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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2011-04-04 11:18 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2011-04-04 11:18 UTC (permalink / raw
  To: gentoo-commits

commit:     5bfc2f1fa057d2311f57dc3528fd45e2b177e49c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  4 11:13:06 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  4 11:13:06 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5bfc2f1f

Fix to latest head

(Portage version: 2.2.0_alpha29/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/pymol/ChangeLog                      |    6 ++-
 sci-chemistry/pymol/files/9999-vmd.patch           |   36 ++++++++++
 sci-chemistry/pymol/files/pymol-9999-shaders.patch |   73 +++++++++++++++++---
 sci-chemistry/pymol/metadata.xml                   |    1 -
 sci-chemistry/pymol/pymol-9999.ebuild              |   46 ++++++------
 5 files changed, 126 insertions(+), 36 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index ad6be4e..256d96c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/pymol
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/9999-vmd.patch,
+  pymol-9999.ebuild, files/pymol-9999-shaders.patch, metadata.xml:
+  Fix to latest head
+
   12 Nov 2010; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
   Synchonized with tree ebuild
 

diff --git a/sci-chemistry/pymol/files/9999-vmd.patch b/sci-chemistry/pymol/files/9999-vmd.patch
new file mode 100644
index 0000000..2fd909f
--- /dev/null
+++ b/sci-chemistry/pymol/files/9999-vmd.patch
@@ -0,0 +1,36 @@
+ setup.py |    8 ++++----
+ 1 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index b0f4dad..4ec5145 100644
+--- a/setup.py
++++ b/setup.py
+@@ -132,8 +132,8 @@ else: # linux or other unix
+               "/usr/include/freetype2",
+ #                 "/users/warren/ext/include",
+ # VMD plugin support
+-#              "contrib/uiuc/plugins/include",
+-#              "contrib/uiuc/plugins/molfile_plugin/src",
++              "contrib/uiuc/plugins/include",
++              "contrib/uiuc/plugins/molfile_plugin/src",
+               "modules/cealign/src",
+ 	      "modules/cealign/src/tnt", ]
+     libs=["GL","GLU","glut","png","z","freetype", "GLEW",
+@@ -153,7 +153,7 @@ else: # linux or other unix
+ # Numeric Python support                    
+ #                ("_PYMOL_NUMPY",None),
+ # VMD plugin support           
+-#               ("_PYMOL_VMD_PLUGINS",None)
++               ("_PYMOL_VMD_PLUGINS",None),
+ 		("NO_MMLIBS",None),
+                 ]
+     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
+@@ -307,7 +307,7 @@ setup ( # Distribution meta-data
+     "layer5/main.c"
+ # VMD plugin support
+     # switch the 0 to 1 to activate the additional source code
+-    ] + 0 * [
++    ] + 1 * [
+ # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
+     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
+     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',

diff --git a/sci-chemistry/pymol/files/pymol-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
index 7f4a24f..853ebff 100644
--- a/sci-chemistry/pymol/files/pymol-9999-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
@@ -1,11 +1,62 @@
-diff -uarN pymol-9999.orig/setup.py pymol-9999/setup.py
---- pymol-9999.orig/setup.py	2008-06-18 11:47:58.000000000 +0200
-+++ pymol-9999/setup.py	2008-06-18 11:48:52.000000000 +0200
-@@ -143,6 +143,7 @@
-     def_macros=[("_PYMOL_MODULE",None),
-                     ("_PYMOL_INLINE",None),
-                     ("_PYMOL_FREETYPE",None),
-+                    ("_PYMOL_OPENGL_SHADERS",None),
- # Numeric Python support                    
- #                        ("_PYMOL_NUMPY",None),
- # VMD plugin support                    
+ layer0/ShaderMgr.c |   16 ++++++++--------
+ layer1/Setting.c   |    2 +-
+ 2 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
+index 929167f..ecb4130 100644
+--- a/layer0/ShaderMgr.c
++++ b/layer0/ShaderMgr.c
+@@ -386,7 +386,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
+ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+   FILE* f;
+   long size;
+-  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
++  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
+ 
+   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
+     "CShaderMgr_ReadShaderFromDisk: fileName='%s'\n", fileName
+@@ -398,16 +398,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+     return NULL;
+   }
+   
+-  pymol_path = getenv("PYMOL_PATH");
+-  if (!pymol_path){
++  pymol_data = getenv("PYMOL_DATA");
++  if (!pymol_data){
+     PRINTFB(G, FB_ShaderMgr, FB_Warnings)
+-      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
++      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
+     return NULL;
+   }
+   /* make this a setting */
+-  shader_path = "/data/shaders/";
+-  fullFile = malloc( sizeof(char) * (strlen(pymol_path)+strlen(shader_path)+strlen(fileName)+1));
+-  fullFile = strcpy(fullFile, pymol_path);
++  shader_path = "/shaders/";
++  fullFile = malloc( sizeof(char) * (strlen(pymol_data)+strlen(shader_path)+strlen(fileName)+1));
++  fullFile = strcpy(fullFile, pymol_data);
+   fullFile = strcat(fullFile, shader_path);
+   fullFile = strcat(fullFile, fileName);
+ 
+@@ -416,7 +416,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+ 
+   if (!f) {
+     PRINTFB(G, FB_ShaderMgr, FB_Errors)
+-      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_PATH='%s'\n", fullFile, pymol_path ENDFB(G);
++      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_DATA='%s'\n", fullFile, pymol_data ENDFB(G);
+     return NULL;
+   } else {
+     PRINTFB(G, FB_ShaderMgr, FB_Blather)
+diff --git a/layer1/Setting.c b/layer1/Setting.c
+index 3aa0b8d..f9b5789 100644
+--- a/layer1/Setting.c
++++ b/layer1/Setting.c
+@@ -3956,7 +3956,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
+     set_b(I, cSetting_line_use_shader, 1);
+     set_b(I, cSetting_sphere_use_shader, 1);
+     set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */
+-    set_s(I, cSetting_shader_path, "data/shaders");
++    set_s(I, cSetting_shader_path, "shaders");
+     set_i(I, cSetting_volume_bit_depth, 8);
+     set_color(I, cSetting_volume_color, "-1");
+     set_f(I, cSetting_volume_layers, 256);

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index cc50a5b..ad86c00 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -6,7 +6,6 @@
 </maintainer>
 <use>
   <flag name='apbs'>Pymol supprt for sci-chemistry/apbs</flag>
-  <flag name='shaders'>Enable shaders support for Pymol</flag>
   <flag name='numpy'>Enable numpy support for Pymol</flag>
   <flag name='vmd'>Builds molfile plugin support</flag>
 </use>

diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 0fda201..38477a3 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.2.3-r1.ebuild,v 1.3 2010/03/23 13:54:53 fauli Exp $
+# $Header: $
 
 EAPI="3"
 
@@ -11,37 +11,39 @@ PYTHON_USE_WITH="tk"
 PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
 
 
-inherit eutils distutils prefix subversion
-
-ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
+inherit eutils distutils prefix subversion versionator
 
 DESCRIPTION="A Python-extensible molecular graphics system."
 HOMEPAGE="http://pymol.sourceforge.net/"
 SRC_URI=""
+ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
 
 LICENSE="PSF-2.2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy shaders vmd"
+IUSE="apbs numpy vmd"
 
 DEPEND="
-		dev-python/numpy
-		dev-python/pmw
-		media-libs/freetype:2
-		media-libs/libpng
-		media-video/mpeg-tools
-		sys-libs/zlib
-		media-libs/freeglut
-		apbs? (
-			dev-libs/maloc
-			sci-chemistry/apbs
-			sci-chemistry/pdb2pqr
-			sci-chemistry/pymol-apbs-plugin
-		)"
+	dev-python/numpy
+	dev-python/pmw
+	media-libs/freetype:2
+	media-libs/glew
+	media-libs/libpng
+	media-video/mpeg-tools
+	sys-libs/zlib
+	media-libs/freeglut
+	apbs? (
+		dev-libs/maloc
+		sci-chemistry/apbs
+		sci-chemistry/pdb2pqr
+		sci-chemistry/pymol-apbs-plugin
+	)"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-data-path.patch
+	epatch \
+		"${FILESDIR}"/${P}-data-path.patch \
+		"${FILESDIR}"/${P}-shaders.patch
 
 	epatch "${FILESDIR}"/${P}-prefix.patch && \
 	eprefixify setup.py
@@ -55,9 +57,7 @@ src_prepare() {
 		-e "s:\(ext_comp_args=\).*:\1[]:g" \
 		"${S}"/setup.py || die "Failed running sed on setup.py"
 
-	use shaders && epatch "${FILESDIR}"/${PN}-1.2.2-shaders.patch
-
-	use vmd && epatch "${FILESDIR}"/1.3.0-vmd.patch
+	use vmd && epatch "${FILESDIR}"/${PV}-vmd.patch
 
 	use numpy && \
 		sed \



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2011-04-28  7:58 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2011-04-28  7:58 UTC (permalink / raw
  To: gentoo-commits

commit:     756d482a75f4c7d7b22f8d83d0fbf3ee42f8f6ef
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 28 07:58:28 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 28 07:58:28 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=756d482a

Fixed patches for current HEAD

(Portage version: 2.2.0_alpha30/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/pymol/ChangeLog                      |    3 ++
 sci-chemistry/pymol/files/pymol-9999-shaders.patch |   32 ++++++++-----------
 2 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 256d96c..d4ba19a 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Apr 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-shaders.patch:
+  Fixed patches for current HEAD
+
   04 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/9999-vmd.patch,
   pymol-9999.ebuild, files/pymol-9999-shaders.patch, metadata.xml:
   Fix to latest head

diff --git a/sci-chemistry/pymol/files/pymol-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
index 853ebff..2caac2d 100644
--- a/sci-chemistry/pymol/files/pymol-9999-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
@@ -1,12 +1,8 @@
- layer0/ShaderMgr.c |   16 ++++++++--------
- layer1/Setting.c   |    2 +-
- 2 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
-index 929167f..ecb4130 100644
---- a/layer0/ShaderMgr.c
-+++ b/layer0/ShaderMgr.c
-@@ -386,7 +386,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
+Index: layer0/ShaderMgr.c
+===================================================================
+--- layer0/ShaderMgr.c	(revision 3945)
++++ layer0/ShaderMgr.c	(working copy)
+@@ -400,7 +400,7 @@
  char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
    FILE* f;
    long size;
@@ -15,7 +11,7 @@ index 929167f..ecb4130 100644
  
    PRINTFB(G, FB_ShaderMgr, FB_Debugging)
      "CShaderMgr_ReadShaderFromDisk: fileName='%s'\n", fileName
-@@ -398,16 +398,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+@@ -412,16 +412,16 @@
      return NULL;
    }
    
@@ -24,8 +20,8 @@ index 929167f..ecb4130 100644
 +  pymol_data = getenv("PYMOL_DATA");
 +  if (!pymol_data){
      PRINTFB(G, FB_ShaderMgr, FB_Warnings)
--      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
-+      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
+-      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n", fileName ENDFB(G);
++      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n", fileName ENDFB(G);
      return NULL;
    }
    /* make this a setting */
@@ -38,7 +34,7 @@ index 929167f..ecb4130 100644
    fullFile = strcat(fullFile, shader_path);
    fullFile = strcat(fullFile, fileName);
  
-@@ -416,7 +416,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+@@ -430,7 +430,7 @@
  
    if (!f) {
      PRINTFB(G, FB_ShaderMgr, FB_Errors)
@@ -47,11 +43,11 @@ index 929167f..ecb4130 100644
      return NULL;
    } else {
      PRINTFB(G, FB_ShaderMgr, FB_Blather)
-diff --git a/layer1/Setting.c b/layer1/Setting.c
-index 3aa0b8d..f9b5789 100644
---- a/layer1/Setting.c
-+++ b/layer1/Setting.c
-@@ -3956,7 +3956,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
+Index: layer1/Setting.c
+===================================================================
+--- layer1/Setting.c	(revision 3945)
++++ layer1/Setting.c	(working copy)
+@@ -3990,7 +3990,7 @@
      set_b(I, cSetting_line_use_shader, 1);
      set_b(I, cSetting_sphere_use_shader, 1);
      set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2011-06-12 10:53 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2011-06-12 10:53 UTC (permalink / raw
  To: gentoo-commits

commit:     b39098ce755dff73d9a6427441bc56aed6847e66
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun  2 08:44:51 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun  2 08:44:51 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b39098ce

