Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci

7 files changed, 103 insertions, 47 deletions

diff --git a/sci-chemistry/burrow-owl/ChangeLog b/sci-chemistry/burrow-owl/ChangeLog
index dc721a3cd..8377c8ba5 100644
--- a/sci-chemistry/burrow-owl/ChangeLog
+++ b/sci-chemistry/burrow-owl/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> burrow-owl-9999.ebuild:
+  Drop Keywords
+
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> burrow-owl-9999.ebuild:
+  Drop Keywords
+
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> burrow-owl-9999.ebuild:
+  Drop Keywords
+
   14 Feb 2012; Justin Lecher <jlec@gentoo.org> -files/1.4-include.patch,
   -burrow-owl-1.4.ebuild, -burrow-owl-9999_pre15.ebuild,
   burrow-owl-9999.ebuild, +files/burrow-owl-9999-impl-dec.patch,
diff --git a/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild b/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
index de9b5b922..42615b4d6 100644
--- a/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
+++ b/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
@@ -15,7 +15,7 @@ EGIT_REPO_URI="git://burrow-owl.git.sourceforge.net/gitroot/burrow-owl/burrow-ow
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
 IUSE="doc examples static-libs"
 
 RDEPEND="
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 8b2e5810d..0f6860d52 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,30 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  files/pymol-9999-prefix.patch, files/pymol-9999-web.patch:
+  Fix for current HEAD, correct desktop entry generation
+
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  files/pymol-9999-prefix.patch, files/pymol-9999-web.patch:
+  Fix for current HEAD, correct desktop entry generation
+
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  files/pymol-9999-prefix.patch, files/pymol-9999-web.patch:
+  Version Bump, correct desktop entry generation
+
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  files/pymol-9999-prefix.patch, files/pymol-9999-web.patch:
+  Add icon to desktop file
+
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  files/pymol-9999-prefix.patch, files/pymol-9999-web.patch:
+  Add desktop entry
+
+  19 Feb 2012; Justin Lecher <jlec@gentoo.org> files/pymol-9999-prefix.patch,
+  files/pymol-9999-web.patch:
+  Fix for latest head
+
   13 Feb 2012; Justin Lecher <jlec@gentoo.org> -files/1.3.0-vmd.patch,
   -files/pymol-0.99_rc10-data-path.patch, -files/pymol-1.2.2-shaders.patch,
   pymol-9999.ebuild, +files/pymol-9999-flags.patch, -files/9999-vmd.patch,
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
new file mode 100644
index 000000000..c7caf1416
--- /dev/null
+++ b/sci-chemistry/pymol/Manifest
@@ -0,0 +1 @@
+DIST pymol.xpm.tar 10240 SHA256 813c450b5acc399387ddc33cc2d747c02afb515e1c3f216be7f7284a09e64819 SHA512 c3f67d4d2d86f814dac17da60efdf9fd9af5dfe84cad67b609af0b5ed825db68b1a4c0bc5233f445bf72d97765fa11e5e42a28c58093169cc51fea392affc9d1 WHIRLPOOL 7d14621523577f56d8a48bb5ffdcbd73dd9ae75934e426b2e7552ed3469e047849f095c0757a5b52ce1f1ccf9e9e88c6acc4edb4910c470be3d786c2b01f7fe5
diff --git a/sci-chemistry/pymol/files/pymol-9999-prefix.patch b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
index 830eb8feb..9b0bad342 100644
--- a/sci-chemistry/pymol/files/pymol-9999-prefix.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
@@ -1,43 +1,57 @@
- setup.py |    8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index ce0d271..2b6fa35 100755
---- a/setup.py
-+++ b/setup.py
-@@ -104,7 +104,7 @@ elif sys.platform=='darwin':
-         inc_dirs=["ov/src",
-                   "layer0","layer1","layer2",
-                   "layer3","layer4","layer5", 
--                  "/usr/X11R6/include",
-+                  "@GENTOO_PORTAGE_EPREFIX@/usr/include",
-                   EXT+"/include",
-                   EXT+"/include/GL",
-                   EXT+"/include/freetype2",
-@@ -120,7 +120,7 @@ elif sys.platform=='darwin':
-                     ]
+Index: setup.py
+===================================================================
+--- setup.py	(revision 3983)
++++ setup.py	(working copy)
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!@GENTOO_PORTAGE_EPREFIX@/usr/bin/env python
+ #
+ # This script only applies if you are performing a Python Distutils-based
+ # installation of PyMOL.
+@@ -35,7 +35,7 @@
+ 	      "modules/cealign/src/tnt" ]
+     libs=["glut32","opengl32","glu32","png"]
+     pyogl_libs = ["glut32","opengl32","glu32"]
+-    lib_dirs=["/usr/lib/w32api"]
++    lib_dirs=["@GENTOO_PORTAGE_EPREFIX@/usr/lib/w32api"]
+     def_macros=[("_PYMOL_MODULE",None),
+                 ("CYGWIN",None),
+                 ("_PYMOL_LIBPNG",None)]
+@@ -87,7 +87,7 @@
+                   "/sw/include/freetype2/freetype",
+                   "/sw/include/freetype2",
+                   "/sw/include",
+-                  "/usr/X11/include",
++                  "@GENTOO_PORTAGE_EPREFIX@/usr/X11/include",
+ 		  "modules/cealign/src",
+ 		  "modules/cealign/src/tnt",
+ 		  #"contrib/uiuc/plugins/include/",
+@@ -114,8 +114,8 @@
          ext_comp_args=[]
          ext_link_args=[
--            "-L/usr/X11R6/lib64", "-lGL", "-lXxf86vm",
-+            "-L@GENTOO_PORTAGE_EPREFIX@/usr/lib64", "-lGL", "-lXxf86vm",
-             "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
-             ]
- #============================================================================
-@@ -159,7 +159,7 @@ else: # linux or other unix
+                        "-L/sw/lib", "-lpng",
+-                       "/usr/X11/lib/libGL.dylib",
+-                       "/usr/X11/lib/libGLU.dylib",
++                       "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGL.dylib",
++                       "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGLU.dylib",
+                        "-lfreeglut",
+                        "-lglew",
+                        "-L/sw/lib/freetype219/lib", "-lfreetype"
+@@ -221,7 +221,7 @@
                   "layer3",
                   "layer4",
                   "layer5",
 -                 "/usr/include/freetype2",
 +                 "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2",
                # VMD plugin support
-                             "contrib/uiuc/plugins/include",
-                             "contrib/uiuc/plugins/molfile_plugin/src",
-@@ -180,7 +180,7 @@ else: # linux or other unix
+               #              "contrib/uiuc/plugins/include",
+               #              "contrib/uiuc/plugins/molfile_plugin/src",
+@@ -242,7 +242,7 @@
                     "GLU",
                     "glut",
                     "GLEW"]
 -    lib_dirs = [ "/usr/X11R6/lib64", ]
-+    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/lib64", ]
++    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/X11R6/lib64", ]
      def_macros = [ ("_PYMOL_MODULE",None),
                     ("_PYMOL_INLINE",None),
                     ("_PYMOL_FREETYPE",None),
diff --git a/sci-chemistry/pymol/files/pymol-9999-web.patch b/sci-chemistry/pymol/files/pymol-9999-web.patch
index fe61f0264..4f4814016 100644
--- a/sci-chemistry/pymol/files/pymol-9999-web.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-web.patch
@@ -1,19 +1,16 @@
- setup.py |    5 +----
- 1 files changed, 1 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 18866a2..366d552 100755
---- a/setup.py
-+++ b/setup.py
-@@ -229,10 +229,7 @@ distribution = setup ( # Distribution meta-data
-                  'pymol/opengl/gl',
+Index: setup.py
+===================================================================
+--- setup.py	(revision 3983)
++++ setup.py	(working copy)
+@@ -292,10 +292,7 @@
                   'pymol/opengl/glu',
                   'pymol/opengl/glut',
--                 'pymol/wizard',
+                  'pymol/wizard',
+-                 'pymol2',
 -                 'web',
 -                 'web/examples',
 -                 'web/javascript', ],
-+                 'pymol/wizard', ],
++                 'pymol2', ],
      ext_modules = [
          Extension("pymol._cmd", [
                  "modules/cealign/src/ccealignmodule.cpp",
diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 908c7fc3c..167184299 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -10,11 +10,11 @@ RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.*"
 PYTHON_USE_WITH="tk"
 PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
 
