Release 6.1.13 nbconvert failing with `TypeError: 'coroutine' object is not subscriptable`

[mriedem]

We have a CI build that runs this notebook:

https://github.com/Qiskit/qiskit-tutorials/blob/stable/0.23.x/tutorials/circuits/1_getting_started_with_qiskit.ipynb

It started failing this morning with this error:

[NbConvertApp] Converting notebook /tmp/qiskit-iqx-tutorials/qiskit/tutorials/circuits/1_getting_started_with_qiskit.ipynb to html
[NbConvertApp] Executing notebook with kernel: python3
Traceback (most recent call last):
  File "/opt/conda/bin/jupyter-nbconvert", line 11, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/opt/conda/lib/python3.8/site-packages/traitlets/config/application.py", line 837, in launch_instance
    app.start()
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 340, in start
    self.convert_notebooks()
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 510, in convert_notebooks
    self.convert_single_notebook(notebook_filename)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 481, in convert_single_notebook
    output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 410, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 179, in from_filename
    return self.from_file(f, resources=resources, **kw)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 197, in from_file
    return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/html.py", line 95, in from_notebook_node
    return super(HTMLExporter, self).from_notebook_node(nb, resources, **kw)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/templateexporter.py", line 307, in from_notebook_node
    nb_copy, resources = super(TemplateExporter, self).from_notebook_node(nb, resources, **kw)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 139, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 316, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/base.py", line 47, in __call__
    return self.preprocess(nb, resources)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 405, in preprocess
    nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/base.py", line 69, in preprocess
    nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 438, in preprocess_cell
    reply, outputs = self.run_cell(cell, cell_index, store_history)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 578, in run_cell
    exec_reply = self._poll_for_reply(parent_msg_id, cell, timeout)
  File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 479, in _poll_for_reply
    if msg['parent_header'].get('msg_id') == msg_id:
TypeError: 'coroutine' object is not subscriptable
sys:1: RuntimeWarning: coroutine 'ZMQSocketChannel.get_msg' was never awaited

The only difference in the package lists was jupyter-client 6.1.13 (note that nbconvert is pinned to 5.6.1 in our case).

I don't know how all of this is related, but was wondering if #623 might be causing some issue.

I have excluded the jupyter-client 6.1.13 version from our build and things are working again. My concern is if this comes back in the next release (6.2?).

[mriedem]

This is the (pip) package list with a successful build:

MarkupSafe-1.1.1
Send2Trash-1.5.0
argon2-cffi-20.1.0
async-generator-1.10
attrs-20.3.0
backcall-0.2.0
bleach-3.3.0
certifi-2020.12.5
cffi-1.14.5
chardet-4.0.0
colorcet-2.0.6
cryptography-3.4.7
cvxpy-1.1.11
cycler-0.10.0
decorator-4.4.2
defusedxml-0.7.1
dill-0.3.3
dlx-1.0.4
docplex-2.20.204
ecos-2.0.7.post1
entrypoints-0.3
fastdtw-0.3.4
fastjsonschema-2.15.0
h5py-3.1.0
ibm-quantum-widgets-1.0.3
idna-2.10
inflection-0.5.1
ipykernel-5.5.3
ipython-7.22.0
ipython-genutils-0.2.0
ipyvue-1.5.0
ipyvuetify-1.6.2
ipywidgets-7.6.3
iqx-0.1.17
jedi-0.18.0
jinja2-2.11.3
joblib-1.0.1
json-logging-1.3.0
jsonschema-3.2.0
jupyter-1.0.0
jupyter-client-6.1.12
jupyter-console-6.4.0
jupyter-core-4.7.1
jupyterlab-pygments-0.1.2
jupyterlab-widgets-1.0.0
kaleidoscope-0.0.12
kiwisolver-1.3.1
llvmlite-0.36.0
lxml-4.6.3
matplotlib-3.4.1
mistune-0.8.4
more-itertools-8.7.0
mpmath-1.2.1
multitasking-0.0.9
nbclient-0.5.3
nbconvert-6.0.7
nbformat-5.1.3
nbresuse-0.4.0
nest-asyncio-1.5.1
networkx-2.5.1
notebook-6.3.0
ntlm-auth-1.5.0
numba-0.53.1
numpy-1.20.1
osqp-0.6.2.post0
packaging-20.9
pandas-1.2.3
pandocfilters-1.4.3
param-1.10.1
parso-0.8.2
pexpect-4.8.0
pickleshare-0.7.5
pillow-8.2.0
plotly-4.14.3
ply-3.11
prometheus-client-0.10.0
prompt-toolkit-3.0.18
psutil-5.8.0
ptyprocess-0.7.0
pybind11-2.6.2
pycparser-2.20
pyct-0.4.8
pydot-1.4.2
pygments-2.8.1
pylatexenc-2.10
pyparsing-2.4.7
pyperclip-1.8.2
pyrsistent-0.17.3
pyscf-1.7.3
python-constraint-1.4.0
python-dateutil-2.8.1
pytz-2021.1
pyzmq-22.0.3
qdldl-0.1.5.post0
qiskit-0.25.0
qiskit-aer-0.8.0
qiskit-aqua-0.9.0
qiskit-finance-0.1.0
qiskit-ibmq-provider-0.12.2
qiskit-ignis-0.6.0
qiskit-machine-learning-0.1.0
qiskit-nature-0.1.0
qiskit-optimization-0.1.0
qiskit-terra-0.17.0
qtconsole-5.0.3
qtpy-1.9.0
quandl-3.6.0
requests-2.25.1
requests-ntlm-1.1.0
retrying-1.3.3
retworkx-0.8.0
scikit-learn-0.24.1
scipy-1.6.1
scs-2.1.2
seaborn-0.11.1
setuptools-54.2.0
six-1.15.0
sparse-0.12.0
sympy-1.7.1
terminado-0.9.4
testpath-0.4.4
threadpoolctl-2.1.0
torch-1.8.0+rocm4.0.1
torchvision-0.9.0
tornado-6.1
traitlets-5.0.5
typing-extensions-3.7.4.3
urllib3-1.26.4
wcwidth-0.2.5
webencodings-0.5.1
websockets-8.1
widgetsnbextension-3.5.1
yfinance-0.1.55

