From 7a5ca6638a91c752c966df86164cf812cac86304 Mon Sep 17 00:00:00 2001
From: Dawn <jiaxin.duan@psi.ch>
Date: Thu, 3 Sep 2026 10:26:17 +0200
Subject: [PATCH] pymol-open-source: wipe stale setuptools build tree + build
 wheel with --no-cache

Two cache layers kept resurrecting a pure-python wheel without _cmd.so:
- modbuild -f re-untars over the old src dir, leaving a stale build/
  tree from a half-failed compile; setup.py packs it as-is
- uv's built-wheel cache (in UV_CACHE_DIR, not ~/.cache/uv) then serves
  that wheel on every rebuild (Prepared in ~550ms = no compile)

rm -rf $SRC_DIR/build in configure + --no-cache on the pymol install
kill both permanently.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 pymol-open-source/build | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/pymol-open-source/build b/pymol-open-source/build
index ac79e25..c4ede00 100755
--- a/pymol-open-source/build
+++ b/pymol-open-source/build
@@ -16,6 +16,11 @@ pbuild::configure() {
     export UV_PYTHON_INSTALL_DIR="$PREFIX/python"
     "$UV" venv --python 3.12 "$PREFIX/venv" || std::die 42 "uv venv failed - is uv at \$UV?"
 
+    # modbuild -f re-untars over the old src dir without deleting extras; a stale
+    # setuptools build/ tree from a failed run then gets packed into the wheel as-is
+    # (pure-python, no _cmd.so). Wipe it so every build compiles from scratch.
+    rm -rf "$SRC_DIR/build"
+
     # stage glm where setup.py's PREFIX_PATH lookup expects it: <prefix>/include/glm.
     # strip_dirs applies to the glm tarball too, so headers land at $SRC_DIR/glm directly
     mkdir -p "$SRC_DIR/deps/include"
@@ -36,7 +41,9 @@ pbuild::install() {
     # -C k=v reaches setup.py as `build_ext --k=v` (_custom_build/backend.py).
     # str2bool accepts ONLY true/false (yes/no -> "Boolean value expected").
     # no-vmd-plugins=false is deliberate: upstream dest is vmd_plugins, false disables them.
-    "$UV" pip install --python "$PREFIX/venv/bin/python" \
+    # --no-cache: never reuse a cached pymol wheel — a poisoned pure-python wheel
+    # (built from a half-failed compile) otherwise gets reinstalled forever
+    "$UV" pip install --no-cache --python "$PREFIX/venv/bin/python" \
         -C use-msgpackc=no -C no-libxml=true -C no-vmd-plugins=false \
         "$SRC_DIR" || \
         std::die 42 "pymol build failed - check system devel RPMs (glew, libpng, freetype, mesa-libGL)"