From 4f630bd81e8cbd647486b0d571fe61684bbe4afc Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefanv@berkeley.edu>
Date: Mon, 30 Jun 2025 17:49:08 -0700
Subject: [PATCH 1/2] =?UTF-8?q?=F0=9F=8E=81=20For=20JATS=20output,=20use?=
 =?UTF-8?q?=20<sup>=20to=20wrap=20parenthetical=20citation?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Closes #2136
---
 .../myst-to-jats/src/transforms/citations.ts  | 24 ++++++-------------
 1 file changed, 7 insertions(+), 17 deletions(-)

diff --git a/packages/myst-to-jats/src/transforms/citations.ts b/packages/myst-to-jats/src/transforms/citations.ts
index 256b4eb19..f3928f57b 100644
--- a/packages/myst-to-jats/src/transforms/citations.ts
+++ b/packages/myst-to-jats/src/transforms/citations.ts
@@ -4,7 +4,7 @@ import { selectAll } from 'unist-util-select';
 import type { GenericNode, GenericParent } from 'myst-common';
 
 /**
- * Add parentheses and separator text to citeGroup nodes as children
+ * Add <sup> tag and separator text to citeGroup with nodes as children
  *
  * This allows us to simply render children and get all the correct formatting.
  */
@@ -21,17 +21,13 @@ export function citeGroupTransform(mdast: GenericParent) {
     node.children.forEach((child) => {
       child.kind = kind;
     });
-    const newChildren: GenericNode[] = [];
-    if (kind === 'parenthetical') {
-      newChildren.push({
-        type: 'text',
-        value: '(',
-      });
-    }
-    newChildren.push(node.children[0]);
+    const wrapper: GenericNode = { type: 'superscript', children: [] };
+    wrapper.children = [];
+
+    wrapper.children.push(node.children[0]);
     const sep = kind === 'parenthetical' ? ';' : ',';
     node.children.slice(1).forEach((child) => {
-      newChildren.push(
+      wrapper.children!.push(
         {
           type: 'text',
           value: `${sep} `,
@@ -39,13 +35,7 @@ export function citeGroupTransform(mdast: GenericParent) {
         child,
       );
     });
-    if (kind === 'parenthetical') {
-      newChildren.push({
-        type: 'text',
-        value: ')',
-      });
-    }
-    node.children = newChildren as any[];
+    node.children = kind == 'parenthetical' ? ([wrapper] as any[]) : wrapper.children;
   });
 }
 

From e1cca3ab036fa6b0a753db2424d0a329e547ac59 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefanv@berkeley.edu>
Date: Mon, 30 Jun 2025 17:53:14 -0700
Subject: [PATCH 2/2] Add changeset

---
 .changeset/young-eggs-work.md | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 .changeset/young-eggs-work.md

diff --git a/.changeset/young-eggs-work.md b/.changeset/young-eggs-work.md
new file mode 100644
index 000000000..3dbf9b9fa
--- /dev/null
+++ b/.changeset/young-eggs-work.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': minor
+---
+
+Wrap parenthetical citations in <sup> tag to group citations