I have a very simple iPython notebook my_nb.ipynb with two simple cells
from mcmc import Tree
a = Tree()
print(a)
This code used to run without problems, but recently has stopped functioning when I run it in Jupyter (and, of course, the code in mcmc.py has not changed). When I run this code with ipython my_nb.ipynb the script runs fine and finishes without error. However, when I open the notebook in Jupyter, the first cell runs fine but the second stalls and never finishes, and the console shows the following error (or warning, really):
Traceback (most recent call last):
File "/usr/lib/python3.8/site-packages/ipykernel/kernelbase.py", line 268, in dispatch_shell
yield gen.maybe_future(handler(stream, idents, msg))
File "/usr/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/usr/lib/python3.8/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/usr/lib/python3.8/site-packages/ipykernel/kernelbase.py", line 542, in execute_request
reply_content = yield gen.maybe_future(
File "/usr/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/usr/lib/python3.8/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/usr/lib/python3.8/site-packages/ipykernel/ipkernel.py", line 287, in do_execute
and should_run_async(code)
File "/usr/lib/python3.8/site-packages/IPython/core/interactiveshell.py", line 2954, in should_run_async
warnings.warn(
DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
Perhaps even more puzzling, if I put all the code in a single cell in the notebook, then the whole code finishes without error both in the command line and in Jupyter.
I have checked this similar thread but my ipykernel is already up to date. In fact, I think all relevant libraries are all at their most current versions:
jupyter core : 4.6.3
jupyter-notebook : 6.1.4
qtconsole : not installed
ipython : 7.18.1
ipykernel : 5.3.4
jupyter client : 6.1.6
jupyter lab : 2.2.7
nbconvert : 5.6.1
ipywidgets : 7.5.1
nbformat : 5.0.6
traitlets : 4.3.3
tornado : 6.0.4-2
terminado : 0.8.3-1
Any help with this will be much appreciated!
By any chance, do you happen to have 'warnings.filterwarnings("error")' or a similar line somewhere in your code?
I just bumped into the same situation just today and have finally traced the problem to this line of code, which was used in my custom package. Once I comment this line out in my code, this Jupyter hanging problem disappeared.
During troubleshooting, I saw this question, so I thought I should write this information down just in case somebody else may benefit from this.