Fix Windows path separator issue in paired notebooks

[Copilot]

Problem

When using the --set-formats command on Windows PowerShell to pair notebooks in different folders:

jupytext --set-formats notebooks//ipynb,scripts//py:percent notebooks/*.ipynb

The command failed with:

Paired paths 'notebooks/example.ipynb','scripts/example.py' do not include 
the current notebook path 'notebooks\example.ipynb'. Current format is 
'notebooks//ipynb', and paired formats are 'notebooks//ipynb,scripts//py:percent'.

Root Cause

The issue was in the separator() function in src/jupytext/paired_paths.py. When determining the appropriate path separator, the function checked if a backslash was present in the path:

if os.path.sep == "\\" and "\\" in path:
    return "\\"
return "/"

However, when base_path() stripped the directory prefix from notebooks\example.ipynb, it returned just 'example' (a bare filename with no separators). The separator('example') call then returned / on Windows because the string didn't contain \, causing a mismatch:

• Input path: notebooks\example.ipynb (backslashes)
• Generated paths: notebooks/example.ipynb, scripts/example.py (forward slashes)
• Path comparison failed due to separator mismatch

Solution

Enhanced the separator() function to properly handle Windows paths in three cases:

1. Path contains \ → return \ (Windows file path)
2. Path contains / but not \ → return / (contents manager/format path)
3. Path has no separators → return \ (bare filename on Windows - the key fix)

This ensures that when rebuilding paths from a bare filename on Windows, the OS separator is used, maintaining consistency with the input path.

Testing

• Added test_paired_paths_windows_relative() to verify the fix with the exact reported scenario
• Verified all existing Windows path tests still pass
• Confirmed Unix/Linux behavior is unchanged
• Verified Jupyter contents manager paths (using /) are preserved on Windows

Fixes issue where Windows users couldn't pair notebooks in different folders using relative paths.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Windows sync different folders</issue_title>
<issue_description>I'm using:

jupytext --set-formats notebooks//ipynb,scripts//py:percent notebooks/*.ipynb

in Windows PowerShell

That command resulted in:

Paired paths 'notebooks/example.ipynb','scripts/example.py' do not include the current notebook path 'notebooks\example.ipynb'. Current format is 'notebooks//ipynb', and paired formats are 'notebooks//ipynb,scripts//py:percent'.

---

I think this is OS specific bug?

NOTE: already using the latest pypi package of jupytext and using VSCode power shell</issue_description>

<agent_instructions>Hi @copilot, can you figure out what should be the pairing instructions on Windows?</agent_instructions>

Comments on the Issue (you are @copilot in this section)

Fixes #1028

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[github-actions]

Thank you for making this pull request.

Did you know? You can try it on Binder: or .

Also, the version of Jupytext developed in this PR can be installed with pip:

HATCH_BUILD_HOOKS_ENABLE=true pip install git+https://github.com/mwouts/jupytext.git@copilot/fix-windows-sync-folders

(this requires nodejs, see more at Developing Jupytext)