update pymol-open-source

pymol-open-source/README.md

@@ -20,9 +20,12 @@ Build options passed as `uv pip install -C k=v` (upstream
 `_custom_build/backend.py` turns them into `build_ext --k=v`):
 
 - `use-msgpackc=no` — no msgpack-c/mmtf-cpp on Ra; disables fast MMTF load
-- `no-libxml=yes` — disables COLLADA export
-- `no-vmd-plugins=no` — disables VMD molfile plugins (needs libnetcdf).
-  `no` is correct: upstream stores the value straight into `vmd_plugins`.
+- `no-libxml=true` — disables COLLADA export
+- `no-vmd-plugins=false` — disables VMD molfile plugins (needs libnetcdf).
+  `false` is correct: upstream stores the value straight into `vmd_plugins`.
+
+Boolean flags take ONLY `true`/`false` — upstream `str2bool` rejects
+`yes`/`no` with "Boolean value expected".
 
 Required system RPMs on the build host (if the compile fails, ask
 sysadmins for): `glew-devel libpng-devel freetype-devel mesa-libGL-devel`.
@@ -46,7 +49,8 @@ module use MX unstable && module load pymol-open-source/3.1.0
 
 ```sh
 which pymol                              # -> .../pymol-open-source/3.1.0/venv/bin/pymol
-readlink -f "$PYMOL_ENV/bin/python"      # must resolve inside the module PREFIX
+readlink -f "$PYMOL_ENV/bin/python"      # system /usr/bin/python3.12 (RPM) is fine;
+                                         # inside $PREFIX/python if uv had to download one
 pymol -cq                                # headless no-op: exits 0 without X
 pymol                                    # Qt GUI check, needs X
 ```

pymol-open-source/build

@@ -16,9 +16,10 @@ 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?"
 
-    # stage glm where setup.py's PREFIX_PATH lookup expects it: <prefix>/include/glm
+    # 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"
-    cp -r "$SRC_DIR/glm-1.0.1/glm" "$SRC_DIR/deps/include/" || \
+    cp -r "$SRC_DIR/glm" "$SRC_DIR/deps/include/" || \
         std::die 42 "glm staging failed - glm tarball missing from SRC_DIR?"
 }
 
@@ -33,9 +34,10 @@ pbuild::install() {
     export CC=gcc CXX=g++
     export PREFIX_PATH="$SRC_DIR/deps"
     # -C k=v reaches setup.py as `build_ext --k=v` (_custom_build/backend.py).
-    # no-vmd-plugins=no is deliberate: upstream dest is vmd_plugins, so `no` disables them.
+    # str2bool accepts ONLY true/false (yes/no -> "Boolean value expected").
+    # no-vmd-plugins=false is deliberate: upstream dest is vmd_plugins, false disables them.
     "$UV" pip install --python "$PREFIX/venv/bin/python" \
-        -C use-msgpackc=no -C no-libxml=yes -C no-vmd-plugins=no \
+        -C use-msgpackc=no -C no-libxml=true -C no-vmd-plugins=false \
         "$SRC_DIR" || \
         std::die 42 "pymol build failed - check system devel RPMs (glew, libpng, freetype, mesa-libGL)"
     # Qt GUI; without it pymol falls back to CLI-only