From 278514e1adb65527c104459ad8f59774d577f730 Mon Sep 17 00:00:00 2001
From: Rowan Cockett <rowanc1@gmail.com>
Date: Mon, 6 Jan 2025 08:53:31 -0700
Subject: [PATCH] =?UTF-8?q?=F0=9F=8C=81=20Join=20gates=20plugin=20before?=
 =?UTF-8?q?=20blocks?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .changeset/slow-cars-smash.md          | 6 ++++++
 packages/myst-cli/src/process/mdast.ts | 4 +---
 packages/myst-transforms/src/basic.ts  | 2 ++
 3 files changed, 9 insertions(+), 3 deletions(-)
 create mode 100644 .changeset/slow-cars-smash.md

diff --git a/.changeset/slow-cars-smash.md b/.changeset/slow-cars-smash.md
new file mode 100644
index 000000000..c5e897706
--- /dev/null
+++ b/.changeset/slow-cars-smash.md
@@ -0,0 +1,6 @@
+---
+"myst-transforms": patch
+"myst-cli": patch
+---
+
+join gates plugin moved before blocks
diff --git a/packages/myst-cli/src/process/mdast.ts b/packages/myst-cli/src/process/mdast.ts
index fb50a03cd..f620767d3 100644
--- a/packages/myst-cli/src/process/mdast.ts
+++ b/packages/myst-cli/src/process/mdast.ts
@@ -25,7 +25,6 @@ import {
   RRIDTransformer,
   RORTransformer,
   DOITransformer,
-  joinGatesPlugin,
   glossaryPlugin,
   abbreviationPlugin,
   reconstructHtmlPlugin,
@@ -197,8 +196,7 @@ export async function transformMdast(
     .use(glossaryPlugin) // This should be before the enumerate plugins
     .use(abbreviationPlugin, { abbreviations: frontmatter.abbreviations })
     .use(indexIdentifierPlugin)
-    .use(enumerateTargetsPlugin, { state }) // This should be after math/container transforms
-    .use(joinGatesPlugin);
+    .use(enumerateTargetsPlugin, { state }); // This should be after math/container transforms
   // Load custom transform plugins
   session.plugins?.transforms.forEach((t) => {
     if (t.stage !== 'document') return;
diff --git a/packages/myst-transforms/src/basic.ts b/packages/myst-transforms/src/basic.ts
index acec0b037..2a0bd2c81 100644
--- a/packages/myst-transforms/src/basic.ts
+++ b/packages/myst-transforms/src/basic.ts
@@ -14,6 +14,7 @@ import { codeBlockToDirectiveTransform, inlineCodeFlattenTransform } from './cod
 import { removeUnicodeTransform } from './removeUnicode.js';
 import { containerChildrenTransform } from './containers.js';
 import { headingDepthTransform } from './headings.js';
+import { joinGatesTransform } from './joinGates.js';
 
 export function basicTransformations(tree: GenericParent, file: VFile, opts?: Record<string, any>) {
   // lifting roles and directives must happen before the mystTarget transformation
@@ -31,6 +32,7 @@ export function basicTransformations(tree: GenericParent, file: VFile, opts?: Re
   headingLabelTransform(tree);
   admonitionBlockquoteTransform(tree); // Must be before header transforms
   admonitionHeadersTransform(tree);
+  joinGatesTransform(tree, file); // This should be before block nesting
   blockNestingTransform(tree);
   // Block metadata may contain labels/html_ids
   blockMetadataTransform(tree, file);