Fix collision with dev-python/webpy, #368947

(Portage version: 2.2.0_alpha37/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/pymol/ChangeLog            |    8 ++++++++
 sci-chemistry/pymol/files/9999-web.patch |   19 +++++++++++++++++++
 sci-chemistry/pymol/metadata.xml         |    7 ++++---
 sci-chemistry/pymol/pymol-9999.ebuild    |    7 +++++--
 4 files changed, 36 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index d4ba19a..e3f6e08 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/9999-web.patch,
+  pymol-9999.ebuild, metadata.xml:
+  Fix collision with dev-python/webpy, #368947
+
+  02 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/9999-web.patch,
+  pymol-9999.ebuild:
+  Fix collision with dev-python/webpy, #368947
+
   28 Apr 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-shaders.patch:
   Fixed patches for current HEAD
 

diff --git a/sci-chemistry/pymol/files/9999-web.patch b/sci-chemistry/pymol/files/9999-web.patch
new file mode 100644
index 0000000..2d6957d
--- /dev/null
+++ b/sci-chemistry/pymol/files/9999-web.patch
@@ -0,0 +1,19 @@
+ setup.py |    5 +----
+ 1 files changed, 1 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index b0f4dad..94d292d 100644
+--- a/setup.py
++++ b/setup.py
+@@ -180,10 +180,7 @@ setup ( # Distribution meta-data
+                 'pymol/opengl/gl',
+                 'pymol/opengl/glu',
+                 'pymol/opengl/glut',
+-                'pymol/wizard',
+-		'web',
+-		'web/examples',
+-		'web/javascript', ],
++                'pymol/wizard', ],
+ 	ext_modules = [
+     Extension("pymol._cmd", [
+     "modules/cealign/src/ccealignmodule.cpp",

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index ad86c00..58b73ca 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -5,8 +5,9 @@
   <email>jlec@gentoo.org</email>
 </maintainer>
 <use>
-  <flag name='apbs'>Pymol supprt for sci-chemistry/apbs</flag>
-  <flag name='numpy'>Enable numpy support for Pymol</flag>
-  <flag name='vmd'>Builds molfile plugin support</flag>
+	<flag name='apbs'>Pymol supprt for sci-chemistry/apbs</flag>
+	<flag name='numpy'>Enable numpy support for Pymol</flag>
+	<flag name='vmd'>Builds molfile plugin support</flag>
+	<flag name="web">Install Pymodule needed for web app support</flag>
 </use>
 </pkgmetadata>

diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 14ff467..53f9bb2 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -20,7 +20,7 @@ ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
 LICENSE="PSF-2.2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="apbs numpy vmd"
+IUSE="apbs numpy vmd web"
 
 DEPEND="
 	dev-python/numpy
@@ -36,7 +36,8 @@ DEPEND="
 		sci-chemistry/apbs
 		sci-chemistry/pdb2pqr
 		sci-chemistry/pymol-apbs-plugin
-	)"
+	)
+	web? ( !dev-python/webpy )"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
@@ -44,6 +45,8 @@ src_prepare() {
 		"${FILESDIR}"/${P}-data-path.patch \
 		"${FILESDIR}"/${P}-shaders.patch
 
+	use web || epatch "${FILESDIR}"/${PV}-web.patch
+
 	epatch "${FILESDIR}"/${P}-prefix.patch && \
 	eprefixify setup.py
 



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2011-08-15 15:55 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2011-08-15 15:55 UTC (permalink / raw
  To: gentoo-commits

commit:     d5fe6f9794ab6175d9b31e6f98af156ca81a42f4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 22 07:19:08 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jul 22 07:19:08 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d5fe6f97

Grap some fedora stuff, fix shadrers patch for current head

(Portage version: 2.2.0_alpha46/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/pymol/ChangeLog                      |    5 +++
 .../pymol/files/pymol-9999-setup.py.patch          |   24 +++++++++++++++
 sci-chemistry/pymol/files/pymol-9999-shaders.patch |   32 +++++++++++--------
 sci-chemistry/pymol/metadata.xml                   |   20 ++++++------
 sci-chemistry/pymol/pymol-9999.ebuild              |   10 ++----
 5 files changed, 60 insertions(+), 31 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index e3f6e08..b007111 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  22 Jul 2011; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  +files/pymol-9999-setup.py.patch, files/pymol-9999-shaders.patch,
+  metadata.xml:
+  Grap some fedora stuff, fix shadrers patch for current head
+
   02 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/9999-web.patch,
   pymol-9999.ebuild, metadata.xml:
   Fix collision with dev-python/webpy, #368947

diff --git a/sci-chemistry/pymol/files/pymol-9999-setup.py.patch b/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
new file mode 100644
index 0000000..1267b96
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
@@ -0,0 +1,24 @@
+ setup.py |    3 ++-
+ 1 files changed, 2 insertions(+), 1 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index b0f4dad..8c82722 100644
+--- a/setup.py
++++ b/setup.py
+@@ -156,7 +156,7 @@ else: # linux or other unix
+ #               ("_PYMOL_VMD_PLUGINS",None)
+ 		("NO_MMLIBS",None),
+                 ]
+-    ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
++    ext_comp_args=[]
+     ext_link_args=[]
+   
+ setup ( # Distribution meta-data
+@@ -174,6 +174,7 @@ setup ( # Distribution meta-data
+                 'pmg_tk/skins',
+                 'pmg_tk/skins/normal',                    
+                 'pmg_wx',
++                'pymol2',
+                 'pymol',
+                 'pymol/contrib',                
+                 'pymol/opengl',

diff --git a/sci-chemistry/pymol/files/pymol-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
index 2caac2d..a20bfe3 100644
--- a/sci-chemistry/pymol/files/pymol-9999-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
@@ -1,8 +1,12 @@
-Index: layer0/ShaderMgr.c
-===================================================================
---- layer0/ShaderMgr.c	(revision 3945)
-+++ layer0/ShaderMgr.c	(working copy)
-@@ -400,7 +400,7 @@
+ layer0/ShaderMgr.c |   16 ++++++++--------
+ layer1/Setting.c   |    2 +-
+ 2 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
+index 4658b96..092aac8 100644
+--- a/layer0/ShaderMgr.c
++++ b/layer0/ShaderMgr.c
+@@ -416,7 +416,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
  char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
    FILE* f;
    long size;
@@ -11,7 +15,7 @@ Index: layer0/ShaderMgr.c
  
    PRINTFB(G, FB_ShaderMgr, FB_Debugging)
      "CShaderMgr_ReadShaderFromDisk: fileName='%s'\n", fileName
-@@ -412,16 +412,16 @@
+@@ -428,16 +428,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
      return NULL;
    }
    
@@ -20,8 +24,8 @@ Index: layer0/ShaderMgr.c
 +  pymol_data = getenv("PYMOL_DATA");
 +  if (!pymol_data){
      PRINTFB(G, FB_ShaderMgr, FB_Warnings)
--      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n", fileName ENDFB(G);
-+      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n", fileName ENDFB(G);
+-      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n" ENDFB(G);
++      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n" ENDFB(G);
      return NULL;
    }
    /* make this a setting */
@@ -34,7 +38,7 @@ Index: layer0/ShaderMgr.c
    fullFile = strcat(fullFile, shader_path);
    fullFile = strcat(fullFile, fileName);
  
-@@ -430,7 +430,7 @@
+@@ -446,7 +446,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
  
    if (!f) {
      PRINTFB(G, FB_ShaderMgr, FB_Errors)
@@ -43,11 +47,11 @@ Index: layer0/ShaderMgr.c
      return NULL;
    } else {
      PRINTFB(G, FB_ShaderMgr, FB_Blather)
-Index: layer1/Setting.c
-===================================================================
---- layer1/Setting.c	(revision 3945)
-+++ layer1/Setting.c	(working copy)
-@@ -3990,7 +3990,7 @@
+diff --git a/layer1/Setting.c b/layer1/Setting.c
+index 29b6bc5..2a70835 100644
+--- a/layer1/Setting.c
++++ b/layer1/Setting.c
+@@ -3991,7 +3991,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
      set_b(I, cSetting_line_use_shader, 1);
      set_b(I, cSetting_sphere_use_shader, 1);
      set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 58b73ca..1a70ddc 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
-<use>
-	<flag name='apbs'>Pymol supprt for sci-chemistry/apbs</flag>
-	<flag name='numpy'>Enable numpy support for Pymol</flag>
-	<flag name='vmd'>Builds molfile plugin support</flag>
-	<flag name="web">Install Pymodule needed for web app support</flag>
-</use>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</maintainer>
+	<use>
+		<flag name="apbs">Pymol supprt for sci-chemistry/apbs</flag>
+		<flag name="numpy">Enable numpy support for Pymol</flag>
+		<flag name="vmd">Builds molfile plugin support</flag>
+		<flag name="web">Install Pymodule needed for web app support</flag>
+	</use>
 </pkgmetadata>

diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 62a7a60..edfdbf2 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -43,22 +43,18 @@ RDEPEND="${DEPEND}"
 src_prepare() {
 	epatch \
 		"${FILESDIR}"/${P}-data-path.patch \
-		"${FILESDIR}"/${P}-shaders.patch
+		"${FILESDIR}"/${P}-shaders.patch \
+		"${FILESDIR}"/${P}-setup.py.patch
 
 	use web || epatch "${FILESDIR}"/${PV}-web.patch
 
 	epatch "${FILESDIR}"/${P}-prefix.patch && \
-	eprefixify setup.py
+		eprefixify setup.py
 
 	# Turn off splash screen.  Please do make a project contribution
 	# if you are able though. #299020
 	epatch "${FILESDIR}"/nosplash-gentoo.patch
 
-	# Respect CFLAGS
-	sed -i \
-		-e "s:\(ext_comp_args=\).*:\1[]:g" \
-		"${S}"/setup.py || die "Failed running sed on setup.py"
-
 	use vmd && epatch "${FILESDIR}"/${PV}-vmd.patch
 
 	use numpy && \



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2011-08-26 16:01 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2011-08-26 16:01 UTC (permalink / raw
  To: gentoo-commits

commit:     7b50469d9a21a586cfb76f7b4fc21937379bc1b0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 18 10:10:06 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Aug 18 10:10:06 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7b50469d

