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Set up ids as a fragment library - #2

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dem-extra1 merged 5 commits into
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setup-fragment-library
Oct 12, 2026
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dem-extra1 merged 5 commits into
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setup-fragment-library

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Before: the repo is a fresh copy of the qwt template, with its example chapters and template wording.

After: the site is Information Theory for Data Science, a fragment library set up the way pds is. Its home page lists the planned topics and links the related libraries, and the sidebar is empty until the first topic page lands.

How: the infrastructure comes from pds, renamed for ids. That includes the ids -> . self-symlink, which lets include paths written as ids/... resolve when the site renders standalone, and its lint, lychee, render and R build exclusions. Where qwt was newer than pds, the PR keeps qwt's version: the preview action pins, the plugin list in .claude/settings.json, the widget-panel CSS and the dependabot comment. CLAUDE.md, AGENTS.md and the Copilot instructions name the UCD-SERG lab manual and Principles of Scientific Writing.

Checked: quarto render --to html with Quarto 1.10.18 completes with no warnings, and typos is clean on the changed prose. An adversarial review of the first commit found template leftovers, and the second commit fixes them.

🤖 Generated with Claude Code

https://claude.ai/code/session_0159834hyPXNNGozz8ZrW5nK


Generated by Claude Code

Replace the qwt template's example chapters with the fragment-library
setup that pds uses: a self-referential ids symlink so include paths
written as ids/... resolve standalone, the symlink removed before lintr
runs, a docked sidebar mirrored by navbar menus, and a home page that
lists the planned topics. The repo's own CLAUDE.md, README and package
metadata now describe ids rather than the template.

Files where the template is newer than pds (action pins in preview.yml,
the plugin list in .claude/settings.json, page-navigation.html, the
widget-panel CSS and the dependabot comment) keep the template's version.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0159834hyPXNNGozz8ZrW5nK
Remove page-navigation.html (Home is not in the sidebar here), point
/new-chapter at root-level topic pages, drop pds-specific lychee
excludes and unused DESCRIPTION imports, keep the self-symlink out of
R CMD build, and reword template and chapter wording.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0159834hyPXNNGozz8ZrW5nK

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link-checker fails on one link: the home page links the sister library at https://morrison-lab.github.io/cds/, which 404s because that site has not published yet. It will exist once Morrison-Lab/cds#2 merges and the publish workflow deploys it, and each PR is blocked on the other in the same way. I added the links checked by hand label, which is the skip the shared link-check workflow provides for this. The weekly link check on main will catch the link if it is still broken after both sites publish.

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


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The README names the qwt template and the pds library and describes the
latex-macros submodule; the Spellcheck workflow flagged all four words.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0159834hyPXNNGozz8ZrW5nK
Address the review nits: chapters/ no longer exists, the preview comment
still described it, _subfiles/ is not created until the first fragment,
and the lint command should restore the symlink even when lint fails.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0159834hyPXNNGozz8ZrW5nK

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Review suggestions, addressed in 2f849c0 along with a Spellcheck fix (pds, qwt and submodule(s) added to inst/WORDLIST; spelling::spell_check_package() is now clean locally):

  • chapters/*.qmd render glob and the stale preview.yml comment: removed and reworded.
  • _subfiles/ in CLAUDE.md: marked as created with the first fragment.
  • lint.md: the symlink restore is now unconditional.
  • Kept as is: the Authors@R name and email (the maintainer's own, as in pds), the appendix heading level and the level-1 slide-break filter (both deliberate pds changes), and bib entries for the starting materials, which come with the first topic page that cites them.

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The Spellcheck job flagged author names, course terms and "symlink" on index.qmd.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0159834hyPXNNGozz8ZrW5nK
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Claude finished review — View run


I reviewed the one commit since the last round, e0efe96. It adds Kullback, Leibler and symlink to inst/WORDLIST. I didn't run spell-check or render the site.

  • Words used on the page: index.qmd uses all three. "Kullback--Leibler" appears at lines 20 and 28, and "symlink" at line 46.
  • List order: the new entries are in the file's existing order.
  • Convention: adding words to the wordlist matches the repo's rule for spell-check fixes.

I found no new issues. The prior review of 2f849c0 (comment of 2026-10-12) was "Ready for merge", and that verdict still stands. The one open item from earlier rounds is unchanged: watch the first CI run for how the spell-check and non-standard-character workflows handle the ids -> . symlink.

Verdict

Ready for merge

Structured Review Data (JSON)
{
  "schema_version": "1.1",
  "reviewer": "claude",
  "commit_sha": "e0efe9647816470975e7609c3a45f86db2967de0",
  "verdict": "CLEAN",
  "findings": [],
  "detailed_assessment": "inst/WORDLIST gained Kullback, Leibler and symlink, all used in index.qmd, in the file's existing order, with no defects found.",
  "holistic_assessment": "The single new commit only fixes spell-check at the source via the wordlist, so the prior clean verdict stands; the remaining risk is the unverified first CI run around the ids symlink."
}

Reviewed commit: e0efe96

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💰 Cost: $0.1593 (review) — run

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github-actions Bot commented Oct 12, 2026 •

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PR Preview Action v1.8.1
Preview removed because the pull request was closed.

2026-10-12 08:05 UTC

@dem-extra1
dem-extra1 merged commit e681f8c into main Oct 12, 2026
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