Hi. Since nbclient v0.5.9 jupyter has had jupyter run (c.f. Command-line interface: jupyter execute by palewire · Pull Request #165 · jupyter/nbclient · GitHub and Changed the default command to `jupyter run`, but left in `execute` as an alias with a deprecation warning by palewire · Pull Request #173 · jupyter/nbclient · GitHub), which is great. However, it seems that jupyter run only works if the notebook that it is operating on has already been run (that is has execution counts that are non null)
As an example: A 1 cell Jupyter notebook named debug.ipynb with print("hello world").
Executing this at the command line works as expected.
(jupyter-run-debug) feickert@ThinkPad-X1:~/Code/debug/jupyter-run-debug$ jupyter run debug.ipynb
{'cells': [{'cell_type': 'code',
'execution_count': 1,
'id': 'aec173a3',
'metadata': {},
'outputs': [{'name': 'stdout',
'output_type': 'stream',
'text': ['hello world\n']}],
'source': ['print("hello world")']}],
'metadata': {'kernelspec': {'display_name': 'Python 3 (ipykernel)',
'language': 'python',
'name': 'python3'},
'language_info': {'codemirror_mode': {'name': 'ipython', 'version': 3},
'file_extension': '.py',
'mimetype': 'text/x-python',
'name': 'python',
'nbconvert_exporter': 'python',
'pygments_lexer': 'ipython3',
'version': '3.9.6'}},
'nbformat': 4,
'nbformat_minor': 5}(jupyter-run-debug) feickert@ThinkPad-X1:~/Code/debug/jupyter-run-debug$ [IPKernelApp] WARNING | Parent appears to have exited, shutting down.
However, if you “Restart & Clear Output” and save (removing the execution count for the cells from the notebook)
and run again you get an error
(jupyter-run-debug) feickert@ThinkPad-X1:~/Code/debug/jupyter-run-debug$ jupyter run debug.ipynb
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/tmp/ipykernel_31410/1794071965.py in <module>
3 {
4 "cell_type": "code",
----> 5 "execution_count": null,
6 "id": "aec173a3",
7 "metadata": {},
NameError: name 'null' is not defined
Traceback (most recent call last):
File "/home/feickert/.pyenv/versions/jupyter-run-debug/bin/jupyter-run", line 8, in <module>
sys.exit(RunApp.launch_instance())
File "/home/feickert/.pyenv/versions/3.9.6/envs/jupyter-run-debug/lib/python3.9/site-packages/jupyter_core/application.py", line 264, in launch_instance
return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
File "/home/feickert/.pyenv/versions/3.9.6/envs/jupyter-run-debug/lib/python3.9/site-packages/traitlets/config/application.py", line 846, in launch_instance
app.start()
File "/home/feickert/.pyenv/versions/3.9.6/envs/jupyter-run-debug/lib/python3.9/site-packages/jupyter_client/runapp.py", line 110, in start
raise Exception("jupyter-run error running '%s'" % filename)
Exception: jupyter-run error running 'debug.ipynb'
(jupyter-run-debug) feickert@ThinkPad-X1:~/Code/debug/jupyter-run-debug$ [IPKernelApp] WARNING | Parent appears to have exited, shutting down.
The NameError of course “makes sense”, but it seems like Jupyter should be able to handle this so that you can execute notebooks from the command line if they have had all output stripped for versioning reasons (let’s ignore the existence of Jupytext for the time being).
Is this a bug? Or am I missing a CLI option to avoid this?
For completeness, here’s my Python 3.9.6 virtual environment arrived at by
$ python -m pip install --upgrade pip setuptools wheel
$ python -m pip install jupyter
$ python -m pip freeze > requirements.txt
$ cat requirements.txt
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
attrs==21.2.0
backcall==0.2.0
bleach==4.1.0
cffi==1.15.0
debugpy==1.5.1
decorator==5.1.0
defusedxml==0.7.1
entrypoints==0.3
ipykernel==6.6.0
ipython==7.30.1
ipython-genutils==0.2.0
ipywidgets==7.6.5
jedi==0.18.1
Jinja2==3.0.3
jsonschema==4.3.0
jupyter==1.0.0
jupyter-client==7.1.0
jupyter-console==6.4.0
jupyter-core==4.9.1
jupyterlab-pygments==0.1.2
jupyterlab-widgets==1.0.2
MarkupSafe==2.0.1
matplotlib-inline==0.1.3
mistune==0.8.4
nbclient==0.5.9
nbconvert==6.3.0
nbformat==5.1.3
nest-asyncio==1.5.4
notebook==6.4.6
packaging==21.3
pandocfilters==1.5.0
parso==0.8.3
pexpect==4.8.0
pickleshare==0.7.5
prometheus-client==0.12.0
prompt-toolkit==3.0.24
ptyprocess==0.7.0
pycparser==2.21
Pygments==2.10.0
pyparsing==3.0.6
pyrsistent==0.18.0
python-dateutil==2.8.2
pyzmq==22.3.0
qtconsole==5.2.2
QtPy==1.11.3
Send2Trash==1.8.0
six==1.16.0
terminado==0.12.1
testpath==0.5.0
tornado==6.1
traitlets==5.1.1
wcwidth==0.2.5
webencodings==0.5.1
widgetsnbextension==3.5.2
