@companion-ai/feynman 0.5.28 → 0.5.30

package/RELEASES.md

@@ -6,6 +6,16 @@ GitHub release notes are generated from the matching `## vX.Y.Z` section in this
 
 ## Unreleased
 
+## v0.5.30 - 2026-10-07
+
+- **Pi 1.1.0.** Claude browser login no longer fails with "localhost refused to connect" when port 53692 is reserved or in use (common with Hyper-V/WSL on Windows); it falls back to a free port. "Servers are busy" provider errors and Mistral stream errors are retried instead of ending the turn, fewer requests fail on context limits, and session costs count long prompts correctly. Adds Claude Haiku 5.5; Feynman's default for Anthropic stays Claude Opus.
+
+## v0.5.29 - 2026-10-07
+
+- **PubMed titles and abstracts keep their italic terms.** Text inside inline tags such as `<i>BRCA1</i>` was dropped, so a title read "patient with germline mutation" instead of "germline BRCA1 mutation", and gene names went missing from abstracts. Thanks to @KennyMcSimpson (#328).
+- **PubMed authors keep all their affiliations.** An author listed with two or more affiliations came back with none. Thanks to @KennyMcSimpson (#327).
+- Security: GHSA-6qxp-vccf-f47h (MCP SDK OAuth client). Feynman's own copies of `@modelcontextprotocol/sdk` move to 1.32.1. pi-web-access still pins 1.27.1 for its separate `npx pi-web-access` MCP server, which Feynman does not run and which does not use the affected OAuth client; it is updated in nicobailon/pi-web-access#522.
+
 ## v0.5.28 - 2026-10-07
 
 - **Pi 1.0.4, pi-subagents 0.76.1, pi-web-access 0.37.0.**

package/extensions/research-tools/science-database-pubmed-parsers.ts

@@ -8,6 +8,14 @@ const xmlParser = new XMLParser({
 	removeNSPrefix: true,
 });
 
+// Object-mode parsing groups tags and loses the order of mixed inline text.
+const orderedTextParser = new XMLParser({
+	preserveOrder: true,
+	removeNSPrefix: true,
+	trimValues: false,
+	parseTagValue: false,
+});
+
 function recordValue(value: unknown): Record<string, unknown> {
 	return value && typeof value === "object" && !Array.isArray(value) ? value as Record<string, unknown> : {};
 }
@@ -49,6 +57,31 @@ function textValue(value: unknown): string | undefined {
 	return parts.length ? parts.join(" ").replace(/\s+/g, " ").trim() : undefined;
 }
 
+function orderedChildren(value: unknown, tag: string): unknown[] {
+	return listValue(value).flatMap((node) => {
+		const children = recordValue(node)[tag];
+		return children === undefined ? [] : [children];
+	});
+}
+
+function orderedText(value: unknown): string {
+	if (typeof value === "string" || typeof value === "number") return String(value);
+	if (Array.isArray(value)) return value.map((node) => orderedText(node)).join("");
+	return Object.entries(recordValue(value))
+		.filter(([key]) => key !== ":@" && !key.startsWith("?"))
+		.map(([, children]) => orderedText(children))
+		.join("");
+}
+
+function orderedTextValue(value: unknown): string | undefined {
+	return orderedText(value).replace(/\s+/g, " ").trim() || undefined;
+}
+
+function orderedPubmedArticles(xml: string): unknown[] {
+	const set = orderedChildren(orderedTextParser.parse(xml), "PubmedArticleSet")[0];
+	return orderedChildren(set, "PubmedArticle");
+}
+
 function dateObject(value: unknown): Record<string, string> | undefined {
 	const record = recordValue(value);
 	const monthMap: Record<string, string> = {
@@ -101,7 +134,8 @@ function parseAuthors(value: unknown): Array<Record<string, unknown>> {
 		const author = recordValue(item);
 		const collective = textValue(author.CollectiveName);
 		if (collective) return { collectiveName: collective, affiliations: [] };
-		const affiliations = listValue(recordValue(author.AffiliationInfo).Affiliation)
+		const affiliations = listValue(author.AffiliationInfo)
+			.flatMap((info) => listValue(recordValue(info).Affiliation))
 			.map((affiliation) => textValue(affiliation))
 			.filter((affiliation): affiliation is string => Boolean(affiliation));
 		return prune({
@@ -113,15 +147,17 @@ function parseAuthors(value: unknown): Array<Record<string, unknown>> {
 	});
 }
 
