paperlint 7.2.0 → 9.0.0

package/skills/paper-pipeline/scripts/extract-ref-facts.harness.mjs

@@ -9,7 +9,7 @@
  * 🔴 THREE MEASUREMENTS HERE — THESE ARE THREE DEFECTS THAT LIVED THE ENTIRE LIFE OF THE PREDECESSOR. Each
  * is pinned by an assertion on a REAL repository file, not a fixture, because all three
  * held exactly because nobody ever passed the real file:
- *   1. `refs.bib` was not in the list of sources (`resolveSource`);
+ *   1. `refs.bib` was never opened;
  *   2. the regex `.bib` required `}` on a separate line and gave 0 entries on both our files;
  *   3. in `.bib` an author is written "LastName, FirstName", but comparison took the last token.
  *
@@ -39,11 +39,18 @@ import {
 import { tmpdir } from "node:os";
 import { dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";
+import { bibReader } from "#src/adapters/bibtex/index";
+import { absolutePath } from "#src/domain/paths";
+import { sha256Hex } from "#src/domain/sha256";
+import { serializeSourcesRecord } from "#src/domain/sources-record";
 import { consumerRoot } from "./consumer.mjs";
 
 const HERE = dirname(fileURLToPath(import.meta.url));
 const ROOT = consumerRoot();
 const X = await import(join(HERE, "extract-ref-facts.mjs"));
+/** The facts' entries of a BibTeX text, read by the one bibtex reader. */
+const factsOf = (text) =>
+  X.factEntries(bibReader.readFile(absolutePath("/p/refs.bib"), text));
 
 // 🔴 PAPERS ROOT — FROM THE DECLARATION, NOT BY THE FIRST CONSUMER'S DIRECTORY NAME (12.09.2026).
 // `package.json` → `paperlint.papersDir`, default `papers`. The same key is read by
@@ -70,38 +77,71 @@ const REAL_PAPERS = existsSync(PAPERS_ROOT)
   : [];
 
 const TMP = realpathSync(mkdtempSync(join(tmpdir(), "extract-ref-facts-")));
+
+/**
+ * What `paperlint build` leaves in a paper's folder (`_build/sources.json`): bibtex opened `refs.bib`.
+ * The paper is read through that record and refused without it, so every paper here is built first.
+ */
+function built(dir) {
+  const digest = (name) => sha256Hex(readFileSync(join(dir, name)));
+  mkdirSync(join(dir, "_build"), { recursive: true });
+  writeFileSync(
+    join(dir, "_build", "sources.json"),
+    serializeSourcesRecord({
+      schema: 1,
+      inputs: [
+        { path: "paper.tex", role: "body" },
+        { path: "refs.bib", role: "preamble" },
+      ],
+      written: [],
+      bibdata: ["refs"],
+      bibtex: {
+        ran: true,
+        databases: ["refs.bib"],
+        keys: [],
+        exit: 0,
+        errors: [],
+      },
+      sha256: {
+        "paper.tex": digest("paper.tex"),
+        "refs.bib": digest("refs.bib"),
+      },
+    }),
+  );
+}
 // Cleanup is attached IMMEDIATELY: assertions throw, and "rmSync at end of file" does not execute precisely in those
 // runs that are red.
 process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
 
