-07-08 11:32:43: Cell Index:1, state:2, exec: undefined. Before Execute individual cell Info 2021-07-08 11:32:43: Cell Index:1, state:2, exec: undefined. Start execution Info 2021-07-08 11:32:43: Cell Index:0, state:3, exec: 1. Executed successfully in executeCell Info 2021-07-08 11:32:43: Cell Index:0, state:3, exec: 1. Execution disposed Info 2021-07-08 11:32:43: Cell Index:1, state:3, exec: undefined. Send code for execution Info 2021-07-08 11:32:43: Cell Index:1, state:3, exec: undefined. Empty cell execution Info 2021-07-08 11:32:43: Cell Index:1, state:3, exec: undefined. Completed successfully Info 2021-07-08 11:32:43: Cell Index:1, state:3, exec: undefined. Completed successfully & resolving Info 2021-07-08 11:32:43: Cell Index:1, state:3, exec: undefined. After Execute individual cell 2 Info 2021-07-08 11:32:43: Cell Index:1, state:3, exec: undefined. Execution disposed Info 2021-07-08 11:32:43: KernelProcess output: Content-Length: 335 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"write to stderr: C:\\Users\\psirv\\Anaconda3\\lib\\site-packages\\traitlets\\traitlets.py:2199: FutureWarning: Supporting extra quotes around Unicode is deprecated in traitlets 5.0. Use 'hmac-sha256' instead of '\"hmac-sha256\"' \u2013 or use CUnicode.\r\n","pid":17564}}Content-Length: 312 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"output","params":{"source":"stderr","out":"C:\\Users\\psirv\\Anaconda3\\lib\\site-packages\\traitlets\\traitlets.py:2199: FutureWarning: Supporting extra quotes around Unicode is deprecated in traitlets 5.0. Use 'hmac-sha256' instead of '\"hmac-sha256\"' \u2013 or use CUnicode.\r\n"}} Info 2021-07-08 11:32:43: Python Daemon (pid: 17564): write to stderr: C:\Users\psirv\Anaconda3\lib\site-packages\traitlets\traitlets.py:2199: FutureWarning: Supporting extra quotes around Unicode is deprecated in traitlets 5.0. Use 'hmac-sha256' instead of '"hmac-sha256"' – or use CUnicode. Info 2021-07-08 11:32:43: KernelProcess output: Content-Length: 116 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"write to stderr: FutureWarning)\r\n","pid":17564}}Content-Length: 93 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"output","params":{"source":"stderr","out":" FutureWarning)\r\n"}}Content-Length: 361 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"write to stderr: C:\\Users\\psirv\\Anaconda3\\lib\\site-packages\\traitlets\\traitlets.py:2154: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '7b65afe3-6949-453f-b9ca-6d4f1b0549d4' instead of 'b\"7b65afe3-6949-453f-b9ca-6d4f1b0549d4\"'.\r\n","pid":17564}}Content-Length: 338 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"output","params":{"source":"stderr","out":"C:\\Users\\psirv\\Anaconda3\\lib\\site-packages\\traitlets\\traitlets.py:2154: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '7b65afe3-6949-453f-b9ca-6d4f1b0549d4' instead of 'b\"7b65afe3-6949-453f-b9ca-6d4f1b0549d4\"'.\r\n"}}Content-Length: 116 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"log","params":{"level":"INFO","msg":"write to stderr: FutureWarning)\r\n","pid":17564}}Content-Length: 93 Content-Type: application/vscode-jsonrpc; charset=utf8 {"jsonrpc":"2.0","method":"output","params":{"source":"stderr","out":" FutureWarning)\r\n"}} Warn 2021-07-08 11:32:43: Kernel 17564 as possibly died, StdErr from Kernel Process C:\Users\psirv\Anaconda3\lib\site-packages\traitlets\traitlets.py:2199: FutureWarning: Supporting extra quotes around Unicode is deprecated in traitlets 5.0. Use 'hmac-sha256' instead of '"hmac-sha256"' – or use CUnicode. Warn 2021-07-08 11:32:43: StdErr from Kernel Process C:\Users\psirv\Anaconda3\lib\site-packages\traitlets\traitlets.py:2199: FutureWarning: Supporting extra quotes around Unicode is deprecated in traitlets 5.0. Use 'hmac-sha256' instead of '"hmac-sha256"' – or use CUnicode. Info 2021-07-08 11:32:43: Python Daemon (pid: 17564): write to stderr: FutureWarning) Warn 2021-07-08 11:32:43: Kernel 17564 as possibly died, StdErr from Kernel Process FutureWarning) Warn 2021-07-08 11:32:43: StdErr from Kernel Process FutureWarning) Info 2021-07-08 11:32:43: Python Daemon (pid: 17564): write to stderr: C:\Users\psirv\Anaconda3\lib\site-packages\traitlets\traitlets.py:2154: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '7b65afe3-6949-453f-b9ca-6d4f1b0549d4' instead of 'b"7b65afe3-6949-453f-b9ca-6d4f1b0549d4"'. Warn 2021-07-08 11:32:43: Kernel 17564 as possibly died, StdErr from Kernel Process C:\Users\psirv\Anaconda3\lib\site-packages\traitlets\traitlets.py:2154: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '7b65afe3-6949-453f-b9ca-6d4f1b0549d4' instead of 'b"7b65afe3-6949-453f-b9ca-6d4f1b0549d4"'. Warn 2021-07-08 11:32:43: StdErr from Kernel Process C:\Users\psirv\Anaconda3\lib\site-packages\traitlets\traitlets.py:2154: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '7b65afe3-6949-453f-b9ca-6d4f1b0549d4' instead of 'b"7b65afe3-6949-453f-b9ca-6d4f1b0549d4"'. Info 2021-07-08 11:32:43: Python Daemon (pid: 17564): write to stderr: FutureWarning) Warn 2021-07-08 11:32:43: Kernel 17564 as possibly died, StdErr from Kernel Process FutureWarning) Warn 2021-07-08 11:32:43: StdErr from Kernel Process FutureWarning) ```

