HEAD fixes

(Portage version: 2.2_rc67/git/Linux x86_64)
 (Signed Manifest commit)

13 files changed, 65 insertions, 163 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 8eae91ff8..d36fe60d0 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,17 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  11 May 2010; Justin Lecher <jlec@gentoo.org>
+  -files/1.2.1/nosplash-gentoo.patch,
+  -files/1.2.1/pymol-1.2.1-data-path.patch,
+  -files/1.2.1/pymol-1.2.1-shaders.patch,
+  -files/1.2.2/pymol-1.2.2-data-path.patch,
+  -files/pymol-1.2.2-data-path.patch, -files/1.2.2/nosplash-gentoo.patch,
+  -files/1.2.2/pymol-1.2.2-shaders.patch, -files/pymol-1.2.2-shaders.patch,
+  pymol-9999.ebuild, +files/pymol-9999-prefix.patch,
+  files/nosplash-gentoo.patch:
+  HAED fixes
+
   30 Mar 2010; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
   Importet tree changes
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index a9f83af21..64ee49ec5 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,26 +1,19 @@
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 Hash: SHA1
 
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 AUX pymol-9999-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8
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 AUX pymol-9999-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
 EBUILD pymol-0.99_rc10.ebuild 2128 RMD160 5f3df016d404f36bb7bb198e25b760448d1c7b86 SHA1 b0bfd0ba6b79b1163f3cab71c35f63f70c031076 SHA256 f05e0b871df5b0443c09eed26779218a64cd68db509bddf988d7224f5f7665c1
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diff --git a/sci-chemistry/pymol/files/1.2.1/nosplash-gentoo.patch b/sci-chemistry/pymol/files/1.2.1/nosplash-gentoo.patch
deleted file mode 100644
index 3125b2856..000000000
--- a/sci-chemistry/pymol/files/1.2.1/nosplash-gentoo.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- modules/pymol/invocation.py	2009-06-25 17:26:27.000000000 +0200
-+++ modules/pymol/invocation.py.new	2009-06-25 17:41:57.000000000 +0200
-@@ -395,6 +395,4 @@
-         if loaded_something and (options.after_load_script!=""):
-             options.deferred.append(options.after_load_script)
-         options.deferred.extend(final_actions)
--        if options.show_splash and not options.no_gui and not restricted:
--            options.deferred.insert(0,"_do__ cmd.splash(1)")
-         
diff --git a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch
deleted file mode 100644
index 86c3fe1f1..000000000
--- a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-data-path.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/commanding.py
---- pymol/modules/pymol/commanding.py	2009-03-31 12:43:14.585834066 +0200
-+++ pymol.new/modules/pymol/commanding.py	2009-03-31 12:44:26.436354330 +0200
-@@ -219,11 +219,11 @@
-                 _self.unlock(0,_self)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
-diff -arNu -uarN pymol/modules/pymol/importing.py pymol.new/modules/pymol/importing.py
---- pymol/modules/pymol/importing.py	2009-03-31 12:43:14.546250540 +0200
-+++ pymol.new/modules/pymol/importing.py	2009-03-31 12:44:48.876657949 +0200
-@@ -191,7 +191,7 @@
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb' }
-         
diff --git a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch b/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch
deleted file mode 100644
index 06f756823..000000000
--- a/sci-chemistry/pymol/files/1.2.1/pymol-1.2.1-shaders.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- pymol-1.2_rc1/setup.py.old  2009-07-17 00:05:10.339203020 -0500
-+++ pymol-1.2_rc1/setup.py      2009-07-17 00:09:03.375274561 -0500
-@@ -138,6 +138,7 @@
-                 ("_PYMOL_INLINE",None),
-                 ("_PYMOL_FREETYPE",None),
-                 ("_PYMOL_LIBPNG",None),
-+                ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support   
diff --git a/sci-chemistry/pymol/files/1.2.2/nosplash-gentoo.patch b/sci-chemistry/pymol/files/1.2.2/nosplash-gentoo.patch
deleted file mode 100644
index 3125b2856..000000000
--- a/sci-chemistry/pymol/files/1.2.2/nosplash-gentoo.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- modules/pymol/invocation.py	2009-06-25 17:26:27.000000000 +0200
-+++ modules/pymol/invocation.py.new	2009-06-25 17:41:57.000000000 +0200
-@@ -395,6 +395,4 @@
-         if loaded_something and (options.after_load_script!=""):
-             options.deferred.append(options.after_load_script)
-         options.deferred.extend(final_actions)
--        if options.show_splash and not options.no_gui and not restricted:
--            options.deferred.insert(0,"_do__ cmd.splash(1)")
-         
diff --git a/sci-chemistry/pymol/files/1.2.2/pymol-1.2.2-data-path.patch b/sci-chemistry/pymol/files/1.2.2/pymol-1.2.2-data-path.patch
deleted file mode 100644
index 86c3fe1f1..000000000
--- a/sci-chemistry/pymol/files/1.2.2/pymol-1.2.2-data-path.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/commanding.py
---- pymol/modules/pymol/commanding.py	2009-03-31 12:43:14.585834066 +0200