-// ── 1. DEFECT #1: `refs.bib` must be in the list of sources ─────────────────
+// ── 1. DEFECT #1: the `.bib` a paper declares is opened ──────────────────────
+//
+// The build recorded that bibtex opened `refs.bib`, and `bibliographyAt` opens it. A fixture paper
+// holds the frozen real `.bib`, so the leg is proven on a real file in every checkout.
 {
-  assert.ok(
-    X.SOURCE_ORDER.includes("refs.bib"),
-    `refs.bib missing from SOURCE_ORDER — this is the defect that kept the .bib leg from ever opening: ${X.SOURCE_ORDER.join(", ")}`,
+  const dir = join(TMP, "declares-real-bib");
+  mkdirSync(dir, { recursive: true });
+  writeFileSync(
+    join(dir, "paper.tex"),
+    "\\documentclass{article}\\begin{document}x\\bibliography{refs}\\end{document}\n",
   );
-  // 🔴 SUBJECT — FIXTURE, real papers ADDITION (12.09.2026). There used to be only a loop over
-  // our two papers with `continue` if file doesn't exist. In this repo they exist, and test is green;
-  // in the extracted pipeline their directories WON'T EXIST — both loops make no iteration, and
-  // harness prints success having checked zero files. "Green over void", a class this base has paid for thrice. Fixture makes an empty run INEXPRESSIBLE: it always lies nearby.
-  //
-  // ⚠️ Directory, not file: `resolveSource` returns the path itself if it IS A FILE, and only for
-  // a directory descends the `SOURCE_ORDER`. A fixture-file would check the wrong branch.
-  {
-    const dir = join(HERE, "fixtures", "real-bib");
-    assert.equal(
-      X.resolveSource(dir),
-      join(dir, "refs.bib"),
-      "resolveSource cannot find the frozen real .bib — .bib leg is dead again",
-    );
-  }
+  writeFileSync(
+    join(dir, "refs.bib"),
+    readFileSync(join(HERE, "fixtures", "real-bib", "refs.bib")),
+  );
+  built(dir);
+  const found = X.bibliographyFrom(dir);
+  assert.deepEqual(
+    found.ok && found.texts.map((t) => t.path),
+    [join(dir, "refs.bib")],
+    `a paper declaring \\bibliography{refs} does not open its refs.bib — the .bib leg is dead again: ${JSON.stringify(found.why ?? "")}`,
+  );
+  // Real consumer papers: whatever each declares is either read or refused WITH A REASON — never a
+  // silent nothing.
   for (const paper of REAL_PAPERS) {
-    const dir = join(PAPERS_ROOT, paper);
-    if (!existsSync(join(dir, "refs.bib"))) continue;
-    assert.equal(
-      X.resolveSource(dir),
-      join(dir, "refs.bib"),
-      `resolveSource cannot find real refs.bib for ${paper} — .bib leg is dead again`,
+    const r = X.bibliographyFrom(join(PAPERS_ROOT, paper));
+    assert.ok(
+      r.ok ? r.texts.length > 0 : r.why.length > 0,
+      `${paper}: neither a bibliography nor a reason`,
     );
   }
 }
@@ -128,7 +168,7 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
     parsed++;
     const text = readFileSync(f, "utf8");
     const want = (text.match(/^@\w+\{/gm) ?? []).length;
-    const got = await X.parseBib(text);
+    const got = factsOf(text);
     assert.ok(
       want > 0,
       `${paper}/refs.bib: no @… entries in file — fixture is broken`,
@@ -170,7 +210,7 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
 @misc{inst2,
   author={{sh-guard contributors}},
   title={Another}, year={2026}}`;
-  const es = await X.parseBib(bib);
+  const es = factsOf(bib);
   assert.deepEqual(
     es.map((e) => e.authors),
     [["Adversa AI"], ["sh-guard contributors"]],
@@ -185,7 +225,7 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
 // single brace — ordinary author, and order "LastName, FirstName" must be unwound.
 {
   const bib = `@misc{human, author={Adversa, Alice}, title={T}, year={2026}}`;
-  const [e] = await X.parseBib(bib);
+  const [e] = factsOf(bib);
   assert.deepEqual(
     e.authors,
     ["Alice Adversa"],
@@ -201,7 +241,7 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
   const bib = `@inproceedings{k1,
   author={Jimenez, Carlos E. and Di Penta, Massimiliano and others},
   title={A Title}, booktitle={ICLR}, year={2024}, note={arXiv:2310.06770}}`;
-  const [e] = await X.parseBib(bib);
+  const [e] = factsOf(bib);
   assert.deepEqual(
     e.authors,
     ["Carlos E. Jimenez", "Massimiliano Di Penta"],
@@ -308,71 +348,17 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
   );
 }
 