This is the pip package list with the failed build:

MarkupSafe-1.1.1
Send2Trash-1.5.0
argon2-cffi-20.1.0
async-generator-1.10
attrs-20.3.0
backcall-0.2.0
bleach-3.3.0
certifi-2020.12.5
cffi-1.14.5
chardet-4.0.0
colorcet-2.0.6
cryptography-3.4.7
cvxpy-1.1.11
cycler-0.10.0
decorator-4.4.2
defusedxml-0.7.1
dill-0.3.3
dlx-1.0.4
docplex-2.20.204
ecos-2.0.7.post1
entrypoints-0.3
fastdtw-0.3.4
fastjsonschema-2.15.0
h5py-3.1.0
ibm-quantum-widgets-1.0.3
idna-2.10
inflection-0.5.1
ipykernel-5.5.3
ipython-7.22.0
ipython-genutils-0.2.0
ipyvue-1.5.0
ipyvuetify-1.6.2
ipywidgets-7.6.3
iqx-0.1.17
jedi-0.18.0
jinja2-2.11.3
joblib-1.0.1
json-logging-1.3.0
jsonschema-3.2.0
jupyter-1.0.0
jupyter-client-6.1.13
jupyter-console-6.4.0
jupyter-core-4.7.1
jupyterlab-pygments-0.1.2
jupyterlab-widgets-1.0.0
kaleidoscope-0.0.12
kiwisolver-1.3.1
llvmlite-0.36.0
lxml-4.6.3
matplotlib-3.4.1
mistune-0.8.4
more-itertools-8.7.0
mpmath-1.2.1
multitasking-0.0.9
nbclient-0.5.3
nbconvert-6.0.7
nbformat-5.1.3
nbresuse-0.4.0
nest-asyncio-1.5.1
networkx-2.5.1
notebook-6.3.0
ntlm-auth-1.5.0
numba-0.53.1
numpy-1.20.1
osqp-0.6.2.post0
packaging-20.9
pandas-1.2.3
pandocfilters-1.4.3
param-1.10.1
parso-0.8.2
pexpect-4.8.0
pickleshare-0.7.5
pillow-8.2.0
plotly-4.14.3
ply-3.11
prometheus-client-0.10.0
prompt-toolkit-3.0.18
psutil-5.8.0
ptyprocess-0.7.0
pybind11-2.6.2
pycparser-2.20
pyct-0.4.8
pydot-1.4.2
pygments-2.8.1
pylatexenc-2.10
pyparsing-2.4.7
pyperclip-1.8.2
pyrsistent-0.17.3
pyscf-1.7.3
python-constraint-1.4.0
python-dateutil-2.8.1
pytz-2021.1
pyzmq-22.0.3
qdldl-0.1.5.post0
qiskit-0.25.0
qiskit-aer-0.8.0
qiskit-aqua-0.9.0
qiskit-finance-0.1.0
qiskit-ibmq-provider-0.12.2
qiskit-ignis-0.6.0
qiskit-machine-learning-0.1.0
qiskit-nature-0.1.0
qiskit-optimization-0.1.0
qiskit-terra-0.17.0
qtconsole-5.0.3
qtpy-1.9.0
quandl-3.6.0
requests-2.25.1
requests-ntlm-1.1.0
retrying-1.3.3
retworkx-0.8.0
scikit-learn-0.24.1
scipy-1.6.1
scs-2.1.2
seaborn-0.11.1
setuptools-54.2.0
six-1.15.0
sparse-0.12.0
sympy-1.7.1
terminado-0.9.4
testpath-0.4.4
threadpoolctl-2.1.0
torch-1.8.0+rocm4.0.1
torchvision-0.9.0
tornado-6.1
traitlets-5.0.5
typing-extensions-3.7.4.3
urllib3-1.26.4
wcwidth-0.2.5
webencodings-0.5.1
websockets-8.1
widgetsnbextension-3.5.1
yfinance-0.1.55

