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pipeio_nb_exec output convention unclear — _executed.ipynb in .src/

When pipeio_nb_exec runs a notebook, it writes the executed output to .src/<name>_executed.ipynb alongside the jupytext .py source. This is confusing because:

  1. .src/ is supposed to contain only .py source files (per CLAUDE.md: "If you find .ipynb in .src/, it's a bug — delete it")
  2. Users expect the executed notebook to be the main .ipynb in the parent workspace dir, or at least clearly documented
  3. The _executed suffix makes it look like a leftover artifact

Suggestion

Either: - Write executed output to the parent workspace dir (alongside the main .ipynb) with a clear naming convention - Document the convention in the pipeio guide - Or add a pipeio_nb_publish step that copies the executed notebook to the workspace dir

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

8dc0d9d Pipeline docs: gitignore docs/pipelines/, relocate hand-authored files
96cd1ec Refactor sharpwaveripple/contracts: extract generic helpers to utils/io, remove pipelines __init__.py
36f9326 Add result note directory and sample note

README:

type: readme

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🐀 Pixecog Project — Compact Overview

Core principles

  • One immutable BIDS raw dataset (raw/) as the canonical baseline
  • Each analysis pipeline ha