-function parsePubmedArticle(value: unknown): Record<string, unknown> {
+function parsePubmedArticle(value: unknown, orderedArticle: unknown): Record<string, unknown> {
 	const articleRoot = recordValue(value);
 	const citation = recordValue(articleRoot.MedlineCitation);
 	const article = recordValue(citation.Article);
 	const journal = recordValue(article.Journal);
 	const issue = recordValue(journal.JournalIssue);
-	const abstract = recordValue(article.Abstract);
-	const abstractParts = listValue(abstract.AbstractText)
-		.map((part) => textValue(part))
+	const orderedCitation = orderedChildren(orderedArticle, "MedlineCitation")[0];
+	const orderedContent = orderedChildren(orderedCitation, "Article")[0];
+	const orderedAbstract = orderedChildren(orderedContent, "Abstract")[0];
+	const abstractParts = orderedChildren(orderedAbstract, "AbstractText")
+		.map((part) => orderedTextValue(part))
 		.filter((part): part is string => Boolean(part));
 	const publicationTypes = listValue(recordValue(article.PublicationTypeList).PublicationType)
 		.map((item) => textValue(item))
@@ -140,7 +176,7 @@ function parsePubmedArticle(value: unknown): Record<string, unknown> {
 		pmid: identifiers.pmid,
 		pmcid: identifiers.pmc,
 		doi: identifiers.doi,
-		title: textValue(article.ArticleTitle),
+		title: orderedTextValue(orderedChildren(orderedContent, "ArticleTitle")[0]),
 		abstract: abstractParts.length ? abstractParts.join("\n") : undefined,
 		journal: prune({
 			title: textValue(journal.Title),
@@ -160,7 +196,8 @@ function parsePubmedArticle(value: unknown): Record<string, unknown> {
 export function parsePubmedArticles(xml: string): Record<string, unknown>[] {
 	const parsed = recordValue(xmlParser.parse(xml));
 	const set = recordValue(parsed.PubmedArticleSet);
-	return listValue(set.PubmedArticle).map((article) => parsePubmedArticle(article));
+	const orderedArticles = orderedPubmedArticles(xml);
+	return listValue(set.PubmedArticle).map((article, index) => parsePubmedArticle(article, orderedArticles[index]));
 }
 
 function jatsArticleId(meta: Record<string, unknown>, type: string): string | undefined {
@@ -238,8 +275,9 @@ export function copyrightFromPubmedXml(xml: string): Map<string, Record<string,
 	const map = new Map<string, Record<string, unknown>>();
 	const parsed = recordValue(xmlParser.parse(xml));
 	const set = recordValue(parsed.PubmedArticleSet);
-	for (const rawArticle of listValue(set.PubmedArticle)) {
-		const article = parsePubmedArticle(rawArticle);
+	const orderedArticles = orderedPubmedArticles(xml);
+	for (const [index, rawArticle] of listValue(set.PubmedArticle).entries()) {
+		const article = parsePubmedArticle(rawArticle, orderedArticles[index]);
 		const pmid = stringValue(article.pmid);
 		if (!pmid) continue;
 		const pubmedArticle = recordValue(rawArticle);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@companion-ai/feynman",
-  "version": "0.5.28",
+  "version": "0.5.30",
   "description": "Research-first CLI agent built on Pi and alphaXiv",
   "license": "MIT",
   "type": "module",
@@ -87,8 +87,8 @@
     "posthog-node": "^5.53.0"
   },
   "peerDependencies": {
-    "@earendil-works/pi-ai": "1.0.4",
-    "@earendil-works/pi-coding-agent": "1.0.4",
+    "@earendil-works/pi-ai": "1.1.0",
+    "@earendil-works/pi-coding-agent": "1.1.0",
     "@earendil-works/pi-tui": "*",
     "typebox": "*"
   },