This is the nbconvert re-install we do with conda:

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:

    - nbconvert==5.6.1

The following packages will be downloaded:

    package                    |            build

    ---------------------------|-----------------

    nbconvert-5.6.1            |   py38h32f6830_1         488 KB  conda-forge

    numpy-1.20.2               |   py38h9894fe3_0         5.8 MB  conda-forge

    openssl-1.1.1k             |       h7f98852_0         2.1 MB  conda-forge

    ------------------------------------------------------------

                                           Total:         8.4 MB

The following NEW packages will be INSTALLED:

  numpy              conda-forge/linux-64::numpy-1.20.2-py38h9894fe3_0

The following packages will be UPDATED:

  openssl                                 1.1.1j-h7f98852_0 --> 1.1.1k-h7f98852_0

The following packages will be DOWNGRADED:

  nbconvert                            6.0.7-py38h578d9bd_3 --> 5.6.1-py38h32f6830_1

[davidbrochart]

My concern is if this comes back in the next release (6.2?).

Thanks for reporting, I will investigate before releasing 6.2.

[jph00]

@davidbrochart we're seeing the same issue in nbdev. I see Apache Beam also has the issue. Might be worth yanking the 6.1.13 release until there's a fix?

(In the meantime, we're pinning our dep version to work around the issue)

[MSeal]

@jph00 6.1.13 is yanked from PyPI and marked as broken in conda now

[jph00]

Thanks Matt! :)

[astafan8]

I have the same issue with 6.2.0 version :( the project is private, so can't share much, let me know what would be helpful

[davidbrochart]

@astafan8 thanks for reporting. I ran nbconvert's test suite in https://github.com/jupyter/nbconvert/pull/1549, and except for an unrelated issue, tests are passing: https://travis-ci.org/github/jupyter/nbconvert/builds/766787036 It would be nice if you could share more details.

[vEpiphyte]

I am seeing the same issue of test failures with the release of 6.2.0; we had a nightly build failure of our doctests. Here is an example failure (which is visible if you login to circleci) https://app.circleci.com/pipelines/github/vertexproject/synapse/6606/workflows/6f31cd70-94e5-425c-aebc-3c5177b1e18f/jobs/26508

Our notebooks use async code extensively, and reviewing the nbconvert unit tests; they do not appear to have any async code used in them. Its possible that there are unexpected interactions with nest-asyncio and native async applications being executed in notebooks?

[astafan8]

The part that is also puzzling me is that this problem appears for a private project which docs structure and content is similar to that of https://github.com/qcodes/qcodes, and on qcodes latest jupyter-client works without problems.

