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Spec 001 T035: compare - #171

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Spec 001, task T035. Replaces #168 after its review (one medium, fixed in the second-last commit); #168 replaced #167 and #165.

Everything in #168 (pdf-export compare; nothing read from a PDF printed unless of a known shape; pdf.js quiet), plus, from #168's review:

  • A diagram joined through a small waypoint was split and its labels read as text: shapes under 4 pt now act as pieces of lines, so clipped segments through a reaction square join their nodes; the shaded-header table still reads its rows. Two more found and fixed: the last section's figures on later pages, and the first heading reaching onto the cover.
  • check-book's and the contents reader's error messages could quote PDF text: pdf.js errors are wrapped in UnreadPdf (src/print/unread.ts), which keeps only the kind; check-book prints the kind and code alone.
  • Every console method is held during a comparison; the hold is tested end to end and restored on failure.

Tests: test/compare/ (58), test/check/unread.test.ts (2). Mutants in tasks.md.

🤖 Generated with Claude Code

adamjohnwright and others added 8 commits November 4, 2026 05:40
pdf-export compare <reference> <new> [--expected <file>], as contracts/cli.md
has it: each side a PDF or a folder, a folder compared file by file by name.
Both sides are read with pdf.js (lines, links, figures as clusters of images
and painted paths) and reduced to FR-012's parts: the cover's title, diagram,
excerpt note and distinct names (counted and hashed; U+2060 and no-break
spaces normalised); the introduction's release and counts; the analysis's
properties; each section's parts by their labels and their text; the
contents' entries and targets; each figure's kind. The literature and edit
history, which name people, are held as hashes. The JSON report gives each
difference by part, field and kind with a count and stable identifiers, list
order as a kind of its own; no section text and no name is printed.
--expected takes the recorded differences, with their reasons.

Tests print a sample document with pdf-export's layout and as a reference
in event-pdf's shape (placeholder names, wording written anew): each part's
difference is caught, and no name appears in any report. 21 mutants, each
caught.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…t strict shapes

One printer (src/compare/output.ts) every reported value passes through:
text read from a PDF is printed only as a count, yes or no, a release, one
of a fixed list, a stable identifier, an analysis token of the service's
form or one of Reactome's species; anything else as a hash and a length,
salted once a run. Tested with names planted everywhere in 300 random
layouts a side.

- H1: the cover title is a hash, said only to be its file's name or not.
- H2: the analysis part ends at the first stable identifier or heading,
  and a property is kept only of its shape.
- M1: a contents target not read on either side is missing-target.
- M2: links, figures and targets read by page; 4,000 sections in 1.25 s
  (30.9 s before on the same layout); a file's bytes not copied twice.
- M3: the sections' order by their longest common subsequence, each
  occurrence of a repeated section compared with its own.
- Lows: --reference-margin; an unreadable file named and a difference;
  --expected refuses unknown keys, keeps an events record to differences
  with events, and lists records matching nothing; docs say what is done.

A second reference layout, unlike the sample's, found that a thin
connector must join a vector figure's shapes. 38 mutants, all caught.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- M1: pdf.js's warnings quoted a PDF's content on standard error. Every
  getDocument reading a PDF that may hold names (compare, check-book, the
  contents' reader) now runs with verbosity ERRORS, and compare holds the
  console while it compares: a library's messages are counted and said
  once with their errors' kinds, never their words. Tested with a PDF
  whose content holds a planted word as an unknown operator.
- M2: a table's hairline borders joined its shaded header into a figure
  and its rows were lost. A line of thin paths now joins clusters only
  where it touches two or more node-sized ones, as a connector does.
- Lows: assertions that kill #167's surviving mutants; a missing path is
  exit 2 in the contract; the token is printed in its canonical form; the
  common subsequence's quadratic case recorded.

10 mutants, all caught.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…by kind

- M1: a connector clipped at a reaction's small square was segments
  touching neither each other nor two nodes, so the diagram was no figure
  and its labels were read as text. Shapes under 4 pt are now pieces of
  lines like thin paths, so the segments and the square are one line,
  which joins the nodes at its ends; a shaded-header table still reads
  its rows.
- Found with it: the last section's figures were sought on its first
  page only, and the first section's heading could reach onto the cover.
- L1: pdf.js's errors quote the file. check-book's and the contents'
  readers turn them into UnreadPdf (src/print/unread.ts), said by kind
  alone, and check-book's stopped line prints kind and code only.
- L2/L3: every console method is held during a comparison, put back on
  failure too, the calls said in one line; each tested.
- L4/L5: the wording of what joins, and of tables still read as figures.

11 mutants, all caught.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Replaced after review: check-book's stop line lost the file and the error kind; the contents reader's privacy test could not fail.

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