From 8530c5ebe0c9ff88a1e4410849351ea8b8799c5e Mon Sep 17 00:00:00 2001
From: claude <claude@alocoq.fr>
Date: Tue, 2 Jun 2026 13:50:01 +0000
Subject: [PATCH] Run Quarto Python kernel inside the project venv, not base
 python
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The global python3 kernelspec hardcodes /usr/bin/python3, so even with
QUARTO_PYTHON pointing at the project venv, Quarto launched the kernel in the
base interpreter — packages installed into the venv (e.g. openpyxl) were not
importable. Register a python3 kernelspec inside the venv via
'ipykernel install --sys-prefix' (kernel.json argv -> the venv's python); since
Quarto runs kernel discovery through QUARTO_PYTHON, the venv's kernelspec is
found ahead of the global one and the kernel runs in the venv.

Bump the completion marker (.verso-complete -> .verso-ready) so venvs built
before this change are rebuilt with the kernelspec.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 services/clsi/app/js/QuartoRunner.js | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/services/clsi/app/js/QuartoRunner.js b/services/clsi/app/js/QuartoRunner.js
index 5a762656f0..4f2cc9cc57 100644
--- a/services/clsi/app/js/QuartoRunner.js
+++ b/services/clsi/app/js/QuartoRunner.js
@@ -168,15 +168,19 @@ function _pythonVenvPrep(venvBaseDir) {
     `if [ -n "$RHASH" ]; then ` +
     `VDIR="$VBASE/$RHASH"; mkdir -p "$VBASE" 2>/dev/null; ` +
     `( flock 9 || exit 0; ` +
-    `if [ ! -f "$VDIR/.verso-complete" ]; then ` +
+    `if [ ! -f "$VDIR/.verso-ready" ]; then ` +
     `echo "Installing Python packages from requirements.txt..."; rm -rf "$VDIR"; ` +
     `python3 -m venv --system-site-packages "$VDIR" ` +
     `&& "$VDIR/bin/pip" install --no-input --disable-pip-version-check -r requirements.txt ` +
-    `&& touch "$VDIR/.verso-complete" ` +
+    // Register a python3 kernelspec INSIDE the venv (argv -> the venv's python)
+    // so Quarto runs the kernel in the venv, not the base /usr/bin/python3 from
+    // the global kernelspec. ipykernel is visible via --system-site-packages.
+    `&& "$VDIR/bin/python3" -m ipykernel install --sys-prefix --name python3 --display-name "Python 3" ` +
+    `&& touch "$VDIR/.verso-ready" ` +
     `|| echo "ERROR: Failed to install Python packages from requirements.txt"; ` +
     `fi ` +
     `) 9>"$VBASE/.$RHASH.lock" 2>&1; ` +
-    `if [ -f "$VDIR/.verso-complete" ]; then export QUARTO_PYTHON="$VDIR/bin/python3"; fi; ` +
+    `if [ -f "$VDIR/.verso-ready" ]; then export QUARTO_PYTHON="$VDIR/bin/python3"; fi; ` +
     `fi; ` +
     `fi; `
   )