DonJayamanne commented 3 years ago

Should be fixed in our new release, will be releasing shortly.

greazer commented 3 years ago

@Psirving, please reopen if this has not been fixed in the next release (happening very very soon)

Psirving commented 3 years ago

I just updated to v2021.8.1013163132. I'm still getting the same result.

Psirving commented 3 years ago

I don't think I have permission to reopen an issue which you closed.

DonJayamanne commented 3 years ago

@Psirving works for me, see here Please could you provide logs:

Jupyter output panel
Toggle Developer tools & go into console window

Psirving commented 3 years ago

My mistake, kind of.

It is working in newly created notebooks only. If I run this cell in an existing notebook, or if I make a copy of a notebook, and run that, It doesn't display. If I copy all of the contents of a notebook to a newly created notebook. It works perfectly. The logs, to me look basically the same.

Logs

Log 1, a new notebook, this displays correctly.

``` Info 2021-07-09 14:30:43: Execute Cells request 1 0 Info 2021-07-09 14:30:43: Execute Cell 0 untitled:Untitled-1.ipynb?jupyter-notebook Info 2021-07-09 14:30:43: Cell Index:0, state:1, exec: 1. User queued cell for execution Info 2021-07-09 14:30:43: Cell Index:0, state:1, exec: 1. Ready to execute Info 2021-07-09 14:30:43: Cell Index:0, state:1, exec: 1. Before Execute individual cell Info 2021-07-09 14:30:43: Cell Index:0, state:1, exec: 1. Start execution Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: undefined. Send code for execution Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: undefined. Wait for jupyter execution Info 2021-07-09 14:30:43: [32mWidget Coordinator sent IPyWidgets_mirror_execute Info 2021-07-09 14:30:43: [32mPosting message to Notebook UI Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:30:43: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:30:43: [32mPosting message to Notebook UI Info 2021-07-09 14:30:43: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:30:43: [32mPosting message to Notebook UI Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: undefined. Kernel switching to busy Info 2021-07-09 14:30:43: Notebook Session status untitled:Untitled-1.ipynb?jupyter-notebook # Busy Info 2021-07-09 14:30:43: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:30:43: [32mPosting message to Notebook UI Info 2021-07-09 14:30:43: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:30:43: [32mPosting message to Notebook UI Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: undefined. Update output Info 2021-07-09 14:30:43: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:30:43: [32mPosting message to Notebook UI Info 2021-07-09 14:30:43: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:30:43: [32mPosting message to Notebook UI Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:30:43: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. Update output Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. Kernel switching to idle Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. Jupyter execution completed Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. Completed successfully Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. Completed successfully & resolving Info 2021-07-09 14:30:43: Notebook Session status untitled:Untitled-1.ipynb?jupyter-notebook # Idle Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. After Execute individual cell 3 Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. Executed successfully in executeCell Info 2021-07-09 14:30:43: Cell Index:0, state:3, exec: 3. Execution disposed ```

Log 2, an existing notebook, this does not display anything.

