jupyter run notebook.ipynb does not work
#7025
Comments
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Thanks @charmoniumQ for opening the issue. Looks like this command might be coming from the |
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Actually Maybe the docs on https://github.com/jupyter/jupyter should also be updated. |
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So the docs should say |
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Yes, they should. @palewire made the change from |
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Closing this issue in favor of the issue above which in the Jupyter pository. |
Description
Docs say that
jupyter run notebook.ipynbwill execute the notebook. It appears that Jupyter is instead trying to evaluate the JSON contents ofnotebook.ipynb. In more complex notebooks, I will get"true" is not definedor"null" is not definedon a specific line of the notebook which contains JSONtrueornull.Reproduce
Source code
{"cells": [{"cell_type": "code", "execution_count": 1, "id": "d3baff75-e7bf-46f3-9ede-b5c0f725123f", "metadata": {}, "outputs": [{"name": "stdout", "output_type": "stream", "text": ["hello world\n"]}], "source": ["import pathlib; pathlib.Path('test').write_text('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": "3.11.4"}}, "nbformat": 4, "nbformat_minor": 5}notebook.ipynbwhich writes a file calledhello.pip install notebookjupyter run notebook.ipynbls -land see thathellodoes not exist.Jupyter did not actually execute the notebook. In notebooks with null execution counts, I will git
"null" is not definedon that line, which seems to indicate that jupyter is simply evaluating the file as a Python expression (which it is not).Expected behavior
jupyter run notebook.ipynbshould actually execute the notebook or change the documentation to not advertise this functionality.Context
Troubleshoot Output
[notice] A new release of pip is available: 23.1.2 -> 23.2.1 [notice] To update, run: pip install --upgrade pip $PATH: /home/sam/box/prov/src/test/kernels/.venv/bin /nix/store/11hrc3lnzp8jyb3afmmy9h4m4c30jkgs-starship-1.15.0/bin /home/sam/.local/share/spack/bin /home/sam/.nix-profile/bin /nix/var/nix/profiles/default/bin /home/sam/.local/share/cargo/bin /usr/local/sbin /usr/local/bin /usr/sbin /usr/bin /sbin /bin /usr/games /usr/local/games /snap/bin /home/sam/.local/binsys.path:
/home/sam/box/prov/src/test/kernels/.venv/bin
/nix/store/xlpbkwgf4nrnr56a3r0k0r32jxlxyf59-python3-3.11.4/lib/python311.zip
/nix/store/xlpbkwgf4nrnr56a3r0k0r32jxlxyf59-python3-3.11.4/lib/python3.11
/nix/store/xlpbkwgf4nrnr56a3r0k0r32jxlxyf59-python3-3.11.4/lib/python3.11/lib-dynload
/home/sam/box/prov/src/test/kernels/.venv/lib/python3.11/site-packages
sys.executable:
/home/sam/box/prov/src/test/kernels/.venv/bin/python
sys.version:
3.11.4 (main, Jun 6 2023, 22:16:46) [GCC 12.3.0]
platform.platform():
Linux-5.15.0-79-generic-x86_64-with-glibc2.37
which -a jupyter:
/home/sam/box/prov/src/test/kernels/.venv/bin/jupyter
pip list:
Package Version
------------------------- -----------
anyio 3.7.1
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
arrow 1.2.3
asttokens 2.2.1
async-lru 2.0.4
attrs 23.1.0
Babel 2.12.1
backcall 0.2.0
beautifulsoup4 4.12.2
bleach 6.0.0
certifi 2023.7.22
cffi 1.15.1
charset-normalizer 3.2.0
comm 0.1.4
debugpy 1.6.7.post1
decorator 5.1.1
defusedxml 0.7.1
executing 1.2.0
fastjsonschema 2.18.0
fqdn 1.5.1
idna 3.4
ipykernel 6.25.1
ipython 8.14.0
