py-pymol: update package, new version 2.5.0 (#28044)

* py-pymol: update package, new version 2.5.0

* ensure legacy plugins still load/work

2 files changed, 50 insertions, 22 deletions

diff --git a/var/spack/repos/builtin/packages/py-pmw-patched/package.py b/var/spack/repos/builtin/packages/py-pmw-patched/package.py
new file mode 100644
index 0000000000..f17bf63452
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pmw-patched/package.py
@@ -0,0 +1,14 @@
+# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyPmwPatched(PythonPackage):
+    """Schrodinger's Fork of Python megawidgets with essential patches applied.
+       Pmw is a toolkit for building high-level compound widgets, or
+       megawidgets, constructed using other widgets as component parts."""
+    homepage = "https://github.com/schrodinger/pmw-patched"
+    git = "https://github.com/schrodinger/pmw-patched"
+
+    version('02-10-2020', commit='8bedfc8747e7757c1048bc5e11899d1163717a43')
diff --git a/var/spack/repos/builtin/packages/py-pymol/package.py b/var/spack/repos/builtin/packages/py-pymol/package.py
index 557caf7692..f62e0c76ab 100644
--- a/var/spack/repos/builtin/packages/py-pymol/package.py
+++ b/var/spack/repos/builtin/packages/py-pymol/package.py
@@ -15,29 +15,43 @@ class PyPymol(PythonPackage):
     homepage = "https://pymol.org"
     url      = "https://github.com/schrodinger/pymol-open-source/archive/v2.4.0.tar.gz"
 
+    version('2.5.0', sha256='aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3')
     version('2.4.0', sha256='5ede4ce2e8f53713c5ee64f5905b2d29bf01e4391da7e536ce8909d6b9116581')
     version('2.3.0', sha256='62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0')
 
-    depends_on('python+tkinter', type=('build', 'run'))
-    depends_on('freetype', type=('build', 'run'))
-    depends_on('glew', type=('build'))
-    depends_on('glm', type=('build'))
-    depends_on('py-numpy', type=('build', 'run'))
-    depends_on('tcsh', type=('build', 'run'))
+    depends_on('python+tkinter@2.7:', type=('build', 'run'), when='@2.3.0:2.4.0')
+    depends_on('python+tkinter@3.6:', type=('build', 'run'), when='@2.5.0:')
+    depends_on('gl')
+    depends_on('glew')
+    depends_on('libpng')
+    depends_on('freetype')
+    depends_on('glm')
+    depends_on('libmmtf-cpp')
+    depends_on('msgpack-c@2.1.5:')
+    depends_on('netcdf-cxx4')
+    depends_on('libxml2')
+    depends_on('py-pmw-patched', type=('build', 'run'))
     depends_on('py-pyqt5', type=('build', 'run'))
-    depends_on('py-pmw', type=('build', 'run'))
-    depends_on('libmmtf-cpp', type=('build', 'run', 'link'))
-    depends_on('msgpack-c', type=('build', 'run'))
-    depends_on('libpng@1.5.13', type=('build', 'run'))
-
-    def setup_build_environment(self, env):
-        include = []
-        library = []
-        for dep in self.spec.dependencies(deptype='link'):
-            query = self.spec[dep.name]
-            include.extend(query.headers.directories)
-
-        env.set('CPATH', ':'.join(include))
-        env.set('LIBRARY_PATH', ':'.join(library))
-        env.set('PREFIX_PATH', self.spec['libpng'].prefix)
-        env.prepend_path('PREFIX_PATH', self.spec['py-pyqt5'].prefix)
+    depends_on('py-numpy', type=('build', 'run'))
+
+    def install_args(self, spec, prefix):
+        args = super(PyPymol, self).install_args(spec, prefix)
+        args.append('--no-launcher')
+        return args
+
+    @run_after('install')
+    def install_launcher(self):
+        binpath = self.prefix.bin
+        mkdirp(self.prefix.bin)
+        fname = join_path(binpath, 'pymol')
+        script = join_path(self.prefix,
+                           self.spec['python'].package.site_packages_dir,
+                           'pymol',
+                           '__init__.py')
+
+        shebang = '#!/bin/sh\n'
+        fdata = 'exec {0} {1} \"$@\"'.format(self.spec['python'].command,
+                                             script)
+        with open(fname, 'w') as new:
+            new.write(shebang + fdata)
+        set_executable(fname)