ci(run-notebook): replace whole-cell bash partition with nbclient

[jhamon]

Purpose

The current run-notebook action partitions each code cell whole-cell: cells containing !pip go entirely to a bash script, the rest go to a Python script. A cell that mixes !pip install with Python imports — a standard Jupyter pattern — fails with import: command not found because bash tries to execute Python as a shell command. See PR #572 / run 25743389812 for a live example.

Solution

Drive notebooks through nbclient, the same tool Project Jupyter ships behind jupyter nbconvert --execute. nbclient launches a real ipykernel and processes cells line-by-line: !pip and other shell magics route through the kernel's magic handlers (subshell), Python runs as Python. Mixed cells work exactly as they do in Colab and Jupyter Lab.

Changes

• New run-notebook.py: 50-line nbclient driver. Takes the notebook path as its only arg. Exits 0 on success, 1 on any cell error, 2 on usage error.
• Updated action.yml: installs nbformat nbclient ipykernel into the runner Python, then invokes the new script. No tempdir, no nested venv, no bash conversion.
• Removed convert-notebook.py (~120 lines).

Net diff: 66 insertions, 137 deletions.

Verification

Tested locally against the notebook from PR #572 (docs/quick-tour/hello-pinecone.ipynb, with !pip install and Python imports in the same cell — the case that breaks today's runner):

$ python .github/actions/run-notebook/run-notebook.py docs/quick-tour/hello-pinecone.ipynb
Executing docs/quick-tour/hello-pinecone.ipynb
PASS — docs/quick-tour/hello-pinecone.ipynb

Notes

• check-structure follow-up. The lint rule "imports must be in the first code cell" was designed around today's runner: under the new runner, a single cell holding !pip install + imports is once again the correct pattern. Either relax the rule to skip pip-only cells when locating "the first code cell," or remove the rule entirely. Separate PR.
• Notebook dep isolation. Notebook deps now install into the runner's Python (the kernel shares its interpreter), not a nested venv. Acceptable for CI (ephemeral runner) and simpler than the previous tempdir/venv dance.
• Per-cell timeout. 600s by default, overridable via NOTEBOOK_CELL_TIMEOUT.
• Soak. Worth running this against a known-passing notebook before merging to confirm no regressions on the existing fleet — let me know if you want me to dual-run on a sample.

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Note

Medium Risk
Changes the CI notebook execution mechanism from a custom conversion/venv+bash flow to nbclient driving a real Jupyter kernel, which may alter dependency/runtime behavior and failure modes across the notebook suite.

Overview
Updates the run-notebook composite action to execute notebooks end-to-end using nbclient/ipykernel instead of converting cells into separate bash/python scripts.

This removes convert-notebook.py, installs nbformat nbclient ipykernel on the runner, and adds run-notebook.py which runs the notebook with a real kernel, returning clearer per-cell errors and supporting mixed !pip + Python cells (with an optional NOTEBOOK_CELL_TIMEOUT).

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