Release 6.1.13 nbconvert failing with TypeError: 'coroutine' object is not subscriptable
#637
Comments
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This is the (pip) package list with a successful build: This is the pip package list with the failed build: This is the nbconvert re-install we do with conda: |
Thanks for reporting, I will investigate before releasing 6.2. |
Fix version of jupyter-client, should be removed when the problem with the version 1.6.2 is fixed upstream. jupyter/jupyter_client#637
1. A new release: jupyter-client 6.1.13 breaks notebooks when getting messages. 2. This is caught by screen diff integration tests of interactive beam. 3. The issue is documented at jupyter/jupyter_client#637 ETA of the fix might be 6.2.x of jupyter-client. 4. Added a timeout=-1 to allow indefinite wait for execution of each notebook cell in integration tests. The default value was 1 second. Instead of timeout each cell, moved the timeout to each test using pytest mark.
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@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) |
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@jph00 6.1.13 is yanked from PyPI and marked as broken in conda now |
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Thanks Matt! :)
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We no more need to fix the version because the wrong package (6.1.13) has been yanked in PyPi jupyter/jupyter_client#637
* We no more need to fix the version because the wrong package (6.1.13) has been yanked in PyPi * jupyter/jupyter_client#637
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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 |
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@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 |
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I am seeing the same issue of test failures with the release of 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? |
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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.
of course! but what exactly would be of help?
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 |
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I pulled 6.2.0 again, there was a API breaking change that I didn't see. |
One thing I noticed between @astafan8's pip freeze output and ours is we're both using |
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Did you try to unpin I had exactly the same issue with |
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 Well, I hope this solution you offer will help. However it looks like a workaround for that separate performance issue of |
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 |
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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. |
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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 |
pinning nbconvert with a particular version that has the templates jupyter/nbgrader#1373 requires also pin jupyter-client to an earlier version jupyter/jupyter_client#637
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I got the error using 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://git@github.com/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 As @kevin-bates pointed out: pinning |
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Maybe worth opening a new issue? This one is for jupyter_client 6.1.13 which was yanked. |
Restrict 'jupyter-client' version to be earlier than 7 to workaround upstream discrepancies. Refs jupyter/jupyter_client#637 Signed-off-by: Ilias Katsakioris <elikatsis@arrikto.com>
Restrict 'jupyter-client' version to be earlier than 7 to workaround upstream discrepancies. Refs jupyter/jupyter_client#637 Signed-off-by: Ilias Katsakioris <elikatsis@arrikto.com> Reviewed-by: Stefano Fioravanzo <stefano@arrikto.com>
Restrict 'jupyter-client' version to be earlier than 7 to workaround upstream discrepancies. Refs jupyter/jupyter_client#637 Signed-off-by: Ilias Katsakioris <elikatsis@arrikto.com> Reviewed-by: Stefano Fioravanzo <stefano@arrikto.com>
as it has error in autograding with version 7.0.2. The discussion about the error is in jupyter/jupyter_client#637
See more in jupyter/jupyter_client#637. Seems version jupyter_client 6.1.13 which was yanked is causing issues
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This remains broken for me for every jupyter client after 6.1.12. |
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Could you elaborate in which context this is happening? |
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@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. |
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This PR should fix it: jupyter/jupyter_console#244 |
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@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. |
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Just wanted to confirm that jupyter/jupyter_console#244 indeed fixed my problem. Thanks, @davidbrochart ! |
Refer to this issue for more details: jupyter/jupyter_client#637
Refer to this issue for more details: jupyter/jupyter_client#637
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:
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?).
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