-inherit distutils eutils prefix subversion versionator
+inherit distutils eutils fdo-mime prefix subversion versionator
 
 DESCRIPTION="A Python-extensible molecular graphics system."
 HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI=""
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${PN}.xpm.tar"
 ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
 
 LICENSE="PSF-2.2"
@@ -40,6 +40,11 @@ DEPEND="
 	web? ( !dev-python/webpy )"
 RDEPEND="${DEPEND}"
 
+src_unpack() {
+	unpack ${A}
+	subversion_src_unpack
+}
+
 src_prepare() {
 	epatch \
 		"${FILESDIR}"/${P}-setup.py.patch \
@@ -51,10 +56,6 @@ src_prepare() {
 	epatch "${FILESDIR}"/${P}-prefix.patch && \
 		eprefixify setup.py
 
-	# Turn off splash screen.  Please do make a project contribution
-	# if you are able though. #299020
-	epatch "${FILESDIR}"/${P}-nosplash.patch
-
 	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
 
 	if use numpy; then
@@ -91,7 +92,7 @@ src_install() {
 
 	cat >> "${T}"/pymol <<- EOF
 	#!/bin/sh
-	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
+	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
 	EOF
 
 	dobin "${T}"/pymol
@@ -103,6 +104,9 @@ src_install() {
 	doins -r examples
 
 	dodoc DEVELOPERS README
+
+	doicon "${WORKDIR}"/${PN}.xpm
+	make_desktop_entry pymol PyMol ${PN} "Graphics;Science;Chemistry"
 }
 
 pkg_postinst() {
@@ -110,4 +114,11 @@ pkg_postinst() {
 	elog "please use pymol config settings"
 	elog "\t set use_shaders, 1"
 	distutils_pkg_postinst
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
 }