Merge remote-tracking branch 'origin/build-pymol'

pymol/README.md

@@ -1,17 +1,52 @@
+# pymol
 
-Installation Remarks: 
+Molecular visualization system. This module ships the **incentive**
+(official Schrodinger) Linux bundle, not the open-source build.
 
-1.) 
-If installed on RH7 (merlin6 nodes), a library is missing for RH8 nodes (RA) : 
+- Upstream: https://pymol.org/ (support: https://www.pymol.org/support.html)
+- License: Schrodinger incentive license required for full features
+
+## How it is built
+
+Per pymol.org support page for Linux (RHEL 8+ supported since v2.5.10):
+download the `PyMOL-<ver>_<build>-Linux-x86_64-py310.tar.bz2` bundle,
+unpack, run `./pymol`. The recipe downloads the bundle from the public
+pymol-storage GCS bucket (sha256-verified), unpacks it and moves the
+bundle contents into `$PREFIX`; the `pymol` launcher sits at the PREFIX
+root, so the modulefile does `prepend-path PATH $PREFIX` (the bundle's
+private `bin/` with its own python is deliberately NOT on PATH).
+
+Versions before 3.1.8 in this module's git history were open-source
+builds (git clone + setup.py) against merlin-era psi-python modules;
+see https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL
+if that route is ever needed again.
+
+### License file
+
+The bundle runs unlicensed with limited features. Site-wide: drop the
+SLM license file at `$PREFIX/share/pymol/license.lic`. Per user: PyMOL
+prompts on first start (get the file from https://pymol.org/dsc/ip/license/).
+
+## Building on Ra
+
+```sh
+module use unstable && module load modbuild/2.1.2
+cd pymol
+modbuild build 3.1.8
+module use MX unstable && module load pymol/3.1.8
 ```
-libGLEW.so.1.10  
+
+## Verifying the install
+
+```sh
+which pymol            # -> /opt/psi/MX/pymol/3.1.8/pymol
+pymol -cq              # headless no-op: exits 0 without X
+pymol                  # GUI check, needs X
 ```
-To overcome this, copy this library from /usr/lib64/libGLEW.so.1.10.0 to the pmodules lib  folder and link accordingly to the right name if neccessary.
 
+## Adding a new version
 
-2.) 
-Installed with the options --no-vmd-plugins --use-msgpackc=no, if these options should be available, probably other dependencies needed. 
-Description from https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL:
-- msgpack-c 2.1.5+ (optional, for fast MMTF loading and export, disable with --use-msgpackc=no)
-- mmtf-cpp (for fast MMTF export, disable with --use-msgpackc=no)
-- libnetcdf (optional, disable with --no-vmd-plugins)
+Check the exact bundle filename on https://pymol.org (the `_0` build
+number and `py310` tag change between releases), update `urls:` if
+needed, add the version + tarball sha256 in `files/config.yaml`, then
+`modbuild build <version>` (modbuild/2.1.2) on a Ra login node.

pymol/build

@@ -1,23 +1,17 @@
 #!/usr/bin/env modbuild
 
-
-
-pbuild::prep() {
-    git clone --depth 1 --branch "v${V_PKG}" https://github.com/schrodinger/pymol-open-source.git
-}
+# Incentive PyMOL: prebuilt Linux bundle from pymol.org, no compile.
+# Default pbuild::prep downloads + sha-verifies + unpacks (urls/shasums in
+# files/config.yaml); the bundle unpacks to pymol/ with the launcher at its root.
 
 pbuild::configure() {
-    #NEEDS GML 
-    git clone -b 0.9.9.8 https://github.com/g-truc/glm.git  $SRC_DIR/glm/
-    cp -r $SRC_DIR/glm/glm/ $SRC_DIR/pymol-open-source/include/
-}
-
-pbuild::compile() {
-    cd "$SRC_DIR/pymol-open-source/"
-    python3 setup.py install --prefix "$PREFIX/" --no-vmd-plugins --use-msgpackc=no
-}
-
-pbuild::install(){
     :
 }
 
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    mv "${SRC_DIR}/pymol/"* "${PREFIX}/"
+}

pymol/files/config.yaml

@@ -1,13 +1,17 @@
+---
 format: 1
 pymol:
   defaults:
     group: MX
     overlay: base
     relstage: unstable
+    urls:
+      # _0 build number and py310 tag are release-specific; check
+      # https://pymol.org/ #download for the exact filename when bumping
+      - url: https://storage.googleapis.com/pymol-storage/installers/PyMOL-${V_PKG}_0-Linux-x86_64-py310.tar.bz2
+  shasums:
+    PyMOL-3.1.8_0-Linux-x86_64-py310.tar.bz2: 69ba3492d6d7c4b6cc3d89d47320fb49ed5fdc2bda1a373b73ce11aad3225a7f
   versions:
-    2.5.0:
+    3.1.8:
       config:
-        build_requires: ["psi-python38/2020.11", "gcc/9.3.0", "cuda/11.0.3"]
-    3.0.0:
-      config:
-        build_requires: ["psi-python39/2021.11", "gcc/9.3.0", "cuda/11.0.3"]
+        relstage: unstable

pymol/modulefile

@@ -1,10 +1,15 @@
 #%Module1.0
 
-module-whatis           "PyMol - molecular visualization system"
-module-url              "https://github.com/schrodinger/pymol-open-source"
-module-license          "-"
-module-maintainer       "Greta Assmann <greta.assmann@psi.ch>"
-
-module-help     "https://pymol.org/2/"
+module-whatis       "PyMOL - molecular visualization system (incentive build)"
+module-url          "https://pymol.org/"
+module-license      "Schrodinger incentive PyMOL - needs license.lic (see module-help)"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
 
+module-help     "
+PyMOL molecular visualization system, official Schrodinger Linux
+bundle. Full features need a license file: place it at
+\$PREFIX/share/pymol/license.lic (site-wide) or let PyMOL prompt
+for it on first start (per user).
+"
 
+prepend-path    PATH    $PREFIX