Matplotlib interactive plotting with Qt causes subsequent cells to hang

Environment data

• VS Code version: version 1.62 (October 2021 release)
• Jupyter Extension version (available under the Extensions sidebar): v2021.10.1001414422
• Python Extension version (available under the Extensions sidebar): v2021.11.1422169775
• OS (Windows | Mac | Linux distro) and version: Ubuntu 18.04 running in WSL2
• Python and/or Anaconda version: 3.9.7
• Type of virtual environment used (N/A | venv | virtualenv | conda | …): conda
• Jupyter server running: Local | Remote | Extension is enabled on ‘WSL: Ubuntu-18.04’

I’m running an X server on my Windows 10 PC to view interactive Qt5 matplotlib plots from Ubuntu 18.04 running in WSL2. Unfortunately a recent update of the Jupyter extension seems to have introduced a bug where only the first cell after the matplotlib qt command runs. I can switch between the last working version (v2021.10.1001393861) and the new version (e.g. v2021.10.1001414422) and reliably reproduce the bug.

Expected behaviour

Manually executing the following three cells should import modules, produce a simple line plot in an interactive window, and print “done”. The most recent update which still produces the expected behaviour is v2021.10.1001393861.

# %%
import numpy as np
from IPython import get_ipython
get_ipython().run_line_magic('matplotlib', 'qt')
import matplotlib.pyplot as plt

# %%
plt.plot(np.linspace(0,1,10))

# %%
print('done')

Actual behaviour

The first two cells execute and the third cell hangs. All subsequent cells hang. Closing the plot has no effect.

Steps to reproduce:

Run these three cells in sequence from the editor using a basic conda environment with matplotlib, numpy, and ipykernel installed.

# %%
import numpy as np
from IPython import get_ipython
get_ipython().run_line_magic('matplotlib', 'qt')
import matplotlib.pyplot as plt

# %%
plt.plot(np.linspace(0,1,10))

# %%
print('done')

Logs

Logs are for the broken version.