It would be nice if you could share more details.

of course! but what exactly would be of help?

pip 21.0.1

Python 3.7.10 (default, Feb 26 2021, 13:06:18) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32

pip freeze:

jupyter-client==6.1.12  # changing this to 6.1.13 or 6.2.0 results in an exception as in the issue descrption

alabaster==0.7.12
apipkg==1.5
appdirs==1.4.4
argon2-cffi==20.1.0
artifacts-keyring==0.3.1
astroid==2.5.2
async-generator==1.10
atomicwrites==1.4.0
attrs==20.3.0
Babel==2.9.0
backcall==0.2.0
black==20.8b1
bleach==3.3.0
bokeh==2.3.0
broadbean==0.10.0
cached-property==1.5.2
cachetools==4.2.1
certifi==2020.12.5
cffi==1.14.5
cftime==1.4.1
chardet==4.0.0
click==7.1.2
cloudpickle==1.6.0
colorama==0.4.4
colorcet==2.0.6
contextlib2==0.6.0.post1
coverage==5.5
cycler==0.10.0
decorator==4.4.2
defusedxml==0.7.1
docutils==0.16
entrypoints==0.3
et-xmlfile==1.0.1
execnet==1.8.0
google-api-core==1.26.3
google-auth==1.28.0
googleapis-common-protos==1.53.0
h5py==3.2.1
holoviews==1.14.2
hypothesis==6.8.5
idna==2.10
imagesize==1.2.0
importlib-metadata==3.10.0
iniconfig==1.1.1
ipykernel==5.5.3
ipython==7.22.0
ipython-genutils==0.2.0
ipywidgets==7.6.3
isort==5.8.0
jedi==0.18.0
Jinja2==2.11.3
jsonpointer==2.1
jsonschema==3.2.0
junit-xml-2==1.9
jupyter==1.0.0
jupyter-console==6.4.0
jupyter-core==4.7.1
jupyterlab-pygments==0.1.2
jupyterlab-widgets==1.0.0
keyring==23.0.1
kiwisolver==1.3.1
lazy-object-proxy==1.6.0
Markdown==3.3.4
MarkupSafe==1.1.1
matplotlib==3.4.1
mccabe==0.6.1
mistune==0.8.4
mypy==0.812
mypy-extensions==0.4.3
nbclient==0.5.3
nbconvert==5.6.1
nbformat==5.1.3
nbsphinx==0.8.3
nest-asyncio==1.5.1
netCDF4==1.5.6
networkx==2.5.1
notebook==6.3.0
numpy==1.20.2
numpydoc==1.1.0
opencensus==0.7.12
opencensus-context==0.1.2
opencensus-ext-azure==1.0.7
openpyxl==3.0.7
packaging==20.9
pandas==1.2.3
pandocfilters==1.4.3
panel==0.11.1
param==1.10.1
parso==0.8.2
pathspec==0.8.1
pbr==5.5.1
pickleshare==0.7.5
Pillow==8.2.0
pluggy==0.13.1
prometheus-client==0.10.0
prompt-toolkit==3.0.18
protobuf==3.15.7
psutil==5.8.0
py==1.10.0
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycodestyle==2.7.0
pycparser==2.20
pyct==0.4.8
pyflakes==2.3.1
Pygments==2.8.1
pylint==2.7.2
pylint-junit==0.3.2
pyparsing==2.4.7
PyQt5==5.12.3
PyQt5-sip==12.8.1
PyQtWebEngine==5.12.1
pyrsistent==0.17.3
pytest==6.2.3
pytest-cov==2.11.1
pytest-forked==1.3.0
pytest-mock==3.5.1
pytest-timeout==1.4.2
pytest-xdist==2.2.1
python-dateutil==2.8.1
pytz==2021.1
PyVISA==1.11.3
PyVISA-sim==0.4.0
pyviz-comms==2.0.1
pywin32==300
pywin32-ctypes==0.2.0
pywinpty==0.5.7
PyYAML==5.4.1
pyzmq==22.0.3
qcodes==0.24.0
QtAwesome==1.0.2
qtconsole==5.0.3
QtPy==1.9.0
regex==2021.4.4
requests==2.25.1
requirements-parser==0.2.0
rope==0.18.0
rsa==4.7.2
ruamel.yaml==0.17.2
ruamel.yaml.clib==0.2.2
schema==0.7.4
scipy==1.6.2
selenium==3.141.0
Send2Trash==1.5.0
six==1.15.0
snowballstemmer==2.1.0
sortedcontainers==2.3.0
Sphinx==2.4.4
sphinx-jsonschema==1.16.8
sphinx-rtd-theme==0.5.2
sphinxcontrib-apidoc==0.3.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==1.0.3
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.4
spyder==3.3.6
spyder-kernels==0.5.2
stringparser==0.5
tabulate==0.8.9
terminado==0.9.4
testpath==0.4.4
toml==0.10.2
tornado==6.1
tqdm==4.60.0
traitlets==5.0.5
typed-ast==1.4.2
typing-extensions==3.7.4.3
urllib3==1.26.4
wcwidth==0.2.5
webencodings==0.5.1
websockets==8.1
widgetsnbextension==3.5.1
wincertstore==0.2
wrapt==1.12.1
xarray==0.17.0
xlrd==2.0.1
zipp==3.4.1