Fixed patches

(Portage version: 2.2.0_alpha51/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/pymol/ChangeLog                      |    4 ++
 sci-chemistry/pymol/files/pymol-9999-prefix.patch  |   33 ++++++++++++-------
 sci-chemistry/pymol/files/pymol-9999-shaders.patch |   32 ++++++++-----------
 3 files changed, 39 insertions(+), 30 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index b007111..e830989 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Aug 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-prefix.patch,
+  files/pymol-9999-shaders.patch:
+  Fixed patches
+
   22 Jul 2011; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
   +files/pymol-9999-setup.py.patch, files/pymol-9999-shaders.patch,
   metadata.xml:

diff --git a/sci-chemistry/pymol/files/pymol-9999-prefix.patch b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
index 2118814..d417d97 100644
--- a/sci-chemistry/pymol/files/pymol-9999-prefix.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
@@ -1,17 +1,26 @@
-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':
+Index: setup.py
+===================================================================
+--- setup.py	(revision 3963)
++++ setup.py	(working copy)
+@@ -101,7 +101,7 @@
+         #
+         # REMEMEBER to use "./ext/bin/python ..."
+         #
+-        EXT = os.getcwd()+"/ext"
++        EXT = "@GENTOO_PORTAGE_EPREFIX@/usr"
+         inc_dirs=["ov/src",
+                   "layer0","layer1","layer2",
+                   "layer3","layer4","layer5", 
+@@ -121,7 +121,7 @@
                      ]
          ext_comp_args=[]
          ext_link_args=[
--	               "-L/usr/X11R6/lib", "-lGL", "-lXxf86vm",
-+	               "-L@GENTOO_PORTAGE_EPREFIX@/usr/lib", "-lGL", "-lXxf86vm",
+-	               "-L/usr/X11R6/lib64", "-lGL", "-lXxf86vm",
++	               "-lGL", "-lXxf86vm",
                     "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
                     ]
  #============================================================================
-@@ -120,7 +120,7 @@ else: # linux or other unix
+@@ -129,7 +129,7 @@
      inc_dirs=["ov/src",
                "layer0","layer1","layer2",
                "layer3","layer4","layer5",
@@ -20,12 +29,12 @@ index 197f827..b39c129 100644
  #                 "/users/warren/ext/include",
  # VMD plugin support
  #              "contrib/uiuc/plugins/include",
-@@ -131,7 +131,7 @@ else: # linux or other unix
+@@ -141,7 +141,7 @@
            ]	
-     pyogl_libs = ["GL","GLU","glut"]
+     pyogl_libs = ["GL","GLU","glut", "GLEW"]
      lib_dirs=[
--        "/usr/X11R6/lib",
-+        "@GENTOO_PORTAGE_EPREFIX@/usr/lib",
+-        "/usr/X11R6/lib64",
++        "@GENTOO_PORTAGE_EPREFIX@/usr/usr/X11R6/lib",
  #        "/users/warren/pymol/ext/lib"
          ]
      def_macros=[("_PYMOL_MODULE",None),

diff --git a/sci-chemistry/pymol/files/pymol-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
index a20bfe3..8517ebe 100644
--- a/sci-chemistry/pymol/files/pymol-9999-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
@@ -1,27 +1,23 @@
- layer0/ShaderMgr.c |   16 ++++++++--------
- layer1/Setting.c   |    2 +-
- 2 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
-index 4658b96..092aac8 100644
---- a/layer0/ShaderMgr.c
-+++ b/layer0/ShaderMgr.c
-@@ -416,7 +416,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
+Index: layer0/ShaderMgr.c
+===================================================================
+--- layer0/ShaderMgr.c	(revision 3963)
++++ layer0/ShaderMgr.c	(working copy)
+@@ -416,7 +416,7 @@
  char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
    FILE* f;
    long size;
 -  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
 +  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
+   size_t res;
  
    PRINTFB(G, FB_ShaderMgr, FB_Debugging)
-     "CShaderMgr_ReadShaderFromDisk: fileName='%s'\n", fileName
-@@ -428,16 +428,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+@@ -429,16 +429,16 @@
      return NULL;
    }
    
 -  pymol_path = getenv("PYMOL_PATH");
 -  if (!pymol_path){
-+  pymol_data = getenv("PYMOL_DATA");
++  pymol_path = getenv("PYMOL_DATA");
 +  if (!pymol_data){
      PRINTFB(G, FB_ShaderMgr, FB_Warnings)
 -      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n" ENDFB(G);
@@ -38,7 +34,7 @@ index 4658b96..092aac8 100644
    fullFile = strcat(fullFile, shader_path);
    fullFile = strcat(fullFile, fileName);
  
-@@ -446,7 +446,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+@@ -447,7 +447,7 @@
  
    if (!f) {
      PRINTFB(G, FB_ShaderMgr, FB_Errors)
@@ -47,11 +43,11 @@ index 4658b96..092aac8 100644
      return NULL;
    } else {
      PRINTFB(G, FB_ShaderMgr, FB_Blather)
-diff --git a/layer1/Setting.c b/layer1/Setting.c
-index 29b6bc5..2a70835 100644
---- a/layer1/Setting.c
-+++ b/layer1/Setting.c
-@@ -3991,7 +3991,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
+Index: layer1/Setting.c
+===================================================================
+--- layer1/Setting.c	(revision 3963)
++++ layer1/Setting.c	(working copy)
+@@ -3991,7 +3991,7 @@
      set_b(I, cSetting_line_use_shader, 1);
      set_b(I, cSetting_sphere_use_shader, 1);
      set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2011-08-31 10:05 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2011-08-31 10:05 UTC (permalink / raw
  To: gentoo-commits

commit:     8b78270e241be7c137bc274fc0ed20918dd616b1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 29 15:09:01 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Aug 29 15:09:01 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8b78270e

Latest changes on HEAD

(Portage version: 2.2.0_alpha51/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/pymol/ChangeLog                      |    3 +++
 sci-chemistry/pymol/files/pymol-9999-shaders.patch |    2 +-
 2 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index e830989..5560aa7 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Aug 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-shaders.patch:
+  Latest changes on HEAD
+
   18 Aug 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-prefix.patch,
   files/pymol-9999-shaders.patch:
   Fixed patches

diff --git a/sci-chemistry/pymol/files/pymol-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
index 8517ebe..f8a762c 100644
--- a/sci-chemistry/pymol/files/pymol-9999-shaders.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
@@ -17,7 +17,7 @@ Index: layer0/ShaderMgr.c
    
 -  pymol_path = getenv("PYMOL_PATH");
 -  if (!pymol_path){
-+  pymol_path = getenv("PYMOL_DATA");
++  pymol_data = getenv("PYMOL_DATA");
 +  if (!pymol_data){
      PRINTFB(G, FB_ShaderMgr, FB_Warnings)
 -      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n" ENDFB(G);



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2011-12-06 16:35 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2011-12-06 16:35 UTC (permalink / raw
  To: gentoo-commits

commit:     812ffb36524400002afd40fc6c2f12b4822ec8e9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  5 16:58:47 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  5 16:58:47 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=812ffb36

Fix pymol-9999-setup.py.patch for current HEAD

(Portage version: 2.2.0_alpha79/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/pymol/ChangeLog                      |    3 +++
 .../pymol/files/pymol-9999-setup.py.patch          |   17 +++++++----------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 5560aa7..0a9b65e 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Dec 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-setup.py.patch:
+  Fix pymol-9999-setup.py.patch for current HEAD
+
   29 Aug 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-shaders.patch:
   Latest changes on HEAD
 

diff --git a/sci-chemistry/pymol/files/pymol-9999-setup.py.patch b/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
index 1267b96..01efe30 100644
--- a/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
@@ -1,20 +1,17 @@
- setup.py |    3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index b0f4dad..8c82722 100644
---- a/setup.py
-+++ b/setup.py
-@@ -156,7 +156,7 @@ else: # linux or other unix
+Index: setup.py
+===================================================================
+--- setup.py	(revision 3972)
++++ setup.py	(working copy)
+@@ -156,7 +156,7 @@
  #               ("_PYMOL_VMD_PLUGINS",None)
  		("NO_MMLIBS",None),
                  ]
--    ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
+-    ext_comp_args=["-ffast-math","-funroll-loops","-O3","-g"]
 +    ext_comp_args=[]
      ext_link_args=[]
    
  setup ( # Distribution meta-data
-@@ -174,6 +174,7 @@ setup ( # Distribution meta-data
+@@ -174,6 +174,7 @@
                  'pmg_tk/skins',
                  'pmg_tk/skins/normal',                    
                  'pmg_wx',



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2012-02-19 12:44 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2012-02-19 12:44 UTC (permalink / raw
  To: gentoo-commits

commit:     b505aeb44d5b3ba28dfb7d949368452d8855ad33
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 13 22:17:17 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 13 22:17:17 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b505aeb4

Update to latest head

(Portage version: 2.2.0_alpha86/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/pymol/ChangeLog                      |   12 ++-
 sci-chemistry/pymol/files/1.3.0-vmd.patch          |   33 -----
 sci-chemistry/pymol/files/9999-vmd.patch           |   36 -----
 sci-chemistry/pymol/files/9999-web.patch           |   19 ---
 sci-chemistry/pymol/files/nosplash-gentoo.patch    |   11 --
 .../pymol/files/pymol-0.99_rc10-data-path.patch    |   64 ---------
 .../pymol/files/pymol-1.2.2-shaders.patch          |   11 --
 .../pymol/files/pymol-9999-data-path.patch         |  137 ++++++++++++++++++--
 sci-chemistry/pymol/files/pymol-9999-flags.patch   |   19 +++
 .../pymol/files/pymol-9999-nosplash.patch          |   15 ++
 sci-chemistry/pymol/files/pymol-9999-prefix.patch  |   69 +++++-----
 .../pymol/files/pymol-9999-setup.py.patch          |   60 ++++++---
 sci-chemistry/pymol/files/pymol-9999-shaders.patch |   58 --------
 sci-chemistry/pymol/files/pymol-9999-vmd.patch     |   36 +++++
 sci-chemistry/pymol/files/pymol-9999-web.patch     |   19 +++
 sci-chemistry/pymol/pymol-9999.ebuild              |   42 ++++---
 16 files changed, 328 insertions(+), 313 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 0a9b65e..8b2e581 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,7 +1,17 @@
 # ChangeLog for sci-chemistry/pymol
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  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,
+  files/pymol-9999-prefix.patch, -files/9999-web.patch,
+  files/pymol-9999-data-path.patch, +files/pymol-9999-nosplash.patch,
+  files/pymol-9999-setup.py.patch, -files/pymol-9999-shaders.patch,
+  +files/pymol-9999-vmd.patch, +files/pymol-9999-web.patch,
+  -files/nosplash-gentoo.patch:
+  Update to latest head
+
   05 Dec 2011; Justin Lecher <jlec@gentoo.org> files/pymol-9999-setup.py.patch:
   Fix pymol-9999-setup.py.patch for current HEAD
 

diff --git a/sci-chemistry/pymol/files/1.3.0-vmd.patch b/sci-chemistry/pymol/files/1.3.0-vmd.patch
deleted file mode 100644
index 0f34a02..0000000
--- a/sci-chemistry/pymol/files/1.3.0-vmd.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3908)
-+++ setup.py	(working copy)
-@@ -130,8 +130,8 @@
-               "/usr/include/freetype2",
- #                 "/users/warren/ext/include",
- # VMD plugin support
--#              "contrib/uiuc/plugins/include",
--#              "contrib/uiuc/plugins/molfile_plugin/src",
-+              "contrib/uiuc/plugins/include",
-+              "contrib/uiuc/plugins/molfile_plugin/src",
-               "modules/cealign/src",
- 	      "modules/cealign/src/tnt", ]
-     libs=["GL","GLU","glut","png","z","freetype",
-@@ -151,7 +151,7 @@
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support           
--#               ("_PYMOL_VMD_PLUGINS",None)
-+               ("_PYMOL_VMD_PLUGINS",None)
-                 ]
-     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
-     ext_link_args=[]
-@@ -299,7 +299,7 @@
-     "layer5/main.c"
- # VMD plugin support
-     # switch the 0 to 1 to activate the additional source code
--    ] + 0 * [
-+    ] + 1 * [
- # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
-     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
-     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',

diff --git a/sci-chemistry/pymol/files/9999-vmd.patch b/sci-chemistry/pymol/files/9999-vmd.patch
deleted file mode 100644
index 2fd909f..0000000
--- a/sci-chemistry/pymol/files/9999-vmd.patch
+++ /dev/null
@@ -1,36 +0,0 @@
- setup.py |    8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index b0f4dad..4ec5145 100644
---- a/setup.py
-+++ b/setup.py
-@@ -132,8 +132,8 @@ else: # linux or other unix
-               "/usr/include/freetype2",
- #                 "/users/warren/ext/include",
- # VMD plugin support
--#              "contrib/uiuc/plugins/include",
--#              "contrib/uiuc/plugins/molfile_plugin/src",
-+              "contrib/uiuc/plugins/include",
-+              "contrib/uiuc/plugins/molfile_plugin/src",
-               "modules/cealign/src",
- 	      "modules/cealign/src/tnt", ]
-     libs=["GL","GLU","glut","png","z","freetype", "GLEW",
-@@ -153,7 +153,7 @@ else: # linux or other unix
- # Numeric Python support                    
- #                ("_PYMOL_NUMPY",None),
- # VMD plugin support           
--#               ("_PYMOL_VMD_PLUGINS",None)
-+               ("_PYMOL_VMD_PLUGINS",None),
- 		("NO_MMLIBS",None),
-                 ]
-     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
-@@ -307,7 +307,7 @@ setup ( # Distribution meta-data
-     "layer5/main.c"
- # VMD plugin support
-     # switch the 0 to 1 to activate the additional source code
--    ] + 0 * [
-+    ] + 1 * [
- # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
-     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
-     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',