-+++ pymol.new/modules/pymol/commanding.py	2009-03-31 12:44:26.436354330 +0200
-@@ -219,11 +219,11 @@
-                 _self.unlock(0,_self)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
-diff -arNu -uarN pymol/modules/pymol/importing.py pymol.new/modules/pymol/importing.py
---- pymol/modules/pymol/importing.py	2009-03-31 12:43:14.546250540 +0200
-+++ pymol.new/modules/pymol/importing.py	2009-03-31 12:44:48.876657949 +0200
-@@ -191,7 +191,7 @@
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb' }
-         
diff --git a/sci-chemistry/pymol/files/1.2.2/pymol-1.2.2-shaders.patch b/sci-chemistry/pymol/files/1.2.2/pymol-1.2.2-shaders.patch
deleted file mode 100644
index 7d0c35d83..000000000
--- a/sci-chemistry/pymol/files/1.2.2/pymol-1.2.2-shaders.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- setup.py.old	2009-10-03 01:01:22.444881137 -0500
-+++ setup.py	2009-10-03 01:01:41.580752440 -0500
-@@ -139,7 +139,7 @@
-                 ("_PYMOL_FREETYPE",None),
-                 ("_PYMOL_LIBPNG",None),
- # OpenGL shaders
--#               ("_PYMOL_OPENGL_SHADERS",None),
-+               ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support           
diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
index 3125b2856..89e811dcf 100644
--- a/sci-chemistry/pymol/files/nosplash-gentoo.patch
+++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch
@@ -1,6 +1,8 @@
---- modules/pymol/invocation.py	2009-06-25 17:26:27.000000000 +0200
-+++ modules/pymol/invocation.py.new	2009-06-25 17:41:57.000000000 +0200
-@@ -395,6 +395,4 @@
+Index: modules/pymol/invocation.py
+===================================================================
+--- modules/pymol/invocation.py	(revision 3908)
++++ modules/pymol/invocation.py	(working copy)
+@@ -398,6 +398,4 @@
          if loaded_something and (options.after_load_script!=""):
              options.deferred.append(options.after_load_script)
          options.deferred.extend(final_actions)
diff --git a/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
deleted file mode 100644
index 86c3fe1f1..000000000
--- a/sci-chemistry/pymol/files/pymol-1.2.2-data-path.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/commanding.py
---- pymol/modules/pymol/commanding.py	2009-03-31 12:43:14.585834066 +0200
-+++ pymol.new/modules/pymol/commanding.py	2009-03-31 12:44:26.436354330 +0200
-@@ -219,11 +219,11 @@
-                 _self.unlock(0,_self)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
-diff -arNu -uarN pymol/modules/pymol/importing.py pymol.new/modules/pymol/importing.py
---- pymol/modules/pymol/importing.py	2009-03-31 12:43:14.546250540 +0200
-+++ pymol.new/modules/pymol/importing.py	2009-03-31 12:44:48.876657949 +0200
-@@ -191,7 +191,7 @@
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb' }
-         
diff --git a/sci-chemistry/pymol/files/pymol-1.2.2-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2.2-shaders.patch
deleted file mode 100644
index 06f756823..000000000
--- a/sci-chemistry/pymol/files/pymol-1.2.2-shaders.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- pymol-1.2_rc1/setup.py.old  2009-07-17 00:05:10.339203020 -0500
-+++ pymol-1.2_rc1/setup.py      2009-07-17 00:09:03.375274561 -0500
-@@ -138,6 +138,7 @@
-                 ("_PYMOL_INLINE",None),
-                 ("_PYMOL_FREETYPE",None),
-                 ("_PYMOL_LIBPNG",None),
-+                ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support   
diff --git a/sci-chemistry/pymol/files/pymol-9999-prefix.patch b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
new file mode 100644
index 000000000..211881435
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
@@ -0,0 +1,31 @@
+diff --git a/setup.py b/setup.py
+index 197f827..b39c129 100644
+--- a/setup.py
++++ b/setup.py
+@@ -112,7 +112,7 @@ elif sys.platform=='darwin':
+                     ]
+         ext_comp_args=[]
+         ext_link_args=[
+-	               "-L/usr/X11R6/lib", "-lGL", "-lXxf86vm",
++	               "-L@GENTOO_PORTAGE_EPREFIX@/usr/lib", "-lGL", "-lXxf86vm",
+                    "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
+                    ]
+ #============================================================================
+@@ -120,7 +120,7 @@ else: # linux or other unix
+     inc_dirs=["ov/src",
+               "layer0","layer1","layer2",
+               "layer3","layer4","layer5",
+-              "/usr/include/freetype2",
++              "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2",
+ #                 "/users/warren/ext/include",
+ # VMD plugin support
+ #              "contrib/uiuc/plugins/include",
+@@ -131,7 +131,7 @@ else: # linux or other unix
+           ]	
+     pyogl_libs = ["GL","GLU","glut"]
+     lib_dirs=[
+-        "/usr/X11R6/lib",
++        "@GENTOO_PORTAGE_EPREFIX@/usr/lib",
+ #        "/users/warren/pymol/ext/lib"
+         ]
+     def_macros=[("_PYMOL_MODULE",None),
diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 7bfef086e..f938474d0 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -17,7 +17,7 @@ SRC_URI=""
 