Info 2021-11-05 13:55:45: Restart requested vscode-interactive:Interactive-1.interactive
Info 2021-11-05 13:55:45: Restart kernel execution
Info 2021-11-05 13:55:45: Cancel pending cells
Info 2021-11-05 13:55:45: Starting raw kernel Python 3.9.7 64-bit ('basic': conda)
Info 2021-11-05 13:55:45: installMissingDependencies /home/grobs/miniconda3/envs/basic/bin/python
Info 2021-11-05 13:55:45: Restarting 51c54e48-3866-4c04-a346-2e2d239ec335
Error 2021-11-05 13:55:45: Failed to get activated conda env variables for basic: /home/grobs/miniconda3/envs/basic/bin/python
Info 2021-11-05 13:55:45: Process Execution: > ~/miniconda3/envs/basic/bin/python -c "import ipykernel"
> ~/miniconda3/envs/basic/bin/python -c "import ipykernel"
Info 2021-11-05 13:55:45: Install Missing Dependencies, Class name = S, completed in 94ms, has a falsy return value, Return Value: undefined
Info 2021-11-05 13:55:45: Kernel launching with ports 9075,9076,9077,9078,9079. Start port is 9000
Info 2021-11-05 13:55:45: Launching kernel daemon for Python 3.9.7 64-bit ('basic': conda) # /home/grobs/miniconda3/envs/basic/bin/python
Error 2021-11-05 13:55:45: Failed to get activated conda env variables for basic: /home/grobs/miniconda3/envs/basic/bin/python
Error 2021-11-05 13:55:45: Failed to get activated conda env variables for basic: /home/grobs/miniconda3/envs/basic/bin/python
Error 2021-11-05 13:55:45: Failed to get activated conda env variables for basic: /home/grobs/miniconda3/envs/basic/bin/python
Info 2021-11-05 13:55:45: Creating daemon process for /home/grobs/miniconda3/envs/basic/bin/python with env variables count 67
Info 2021-11-05 13:55:45: Process Execution: > ~/miniconda3/envs/basic/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> ~/miniconda3/envs/basic/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
Info 2021-11-05 13:55:45: Starting kernel from scratch with options {"env":{"USER":"grobs","VSCODE_WSL_EXT_LOCATION":"/mnt/c/Users/gawr/.vscode/extensions/ms-vscode-remote.remote-wsl-0.58.5","SHLVL":"2","WT_PROFILE_ID":"{c6eaf9f4-32a7-5fdc-b5cf-066e8a4b1e40}","HOME":"/home/grobs","WSL_DISTRO_NAME":"Ubuntu-18.04","LOGNAME":"grobs","WSL_INTEROP":"/run/WSL/2332_interop","NAME":"Code","_":"/home/grobs/miniconda3/envs/basic/bin/python","TERM":"xterm-256color","PATH":"/home/grobs/.vscode-server/bin/b3318bc0524af3d74034b8bb8a64df0ccf35549a/bin:/usr/local/freesurfer/7.2.0/bin:/usr/local/freesurfer/7.2.0/fsfast/bin:/usr/local/freesurfer/7.2.0/tktools:/usr/local/freesurfer/7.2.0/mni/bin:/home/grobs/miniconda3/envs/basic/bin:/home/grobs/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program 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Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): Execute rpc method exec_module in DS Daemon
Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): Execute rpc method exec_module from /home/grobs/miniconda3/envs/basic/bin/python
Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): Exec module in DS Kernel Launcher Daemon ipykernel_launcher with args ['--ip=127.0.0.1', '--stdin=9078', '--control=9076', '--hb=9075', '--Session.signature_scheme="hmac-sha256"', '--Session.key=b"9b7d1f68-95da-4329-a6d1-edf9306bd29d"', '--shell=9077', '--transport="tcp"', '--iopub=9079', '--f=/tmp/tmp-6542xDnxgKHM6b5k.json']
Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): Exec in DS Kernel Launcher Daemon (observable) ipykernel_launcher with args ['--ip=127.0.0.1', '--stdin=9078', '--control=9076', '--hb=9075', '--Session.signature_scheme="hmac-sha256"', '--Session.key=b"9b7d1f68-95da-4329-a6d1-edf9306bd29d"', '--shell=9077', '--transport="tcp"', '--iopub=9079', '--f=/tmp/tmp-6542xDnxgKHM6b5k.json']
Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): Exec in DS Kernel Launcher Daemon (observable) ['/home/grobs/miniconda3/envs/basic/bin/python', '-m', 'ipykernel_launcher', '--ip=127.0.0.1', '--stdin=9078', '--control=9076', '--hb=9075', '--Session.signature_scheme="hmac-sha256"', '--Session.key=b"9b7d1f68-95da-4329-a6d1-edf9306bd29d"', '--shell=9077', '--transport="tcp"', '--iopub=9079', '--f=/tmp/tmp-6542xDnxgKHM6b5k.json']
Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): Exec in DS Kernel Launcher Daemon (observable)
Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): Kernel launched, with PID 6947
Warn 2021-11-05 13:55:45: Python Daemon (pid: 6946): Waiting for Kernel to die 6947
Info 2021-11-05 13:55:45: Launching kernel daemon, Class name = p, completed in 45ms, has a truthy return value, Arg 1: <Uri:/home/grobs/meg_analysis/for_notebook.py>, Arg 2: "/home/grobs/meg_analysis", Arg 3: {"interpreterPath":"/home/grobs/miniconda3/envs/basic/bin/python","name":"python397jvsc74a57bd0ea5d3ea4e504429a544d1553bc21d85a7673a48ee674c84e04ac5ffc06b339d4","argv":["python","-m","ipykernel_launcher","--ip=127.0.0.1","--stdin=9078","--control=9076","--hb=9075","--Session.signature_scheme=\"hmac-sha256\"","--Session.key=b\"9b7d1f68-95da-4329-a6d1-edf9306bd29d\"","--shell=9077","--transport=\"tcp\"","--iopub=9079","--f=/tmp/tmp-6542xDnxgKHM6b5k.json"],"language":"python","path":"python","display_name":"Python 3.9.7 64-bit ('basic': conda)","metadata":{"interpreter":{"sysPrefix":"/home/grobs/miniconda3/envs/basic","envType":"Conda","envName":"basic","envPath":"/home/grobs/miniconda3/envs/basic","path":"/home/grobs/miniconda3/envs/basic/bin/python","architecture":3,"sysVersion":"3.9.7 (default, Sep 16 2021, 13:09:58) \n[GCC 7.5.0]","version":{"raw":"3.9.7","major":3,"minor":9,"patch":7,"build":[],"prerelease":["final","0"]},"companyDisplayName":"Anaconda, Inc.","displayName":"Python 3.9.7 64-bit ('basic': conda)"}},"env":{}}, Arg 4: {"sysPrefix":"/home/grobs/miniconda3/envs/basic","envType":"Conda","envName":"basic","envPath":"/home/grobs/miniconda3/envs/basic","path":"/home/grobs/miniconda3/envs/basic/bin/python","architecture":3,"sysVersion":"3.9.7 (default, Sep 16 2021, 13:09:58) \n[GCC 7.5.0]","version":{"raw":"3.9.7","major":3,"minor":9,"patch":7,"build":[],"prerelease":["final","0"]},"companyDisplayName":"Anaconda, Inc.","displayName":"Python 3.9.7 64-bit ('basic': conda)"}, Return Value: <Return value cannot be serialized for logging>
Info 2021-11-05 13:55:45: Launching kernel in kernelProcess.ts, Class name = y, completed in 45ms, has a truthy return value, Arg 1: "/home/grobs/meg_analysis", Return Value: 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Info 2021-11-05 13:55:45: KernelProcess output: Content-Length: 368
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "write to stderr: /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '\"hmac-sha256\"' if you require traitlets >=5.\n", "pid": 6946}}
Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): write to stderr: /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5.