diff --git a/sci-chemistry/pymol/files/9999-web.patch b/sci-chemistry/pymol/files/9999-web.patch
deleted file mode 100644
index 2d6957d..0000000
--- a/sci-chemistry/pymol/files/9999-web.patch
+++ /dev/null
@@ -1,19 +0,0 @@
- setup.py |    5 +----
- 1 files changed, 1 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index b0f4dad..94d292d 100644
---- a/setup.py
-+++ b/setup.py
-@@ -180,10 +180,7 @@ setup ( # Distribution meta-data
-                 'pymol/opengl/gl',
-                 'pymol/opengl/glu',
-                 'pymol/opengl/glut',
--                'pymol/wizard',
--		'web',
--		'web/examples',
--		'web/javascript', ],
-+                'pymol/wizard', ],
- 	ext_modules = [
-     Extension("pymol._cmd", [
-     "modules/cealign/src/ccealignmodule.cpp",

diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
deleted file mode 100644
index 89e811d..0000000
--- a/sci-chemistry/pymol/files/nosplash-gentoo.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-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)
--        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/pymol-0.99_rc10-data-path.patch b/sci-chemistry/pymol/files/pymol-0.99_rc10-data-path.patch
deleted file mode 100644
index 286489f..0000000
--- a/sci-chemistry/pymol/files/pymol-0.99_rc10-data-path.patch
+++ /dev/null
@@ -1,64 +0,0 @@
---- pymol-0.99rc8/modules/pymol/commanding.py	2007-04-18 02:11:48.000000000 -0400
-+++ commanding.py	2007-04-24 02:17:53.000000000 -0400
-@@ -129,11 +129,11 @@
-                 unlock(0)
-             r = DEFAULT_SUCCESS
-             if show_splash==1: # generic / open-source
--                png_path = cmd.exp_path("$PYMOL_PATH/data/pymol/splash.png")
-+                png_path = cmd.exp_path("$PYMOL_DATA/pymol/splash.png")
-             elif show_splash==2: # evaluation builds
--                png_path = cmd.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
-+                png_path = cmd.exp_path("$PYMOL_DATA/pymol/epymol.png")
-             else: # incentive builds
--                png_path = cmd.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
-+                png_path = cmd.exp_path("$PYMOL_DATA/pymol/ipymol.png")
-             if os.path.exists(png_path):
-                 cmd.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
-         else:
---- pymol-0.99rc8/modules/pymol/fitting.py	2007-04-18 02:11:48.000000000 -0400
-+++ fitting.py	2007-04-24 02:18:07.000000000 -0400
-@@ -61,7 +61,7 @@
-         r = DEFAULT_ERROR
-         source = selector.process(source)
-         target = selector.process(target)
--        mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
-+        mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
-         if object==None: object=''
-         try:
-             lock()
---- pymol-0.99rc8/modules/pymol/importing.py	2007-04-18 02:11:47.000000000 -0400
-+++ importing.py	2007-04-24 02:18:46.000000000 -0400
-@@ -177,7 +177,7 @@
-         r = DEFAULT_ERROR
-         
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                       'pymol' : 'pymol',
-                       'rgb' : 'rgb' }
- 
---- pymol-0.99rc8/modules/pymol/wizard/mutagenesis.py	2007-04-18 02:11:50.000000000 -0400
-+++ mutagenesis.py	2007-04-24 04:08:44.000000000 -0400
-@@ -35,8 +35,8 @@
- 
-         self.dep = default_dep
- 
--        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
-+        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_ind.pkl")
-         self.load_library()
-         self.status = 0 # 0 no selection, 1 mutagenizing
-         self.bump_check = 1
-@@ -108,8 +108,8 @@
-     def load_library(self):
-         if self.dep == 'dep':
-             if not hasattr(self,'dep_library'):
--                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
-+                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_dep.pkl")
-             
-     def set_mode(self,mode):
-         if mode in self.modes:
-

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 7d0c35d..0000000
--- a/sci-chemistry/pymol/files/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/pymol-9999-data-path.patch b/sci-chemistry/pymol/files/pymol-9999-data-path.patch
index 86c3fe1..e865bfd 100644
--- a/sci-chemistry/pymol/files/pymol-9999-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-data-path.patch
@@ -1,7 +1,101 @@
-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 @@
+ layer0/ShaderMgr.c                  |   16 ++++++++--------
+ layer1/Setting.c                    |    2 +-
+ modules/chempy/__init__.py          |    2 +-
+ modules/chempy/tinker/__init__.py   |    2 +-
+ modules/pymol/commanding.py         |    6 +++---
+ modules/pymol/importing.py          |    2 +-
+ modules/pymol/wizard/mutagenesis.py |    4 ++--
+ 7 files changed, 17 insertions(+), 17 deletions(-)
+
+diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
+index cc760ae..364277f 100644
+--- a/layer0/ShaderMgr.c
++++ b/layer0/ShaderMgr.c
+@@ -385,7 +385,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
+ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+   FILE* f;
+   long size;
+-  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
++  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
+   size_t res;
+ 
+   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
+@@ -398,16 +398,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+     return NULL;
+   }
+   
+-  pymol_path = getenv("PYMOL_PATH");
+-  if (!pymol_path){
++  pymol_data = getenv("PYMOL_DATA");
++  if (!pymol_data){
+     PRINTFB(G, FB_ShaderMgr, FB_Warnings)
+-      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n" ENDFB(G);
++      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n" ENDFB(G);
+     return NULL;
+   }
+   /* make this a setting */
+-  shader_path = "/data/shaders/";
+-  fullFile = malloc( sizeof(char) * (strlen(pymol_path)+strlen(shader_path)+strlen(fileName)+1));
+-  fullFile = strcpy(fullFile, pymol_path);
++  shader_path = "/shaders/";
++  fullFile = malloc( sizeof(char) * (strlen(pymol_data)+strlen(shader_path)+strlen(fileName)+1));
++  fullFile = strcpy(fullFile, pymol_data);
+   fullFile = strcat(fullFile, shader_path);
+   fullFile = strcat(fullFile, fileName);
+ 
+@@ -416,7 +416,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+ 
+   if (!f) {
+     PRINTFB(G, FB_ShaderMgr, FB_Errors)
+-      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_PATH='%s'\n", fullFile, pymol_path ENDFB(G);
++      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_DATA='%s'\n", fullFile, pymol_data ENDFB(G);
+     return NULL;
+   } else {
+     PRINTFB(G, FB_ShaderMgr, FB_Blather)
+diff --git a/layer1/Setting.c b/layer1/Setting.c
+index c2b8bbb..4c6fdb7 100644
+--- a/layer1/Setting.c
++++ b/layer1/Setting.c
+@@ -4375,7 +4375,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
+     set_b(I, cSetting_line_use_shader, 1);
+     set_b(I, cSetting_sphere_use_shader, 1);
+     set_b(I, cSetting_use_shaders, 0);
+-    set_s(I, cSetting_shader_path, "data/shaders");
++    set_s(I, cSetting_shader_path, "shaders");
+     set_i(I, cSetting_volume_bit_depth, 8);
+     set_color(I, cSetting_volume_color, "-1");
+     set_f(I, cSetting_volume_layers, 256);
+diff --git a/modules/chempy/__init__.py b/modules/chempy/__init__.py
+index 23dbe45..795a223 100644
+--- a/modules/chempy/__init__.py
++++ b/modules/chempy/__init__.py
+@@ -235,7 +235,7 @@ if os.environ.has_key('CHEMPY_DATA'):  #
+ elif os.environ.has_key('PYMOL_DATA'):
+     path = os.environ['PYMOL_DATA'] + '/chempy/'
+ elif os.environ.has_key('PYMOL_PATH'):
+-    path = os.environ['PYMOL_PATH'] + '/data/chempy/'   
++    path = os.environ['PYMOL_PATH'] + '/chempy/'   
+ elif os.environ.has_key('FREEMOL_MODULES'):
+     path = os.environ['FREEMOL_MODULES'] + '/chempy/'
+ else:
+diff --git a/modules/chempy/tinker/__init__.py b/modules/chempy/tinker/__init__.py
+index a2d8eb1..1e48f81 100644
+--- a/modules/chempy/tinker/__init__.py
++++ b/modules/chempy/tinker/__init__.py
+@@ -147,7 +147,7 @@ else:
+ 
+ if os.environ.has_key('PYMOL_PATH'):
+     pymol_path = os.environ['PYMOL_PATH']
+-    test_path = pymol_path + '/data/chempy/tinker/'
++    test_path = pymol_path + '/chempy/tinker/'
+     if os.path.exists(test_path):
+         params_path = test_path
+ 
+diff --git a/modules/pymol/commanding.py b/modules/pymol/commanding.py
+index 5a202d0..5cb27a6 100644
+--- a/modules/pymol/commanding.py
++++ b/modules/pymol/commanding.py
+@@ -219,11 +219,11 @@ USAGE
                  _self.unlock(0,_self)
              r = DEFAULT_SUCCESS
              if show_splash==1: # generic / open-source
@@ -16,15 +110,38 @@ diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/comma
              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 @@
+diff --git a/modules/pymol/importing.py b/modules/pymol/importing.py
+index 457ace7..7cc2953 100644
+--- a/modules/pymol/importing.py
++++ b/modules/pymol/importing.py
+@@ -191,7 +191,7 @@ SEE ALSO
      '''
          r = DEFAULT_ERROR
          
 -        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
 +        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
                     'pymol' : 'pymol',
-                    'rgb' : 'rgb' }
-         
+                    'rgb' : 'rgb',
+                    'greyscale': 'greyscale' }
+diff --git a/modules/pymol/wizard/mutagenesis.py b/modules/pymol/wizard/mutagenesis.py
+index 8a5250d..6c1b26c 100644
+--- a/modules/pymol/wizard/mutagenesis.py
++++ b/modules/pymol/wizard/mutagenesis.py
+@@ -53,7 +53,7 @@ class Mutagenesis(Wizard):
+         self.dep = default_dep
+ 
+         self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
++                                           "/chempy/sidechains/sc_bb_ind.pkl")
+         self.load_library()
+         self.status = 0 # 0 no selection, 1 mutagenizing
+         self.bump_check = 1
+@@ -218,7 +218,7 @@ class Mutagenesis(Wizard):
+         if self.dep == 'dep':
+             if not hasattr(self,'dep_library'):
+                 self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
++                                           "/chempy/sidechains/sc_bb_dep.pkl")
+             
+     def set_mode(self,mode):
+         cmd=self.cmd

diff --git a/sci-chemistry/pymol/files/pymol-9999-flags.patch b/sci-chemistry/pymol/files/pymol-9999-flags.patch
new file mode 100644
index 0000000..9bdba45
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-flags.patch
@@ -0,0 +1,19 @@
+ setup.py |    5 +----
+ 1 files changed, 1 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 2b6fa35..9c0556d 100755
+--- a/setup.py
++++ b/setup.py
+@@ -197,10 +197,7 @@ else: # linux or other unix
+                    ("_PYMOL_GL_CALLLISTS",None),
+                    ("OPENGL_ES_2",None),
+                    ]
+-    ext_comp_args = [ "-ffast-math",
+-                      "-funroll-loops",
+-                      "-O3",
+-                      "-g" ]
++    ext_comp_args = []
+     ext_link_args = []
+ 
+ 

diff --git a/sci-chemistry/pymol/files/pymol-9999-nosplash.patch b/sci-chemistry/pymol/files/pymol-9999-nosplash.patch
new file mode 100644
index 0000000..b296285
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-nosplash.patch
@@ -0,0 +1,15 @@
+ modules/pymol/invocation.py |    2 --
+ 1 files changed, 0 insertions(+), 2 deletions(-)
+
+diff --git a/modules/pymol/invocation.py b/modules/pymol/invocation.py
+index de47849..c5f4487 100644
+--- a/modules/pymol/invocation.py
++++ b/modules/pymol/invocation.py
+@@ -397,7 +397,5 @@ if __name__=='pymol.invocation':
+         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)")
+         if options.full_screen:
+             options.deferred.append("_do__ full_screen on")

