jupytext | Jupyter Notebooks as Markdown Documents

My current hook looks like this:

Is is possible to add papermill parameters to a jupyter notebook manually, e.g. in an editor? Is it possible to add papermill parameters to a .py file and have them persist when converted to a .pynb file?

Context:

I am working on running jupyter notebooks in an automated way via Papermill. I would like to add parameters to a notebook manually rather than using jupyter or jupyter lab interfaces. Ideally these parameters could be added to a python script .py file first. Upon converting the .py file to a .ipynb file the parameters would persist.

My desired workflow looks like this:

1. Store generic notebook as a < notebook >.py file with parameters in version control repository
2. Convert python script < notebook >.py to jupyter notebook < notebook >.ipynb
3. Run < notebook >.ipynb via papermill and pass parameters to it
4. Use nbconvert to produce output pdf with no code (using exclude_input argument)

Steps 1-3 will be run via a script that can be auotmated. I want to use jupytext to avoid storing the notebooks and all their associated metadata. Currently, the only way I can find to add parameters to a notebook is to add them via jupyter/(lab) interfaces. Then I can run the notebook with papermill. However, this doesn't work with the jupytext conversion.

*Note I would have added the "jupytext" tag to this but it doesn't exist yet and I don't have enough rep to create

gooseberry's answer appears to be the correct one.

However, it doesn't actually appear to be necessary to add a parameters tag to your notebook in order to inject parameters via papermill. While papermill will give a no cell with tag parameters found in notebook warning it will still inject the parameters. Additionally, your output notebook from papermill will have a new cell:

I'm trying to install jupyter-book on NixOS. I have this flake:

I'm looking for a good way to convert .ipynb to .py files in VSCode. So far I've tried:

• the "Export As" Option built into vscode. Not ideal as it produces the following at the start of the script, as well as "Run Cell", "Run Below", etc. buttons/links:

"To add a new cell, type '# %%' To add a new markdown cell, type '# %% [markdown]' %% from IPython import get_ipython"

• nbconvert. I usually insert this as a command in the script itself (https://stackoverflow.com/a/19779226/14198216) so it's automatically converted and saved once run. But this also leaves "Run Cell" etc, as well as execution markings (ex: "In [1]")

• jupytext. I also usually insert this as a command. At the start of the .py, it produces:

-- coding: utf-8 -- --- jupyter: jupytext: text_representation:

Is there a nice, minimalist solution that doesn't insert a bunch of gunk (which needs to be manually edited out) in the .py version of my notebooks and can be easily/automatically executed from the notebook itself? This could also be setting tweaks that I'm currently unaware of that can make one of the things I mentioned work better.

Thanks in advance.

I've got a directory structure to my notebooks:

• main.py
• notebooks/
  • notebook.py
  • notebook.ipynb

The notebook.py file and notebook.ipynb file are linked with JupyText: we keep the .py file in source control (without outputs or metadata) and we use the .ipynb file as a regular notebook. IntelliJ gives us the opportunity to run cells from both files, but unfortunately, with different working directories. This means that referring to files becomes a real headache because the relative path begins with either ./ or ../

To fix this, I've done a filthy hack: at the root level (next to the main.py) I've defined a project_root.py with the following function: