paperlint 13.2.0 → 13.3.0

package/skills/assess-novelty/scripts/script_edges.test.ts

@@ -0,0 +1,174 @@
+/**
+ * candidate_page.ts and novelty_reader_brief.ts, the edges the other tests do not reach: the fallbacks for a
+ * missing field, a missing file, a wrong argument count. Each case runs the script as a process on a fixture copy.
+ * Run: npx vitest run skills/assess-novelty/scripts/script_edges.test.ts
+ */
+import {
+  cpSync,
+  mkdirSync,
+  mkdtempSync,
+  readFileSync,
+  realpathSync,
+  rmSync,
+  writeFileSync,
+} from "node:fs";
+import { spawnSync } from "node:child_process";
+import { tmpdir } from "node:os";
+import { dirname, join } from "node:path";
+import { fileURLToPath } from "node:url";
+import assert from "node:assert/strict";
+import { test } from "vitest";
+
+const here = dirname(fileURLToPath(import.meta.url));
+const FIXTURE = join(here, "fixtures", "novelty");
+const PAGE = join(here, "candidate_page.ts");
+const BRIEF = join(here, "novelty_reader_brief.ts");
+const PNG = Buffer.from(
+  "iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAADUlEQVR42mP8z8BQDwAEhQGAhKmMIQAAAABJRU5ErkJggg==",
+  "base64",
+);
+const SENTENCE = "A sentence of at least eight words, quoted from the text.";
+
+const node = (script: string, ...args: string[]) => {
+  const r = spawnSync(process.execPath, [script, ...args], {
+    encoding: "utf8",
+  });
+  return { code: r.status, out: r.stdout, err: r.stderr };
+};
+
+const withDir = (body: (dir: string) => void) => {
+  const dir = realpathSync(mkdtempSync(join(tmpdir(), "script-edges-")));
+  try {
+    body(dir);
+  } finally {
+    rmSync(dir, { recursive: true, force: true });
+  }
+};
+
+const paperWith = (dir: string, ids: string[]) => {
+  cpSync(FIXTURE, dir, { recursive: true });
+  const siblings = join(dir, "siblings");
+  for (const d of ["candidates", "data/crops"])
+    mkdirSync(join(siblings, d), { recursive: true });
+  for (const id of ids) {
+    writeFileSync(
+      join(siblings, "candidates", `${id}.json`),
+      JSON.stringify({
+        id,
+        title: "A title",
+        url: `https://example.org/${id}`,
+        text: `siblings/data/${id}.txt`,
+        found_by: [{ source: "paper.tex ref1" }],
+        summary: "What it does.",
+        abstract: { page: 1, text: SENTENCE },
+        conclusion: { page: 2, text: SENTENCE },
+        passages: [
+          {
+            claim: "P5-1",
+            page: 1,
+            quote: SENTENCE,
+            crop: `siblings/data/crops/${id}-1.png`,
+            meaning: "It matters.",
+          },
+        ],
+        suggestion: "cite",
+        suggestion_why: "Because.",
+      }),
+    );
+    writeFileSync(join(siblings, "data", `${id}.txt`), `${SENTENCE}\n`);
+    writeFileSync(join(siblings, "data", "crops", `${id}-1.png`), PNG);
+  }
+};
+
+const setJson = (dir: string, file: string, change: (j: any) => any) => {
+  const p = join(dir, "siblings", file);
+  writeFileSync(p, JSON.stringify(change(JSON.parse(readFileSync(p, "utf8")))));
+};
+
+test("candidate_page: usage, no candidates, a broken candidate file", () => {
+  assert.equal(node(PAGE).code, 2, "no arguments is a usage error");
+  assert.match(node(PAGE).err, /usage: node candidate_page.ts/);
+  withDir((dir) => {
+    cpSync(FIXTURE, dir, { recursive: true });
+    const r = node(PAGE, "build", dir, join(dir, "out.html"));
+    assert.equal(r.code, 1);