diff --git a/sci-chemistry/pymol/files/pymol-9999-prefix.patch b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
index d417d97..830eb8f 100644
--- a/sci-chemistry/pymol/files/pymol-9999-prefix.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
@@ -1,40 +1,43 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3963)
-+++ setup.py	(working copy)
-@@ -101,7 +101,7 @@
-         #
-         # REMEMEBER to use "./ext/bin/python ..."
-         #
--        EXT = os.getcwd()+"/ext"
-+        EXT = "@GENTOO_PORTAGE_EPREFIX@/usr"
+ 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", 
-@@ -121,7 +121,7 @@
+-                  "/usr/X11R6/include",
++                  "@GENTOO_PORTAGE_EPREFIX@/usr/include",
+                   EXT+"/include",
+                   EXT+"/include/GL",
+                   EXT+"/include/freetype2",
+@@ -120,7 +120,7 @@ elif sys.platform=='darwin':
                      ]
          ext_comp_args=[]
          ext_link_args=[
--	               "-L/usr/X11R6/lib64", "-lGL", "-lXxf86vm",
-+	               "-lGL", "-lXxf86vm",
-                    "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
-                    ]
+-            "-L/usr/X11R6/lib64", "-lGL", "-lXxf86vm",
++            "-L@GENTOO_PORTAGE_EPREFIX@/usr/lib64", "-lGL", "-lXxf86vm",
+             "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
+             ]
  #============================================================================
-@@ -129,7 +129,7 @@
-     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",
-@@ -141,7 +141,7 @@
-           ]	
-     pyogl_libs = ["GL","GLU","glut", "GLEW"]
-     lib_dirs=[
--        "/usr/X11R6/lib64",
-+        "@GENTOO_PORTAGE_EPREFIX@/usr/usr/X11R6/lib",
- #        "/users/warren/pymol/ext/lib"
-         ]
-     def_macros=[("_PYMOL_MODULE",None),
+@@ -159,7 +159,7 @@ else: # linux or other unix
+                  "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
+                    "GLU",
+                    "glut",
+                    "GLEW"]
+-    lib_dirs = [ "/usr/X11R6/lib64", ]
++    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/lib64", ]
+     def_macros = [ ("_PYMOL_MODULE",None),
+                    ("_PYMOL_INLINE",None),
+                    ("_PYMOL_FREETYPE",None),

diff --git a/sci-chemistry/pymol/files/pymol-9999-setup.py.patch b/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
index 01efe30..076d690 100644
--- a/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
@@ -1,21 +1,39 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3972)
-+++ setup.py	(working copy)
-@@ -156,7 +156,7 @@
- #               ("_PYMOL_VMD_PLUGINS",None)
- 		("NO_MMLIBS",None),
-                 ]
--    ext_comp_args=["-ffast-math","-funroll-loops","-O3","-g"]
-+    ext_comp_args=[]
-     ext_link_args=[]
-   
- setup ( # Distribution meta-data
-@@ -174,6 +174,7 @@
-                 'pmg_tk/skins',
-                 'pmg_tk/skins/normal',                    
-                 'pmg_wx',
-+                'pymol2',
-                 'pymol',
-                 'pymol/contrib',                
-                 'pymol/opengl',
+ setup.py |   28 ----------------------------
+ 1 files changed, 0 insertions(+), 28 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 18866a2..705b0c5 100755
+--- a/setup.py
++++ b/setup.py
+@@ -487,31 +487,3 @@ distribution = setup ( # Distribution meta-data
+                   define_macros = def_macros
+                   )
+         ])
+-
+-# make available for setup2.py
+-try:
+-    site_packages = distribution.command_obj['install'].install_libbase
+-except KeyError:
+-    print """
+- Error: Please run, 'setup.py install' not 'setup build' or other variant.
+-
+-"""
+-    sys.exit(2)
+-
+-f = open('setup3.py', 'w')
+-print >> f, 'site_packages =', repr(site_packages)
+-f.close()
+-
+-print '''
+- After running:
+-
+-     python setup.py install
+-     
+- Please run, to complete the installation:
+-
+-     python setup2.py install
+-
+- To uninstall PyMOL, run:
+-
+-     python setup2.py uninstall
+-'''

diff --git a/sci-chemistry/pymol/files/pymol-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch
deleted file mode 100644
index f8a762c..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-shaders.patch
+++ /dev/null
@@ -1,58 +0,0 @@
-Index: layer0/ShaderMgr.c
-===================================================================
---- layer0/ShaderMgr.c	(revision 3963)
-+++ layer0/ShaderMgr.c	(working copy)
-@@ -416,7 +416,7 @@
- char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
-   FILE* f;
-   long size;
--  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
-+  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
-   size_t res;
- 
-   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
-@@ -429,16 +429,16 @@
-     return NULL;
-   }
-   
--  pymol_path = getenv("PYMOL_PATH");
--  if (!pymol_path){
-+  pymol_data = getenv("PYMOL_DATA");
-+  if (!pymol_data){
-     PRINTFB(G, FB_ShaderMgr, FB_Warnings)
--      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n" ENDFB(G);
-+      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n" ENDFB(G);
-     return NULL;
-   }
-   /* make this a setting */
--  shader_path = "/data/shaders/";
--  fullFile = malloc( sizeof(char) * (strlen(pymol_path)+strlen(shader_path)+strlen(fileName)+1));
--  fullFile = strcpy(fullFile, pymol_path);
-+  shader_path = "/shaders/";
-+  fullFile = malloc( sizeof(char) * (strlen(pymol_data)+strlen(shader_path)+strlen(fileName)+1));
-+  fullFile = strcpy(fullFile, pymol_data);
-   fullFile = strcat(fullFile, shader_path);
-   fullFile = strcat(fullFile, fileName);
- 
-@@ -447,7 +447,7 @@
- 
-   if (!f) {
-     PRINTFB(G, FB_ShaderMgr, FB_Errors)
--      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_PATH='%s'\n", fullFile, pymol_path ENDFB(G);
-+      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_DATA='%s'\n", fullFile, pymol_data ENDFB(G);
-     return NULL;
-   } else {
-     PRINTFB(G, FB_ShaderMgr, FB_Blather)
-Index: layer1/Setting.c
-===================================================================
---- layer1/Setting.c	(revision 3963)
-+++ layer1/Setting.c	(working copy)
-@@ -3991,7 +3991,7 @@
-     set_b(I, cSetting_line_use_shader, 1);
-     set_b(I, cSetting_sphere_use_shader, 1);
-     set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */
--    set_s(I, cSetting_shader_path, "data/shaders");
-+    set_s(I, cSetting_shader_path, "shaders");
-     set_i(I, cSetting_volume_bit_depth, 8);
-     set_color(I, cSetting_volume_color, "-1");
-     set_f(I, cSetting_volume_layers, 256);

diff --git a/sci-chemistry/pymol/files/pymol-9999-vmd.patch b/sci-chemistry/pymol/files/pymol-9999-vmd.patch
new file mode 100644
index 0000000..cf47082
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-vmd.patch
@@ -0,0 +1,36 @@
+ setup.py |    8 ++++----
+ 1 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 366d552..ce0d271 100755
+--- a/setup.py
++++ b/setup.py
+@@ -161,8 +161,8 @@ else: # linux or other unix
+                  "layer5",
+                  "/usr/include/freetype2",
+               # VMD plugin support
+-              #              "contrib/uiuc/plugins/include",
+-              #              "contrib/uiuc/plugins/molfile_plugin/src",
++                            "contrib/uiuc/plugins/include",
++                            "contrib/uiuc/plugins/molfile_plugin/src",
+                  "modules/cealign/src",
+                  "modules/cealign/src/tnt",
+                  "generated/include",
+@@ -190,7 +190,7 @@ else: # linux or other unix
+                    # Numeric Python support                    
+                    #                ("_PYMOL_NUMPY",None),
+                    # VMD plugin support           
+-                   #               ("_PYMOL_VMD_PLUGINS",None)
++                                  ("_PYMOL_VMD_PLUGINS",None),
+                    ("_PYMOL_CGO_DRAWARRAYS",None),
+                    ("_PYMOL_CGO_DRAWBUFFERS",None),
+                    ("_CGO_DRAWARRAYS",None),
+@@ -354,7 +354,7 @@ distribution = setup ( # Distribution meta-data
+                 "layer5/main.c"
+                 # VMD plugin support
+                 # switch the 0 to 1 to activate the additional source code
+-                ] + 0 * [
++                ] + 1 * [
+                 # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
+                 'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
+                 'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',

diff --git a/sci-chemistry/pymol/files/pymol-9999-web.patch b/sci-chemistry/pymol/files/pymol-9999-web.patch
new file mode 100644
index 0000000..fe61f02
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-web.patch
@@ -0,0 +1,19 @@
+ 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',
+                  'pymol/opengl/glu',
+                  'pymol/opengl/glut',
+-                 'pymol/wizard',
+-                 'web',
+-                 'web/examples',
+-                 'web/javascript', ],
++                 'pymol/wizard', ],
+     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 edfdbf2..908c7fc 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI=4
 
-PYTHON_DEPEND="2:2.6"
+PYTHON_DEPEND="2:2.7"
 SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="2.4 2.5 3.*"
+RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.*"
 PYTHON_USE_WITH="tk"
 PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
 
@@ -42,28 +42,31 @@ RDEPEND="${DEPEND}"
 
 src_prepare() {
 	epatch \
+		"${FILESDIR}"/${P}-setup.py.patch \
 		"${FILESDIR}"/${P}-data-path.patch \
-		"${FILESDIR}"/${P}-shaders.patch \
-		"${FILESDIR}"/${P}-setup.py.patch
+		"${FILESDIR}"/${P}-flags.patch
 
-	use web || epatch "${FILESDIR}"/${PV}-web.patch
+	use web || epatch "${FILESDIR}"/${P}-web.patch
 
 	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 "${FILESDIR}"/nosplash-gentoo.patch
+	epatch "${FILESDIR}"/${P}-nosplash.patch
 
-	use vmd && epatch "${FILESDIR}"/${PV}-vmd.patch
+	use vmd && epatch "${FILESDIR}"/${P}-vmd.patch
 
-	use numpy && \
+	if use numpy; then
 		sed \
 			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py
+			-i setup.py || die
+	fi
 
 	rm ./modules/pmg_tk/startup/apbs_tools.py || die
 
+	echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die
+
 	# python 3.* fix
 	# sed '452,465d' -i setup.py
 	distutils_src_prepare
@@ -84,20 +87,27 @@ src_install() {
 		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
 	EOF
 
-	doenvd "${T}"/20pymol || die "Failed to install env.d file."
+	doenvd "${T}"/20pymol
 
 	cat >> "${T}"/pymol <<- EOF
 	#!/bin/sh
 	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
 	EOF
 
-	dobin "${T}"/pymol || die "Failed to install wrapper."
+	dobin "${T}"/pymol
 
 	insinto /usr/share/pymol
-	doins -r test data scripts || die "no shared data"
+	doins -r test data scripts
 
 	insinto /usr/share/pymol/examples
-	doins -r examples || die "Failed to install docs."
+	doins -r examples
+
+	dodoc DEVELOPERS README
+}
 
-	dodoc DEVELOPERS README || die "Failed to install docs."
+pkg_postinst() {
+	elog "\t USE=shaders was removed,"
+	elog "please use pymol config settings"
+	elog "\t set use_shaders, 1"
+	distutils_pkg_postinst
 }



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2012-02-20 14:30 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2012-02-20 14:30 UTC (permalink / raw
  To: gentoo-commits

commit:     729c8534f774efc7b0124e16ab8766096093498c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 19 13:18:34 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 19 13:18:34 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=729c8534

Fix for current HEAD, correct desktop entry generation

(Portage version: 2.2.0_alpha87/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/pymol/ChangeLog                     |   24 +++++++
 sci-chemistry/pymol/files/pymol-9999-prefix.patch |   70 ++++++++++++--------
 sci-chemistry/pymol/files/pymol-9999-web.patch    |   19 +++---
 sci-chemistry/pymol/pymol-9999.ebuild             |   25 +++++--
 4 files changed, 92 insertions(+), 46 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 8b2e581..0f6860d 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/files/pymol-9999-prefix.patch b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
index 830eb8f..9b0bad3 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 fe61f02..4f48140 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 908c7fc..1671842 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
 }



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2012-03-29  9:07 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2012-03-29  9:07 UTC (permalink / raw
  To: gentoo-commits

commit:     ed1028a1b6c2a45f42d1275023094d3195bd1ad9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 29 09:07:09 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 29 09:07:09 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ed1028a1

