Pair ipynb with files in subfolders one level down

[hectormz]

I would like to pair .ipynb files with .py files according to this structure:

.
├── jupytext.toml
├── Alpha/
│   ├── notebooks_py/
│   │   └── notebook.py
│   └── notebook.ipynb
├── Beta/
│   ├── notebooks_py/
│   │   └── notebook.py
│   └── notebook.ipynb
└── Gamma/
    ├── notebooks_py/
    │   └── notebook.py
    └── notebook.ipynb

I haven't been able to figure this out. I am able to get it to work if I switch the locations of the .ipynb and .py files and use this in in my config:

[formats]
"notebooks_ipynb/" = "ipynb"
"./" = "py:percent"

I am open to manually pairing each .py and .ipynb pair or putting jupytext.toml config files in each project directory if that will help (Alpha, Beta, Gamma)

[hectormz]

I seem to be able to achieve what I want (from some other, old issues) using:

formats = "ipynb,_notebooks_py//py:percent,notebooks_md//md"

although I'm not sure what the equivalent is for the other style (for completeness)

[formats]
...
...
...
``
Maybe @mwouts has an idea. It would be good to expand the config section to cover this type of organization/pairing

[VRConservation]

Hi,
I'm having the same issue when I use

jupytext --sync *.ipynb

It only syncs the notebooks in the folder that I cd into. So, If I have paired notebooks in separate folders, I have to cd into each folder and issue the command. Is there any way to sync across an entire folder and all subfolders?

[mwouts]

Hi @VRConservation , can you use the globstar operator for this?

shopt -s globstar
jupytext --sync **/*.ipynb
jupytext --sync {dir_a,dir_b,dir_c}/**/*.ipynb

@hectormz sorry that I missed this issue, indeed in the dict-like representation you can't have an empty prefix at the moment, I will fix that in a future version.

[VRConservation]

Thanks, Marc. I'll try this. My workaround was to create a python script in the root directory that defined the folder locations as variables then ran a for loop: ```python for folder in folders: os.chdir(folder) subprocess.run(["jupytext", "--sync", "*.ipynb"], check=True) os.chdir(orig_dir) ``` Depends on `import os, subprocess` as well as defining orig_dir. From: Marc Wouts ***@***.***> Sent: Sunday, June 2, 2024 6:14 PM To: mwouts/jupytext ***@***.***> Cc: VRConservation ***@***.***>; Mention ***@***.***> Subject: Re: [mwouts/jupytext] Pair ipynb with files in subfolders one level down (Issue #1144) Hi @VRConservation<https://github.com/VRConservation> , can you use the globstar operator<https://askubuntu.com/questions/1010707/how-to-enable-the-double-star-globstar-operator> for this? shopt -s globstar jupytext --sync **/*.ipynb jupytext --sync {dir_a,dir_b,dir_c}/**/*.ipynb @hectormz<https://github.com/hectormz> sorry that I missed this issue, indeed in the dict-like representation you can't have an empty prefix at the moment, I will fix that in a future version. - Reply to this email directly, view it on GitHub<#1144 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOTZCQ6KSYLSZCRKRDUZAN3ZFNHENAVCNFSM6AAAAAA6HQ2SUCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBTHE2DOMZXGM>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>