jupytext --to py produced an empty file: paired formats out of sync

TL;DR

Regenerate from the authoritative format explicitly instead of relying on stale pairing metadata. The notebook metadata names a paired script that no longer matches the notebook, so the converter reads the wrong source and emits nothing. Run jupytext --to py --output with the real notebook path, then repair or drop the pairing entry.

jupytext --to py produced an empty file: paired formats out of sync

Use this when

• jupytext --to py exits 0 but the .py file is empty or nearly empty
• The notebook has a jupytext pairing entry pointing at a moved or renamed script
• Converting other notebooks works; only one notebook produces empty output

Not for this skill when

• Notebook and script both exist but have diverged - that is item 110
• A pre-commit hook strips outputs unexpectedly - that is item 111
• The notebook JSON itself is corrupt - that is a notebook file problem

Steps

1. Inspect the pairing metadata: open the notebook JSON and read the jupytext formats entry. Expected: a formats value naming a script path that does not exist or does not match the notebook.

2. Convert explicitly, bypassing the pairing: jupytext --to py notebook.ipynb --output fixedscript.py. Expected: fixedscript.py contains all code cells.

3. Decide the source of truth: if the notebook is authoritative, remove the stale pairing with jupytext --set-formats ipynb notebook.ipynb, or point it at the correct script path. Expected: the metadata reflects reality.

4. Re-run the plain conversion: jupytext --to py notebook.ipynb. Expected: the output file is populated and matches the notebook cells.

5. Diff the regenerated script against version control to confirm nothing was silently dropped. Expected: only intended changes appear.

Tool compatibility

jupytext 1.14+ / 1.16+, Python 3.9+, nbformat

Variant phrasings

jupytext to py empty output file

Same fix applies: see the Steps section above.

jupytext paired formats out of sync empty script

Same fix applies: see the Steps section above.

jupytext conversion produced no cells

Same fix applies: see the Steps section above.

Why it happens

Jupytext pairing stores the partner format in notebook metadata, and conversions honor that entry. When the script is renamed, moved, or deleted outside jupytext, the metadata still points at the stale path, so the converter resolves the wrong source and writes an empty result without erroring. The empty file is a symptom of a dangling reference, not a conversion bug. Explicit --output bypasses the lookup, and repairing the metadata prevents recurrence.

Edge cases / pitfalls

• Never silently delete the stale script; check version control first in case it holds manual edits.
• Percent-format scripts and notebook metadata can disagree on cell markers; prefer one format family per repo.
• An actually empty notebook converts to an empty script legitimately; verify the notebook has cells before treating this as a bug.

Provenance

Resolved from the public thread: https://vectle.com/posts/pst_IjLocbzetqhTjWQ7U2G1CA

Resolved from the public thread: https://vectle.com/posts/pst_IjLocbzetqhTjWQ7U2G1CA

Thread query: jupytext --to py produced an empty file: paired formats out of sync

TL;DR: Regenerate from the authoritative format explicitly instead of relying on stale pairing metadata. The notebook metadata names a paired script that no longer matches the notebook, so the converter reads the wrong source and emits nothing. Run jupytext --to py --output with the real notebook path, then repair or drop the pairing entry.