Import tree changes

(Portage version: 2.2.0_alpha96/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/pymol/ChangeLog                      |    4 ++++
 .../pymol/files/pymol-9999-data-path.patch         |   18 +++++++++++-------
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 3aee674..78f20cb 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Mar 2012; Justin Lecher <jlec@gentoo.org>
+  files/pymol-9999-data-path.patch:
+  Import tree changes
+
   04 Mar 2012; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
   Block pypy usage
 

diff --git a/sci-chemistry/pymol/files/pymol-9999-data-path.patch b/sci-chemistry/pymol/files/pymol-9999-data-path.patch
index e865bfd..a2b09bb 100644
--- a/sci-chemistry/pymol/files/pymol-9999-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-data-path.patch
@@ -4,8 +4,8 @@
  modules/chempy/tinker/__init__.py   |    2 +-
  modules/pymol/commanding.py         |    6 +++---
  modules/pymol/importing.py          |    2 +-
- modules/pymol/wizard/mutagenesis.py |    4 ++--
- 7 files changed, 17 insertions(+), 17 deletions(-)
+ modules/pymol/wizard/mutagenesis.py |    8 ++++----
+ 7 files changed, 19 insertions(+), 19 deletions(-)
 
 diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
 index cc760ae..364277f 100644
@@ -74,7 +74,7 @@ index 23dbe45..795a223 100644
      path = os.environ['PYMOL_DATA'] + '/chempy/'
  elif os.environ.has_key('PYMOL_PATH'):
 -    path = os.environ['PYMOL_PATH'] + '/data/chempy/'   
-+    path = os.environ['PYMOL_PATH'] + '/chempy/'   
++    path = os.environ['PYMOL_PATH'] + '/chempy/'
  elif os.environ.has_key('FREEMOL_MODULES'):
      path = os.environ['FREEMOL_MODULES'] + '/chempy/'
  else:
@@ -127,20 +127,24 @@ diff --git a/modules/pymol/wizard/mutagenesis.py b/modules/pymol/wizard/mutagene
 index 8a5250d..6c1b26c 100644
 --- a/modules/pymol/wizard/mutagenesis.py
 +++ b/modules/pymol/wizard/mutagenesis.py
-@@ -53,7 +53,7 @@ class Mutagenesis(Wizard):
+@@ -52,8 +52,8 @@ class Mutagenesis(Wizard):
+         
          self.dep = default_dep
  
-         self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
 -                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
++        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
 +                                           "/chempy/sidechains/sc_bb_ind.pkl")
          self.load_library()
          self.status = 0 # 0 no selection, 1 mutagenizing
          self.bump_check = 1
-@@ -218,7 +218,7 @@ class Mutagenesis(Wizard):
+@@ -217,8 +217,8 @@ class Mutagenesis(Wizard):
+     def load_library(self):
          if self.dep == 'dep':
              if not hasattr(self,'dep_library'):
-                 self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
 -                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
++                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
 +                                           "/chempy/sidechains/sc_bb_dep.pkl")
              
      def set_mode(self,mode):



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2012-05-02 19:22 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2012-05-02 19:22 UTC (permalink / raw
  To: gentoo-commits

commit:     343709f993aaf8c97385c4b33c5984c56991cba9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed May  2 18:06:12 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed May  2 18:06:12 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=343709f9

sci-chemistry/pymol: Fix for latest HEAD

(Portage version: 2.2.0_alpha101/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/pymol/ChangeLog                  |    3 +++
 sci-chemistry/pymol/files/pymol-9999-web.patch |    2 +-
 2 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index d8f7712..98f4ebc 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 May 2012; Justin Lecher <jlec@gentoo.org> files/pymol-9999-web.patch:
+  Fix for latest HEAD
+
   29 Mar 2012; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
   Add new icon files provided by Ramiro Téllez Sanz
 

diff --git a/sci-chemistry/pymol/files/pymol-9999-web.patch b/sci-chemistry/pymol/files/pymol-9999-web.patch
index 4f48140..2293670 100644
--- a/sci-chemistry/pymol/files/pymol-9999-web.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-web.patch
@@ -6,6 +6,7 @@ Index: setup.py
                   'pymol/opengl/glu',
                   'pymol/opengl/glut',
                   'pymol/wizard',
+                  'pymol/plugins',
 -                 'pymol2',
 -                 'web',
 -                 'web/examples',
@@ -13,4 +14,3 @@ Index: setup.py
 +                 'pymol2', ],
      ext_modules = [
          Extension("pymol._cmd", [
-                 "modules/cealign/src/ccealignmodule.cpp",



^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2013-02-15 15:52 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2013-02-15 15:52 UTC (permalink / raw
  To: gentoo-commits

commit:     37524e665700b37970924243853f1bef9bb7c6ba
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 15 15:53:06 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 15 15:53:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37524e66

sci-chemistry/pymol: adopt to current HEAD

Package-Manager: portage-2.2.0_alpha163

---
 sci-chemistry/pymol/ChangeLog                      |    7 +
 .../pymol/files/pymol-9999-data-path.patch         |  151 --------------------
 sci-chemistry/pymol/files/pymol-9999-flags.patch   |   18 ++--
 .../pymol/files/pymol-9999-nosplash.patch          |   15 --
 sci-chemistry/pymol/files/pymol-9999-prefix.patch  |   52 +++-----
 .../pymol/files/pymol-9999-setup.py.patch          |   39 -----
 sci-chemistry/pymol/files/pymol-9999-vmd.patch     |   36 -----
 sci-chemistry/pymol/files/pymol-9999-web.patch     |   16 --
 sci-chemistry/pymol/metadata.xml                   |    2 -
 sci-chemistry/pymol/pymol-9999.ebuild              |   50 +------
 10 files changed, 40 insertions(+), 346 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index c88876a..fe1b0b7 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Feb 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  -files/pymol-9999-data-path.patch, files/pymol-9999-flags.patch,
+  -files/pymol-9999-nosplash.patch, files/pymol-9999-prefix.patch,
+  -files/pymol-9999-setup.py.patch, -files/pymol-9999-vmd.patch,
+  -files/pymol-9999-web.patch, metadata.xml:
+  adopt to current HEAD
+
   29 Jan 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild, metadata.xml:
   Bump python eclass
 

diff --git a/sci-chemistry/pymol/files/pymol-9999-data-path.patch b/sci-chemistry/pymol/files/pymol-9999-data-path.patch
deleted file mode 100644
index a2b09bb..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-data-path.patch
+++ /dev/null
@@ -1,151 +0,0 @@
- layer0/ShaderMgr.c                  |   16 ++++++++--------
- layer1/Setting.c                    |    2 +-
- modules/chempy/__init__.py          |    2 +-
- modules/chempy/tinker/__init__.py   |    2 +-
- modules/pymol/commanding.py         |    6 +++---
- modules/pymol/importing.py          |    2 +-
- modules/pymol/wizard/mutagenesis.py |    8 ++++----
- 7 files changed, 19 insertions(+), 19 deletions(-)
-
-diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
-index cc760ae..364277f 100644
---- a/layer0/ShaderMgr.c
-+++ b/layer0/ShaderMgr.c
-@@ -385,7 +385,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
- char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
-   FILE* f;
-   long size;
--  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
-+  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
-   size_t res;
- 
-   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
-@@ -398,16 +398,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
-     return NULL;
-   }
-   
--  pymol_path = getenv("PYMOL_PATH");
--  if (!pymol_path){
-+  pymol_data = getenv("PYMOL_DATA");
-+  if (!pymol_data){
-     PRINTFB(G, FB_ShaderMgr, FB_Warnings)
--      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files from disk\n" ENDFB(G);
-+      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n" ENDFB(G);
-     return NULL;
-   }
-   /* make this a setting */
--  shader_path = "/data/shaders/";
--  fullFile = malloc( sizeof(char) * (strlen(pymol_path)+strlen(shader_path)+strlen(fileName)+1));
--  fullFile = strcpy(fullFile, pymol_path);
-+  shader_path = "/shaders/";
-+  fullFile = malloc( sizeof(char) * (strlen(pymol_data)+strlen(shader_path)+strlen(fileName)+1));
-+  fullFile = strcpy(fullFile, pymol_data);
-   fullFile = strcat(fullFile, shader_path);
-   fullFile = strcat(fullFile, fileName);
- 
-@@ -416,7 +416,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
- 
-   if (!f) {
-     PRINTFB(G, FB_ShaderMgr, FB_Errors)
--      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_PATH='%s'\n", fullFile, pymol_path ENDFB(G);
-+      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_DATA='%s'\n", fullFile, pymol_data ENDFB(G);
-     return NULL;
-   } else {
-     PRINTFB(G, FB_ShaderMgr, FB_Blather)
-diff --git a/layer1/Setting.c b/layer1/Setting.c
-index c2b8bbb..4c6fdb7 100644
---- a/layer1/Setting.c
-+++ b/layer1/Setting.c
-@@ -4375,7 +4375,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
-     set_b(I, cSetting_line_use_shader, 1);
-     set_b(I, cSetting_sphere_use_shader, 1);
-     set_b(I, cSetting_use_shaders, 0);
--    set_s(I, cSetting_shader_path, "data/shaders");
-+    set_s(I, cSetting_shader_path, "shaders");
-     set_i(I, cSetting_volume_bit_depth, 8);
-     set_color(I, cSetting_volume_color, "-1");
-     set_f(I, cSetting_volume_layers, 256);
-diff --git a/modules/chempy/__init__.py b/modules/chempy/__init__.py
-index 23dbe45..795a223 100644
---- a/modules/chempy/__init__.py
-+++ b/modules/chempy/__init__.py
-@@ -235,7 +235,7 @@ if os.environ.has_key('CHEMPY_DATA'):  #
- elif os.environ.has_key('PYMOL_DATA'):
-     path = os.environ['PYMOL_DATA'] + '/chempy/'
- elif os.environ.has_key('PYMOL_PATH'):
--    path = os.environ['PYMOL_PATH'] + '/data/chempy/'   
-+    path = os.environ['PYMOL_PATH'] + '/chempy/'
- elif os.environ.has_key('FREEMOL_MODULES'):
-     path = os.environ['FREEMOL_MODULES'] + '/chempy/'
- else:
-diff --git a/modules/chempy/tinker/__init__.py b/modules/chempy/tinker/__init__.py
-index a2d8eb1..1e48f81 100644
---- a/modules/chempy/tinker/__init__.py
-+++ b/modules/chempy/tinker/__init__.py
-@@ -147,7 +147,7 @@ else:
- 
- if os.environ.has_key('PYMOL_PATH'):
-     pymol_path = os.environ['PYMOL_PATH']
--    test_path = pymol_path + '/data/chempy/tinker/'
-+    test_path = pymol_path + '/chempy/tinker/'
-     if os.path.exists(test_path):
-         params_path = test_path
- 
-diff --git a/modules/pymol/commanding.py b/modules/pymol/commanding.py
-index 5a202d0..5cb27a6 100644
---- a/modules/pymol/commanding.py
-+++ b/modules/pymol/commanding.py
-@@ -219,11 +219,11 @@ USAGE
-                 _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 --git a/modules/pymol/importing.py b/modules/pymol/importing.py
-index 457ace7..7cc2953 100644
---- a/modules/pymol/importing.py
-+++ b/modules/pymol/importing.py
-@@ -191,7 +191,7 @@ SEE ALSO
-     '''
-         r = DEFAULT_ERROR
-         
--        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
-+        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
-                    'pymol' : 'pymol',
-                    'rgb' : 'rgb',
-                    'greyscale': 'greyscale' }
-diff --git a/modules/pymol/wizard/mutagenesis.py b/modules/pymol/wizard/mutagenesis.py
-index 8a5250d..6c1b26c 100644
---- a/modules/pymol/wizard/mutagenesis.py
-+++ b/modules/pymol/wizard/mutagenesis.py
-@@ -52,8 +52,8 @@ class Mutagenesis(Wizard):
-         
-         self.dep = default_dep
- 
--        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
-+        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_ind.pkl")
-         self.load_library()
-         self.status = 0 # 0 no selection, 1 mutagenizing
-         self.bump_check = 1
-@@ -217,8 +217,8 @@ class Mutagenesis(Wizard):
-     def load_library(self):
-         if self.dep == 'dep':
-             if not hasattr(self,'dep_library'):
--                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
--                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
-+                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
-+                                           "/chempy/sidechains/sc_bb_dep.pkl")
-             
-     def set_mode(self,mode):
-         cmd=self.cmd

diff --git a/sci-chemistry/pymol/files/pymol-9999-flags.patch b/sci-chemistry/pymol/files/pymol-9999-flags.patch
index 9bdba45..528e220 100644
--- a/sci-chemistry/pymol/files/pymol-9999-flags.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-flags.patch
@@ -1,11 +1,11 @@
- setup.py |    5 +----
- 1 files changed, 1 insertions(+), 4 deletions(-)
+ pymol/setup.py | 5 +----
+ 1 file changed, 1 insertion(+), 4 deletions(-)
 
