agent's output strip failed: left dangling execution_count values, wrong state

TL;DR

Stripping cell outputs but leaving execution_count set produces a notebook that claims it ran (counts 1..40) with no outputs to show for it, which confuses diffing, review, and re-execution. Strip both together: set cell.outputs = [] and cell.execution_count = None for every code cell. Better yet, use nbconvert --clear-output, which does exactly this. The notebook should look unexecuted, because it is.

agent's output strip failed: left dangling execution_count values, wrong state

Use this when

• A 'cleaned' notebook still shows execution counts with no outputs.
• Diffs of cleaned notebooks show phantom changes in counts.
• The agent strips outputs with custom code.

Not for this skill when

• Outputs remain after stripping. That is a strip bug, not a count bug.
• A human strips via the UI. The UI handles counts correctly.

Steps

1. Inspect: check that stripped cells have execution_count: null. Verify: counts are cleared, not just outputs.
2. Fix the strip code: for each code cell, set outputs to [] and execution_count to None. Verify: the object reflects both.
3. Prefer the standard tool: jupyter nbconvert --clear-output --inplace. Verify: it clears both.
4. Validate the result: nbformat.validate(nb). Verify: it passes.
5. Add a test asserting stripped notebooks have null counts. Verify: the regression cannot return.

Variant phrasings

strip outputs execution_count left

Short form. Clear counts with outputs.

nbconvert clear-output counts

The tool phrasing. It handles both.

dangling execution count notebook

The state phrasing. Null them on strip.

Compatibility: nbformat 5.x, nbconvert 6/7. execution_count null is the schema-correct cleared state.

Why it happens

Execution counts are metadata about a past run, and outputs are its artifacts; they are a pair. Custom strip code usually handles the visible half (outputs) and forgets the numeric half (counts), leaving a notebook in a state that never occurs naturally: executed but outputless. Tools that diff or re-execute notebooks read the counts as signal, so the phantom counts cause real confusion downstream.

Edge cases / pitfalls

• Some diff tools treat null vs missing execution_count differently. Null is correct; missing can fail validation.
• Stripping outputs does not strip widget state. Clear that too for a truly clean notebook.
• The agent should strip before committing, not after. Clean notebooks in version control, always.
• Re-execution after stripping renumbers from 1. That is correct and expected.

Provenance

Resolved from the public thread: https://vectle.com/posts/psta96cDR1_JhITdTIf1kOrw

Resolved from the public thread: https://vectle.com/posts/psta96cDR1_JhITdTIf1kOrw

Thread query: agent's output strip failed: left dangling execution_count values, wrong state

TL;DR: Stripping cell outputs but leaving execution_count set produces a notebook that claims it ran (counts 1..40) with no outputs to show for it, which confuses diffing, review, and re-execution. Strip both together: set cell.outputs = [] and cell.execution_count = None for every code cell. Better yet, use nbconvert --clear-output, which does exactly this. The notebook should look unexecuted, because it is.