[davidbrochart]

I pulled 6.2.0 again, there was a API breaking change that I didn't see. I will fix it and make a 7.0.0 alpha0.

[mriedem]

@astafan8 thanks for reporting. I ran nbconvert's test suite in jupyter/nbconvert#1549, and except for an unrelated issue, tests are passing: https://travis-ci.org/github/jupyter/nbconvert/builds/766787036 It would be nice if you could share more details.

One thing I noticed between @astafan8's pip freeze output and ours is we're both using nbconvert 5.6.1 (we're capped on that project until https://github.com/jupyter/nbconvert/issues/1439 is fixed). So running latest nbconvert unit tests with latest jupyter-client might not show the issue but what about nbconvert==5.6.1?

[kirienko]

Did you try to unpin nbconvert instead of downgrading jupyter-client? It seems to be more beneficial in a long run, since nbconvert-5.6.1 is still aimed to support python-2 and python<3.7.

I had exactly the same issue with nbconvert restricted to <6, but without jupyter_client involved, and unpinning nbconvert resolved the problem.

[mriedem]

Did you try to unpin nbconvert instead of downgrading jupyter-client? It seems to be more beneficial in a long run, since nbconvert-5.6.1 is still aimed to support python-2 and python<3.7.

I had exactly the same issue with nbconvert restricted to <6, but without jupyter_client involved, and unpinning nbconvert resolved the problem.

In my case we're pulling in jupyter-client as a transitive dependency. We're capping nbconvert for a separate reason: https://github.com/jupyter/nbconvert/issues/1439

[kirienko]

Did you try to unpin nbconvert instead of downgrading jupyter-client? It seems to be more beneficial in a long run, since nbconvert-5.6.1 is still aimed to support python-2 and python<3.7. I had exactly the same issue with nbconvert restricted to <6, but without jupyter_client involved, and unpinning nbconvert resolved the problem.

In my case we're pulling in jupyter-client as a transitive dependency. We're capping nbconvert for a separate reason: jupyter/nbconvert#1439

This performance regression was a good reason to stick to an older version of nbconvert, I fully agree. We thought the same way before it screwed up completely, and we had not another option but unpin it. (I also already faced the dependency issues related to the oldness of 5.6.1 on newer systems.)

Well, I hope this solution you offer will help. However it looks like a workaround for that separate performance issue of nbconvert you mentioned.

[mriedem]

One thing I noticed between @astafan8's pip freeze output and ours is we're both using nbconvert 5.6.1 (we're capped on that project until jupyter/nbconvert#1439 is fixed). So running latest nbconvert unit tests with latest jupyter-client might not show the issue but what about nbconvert==5.6.1?

Recreated here jupyter/nbconvert/pull/1550 with jupyter-client 6.2.0 and nbconvert 5.6.1:

https://travis-ci.org/github/jupyter/nbconvert/jobs/766808690#L1370

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f3e7ca1dd30>

msg_id = '238d6f9e-e6ea4495439b51dfd5175f5b_1'

cell = {'cell_type': 'code', 'metadata': {}, 'outputs': [], 'source': 'from __future__ import print_function\nfrom IPython.display import clear_output'}

timeout = 1

    def _poll_for_reply(self, msg_id, cell=None, timeout=None):

        try:

            # check with timeout if kernel is still alive

            msg = self.kc.shell_channel.get_msg(timeout=timeout)

>           if msg['parent_header'].get('msg_id') == msg_id:

E           TypeError: 'coroutine' object is not subscriptable

[davidbrochart]

See https://github.com/jupyter/nbconvert/pull/1549#issuecomment-818734169

[astafan8]

allow me to report that indeed, using the latest nbconvert as opposed to 5.6.1 removed the issue, and luckily we did not experience any slowdowns in the docs build mentioned in jupyter/nbconvert#1439 .