-// ── 7. markdown: reference list, source lines, `et al.`, appendix ───
-{
-  const md = [
-    "# Paper",
-    "",
-    "## 1. Intro",
-    "",
-    "Prose.",
-    "",
-    "## References",
-    "",
-    "1. C. Yang, Z. Zhao, L. Zhang. *KNighter: Transforming Static Analysis.* arXiv:2503.09002, 2025.",
-    "2. Z. Xiang et al. *Another Work.* ICSE 2024. arXiv:2401.00001",
-    "",
-    "## Appendix A",
-    "",
-    "1. Not a reference at all.",
-    "",
-  ].join("\n");
-  const es = X.parseMarkdownRefs(md);
-  assert.equal(
-    es.length,
-    2,
-    `heading must close the reference list, parsed ${es.length}`,
-  );
-  assert.equal(
-    es[0].line,
-    9,
-    `line of first entry is ${es[0].line}, but it is ninth in file`,
-  );
-  assert.equal(es[0].title, "KNighter: Transforming Static Analysis");
-  assert.equal(es[1].truncated, true, "`et al.` must be marked as truncation");
-  assert.deepEqual(es[1].authors, ["Z. Xiang"]);
-  assert.equal(es[1].year, "2024");
-}
-
-// ── 8. `## References` inside ```-block does NOT open list ──────────────────
-// Papers in this repo cite their own markup in pieces; the old `split` would open
-// bibliography in the middle of a code example.
-{
-  const md = [
-    "# P",
-    "",
-    "## Body",
-    "",
-    "```md",
-    "## References",
-    "",
-    "1. Fake. *X.* arXiv:1111.11111",
-    "```",
-    "",
-  ].join("\n");
-  assert.deepEqual(
-    X.parseMarkdownRefs(md),
-    [],
-    "heading inside ```-block is not a heading",
-  );
-}
-
-// ── 9. CLI: ZERO ENTRIES — REFUSAL, not empty facts ─────────────────────────
+// ── 7. CLI: ZERO ENTRIES — REFUSAL, not empty facts ─────────────────────────
 {
   const { spawnSync } = await import("node:child_process");
   const dir = join(TMP, "empty");
   mkdirSync(dir, { recursive: true });
-  writeFileSync(join(dir, "paper.md"), "# P\n\nNo links at all.\n");
+  writeFileSync(
+    join(dir, "paper.tex"),
+    "\\documentclass{article}\\begin{document}x\\bibliography{refs}\\end{document}\n",
+  );
+  writeFileSync(join(dir, "refs.bib"), "% no entries at all\n");
+  built(dir);
   const r = spawnSync(
     "node",
     [join(HERE, "extract-ref-facts.mjs"), dir, "--offline"],
@@ -393,7 +379,7 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
   );
 }
 
-// ── 10. CLI: no source — also refusal, not silence ─────────────────────────
+// ── 8. CLI: no source — also refusal, not silence ─────────────────────────
 {
   const { spawnSync } = await import("node:child_process");
   const dir = join(TMP, "nosrc");
@@ -405,25 +391,25 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
   );
   assert.equal(r.status, 1);
   assert.ok(
-    /refs\.bib/u.test(r.stderr),
-    "message must list sources, including refs.bib",
+    /no paper\.tex/u.test(r.stderr),
+    `message must say what is missing: ${r.stderr}`,
   );
 }
 
-// ── 11. end-to-end: real paper → facts, freshness is computed ───────────────
+// ── 9. end-to-end: real paper → facts, freshness is computed ───────────────
 {
   const { spawnSync } = await import("node:child_process");
   const dir = join(TMP, "e2e");
   mkdirSync(join(dir, "repro"), { recursive: true });
-  const paper = [
-    "# P",
-    "",
-    "## References",
-    "",
-    "1. A. Lovelace, G. Hopper. *A Study.* arXiv:2503.09002, 2025.",
-    "",
-  ].join("\n");
-  writeFileSync(join(dir, "paper.md"), paper);
+  const paper =
+    "@misc{lovelace2025,\n  author={Lovelace, Ada and Hopper, Grace},\n  title={A Study},\n" +
+    "  note={arXiv:2503.09002},\n  year={2025}}\n";
+  writeFileSync(join(dir, "refs.bib"), paper);
+  writeFileSync(
+    join(dir, "paper.tex"),
+    "\\documentclass{article}\\begin{document}x\\bibliography{refs}\\end{document}\n",
+  );
+  built(dir);
   writeFileSync(
     join(dir, "repro", "refs-cache.json"),
     JSON.stringify({
@@ -454,6 +440,6 @@ process.on("exit", () => rmSync(TMP, { recursive: true, force: true }));
 }
 
 console.log(
-  "✓ extract-ref-facts: refs.bib in sources, both real .bib parse completely, name order unwound, " +
+  "✓ extract-ref-facts: the declared refs.bib is opened, both real .bib parse completely, name order unwound, " +
     "arXiv-DOI does not go to CrossRef, registry readers run on raw bodies, zero entries = refusal",
 );