Info 2021-11-05 13:55:45: KernelProcess output: Content-Length: 344
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "output", "params": {"source": "stderr", "out": "/home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '\"hmac-sha256\"' if you require traitlets >=5.\n"}}Content-Length: 114
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "write to stderr:   warn(\n", "pid": 6946}}Content-Length: 90
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "output", "params": {"source": "stderr", "out": "  warn(\n"}}Content-Length: 380
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "write to stderr: /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '9b7d1f68-95da-4329-a6d1-edf9306bd29d' instead of 'b\"9b7d1f68-95da-4329-a6d1-edf9306bd29d\"'.\n", "pid": 6946}}Content-Length: 356
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "output", "params": {"source": "stderr", "out": "/home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '9b7d1f68-95da-4329-a6d1-edf9306bd29d' instead of 'b\"9b7d1f68-95da-4329-a6d1-edf9306bd29d\"'.\n"}}Content-Length: 114
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "write to stderr:   warn(\n", "pid": 6946}}Content-Length: 90
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "output", "params": {"source": "stderr", "out": "  warn(\n"}}
Warn 2021-11-05 13:55:45: Kernel 6946 as possibly died, StdErr from Kernel Process /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5.

Warn 2021-11-05 13:55:45: StdErr from Kernel Process /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5.

Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): write to stderr:   warn(

Warn 2021-11-05 13:55:45: Kernel 6946 as possibly died, StdErr from Kernel Process   warn(

Warn 2021-11-05 13:55:45: StdErr from Kernel Process   warn(

Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): write to stderr: /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '9b7d1f68-95da-4329-a6d1-edf9306bd29d' instead of 'b"9b7d1f68-95da-4329-a6d1-edf9306bd29d"'.

Warn 2021-11-05 13:55:45: Kernel 6946 as possibly died, StdErr from Kernel Process /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '9b7d1f68-95da-4329-a6d1-edf9306bd29d' instead of 'b"9b7d1f68-95da-4329-a6d1-edf9306bd29d"'.

Warn 2021-11-05 13:55:45: StdErr from Kernel Process /home/grobs/miniconda3/envs/basic/lib/python3.9/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '9b7d1f68-95da-4329-a6d1-edf9306bd29d' instead of 'b"9b7d1f68-95da-4329-a6d1-edf9306bd29d"'.

Info 2021-11-05 13:55:45: Python Daemon (pid: 6946): write to stderr:   warn(

Warn 2021-11-05 13:55:45: Kernel 6946 as possibly died, StdErr from Kernel Process   warn(