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
 IUSE="apbs numpy shaders vmd"
 
 DEPEND="
@@ -37,11 +37,10 @@ DEPEND="
 RDEPEND="${DEPEND}"
 RESTRICT_PYTHON_ABIS="3.* 2.4"
 
-
 src_prepare() {
-	epatch "${FILESDIR}"/1.2.2-data-path.patch
+	epatch "${FILESDIR}"/${P}-data-path.patch
 
-	epatch "${FILESDIR}"/1.2.2-prefix.patch && \
+	epatch "${FILESDIR}"/${P}-prefix.patch && \
 	eprefixify setup.py
 
 	# Turn off splash screen.  Please do make a project contribution
@@ -60,15 +59,20 @@ src_prepare() {
 
 	use vmd && \
 		sed \
-			-e 's:\] + 0 \* \[:] + 1 * [:g' \
-			-e '/contrib\/uiuc\/plugins/s:^#::g' \
-			-e '/PYMOL_VMD_PLUGINS/s:^#::g' \
+			-e '/PYMOL_VMD/s:^#::g' \
+			-e 's:    ] + 0 * [:    ] + 1 * [:g' \
 			-i setup.py
 
 	use numpy && \
 		sed \
 			-e '/PYMOL_NUMPY/s:^#::g' \
 			-i setup.py
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	# python 3.* fix
+	# sed '452,465d' -i setup.py
+	distutils_src_prepare
 }
 
 src_configure() {