``` Info 2021-07-09 14:31:38: Execute Cells request 1 0 Info 2021-07-09 14:31:38: Execute Cell 0 file:///c%3A/Users/psirving/OneDrive%20-%20University%20of%20North%20Carolina%20at%20Chapel%20Hill/GitHub/JNBTools/JNB-example/3d_test.ipynb Info 2021-07-09 14:31:38: Cell Index:0, state:1, exec: 2. User queued cell for execution Info 2021-07-09 14:31:38: Cell Index:0, state:1, exec: 2. Ready to execute Info 2021-07-09 14:31:38: Cell Index:0, state:1, exec: 2. Before Execute individual cell Info 2021-07-09 14:31:38: Cell Index:0, state:1, exec: 2. Start execution Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: undefined. Send code for execution Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: undefined. Wait for jupyter execution Info 2021-07-09 14:31:38: [32mWidget Coordinator sent IPyWidgets_mirror_execute Info 2021-07-09 14:31:38: [32mPosting message to Notebook UI Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:31:38: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:31:38: [32mPosting message to Notebook UI Info 2021-07-09 14:31:38: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:31:38: [32mPosting message to Notebook UI Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: undefined. Kernel switching to busy Info 2021-07-09 14:31:38: Notebook Session status file:///c%3A/Users/psirving/OneDrive%20-%20University%20of%20North%20Carolina%20at%20Chapel%20Hill/GitHub/JNBTools/JNB-example/3d_test.ipynb # Busy Info 2021-07-09 14:31:38: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:31:38: [32mPosting message to Notebook UI Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: undefined. Update output Info 2021-07-09 14:31:38: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:31:38: [32mPosting message to Notebook UI Info 2021-07-09 14:31:38: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:31:38: [32mPosting message to Notebook UI Info 2021-07-09 14:31:38: [32mWidget Coordinator sent IPyWidgets_msg Info 2021-07-09 14:31:38: [32mPosting message to Notebook UI Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_iopub_msg_handled Info 2021-07-09 14:31:38: [32mWidget Coordinator received IPyWidgets_msg_received Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. Update output Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. Kernel switching to idle Info 2021-07-09 14:31:38: Notebook Session status file:///c%3A/Users/psirving/OneDrive%20-%20University%20of%20North%20Carolina%20at%20Chapel%20Hill/GitHub/JNBTools/JNB-example/3d_test.ipynb # Idle Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. Jupyter execution completed Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. Completed successfully Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. Completed successfully & resolving Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. After Execute individual cell 3 Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. Executed successfully in executeCell Info 2021-07-09 14:31:38: Cell Index:0, state:3, exec: 3. Execution disposed ```

DonJayamanne commented 3 years ago

Odd, I can replicate in stable however it works in insiders. Please could you install VS Code insiders and try this out, its possible its related to an upstream issue (in vsocde) & its been fixed there. Appreciate your help.

Psirving commented 3 years ago

Yup, works perfect with insiders. Thanks so much!

DonJayamanne commented 3 years ago

Sounds like a bug in vscode stable that's fixed in insiders. I'll try to keep an eye out for this when the next version of vscode gets released

microsoft / vscode-jupyter