fix: move execution transform much earlier

Author: agoose77

packages/myst-cli/src/process/mdast.ts

@@ -183,6 +183,19 @@ export async function transformMdast(
   // This needs to come before basic transformations since it may add labels to blocks
   liftCodeMetadataToBlock(session, vfile, mdast);
 
+  if (execute && !frontmatter.skip_execution) {
+    const cachePath = path.join(session.buildPath(), 'execute');
+    await kernelExecutionTransform(mdast, vfile, {
+      basePath: session.sourcePath(),
+      cache: new LocalDiskCache<(IExpressionResult | IOutput[])[]>(cachePath),
+      sessionFactory: () => session.jupyterSessionManager(),
+      frontmatter: frontmatter,
+      ignoreCache: false,
+      errorIsFatal: false,
+      log: session.log,
+    });
+  }
+
   const pipe = unified()
     .use(reconstructHtmlPlugin) // We need to group and link the HTML first
     .use(htmlPlugin, { htmlHandlers }) // Some of the HTML plugins need to operate on the transformed html, e.g. figure caption transforms
@@ -226,18 +239,6 @@ export async function transformMdast(
   // Combine file-specific citation renderers with project renderers from bib files
   const fileCitationRenderer = combineCitationRenderers(cache, ...rendererFiles);
 
-  if (execute && !frontmatter.skip_execution) {
-    const cachePath = path.join(session.buildPath(), 'execute');
-    await kernelExecutionTransform(mdast, vfile, {
-      basePath: session.sourcePath(),
-      cache: new LocalDiskCache<(IExpressionResult | IOutput[])[]>(cachePath),
-      sessionFactory: () => session.jupyterSessionManager(),
-      frontmatter: frontmatter,
-      ignoreCache: false,
-      errorIsFatal: false,
-      log: session.log,
-    });
-  }
   transformRenderInlineExpressions(mdast, vfile);
   await transformOutputsToCache(session, mdast, kind, { minifyMaxCharacters });
   liftOutputs(session, mdast, vfile, {