From 824b873c69e285d0c8107cc775371c8ee6b4dbe4 Mon Sep 17 00:00:00 2001
From: claude <claude@alocoq.fr>
Date: Sun, 31 May 2026 14:08:08 +0000
Subject: [PATCH] =?UTF-8?q?Fix=20QuartoRunner:=20drop=20--output=20flag=20?=
 =?UTF-8?q?to=20let=20Quarto=20run=20full=20typst=E2=86=92PDF=20pipeline?=
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--to typst combined with --output output.pdf caused Quarto to write a
Typst source file (.typ content) named output.pdf instead of invoking
the typst compiler, producing a text file that the PDF viewer could not
render (hence 'markdown not rendered' — it was literally showing the raw
.typ markup). Fix: let Quarto name the PDF after the input file
(main.qmd → main.pdf) and rename to output.pdf with mv afterwards.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 services/clsi/app/js/QuartoRunner.js | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/services/clsi/app/js/QuartoRunner.js b/services/clsi/app/js/QuartoRunner.js
index c664bc5691..75ad7bf404 100644
--- a/services/clsi/app/js/QuartoRunner.js
+++ b/services/clsi/app/js/QuartoRunner.js
@@ -52,18 +52,19 @@ function _buildQuartoCommand(mainFile) {
   // Run through a POSIX shell so stderr is merged into stdout (2>&1).
   // Quarto writes all progress and error messages to stderr; without this
   // the log panel would be empty on failure.
-  // LocalCommandRunner replaces $COMPILE_DIR before the shell sees the
-  // string, so no shell variable expansion occurs for that token.
-  const quartoArgs = [
-    'quarto',
-    'render',
-    `$COMPILE_DIR/${mainFile}`,
-    '--to',
-    'typst',
-    '--output',
-    'output.pdf',
-  ].join(' ')
-  return ['/bin/sh', '-c', `${quartoArgs} 2>&1`]
+  // LocalCommandRunner replaces $COMPILE_DIR before the shell sees it.
+  //
+  // Do NOT pass --output: combining --to typst with --output *.pdf causes
+  // Quarto to write a Typst source file (.typ) with a .pdf extension instead
+  // of running the full typst→PDF pipeline. Instead, let Quarto name the PDF
+  // after the source file (main.qmd → main.pdf) and rename it afterwards.
+  const inputPath = `$COMPILE_DIR/${mainFile}`
+  const pdfName = mainFile.replace(/\.[^/.]+$/, '') + '.pdf'
+  const renderedPdf = `$COMPILE_DIR/${pdfName}`
+  const cmd =
+    `quarto render ${inputPath} --to typst 2>&1 && ` +
+    `mv ${renderedPdf} $COMPILE_DIR/output.pdf`
+  return ['/bin/sh', '-c', cmd]
 }
 
 function _writeLogOutput(compileName, directory, output, callback) {