[mriedem]

allow me to report that indeed, using the latest nbconvert as opposed to 5.6.1 removed the issue, and luckily we did not experience any slowdowns in the docs build mentioned in jupyter/nbconvert#1439 .

Cool. Note that the performance slowdown issue there is because we're using object storage with s3fs to back our user notebook pods rather than PVCs (with zero-to-jupyterhub-k8s). The entrypoint import times can get slow with s3fs.

[marius311]

I could quite follow if the above comments indicate a fix is already in place, but I also had CI fail with this exact error so just wanted to report here in case its helpful.

I also have nbconvert<6 (so 5.6.1) pinned, and I also confirm that pinning jupyter-client==6.1.12 fixes the issue.

Here's the traceback from the CI job: https://github.com/marius311/CMBLensing.jl/runs/2302363389?check_suite_focus=true#step:4:4342

The exact command that fails is jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1 $filename (here)

[davidbrochart]

Both releases 6.1.13 and 6.2.0 have been pulled, we are working towards a 7.0.0 release, see #642.

[qci-amos]

This issue appears to have cropped up again with jupyter-client 7.0.0 released a couple hours ago: https://pypi.org/project/jupyter-client/#history

[kevin-bates]

What a drag. Looks like this item slipped through the 7.0 cracks.

It seems that the solution to this, when nbconvert < 6 is required, is to cap jupyter_client < 7.0 or (preferably) update nbconvert with this guidance: https://github.com/jupyter/nbconvert/pull/1549#issuecomment-818734169.

If the second approach is adopted, it looks like there are 3 locations within preprocessors/execute.py that should be updated - two related to shell messages, the third related to iopub. Haven't looked for other calls to KernelClient.xxx_channel.get_msg() but all would be candidates to convert to KernelClient.get_xxx_msg().

[avivajpeyi]