-diff --git a/setup.py b/setup.py
-index 2b6fa35..9c0556d 100755
---- a/setup.py
-+++ b/setup.py
-@@ -197,10 +197,7 @@ else: # linux or other unix
+diff --git a/pymol/setup.py b/pymol/setup.py
+index b8d7070..7fc11fb 100644
+--- a/pymol/setup.py
++++ b/pymol/setup.py
+@@ -252,10 +252,7 @@ else: # linux or other unix
                     ("_PYMOL_GL_CALLLISTS",None),
                     ("OPENGL_ES_2",None),
                     ]
@@ -14,6 +14,6 @@ index 2b6fa35..9c0556d 100755
 -                      "-O3",
 -                      "-g" ]
 +    ext_comp_args = []
-     ext_link_args = []
- 
  
+ def get_pymol_version():
+     return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0]

diff --git a/sci-chemistry/pymol/files/pymol-9999-nosplash.patch b/sci-chemistry/pymol/files/pymol-9999-nosplash.patch
deleted file mode 100644
index b296285..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-nosplash.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- modules/pymol/invocation.py |    2 --
- 1 files changed, 0 insertions(+), 2 deletions(-)
-
-diff --git a/modules/pymol/invocation.py b/modules/pymol/invocation.py
-index de47849..c5f4487 100644
---- a/modules/pymol/invocation.py
-+++ b/modules/pymol/invocation.py
-@@ -397,7 +397,5 @@ if __name__=='pymol.invocation':
-         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)")
-         if options.full_screen:
-             options.deferred.append("_do__ full_screen on")

diff --git a/sci-chemistry/pymol/files/pymol-9999-prefix.patch b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
index 9b0bad3..0334845 100644
--- a/sci-chemistry/pymol/files/pymol-9999-prefix.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
@@ -1,33 +1,17 @@
-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 @@
+ pymol/setup.py | 10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/pymol/setup.py b/pymol/setup.py
+index b8d7070..378bbf6 100644
+--- a/pymol/setup.py
++++ b/pymol/setup.py
+@@ -185,12 +185,12 @@ elif sys.platform=='darwin':
                    "/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/sw/lib", "-lpng",
 -                       "/usr/X11/lib/libGL.dylib",
@@ -37,21 +21,21 @@ Index: setup.py
                         "-lfreeglut",
                         "-lglew",
                         "-L/sw/lib/freetype219/lib", "-lfreetype"
-@@ -221,7 +221,7 @@
-                  "layer3",
-                  "layer4",
-                  "layer5",
+@@ -220,7 +220,7 @@ elif sys.platform=='darwin':
+ else: # linux or other unix
+ 
+     inc_dirs += [
 -                 "/usr/include/freetype2",
 +                 "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2",
-               # VMD plugin support
-               #              "contrib/uiuc/plugins/include",
-               #              "contrib/uiuc/plugins/molfile_plugin/src",
-@@ -242,7 +242,7 @@
+                  ]
+     libs = [ "GL",
+              "GLU",
+@@ -235,7 +235,7 @@ else: # linux or other unix
                     "GLU",
                     "glut",
                     "GLEW"]
 -    lib_dirs = [ "/usr/X11R6/lib64", ]
 +    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/X11R6/lib64", ]
-     def_macros = [ ("_PYMOL_MODULE",None),
+     def_macros += [
                     ("_PYMOL_INLINE",None),
                     ("_PYMOL_FREETYPE",None),

diff --git a/sci-chemistry/pymol/files/pymol-9999-setup.py.patch b/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
deleted file mode 100644
index 076d690..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-setup.py.patch
+++ /dev/null
@@ -1,39 +0,0 @@
- setup.py |   28 ----------------------------
- 1 files changed, 0 insertions(+), 28 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 18866a2..705b0c5 100755
---- a/setup.py
-+++ b/setup.py
-@@ -487,31 +487,3 @@ distribution = setup ( # Distribution meta-data
-                   define_macros = def_macros
-                   )
-         ])
--
--# make available for setup2.py
--try:
--    site_packages = distribution.command_obj['install'].install_libbase
--except KeyError:
--    print """
-- Error: Please run, 'setup.py install' not 'setup build' or other variant.
--
--"""
--    sys.exit(2)
--
--f = open('setup3.py', 'w')
--print >> f, 'site_packages =', repr(site_packages)
--f.close()
--
--print '''
-- After running:
--
--     python setup.py install
--     
-- Please run, to complete the installation:
--
--     python setup2.py install
--
-- To uninstall PyMOL, run:
--
--     python setup2.py uninstall
--'''

diff --git a/sci-chemistry/pymol/files/pymol-9999-vmd.patch b/sci-chemistry/pymol/files/pymol-9999-vmd.patch
deleted file mode 100644
index cf47082..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-vmd.patch
+++ /dev/null
@@ -1,36 +0,0 @@
- setup.py |    8 ++++----
- 1 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 366d552..ce0d271 100755
---- a/setup.py
-+++ b/setup.py
-@@ -161,8 +161,8 @@ else: # linux or other unix
-                  "layer5",
-                  "/usr/include/freetype2",
-               # VMD plugin support
--              #              "contrib/uiuc/plugins/include",
--              #              "contrib/uiuc/plugins/molfile_plugin/src",
-+                            "contrib/uiuc/plugins/include",
-+                            "contrib/uiuc/plugins/molfile_plugin/src",
-                  "modules/cealign/src",
-                  "modules/cealign/src/tnt",
-                  "generated/include",
-@@ -190,7 +190,7 @@ else: # linux or other unix
-                    # Numeric Python support                    
-                    #                ("_PYMOL_NUMPY",None),
-                    # VMD plugin support           
--                   #               ("_PYMOL_VMD_PLUGINS",None)
-+                                  ("_PYMOL_VMD_PLUGINS",None),
-                    ("_PYMOL_CGO_DRAWARRAYS",None),
-                    ("_PYMOL_CGO_DRAWBUFFERS",None),
-                    ("_CGO_DRAWARRAYS",None),
-@@ -354,7 +354,7 @@ distribution = setup ( # Distribution meta-data
-                 "layer5/main.c"
-                 # VMD plugin support
-                 # switch the 0 to 1 to activate the additional source code
--                ] + 0 * [
-+                ] + 1 * [
-                 # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
-                 'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
-                 'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',

diff --git a/sci-chemistry/pymol/files/pymol-9999-web.patch b/sci-chemistry/pymol/files/pymol-9999-web.patch
deleted file mode 100644
index 2293670..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-web.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Index: setup.py
-===================================================================
---- setup.py	(revision 3983)
-+++ setup.py	(working copy)
-@@ -292,10 +292,7 @@
-                  'pymol/opengl/glu',
-                  'pymol/opengl/glut',
-                  'pymol/wizard',
-                  'pymol/plugins',
--                 'pymol2',
--                 'web',
--                 'web/examples',
--                 'web/javascript', ],
-+                 'pymol2', ],
-     ext_modules = [
-         Extension("pymol._cmd", [

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 8ada2f2..388b22d 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -7,7 +7,5 @@
   <use>
     <flag name="apbs">Pymol supprt for sci-chemistry/apbs</flag>
     <flag name="numpy">Enable numpy support for Pymol</flag>
-    <flag name="vmd">Builds molfile plugin support</flag>
-    <flag name="web">Install Pymodule needed for web app support</flag>
   </use>
 </pkgmetadata>

diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 00dc372..12bf73d 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -17,7 +17,7 @@ ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
 LICENSE="PSF-2.2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs numpy vmd web"
+IUSE="apbs +numpy"
 
 DEPEND="
 	dev-python/numpy
@@ -34,7 +34,7 @@ DEPEND="
 		sci-chemistry/pdb2pqr
 		sci-chemistry/pymol-apbs-plugin
 	)
-	web? ( !dev-python/webpy )"
+	!dev-python/webpy"
 RDEPEND="${DEPEND}"
 
 src_unpack() {
@@ -44,15 +44,10 @@ src_unpack() {
 
 python_prepare_all() {
 	local PATCHES=(
-		"${FILESDIR}"/${P}-setup.py.patch
-		"${FILESDIR}"/${P}-data-path.patch
 		"${FILESDIR}"/${P}-flags.patch
 		"${FILESDIR}"/${P}-prefix.patch
 		)
 
-	use web || PATCHES+=( "${FILESDIR}"/${P}-web.patch )
-	use vmd && PATCHES+=( "${FILESDIR}"/${P}-vmd.patch )
-
 	if use numpy; then
 		sed \
 			-e '/PYMOL_NUMPY/s:^#::g' \
@@ -61,12 +56,8 @@ python_prepare_all() {
 
 	rm ./modules/pmg_tk/startup/apbs_tools.py || die
 
-	python_export python2_7 EPYTHON PYTHON_SITEDIR
-	echo "site_packages = \'$(python_get_sitedir)\'" > setup3.py || die
-
 	sed \
 		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
 		-i setup.py || die
 
 	distutils-r1_python_prepare_all
@@ -79,47 +70,18 @@ src_prepare() {
 	distutils-r1_src_prepare
 }
 
+python_install() {
+	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
+}
+
 python_install_all() {
 	distutils-r1_python_install_all
 
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	cat >> "${T}"/pymol <<- EOF
-	#!/bin/sh
-	${EPYTHON} -O \${PYMOL_PATH}/__init__.py -q \$*
-	EOF
-
-	dobin "${T}"/pymol
-
-	insinto /usr/share/pymol
-	doins -r test data scripts
-
-	insinto /usr/share/pymol/examples
-	doins -r examples
-
-	dodoc DEVELOPERS README
-
 	doicon "${WORKDIR}"/${PN}.{xpm,png}
 	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
 }
 
 pkg_postinst() {
-	elog "\t USE=shaders was removed,"
-	elog "please use pymol config settings (~/.pymolrc)"
-	elog "\t set use_shaders, 1"
-	elog "in case of crashes, please deactivate this experimental feature by setting"
-	elog "\t set use_shaders, 0"
-	elog "\t set sphere_mode, 0"
 	fdo-mime_desktop_database_update
 	fdo-mime_mime_database_update
 }


