ci: drop duplicate graphviz install from notebook env setup

[AlexanderFengler]

Mechanical drift healing (weekly audit-drift session, 2026-08-17).

• .github/setup-env-notebooks/action.yml installed graphviz twice: PRs ci: install the graphviz binary for notebook checks #1184 and ci: run the notebook drift check weekly, and fix its environment #1188 landed within two hours of each other on 2026-08-13 and each added an apt-get update && apt-get install -y graphviz step.
• Keeps the first step (and its comment); drops the second. Net −8 lines.
• Saves a redundant apt-get update on each of the 4 notebook shards per drift run.

No behavior change — dot is still on PATH for every notebook job. Verified the action still parses and retains exactly one graphviz step.

Context: the hssm-notebooks freshness budget went red because run 31734899653 (2026-08-13 19:15 UTC) failed all 4 shards on ExecutableNotFound: 'dot' — that run started before either graphviz fix merged. A fresh notebook run is in flight to clear the budget: https://github.com/lnccbrown/HSSM/actions/runs/32063688775

Summary by CodeRabbit

• Chores
  • Streamlined notebook environment setup by removing a redundant Graphviz installation step.
  • Notebook dependency installation remains unchanged.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 9013014f-d85d-4318-bd0f-4cf9d4e9e209

📥 Commits

Reviewing files that changed from the base of the PR and between 5e8610b and 4227670.

📒 Files selected for processing (1)

• .github/setup-env-notebooks/action.yml

💤 Files with no reviewable changes (1)

• .github/setup-env-notebooks/action.yml

Included review availability: Your plan includes up to 2 reviews per rolling hour; 1 remains after this review.

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📝 Walkthrough

Walkthrough

This pull request removes a duplicate Graphviz installation step from the notebook setup composite action. The action now continues from the existing Graphviz setup to the hssm installation step.

Changes

Notebook environment setup

Layer / File(s)	Summary
Remove duplicate Graphviz step .github/setup-env-notebooks/action.yml	The composite action removes a repeated Graphviz installation step and its comments. The next step remains the hssm installation.

Estimated code review effort: 1 (Trivial) | ~2 minutes

Merge Risk: ⚪ Minimal · up to 42276

This localized cleanup removes a redundant Graphviz installation while retaining the step that provides dot for notebook jobs; no actionable merge-blocking risk remains beyond normal checks.

Possibly related PRs

• lnccbrown/HSSM#1184: This PR appears related because it added the duplicate Graphviz installation step in the same composite action.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the removal of the duplicate Graphviz installation from the notebook environment setup.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch drift/2026-08-17-notebook-toolchain

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