isoduration 20.11.0
jedi 0.19.0
Jinja2 3.1.2
json5 0.9.14
jsonpointer 2.4
jsonschema 4.19.0
jsonschema-specifications 2023.7.1
jupyter_client 8.3.1
jupyter_core 5.3.1
jupyter-events 0.7.0
jupyter-lsp 2.2.0
jupyter_server 2.7.2
jupyter_server_terminals 0.4.4
jupyterlab 4.0.5
jupyterlab-pygments 0.2.2
jupyterlab_server 2.24.0
MarkupSafe 2.1.3
matplotlib-inline 0.1.6
mistune 3.0.1
nbclient 0.8.0
nbconvert 7.8.0
nbformat 5.9.2
nest-asyncio 1.5.7
notebook 7.0.3
notebook_shim 0.2.3
overrides 7.4.0
packaging 23.1
pandocfilters 1.5.0
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
pip 23.1.2
platformdirs 3.10.0
prometheus-client 0.17.1
prompt-toolkit 3.0.39
psutil 5.9.5
ptyprocess 0.7.0
pure-eval 0.2.2
pycparser 2.21
Pygments 2.16.1
python-dateutil 2.8.2
python-json-logger 2.0.7
PyYAML 6.0.1
pyzmq 25.1.1
referencing 0.30.2
requests 2.31.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rpds-py 0.10.0
Send2Trash 1.8.2
setuptools 65.5.0
six 1.16.0
sniffio 1.3.0
soupsieve 2.4.1
stack-data 0.6.2
terminado 0.17.1
tinycss2 1.2.1
tornado 6.3.3
traitlets 5.9.0
uri-template 1.3.0
urllib3 2.0.4
wcwidth 0.2.6
webcolors 1.13
webencodings 0.5.1
websocket-client 1.6.2
jupyter run --debug
jupyter run --debug Untitled.ipynb [RunApp] Searching ['/home/sam/box/prov/src/test/kernels/.venv/etc/jupyter', '/home/sam/.config/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files [RunApp] Looking for jupyter_config in /etc/jupyter [RunApp] Looking for jupyter_config in /usr/local/etc/jupyter [RunApp] Looking for jupyter_config in /home/sam/.config/jupyter [RunApp] Looking for jupyter_config in /home/sam/box/prov/src/test/kernels/.venv/etc/jupyter [RunApp] Looking for jupyter run_config in /etc/jupyter [RunApp] Looking for jupyter run_config in /usr/local/etc/jupyter [RunApp] Looking for jupyter run_config in /home/sam/.config/jupyter [RunApp] Looking for jupyter run_config in /home/sam/box/prov/src/test/kernels/.venv/etc/jupyter [RunApp] Connection File not found: /home/sam/.local/share/jupyter/runtime/kernel-2385632.json 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [RunApp] Instantiating kernel 'Python 3 (ipykernel)' with kernel provisioner: local-provisioner [RunApp] Starting kernel: ['/home/sam/box/prov/src/test/kernels/.venv/bin/python', '-m', 'ipykernel_launcher', '-f', '/home/sam/.local/share/jupyter/runtime/kernel-2385632.json', 'Untitled.ipynb'] [RunApp] Connecting to: tcp://127.0.0.1:34447 [RunApp] connecting iopub channel to tcp://127.0.0.1:50623 [RunApp] Connecting to: tcp://127.0.0.1:50623 [RunApp] connecting shell channel to tcp://127.0.0.1:43263 [RunApp] Connecting to: tcp://127.0.0.1:43263 [RunApp] connecting stdin channel to tcp://127.0.0.1:51469 [RunApp] Connecting to: tcp://127.0.0.1:51469 [RunApp] connecting heartbeat channel to tcp://127.0.0.1:40461 [RunApp] connecting control channel to tcp://127.0.0.1:34447 [RunApp] Connecting to: tcp://127.0.0.1:34447 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [RunApp] jupyter run: starting... [RunApp] jupyter run: executing `Untitled.ipynb` {'cells': [{'cell_type': 'code', 'execution_count': 1, 'id': 'd3baff75-e7bf-46f3-9ede-b5c0f725123f', 'metadata': {}, 'outputs': [{'name': 'stdout', 'output_type': 'stream', 'text': ['hello world\n']}], 'source': ["import pathlib; pathlib.Path('test').write_text('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': '3.11.4'}}, 'nbformat': 4, 'nbformat_minor': 5}The text was updated successfully, but these errors were encountered: