[d-morrison]

Requested by Ezra · project thread

Closes #165.

Why

mds already treats 40 mcs definitions as prerequisites (391 edges in its published dependency-graph.json), but mcs publishes no graph of its own. Because of that, no tree can show how the mcs definitions depend on each other, and the cross-repo tree on lds leaves mcs out entirely. This PR is step 1 of the plan from Ezra's thread. Step 2 adds a combined mcs+mds tree to mds. Step 3 adds mcs to the lds all-notes tree, then a radial layout and grouping (lds#2298).

What changed

• tools/build_dependency_graph.py and dependency-graph.js: copied unchanged from lds. The lds JavaScript has the guard from lds#1698 that the mds, pds and sds copies lack (lds#2412).
• _quarto-website.yml: a pre-render step builds dependency-graph.json from the top-level pages, and the script and JSON are published as resources. A Dependency Tree entry is added at the end of Math Reference in both the navbar and the sidebar.
• dependency-tree.qmd: the tree page, HTML only (like lds's all-notes tree), since the tree is drawn in the browser. Only this page loads the script. The chapters/ pages reuse 105 of the same ids and share three page names (sets, relations, induction), so loading the script site-wide would draw per-div graphs on chapter pages that link to the wrong page.
• .gitignore: ignores the generated JSON, as mds does.
• CLAUDE.md: names the new files in the layout list.

Size

The diff is over the 300-line cap only because of tools/build_dependency_graph.py and dependency-graph.js (516 lines), which are byte-identical copies of the lds files. They are copied, not written here (mechanical, content-identical). The rest of the PR is about 40 lines.

Scope

The graph covers only the Math Reference pages, because those are the pages the other sites link to. Graphing chapters/ needs the builder to handle several page directories, so that is a follow-up.

Verification

• The builder reports 162 nodes, 300 edges, 0 cycles and 0 forward references. All 40 mcs nodes in mds's graph match a node here by id, so the cross-site tree will join them.
• quarto render dependency-tree.qmd --to html succeeds. The rendered page loads the script once, and the theorem link resolves to ./proof-writing.html#def-theorem.
• I ran the script on the rendered page under jsdom (no browser). It drew 162 boxes, each linking to its page, for example expressions-algorithms.html#def-algorithm.

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Generated by Claude Code

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[d-morrison]

Addressed in e83304b:

• CLAUDE.md: the layout list now names tools/build_dependency_graph.py, dependency-graph.js and dependency-tree.qmd. It also covers the pre-render step and the git-ignored JSON, and says the builder and script are copies of the lds ones.
• dependency-tree.qmd: the page is now HTML only, as lds's all-notes tree is. It renders to _site/dependency-tree.html and nothing else.

Deferred: dependency-graph.js fetch failure. This file is a byte-identical copy of lds's chapters/dependency-graph.js, and four repos share it. Changing it here alone would add a fifth variant to the drift that lds#2412 already tracks. I've added the "graph unavailable" message to that issue, so all the copies get it together: https://github.com/Morrison-Lab/lds/issues/2412

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Posted by Claude Code (AI agent) --- not written by a human.

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Generated by Claude Code

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[github-actions]

Claude finished review — View run

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I fetched PR 166 live just now. It is open, not a draft and not merged, and its head is 749d8c44bd8c1cbe0f09938bd9c014de33f19654. That is the commit I reviewed, so the review above stands.

Verdict

Ready for merge

Structured Review Data (JSON)

{
  "schema_version": "1.1",
  "reviewer": "claude",
  "commit_sha": "749d8c44bd8c1cbe0f09938bd9c014de33f19654",
  "verdict": "CLEAN",
  "findings": [],
  "detailed_assessment": "The dependency-tree.qmd front matter now declares only html, matching the script loading, and CLAUDE.md documents the new graph files; the silent fetch catch in dependency-graph.js is a deliberate, non-blocking suggestion.",
  "holistic_assessment": "Both blocking items from the prior round are resolved, scope remains limited to the dependency graph feature, and regression risk to existing chapters is low."
}

Reviewed commit: 749d8c4

[github-actions]

💰 Cost: $0.2105 (review) — run

[github-actions]

PR Preview Action v1.8.2
🚀 Preview available at: https://Morrison-Lab.github.io/mcs/pr-preview/pr-166/

_{Built to branch gh-pages at 2026-11-12 23:09 UTC.}

[d-morrison]

Cross-harness review (agy Flash) on 749d8c4: VERDICT: CLEAN

The dependency-graph builder and viewer are consistent with the navigation, .gitignore and CLAUDE.md entries; no logic bugs or broken targets found. Reviewed from the diff only; the page was not rendered by me.

Posted by Claude Code (AI agent) --- not written by a human.