I got the error using jupyter-client==7.0.5 and nbconvert==5.6.1

Full pip freeze:

``` aesara-theano-fallback==0.0.4 alabaster==0.7.12 anyio==3.3.2 argcomplete==1.12.3 argon2-cffi==21.1.0 arviz==0.11.4 astropy==4.0.1 astroquery==0.4.3 attrs==20.3.0 autograd==1.3 Babel==2.9.1 backcall==0.2.0 backports.entry-points-selectable==1.1.0 beautifulsoup4==4.10.0 black==21.9b0 bleach==4.1.0 bokeh==2.4.0 cached-property==1.5.2 cachetools==4.2.4 celerite2==0.2.0 certifi==2021.5.30 cffi==1.14.6 cfgv==3.3.1 cftime==1.5.1 charset-normalizer==2.0.6 click==7.1.2 colorama==0.4.4 corner==2.2.1 cryptography==35.0.0 cycler==0.10.0 Cython==0.29.16 debugpy==1.5.0 decorator==5.1.0 defusedxml==0.7.1 dill==0.3.4 distlib==0.3.3 docutils==0.16 entrypoints==0.3 exoplanet==0.5.1 exoplanet-core==0.1.2 fastprogress==1.0.0 fbpca==1.0 filelock==3.3.0 flake8==3.9.2 future==0.18.2 gitdb==4.0.7 GitPython==3.1.24 greenlet==1.1.2 h5py==3.2.1 html5lib==1.1 identify==2.3.0 idna==3.2 imagesize==1.2.0 importlib-metadata==4.8.1 importlib-resources==5.2.2 iniconfig==1.1.1 ipykernel==6.4.1 ipython==7.28.0 ipython-genutils==0.2.0 ipywidgets==7.6.5 isort==5.9.3 jedi==0.18.0 jeepney==0.7.1 Jinja2==3.0.2 joblib==1.0.1 jsonschema==4.0.1 jupyter==1.0.0 jupyter-book==0.11.3 jupyter-cache==0.4.3 jupyter-client==7.0.5 jupyter-console==6.4.0 jupyter-core==4.8.1 jupyter-server==1.11.1 jupyter-server-mathjax==0.2.3 jupyter-sphinx==0.3.2 jupyterlab-widgets==1.0.2 jupytext==1.10.3 kaleido==0.2.1 keyring==23.2.1 kiwisolver==1.3.2 latexcodec==2.0.1 lightkurve==2.0.11 linkify-it-py==1.0.1 markdown-it-py==0.6.2 MarkupSafe==2.0.1 matplotlib==3.4.3 matplotlib-inline==0.1.3 mccabe==0.6.1 mdit-py-plugins==0.2.6 memoization==0.4.0 mimeparse==0.1.3 mistune==0.8.4 mpi4py==3.0.2 mpmath==1.1.0 mypy-extensions==0.4.3 myst-nb==0.12.3 myst-parser==0.13.7 nbclient==0.5.4 nbconvert==5.6.1 nbdime==3.1.0 nbformat==5.1.3 nest-asyncio==1.5.1 netCDF4==1.5.7 nodeenv==1.6.0 notebook==6.4.4 numpy==1.18.2 oktopus==0.1.2 packaging==21.0 pandas==0.25.3 pandocfilters==1.5.0 parso==0.8.2 pathspec==0.9.0 patsy==0.5.2 pexpect==4.8.0 pickleshare==0.7.5 Pillow==8.3.2 platformdirs==2.4.0 plotly==5.3.1 pluggy==1.0.0 pre-commit==2.15.0 prometheus-client==0.11.0 prompt-toolkit==3.0.20 ptyprocess==0.7.0 py==1.10.0 pybtex==0.24.0 pybtex-docutils==1.0.1 pycodestyle==2.7.0 pycparser==2.20 pydata-sphinx-theme==0.6.3 pyerfa==2.0.0 pyflakes==2.3.1 Pygments==2.10.0 pymc3==3.11.4 pymc3-ext==0.1.0 pyparsing==2.4.7 pyrsistent==0.18.0 pytest==6.2.5 python-dateutil==2.8.2 pytz==2021.3 pyvo==1.1 PyYAML==5.4.1 pyzmq==22.3.0 qtconsole==5.1.1 QtPy==1.11.2 regex==2021.9.30 requests==2.26.0 requests-unixsocket==0.2.0 scikit-learn==1.0 scipy==1.4.1 SecretStorage==3.3.1 semver==2.13.0 Send2Trash==1.8.0 six==1.16.0 smmap==4.0.0 sniffio==1.2.0 snowballstemmer==2.1.0 soupsieve==2.2.1 Sphinx==3.5.4 sphinx-book-theme==0.1.5 sphinx-comments==0.0.3 sphinx-copybutton==0.4.0 sphinx-external-toc==0.2.3 sphinx-jupyterbook-latex==0.4.3 sphinx-multitoc-numbering==0.1.3 sphinx-panels==0.5.2 sphinx-thebe==0.0.10 sphinx-togglebutton==0.2.3 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-bibtex==2.2.1 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 SQLAlchemy==1.4.25 tenacity==8.0.1 terminado==0.12.1 -e git+ssh://[email protected]/dfm/tess-atlas.git@746de72905b4f134e286d699e96200e978c19b60#egg=tess_atlas testbook==0.4.2 testpath==0.5.0 Theano-PyMC==1.1.2 threadpoolctl==3.0.0 toml==0.10.2 tomli==1.2.1 tornado==6.1 tqdm==4.62.3 traitlets==5.1.0 typed-ast==1.4.3 typing-extensions==3.10.0.2 uc-micro-py==1.0.1 uncertainties==3.1.6 urllib3==1.26.7 virtualenv==20.8.1 wcwidth==0.2.5 webencodings==0.5.1 websocket-client==1.2.1 widgetsnbextension==3.5.1 xarray==0.19.0 zipp==3.6.0 ```

I am using myst-nb, which requires nbconvert~=5.6

As @kevin-bates pointed out: pinning jupyter_client==6.1.12 fixes the issue for me

[davidbrochart]

Maybe worth opening a new issue? This one is for jupyter_client 6.1.13 which was yanked.

[NeilGirdhar]

This remains broken for me for every jupyter client after 6.1.12.

[davidbrochart]

Could you elaborate in which context this is happening?

[NeilGirdhar]

@davidbrochart Sure. I run jupyter console in a Python 3.9 virtual environment created by poetry and I can't import anything. If I install jupyter-client 6.1.12, the problem goes away.

[davidbrochart]

This PR should fix it: https://github.com/jupyter/jupyter_console/pull/244 But I don't have the rights to merge it.

[MSeal]

@davidbrochart I just merged the PR -- though I need ping someone with release privilages to add me or run a patch release for the repo. I'll check if I can get that added for this week so we can unblock it.

[NeilGirdhar]

Just wanted to confirm that https://github.com/jupyter/jupyter_console/pull/244 indeed fixed my problem. Thanks, @davidbrochart !