Warn 2021-11-05 13:55:45: StdErr from Kernel Process   warn(

Warn 2021-11-05 13:55:46: Didn't get response for requestKernelInfo
Info 2021-11-05 13:55:46: Got new session f6e53168-9725-4307-bc43-8ed54a7f0ed1
Info 2021-11-05 13:55:46: Started new restart session
Info 2021-11-05 13:55:46: shutdownSession 51c54e48-3866-4c04-a346-2e2d239ec335, .jvsc74a57bd0ea5d3ea4e504429a544d1553bc21d85a7673a48ee674c84e04ac5ffc06b339d4./home/grobs/miniconda3/envs/basic/python./home/grobs/miniconda3/envs/basic/python.-m#ipykernel_launcher - start
Info 2021-11-05 13:55:46: Session can be shutdown .jvsc74a57bd0ea5d3ea4e504429a544d1553bc21d85a7673a48ee674c84e04ac5ffc06b339d4./home/grobs/miniconda3/envs/basic/python./home/grobs/miniconda3/envs/basic/python.-m#ipykernel_launcher
Info 2021-11-05 13:55:46: Dispose Kernel process
Info 2021-11-05 13:55:46: kill daemon
Info 2021-11-05 13:55:46: UpdateWorkingDirectoryAndPath in Kernel
Info 2021-11-05 13:55:46: KernelProcess output: Content-Length: 131
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": 6928}}
Info 2021-11-05 13:55:46: Python Daemon (pid: 6928): Execute rpc method kill_kernel in DS Daemon
Info 2021-11-05 13:55:46: KernelProcess output: Content-Length: 168
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "Execute rpc method kill_kernel from /home/grobs/miniconda3/envs/basic/bin/python", "pid": 6928}}Content-Length: 128
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "Kill kernel in DS Kernel Launcher Daemon", "pid": 6928}}Content-Length: 138
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "Kill kernel in DS Kernel Launcher Daemon, pid 6929", "pid": 6928}}
Info 2021-11-05 13:55:46: Python Daemon (pid: 6928): Execute rpc method kill_kernel from /home/grobs/miniconda3/envs/basic/bin/python
Info 2021-11-05 13:55:46: KernelProcess output: Content-Length: 43
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "id": 2, "result": null}
Info 2021-11-05 13:55:46: Python Daemon (pid: 6928): Kill kernel in DS Kernel Launcher Daemon
Info 2021-11-05 13:55:46: Python Daemon (pid: 6928): Kill kernel in DS Kernel Launcher Daemon, pid 6929
Info 2021-11-05 13:55:46: Dispose Kernel process
Info 2021-11-05 13:55:46: shutdownSession 51c54e48-3866-4c04-a346-2e2d239ec335, .jvsc74a57bd0ea5d3ea4e504429a544d1553bc21d85a7673a48ee674c84e04ac5ffc06b339d4./home/grobs/miniconda3/envs/basic/python./home/grobs/miniconda3/envs/basic/python.-m#ipykernel_launcher - shutdown complete
Info 2021-11-05 13:55:46: Dispose Kernel process
Info 2021-11-05 13:55:46: KernelProcess Exit Exit - undefined 
Info 2021-11-05 13:55:46: changeDirectoryIfPossible
Info 2021-11-05 13:55:46: Executing (status Idle) silently Code = import os\nimport sys\n%cd "/home/grobs/meg_analysis"\nif os.getcwd() not in sys.path:\nsys.path.ins
Info 2021-11-05 13:55:46: Executing silently Code (completed) = import os\nimport sys\n%cd "/home/grobs/meg_analysis"\nif os.getcwd() not in sys.path:\nsys.path.ins
Info 2021-11-05 13:55:46: Executing (status Idle) silently Code = %config Completer.use_jedi = False
Info 2021-11-05 13:55:46: Executing silently Code (completed) = %config Completer.use_jedi = False
Info 2021-11-05 13:55:46: Executing (status Idle) silently Code = %config InlineBackend.figure_formats = ['png']
Info 2021-11-05 13:55:46: Executing silently Code (completed) = %config InlineBackend.figure_formats = ['png']
Info 2021-11-05 13:55:46: Executing (status Idle) silently Code = import sys\nprint(sys.executable)
Info 2021-11-05 13:55:46: Executing silently Code (completed) = import sys\nprint(sys.executable)
Info 2021-11-05 13:55:46: Waiting for idle on (kernel): f6e53168-9725-4307-bc43-8ed54a7f0ed1 -> idle
Info 2021-11-05 13:55:46: Finished waiting for idle on (kernel): f6e53168-9725-4307-bc43-8ed54a7f0ed1 -> idle
Info 2021-11-05 13:55:46: Executing (status Idle) silently Code = __file__ = '/home/grobs/meg_analysis/for_notebook.py'
Info 2021-11-05 13:55:46: Executing silently Code (completed) = __file__ = '/home/grobs/meg_analysis/for_notebook.py'
Info 2021-11-05 13:55:49: Adding hash for 1 = f475ed43daca with 4 lines
Info 2021-11-05 13:55:49: Finished execution for 947da0d4-029b-42e4-95c3-0cb50299cadd
Info 2021-11-05 13:55:49: KernelProcess output: Content-Length: 182
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "log", "params": {"level": "INFO", "msg": "write to stderr: QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-grobs'\n", "pid": 6946}}
Info 2021-11-05 13:55:49: Python Daemon (pid: 6946): write to stderr: QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-grobs'

Info 2021-11-05 13:55:49: KernelProcess output: Content-Length: 158
Content-Type: application/vscode-jsonrpc; charset=utf8

{"jsonrpc": "2.0", "method": "output", "params": {"source": "stderr", "out": "QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-grobs'\n"}}
Warn 2021-11-05 13:55:49: Kernel 6946 as possibly died, StdErr from Kernel Process QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-grobs'

Warn 2021-11-05 13:55:49: StdErr from Kernel Process QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-grobs'

Info 2021-11-05 13:55:51: Adding hash for 2 = 4e7389085c14 with 2 lines
Info 2021-11-05 13:55:51: Finished execution for 712c2e7e-96af-4461-9f56-462b20f92946
Info 2021-11-05 13:55:54: Adding hash for 3 = fcecaaa62083 with 2 lines

[rchiodo]

Thanks for the bug. This commit might have caused this problem (at least it’s the only thing that would interfere with comm like that)

https://github.com/microsoft/vscode-jupyter/commit/01ff4cce9e79a6e050f637f7253c99b7432629c6

I can repro, so we should be able to debug it to see why.

[aroyphillips]

I would also like to add that this qt plotting feature is important for my work as well. Any work around to be able to scroll through the MNE output plots on my computer connected to a remote server are welcome