+    assert.match(r.err, /no candidates in/);
+  });
+  withDir((dir) => {
+    paperWith(dir, ["a1"]);
+    writeFileSync(join(dir, "siblings", "candidates", "a1.json"), "{not json");
+    const r = node(PAGE, "build", dir, join(dir, "out.html"));
+    assert.equal(r.code, 1, "a candidate file that is not JSON is refused");
+  });
+});
+
+test("candidate_page build: a page config without session or pdfs, claims without sentences or absent", () => {
+  withDir((dir) => {
+    paperWith(dir, ["a1"]);
+    writeFileSync(join(dir, "siblings", "candidate-page.json"), "{}");
+    setJson(dir, "novelty.json", (j) => {
+      delete j.claims[0].sentence;
+      return j;
+    });
+    const out = join(dir, "out.html");
+    const r = node(PAGE, "build", dir, out);
+    assert.equal(r.code, 0, r.err);
+    assert.match(readFileSync(out, "utf8"), /"session":""/);
+    setJson(dir, "novelty.json", (j) => {
+      delete j.claims;
+      return j;
+    });
+    assert.equal(node(PAGE, "build", dir, out).code, 0);
+    assert.match(readFileSync(out, "utf8"), /"claims":\{\}/);
+  });
+});
+
+test("candidate_page export: a flat folder, a wrapped document, no reason, an already decided and an undecided candidate", () => {
+  withDir((dir) => {
+    paperWith(dir, ["a1", "a2", "a3"]);
+    setJson(dir, "candidates/a2.json", (j) => ({
+      ...j,
+      decision: {
+        choice: "skip",
+        reason: "r",
+        at: "2026-01-01T00:00:00Z",
+        source: "chat",
+      },
+    }));
+    const flat = join(dir, "dump");
+    mkdirSync(flat);
+    writeFileSync(
+      join(flat, "a1.json"),
+      JSON.stringify({ data: { choice: "cite" } }),
+    );
+    const r = node(PAGE, "export", dir, flat);
+    assert.equal(r.code, 0, r.err);
+    assert.match(r.out, /^a1: cite$/m, "no reason, no dash");
+    assert.match(r.out, /^still undecided: a3$/m, "a2 decided already, a3 not");
+  });
+});
+
+test("novelty_reader_brief: a missing novelty.json, no neighbours, a neighbour without title or url", () => {
+  withDir((dir) => {
+    const check = node(BRIEF, "check", dir, "n1");
+    assert.equal(check.code, 1);
+    assert.match(check.err, /cannot read .*novelty\.json/);
+    mkdirSync(join(dir, "siblings"));
+    writeFileSync(join(dir, "siblings", "novelty.json"), "{}");
+    const none = node(BRIEF, dir, "n1");
+    assert.equal(none.code, 1);
+    assert.match(none.err, /no neighbour n1 in novelty\.json \(have: \)/);
+    assert.equal(node(BRIEF, "check", dir, "n1").code, 1);
+    writeFileSync(
+      join(dir, "siblings", "novelty.json"),
+      JSON.stringify({ neighbours: [{ id: "n1", text: "t.txt" }] }),
+    );
+    const missing = node(BRIEF, dir, "n1");
+    assert.equal(missing.code, 2);
+    assert.match(missing.err, /arxiv\.org\/pdf\/<id>/);
+    writeFileSync(join(dir, "t.txt"), "");
+    const brief = node(BRIEF, dir, "n1");
+    assert.equal(brief.code, 0, brief.err);
+    assert.match(brief.out, /Neighbour: n1 — {2}\n/);
+  });
+});

package/src/doctor.ts

@@ -95,8 +95,10 @@ export const PROGRAMS: readonly Program[] = [
   {
     bin: "python3",
     from: "your system",
-    without: "the analysis and report scripts do not start",
-    install: "apt-get install -y python3",
+    without:
+      "the analysis and report scripts and the novelty checks (assess-novelty) do not start",
+    install:
+      "apt-get install -y python3; crop_quote.py also needs PyMuPDF: pip install pymupdf",
   },
 ];