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2013-02-19 19:35 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2013-02-19 19:35 UTC (permalink / raw
  To: gentoo-commits

commit:     e4f5b3533db0f3b40cbcfeee0adbcc8684c37972
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 18 20:22:05 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 18 20:22:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e4f5b353

sci-chemistry/pymol: Adapt to current HEAD

Package-Manager: portage-2.2.0_alpha163

---
 sci-chemistry/pymol/ChangeLog                     |    4 ++
 sci-chemistry/pymol/files/pymol-9999-flags.patch  |   19 ----------
 sci-chemistry/pymol/files/pymol-9999-prefix.patch |   41 ---------------------
 sci-chemistry/pymol/metadata.xml                  |    1 -
 sci-chemistry/pymol/pymol-9999.ebuild             |   20 +++--------
 5 files changed, 9 insertions(+), 76 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index fe1b0b7..9652f4b 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Feb 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  -files/pymol-9999-flags.patch, -files/pymol-9999-prefix.patch, metadata.xml:
+  Adapt to current HEAD
+
   15 Feb 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
   -files/pymol-9999-data-path.patch, files/pymol-9999-flags.patch,
   -files/pymol-9999-nosplash.patch, files/pymol-9999-prefix.patch,

diff --git a/sci-chemistry/pymol/files/pymol-9999-flags.patch b/sci-chemistry/pymol/files/pymol-9999-flags.patch
deleted file mode 100644
index 528e220..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-flags.patch
+++ /dev/null
@@ -1,19 +0,0 @@
- pymol/setup.py | 5 +----
- 1 file changed, 1 insertion(+), 4 deletions(-)
-
-diff --git a/pymol/setup.py b/pymol/setup.py
-index b8d7070..7fc11fb 100644
---- a/pymol/setup.py
-+++ b/pymol/setup.py
-@@ -252,10 +252,7 @@ else: # linux or other unix
-                    ("_PYMOL_GL_CALLLISTS",None),
-                    ("OPENGL_ES_2",None),
-                    ]
--    ext_comp_args = [ "-ffast-math",
--                      "-funroll-loops",
--                      "-O3",
--                      "-g" ]
-+    ext_comp_args = []
- 
- def get_pymol_version():
-     return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0]

diff --git a/sci-chemistry/pymol/files/pymol-9999-prefix.patch b/sci-chemistry/pymol/files/pymol-9999-prefix.patch
deleted file mode 100644
index 0334845..0000000
--- a/sci-chemistry/pymol/files/pymol-9999-prefix.patch
+++ /dev/null
@@ -1,41 +0,0 @@
- pymol/setup.py | 10 +++++-----
- 1 file changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/pymol/setup.py b/pymol/setup.py
-index b8d7070..378bbf6 100644
---- a/pymol/setup.py
-+++ b/pymol/setup.py
-@@ -185,12 +185,12 @@ elif sys.platform=='darwin':
-                   "/sw/include/freetype2/freetype",
-                   "/sw/include/freetype2",
-                   "/sw/include",
--                  "/usr/X11/include",
-+                  "@GENTOO_PORTAGE_EPREFIX@/usr/X11/include",
-                   ]
-         ext_link_args=[
-                        "-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"
-@@ -220,7 +220,7 @@ elif sys.platform=='darwin':
- else: # linux or other unix
- 
-     inc_dirs += [
--                 "/usr/include/freetype2",
-+                 "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2",
-                  ]
-     libs = [ "GL",
-              "GLU",
-@@ -235,7 +235,7 @@ else: # linux or other unix
-                    "GLU",
-                    "glut",
-                    "GLEW"]
--    lib_dirs = [ "/usr/X11R6/lib64", ]
-+    lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/X11R6/lib64", ]
-     def_macros += [
-                    ("_PYMOL_INLINE",None),
-                    ("_PYMOL_FREETYPE",None),

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 388b22d..e2aa7cd 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -6,6 +6,5 @@
   </maintainer>
   <use>
     <flag name="apbs">Pymol supprt for sci-chemistry/apbs</flag>
-    <flag name="numpy">Enable numpy support for Pymol</flag>
   </use>
 </pkgmetadata>

diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 12bf73d..cd05037 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -17,7 +17,7 @@ ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
 LICENSE="PSF-2.2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs +numpy"
+IUSE="apbs"
 
 DEPEND="
 	dev-python/numpy
@@ -43,23 +43,13 @@ src_unpack() {
 }
 
 python_prepare_all() {
-	local PATCHES=(
-		"${FILESDIR}"/${P}-flags.patch
-		"${FILESDIR}"/${P}-prefix.patch
-		)
-
-	if use numpy; then
-		sed \
-			-e '/PYMOL_NUMPY/s:^#::g' \
-			-i setup.py || die
-	fi
-
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
 	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args/s:=.*$:=:g" \
 		-i setup.py || die
 
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
 	distutils-r1_python_prepare_all
 
 	eprefixify setup.py


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2014-10-20 18:01 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2014-10-20 18:01 UTC (permalink / raw
  To: gentoo-commits

commit:     5f7b312a1fa336fc5f4b98909502579ce5557155
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 20 18:00:45 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 20 18:01:10 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f7b312a

sci-chemistry/pymol: Fix broken plugin listing

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog                      |  4 ++++
 sci-chemistry/pymol/files/pymol-9999-listing.patch | 17 +++++++++++++++++
 sci-chemistry/pymol/pymol-9999.ebuild              |  1 +
 3 files changed, 22 insertions(+)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 2cce805..0364715 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   20 Oct 2014; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  +files/pymol-9999-listing.patch:
+  Fix broken plugin listing
+
+  20 Oct 2014; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
   +files/pymol-9999-options.patch:
   Fix upstream buildsystem
 

diff --git a/sci-chemistry/pymol/files/pymol-9999-listing.patch b/sci-chemistry/pymol/files/pymol-9999-listing.patch
new file mode 100644
index 0000000..1b4039c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-listing.patch
@@ -0,0 +1,17 @@
+ pymol/modules/pymol/plugins/repository.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pymol/modules/pymol/plugins/repository.py b/pymol/modules/pymol/plugins/repository.py
+index 9697f68..9820fac 100644
+--- a/pymol/modules/pymol/plugins/repository.py
++++ b/pymol/modules/pymol/plugins/repository.py
+@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
+ 
+     def fetchjson(self, url):
+         handle = urlopen('https://api.github.com' + url)
+-        return eval(handle.read())
++        ret = handle.read().replace("false", "False")
++        return eval(ret)
+ 
+ class LocalRepository(Repository):
+     def __init__(self, url):

diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index a811e69..cbc6a4b 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -39,6 +39,7 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
 	"${FILESDIR}"/${P}-options.patch
+	"${FILESDIR}"/${P}-listing.patch
 )
 
 src_unpack() {


^ permalink raw reply related	[flat|nested] 15+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
@ 2014-10-30 13:48 Justin Lecher
  0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2014-10-30 13:48 UTC (permalink / raw
  To: gentoo-commits

commit:     ecb0dc0854f860d87e7ebd237d3c83ef8f815444
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 30 13:48:47 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct 30 13:48:47 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecb0dc08

sci-chemistry/pymol: Make it really multi py ABI ready; use internal apbs plugin

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog                    |   4 +
 sci-chemistry/pymol/files/pymol-9999-tk8.6.patch | 163 +++++++++++++++++++++++
 sci-chemistry/pymol/pymol-9999.ebuild            |  21 ++-
 3 files changed, 183 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 67954f0..15af521 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Oct 2014; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+  +files/pymol-9999-tk8.6.patch:
+  Make it really multi py ABI ready; use internal apbs plugin
+
   27 Oct 2014; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
   Add missing PYTHON_USEDEP
 

diff --git a/sci-chemistry/pymol/files/pymol-9999-tk8.6.patch b/sci-chemistry/pymol/files/pymol-9999-tk8.6.patch
new file mode 100644
index 0000000..c4fa209
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-9999-tk8.6.patch
@@ -0,0 +1,163 @@
+ pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++++++++++++++---------------
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py b/pymol/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..ad82df3 100644
+--- a/pymol/modules/pmg_tk/startup/apbs_tools.py
++++ b/pymol/modules/pmg_tk/startup/apbs_tools.py
+@@ -612,7 +612,7 @@ class APBSTools2:
+         # Set up the Main page
+         page = self.notebook.add('Main')
+         group = Pmw.Group(page,tag_text='Main options')
+-        group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++        group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+         self.selection = Pmw.EntryField(group.interior(),
+                                         labelpos='w',
+                                         label_text='Selection to use: ',
+@@ -658,7 +658,7 @@ class APBSTools2:
+         page = self.notebook.add('Configuration')
+ 
+         group = Pmw.Group(page,tag_text='Dielectric Constants')
+-        group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++        group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+         group.grid(column=0, row=0)
+         self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w',
+                                    label_text = 'Protein Dielectric:',
+@@ -677,7 +677,7 @@ class APBSTools2:
+             #entry.pack(side='left',fill='both',expand=1,padx=4) # side-by-side
+             entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical
+         group = Pmw.Group(page,tag_text='Other')
+-        group.pack(fill='both',expand=1, padx=4, pady=5)
++        group.grid(padx=4, pady=5, sticky=(N, S, E, W))
+         group.grid(column=1, row=1,columnspan=4)
+         self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',
+                                               label_text = 'Maximum Memory Allowed (MB):',
+@@ -735,7 +735,7 @@ class APBSTools2:
+ 
+ 
+         group = Pmw.Group(page,tag_text='Ions')
+-        group.pack(fill='both',expand=1, padx=4, pady=5)
++        group.grid(padx=4, pady=5, sticky=(N, S, E, W))
+         group.grid(column=0, row=1, )
+         self.ion_plus_one_conc = Pmw.EntryField(group.interior(),
+                                                 labelpos='w',
+@@ -794,7 +794,7 @@ class APBSTools2:
+             entry.pack(fill='x',expand=1,padx=4)
+ 
+         group = Pmw.Group(page,tag_text = 'Coarse Mesh Length')
+-        group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++        group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+         group.grid(column = 1, row = 0)
+         for coord in 'x y z'.split():
+             setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(),
+@@ -809,7 +809,7 @@ class APBSTools2:
+ 
+ 
+         group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+-        group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++        group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+         group.grid(column = 2, row = 0)
+         for coord in 'x y z'.split():
+             setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(),
+@@ -824,7 +824,7 @@ class APBSTools2:
+ 
+ 
+         group = Pmw.Group(page,tag_text = 'Grid Center')
+-        group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++        group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+         group.grid(column = 3, row = 0)
+         for coord in 'x y z'.split():
+             setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(),
+@@ -838,7 +838,7 @@ class APBSTools2:
+             getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
+ 
+         group = Pmw.Group(page,tag_text = 'Grid Points')
+-        group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++        group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+         group.grid(column = 4, row = 0)
+         for coord in 'x y z'.split():
+             setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(),
+@@ -856,7 +856,7 @@ class APBSTools2:
+         page.grid_columnconfigure(5,weight=1)
+         page = self.notebook.add('Program Locations')
+         group = Pmw.Group(page,tag_text='Locations')
+-        group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++        group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+         def quickFileValidation(s):
+             if s == '': return Pmw.PARTIAL
+             elif os.path.isfile(s): return Pmw.OK
+@@ -955,7 +955,7 @@ protein residues and AMBER charges.  If wish that behavior, simply delete the "p
+         
+         page = self.notebook.add('Temp File Locations')
+         group = Pmw.Group(page,tag_text='Locations')
+-        group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++        group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+         self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
+                                                            labelpos = 'w',
+                                                            label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
+@@ -1003,17 +1003,17 @@ by setting the environment variable TEMP.
+         page = self.notebook.add('Visualization (1)')
+         group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
+         self.visualization_group_1 = group
+-        group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++        group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ 
+         page = self.notebook.add('Visualization (2)')
+         group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
+         self.visualization_group_2 = group
+-        group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++        group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ 
+         # Create a couple of other empty pages
+         page = self.notebook.add('About')
+         group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
+-        group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++        group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+         text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
+ 
+ Documentation may be found at
+@@ -2271,7 +2271,7 @@ class VisualizationGroup(Pmw.Group):
+             self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
+             self.update_buttonbox.pack(side=LEFT)
+             self.update_buttonbox.add('Update',command=self.refresh)
+-            self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++            self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+ 
+             self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
+             self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
+@@ -2322,7 +2322,7 @@ class VisualizationGroup(Pmw.Group):
+             bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
+             Pmw.alignlabels(bars)
+             for bar in bars: bar.pack(side=LEFT)
+-            self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++            self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+ 
+             self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
+             self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
+@@ -2337,7 +2337,7 @@ class VisualizationGroup(Pmw.Group):
+                                   text = """Follows same coloring as surface.""",
+                                   )
+             label.pack()
+-            self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++            self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+ 
+             self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
+             self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
+@@ -2356,7 +2356,7 @@ class VisualizationGroup(Pmw.Group):
+                                             entryfield_validate = {'validator' : 'real', 'min':0}
+                                             )
+             self.pos_surf_val.pack(side=LEFT)
+-            self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++            self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+ 
+             self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
+             self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
+@@ -2375,7 +2375,7 @@ class VisualizationGroup(Pmw.Group):
+                                             entryfield_validate = {'validator' : 'real', 'max':0}
+                                             )
+             self.neg_surf_val.pack(side=LEFT)
+-            self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++            self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+ 
+ 
+ 

diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index cd57153..957afd0 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -32,11 +32,13 @@ DEPEND="
 	apbs? (
 		sci-chemistry/apbs[${PYTHON_USEDEP}]
 		sci-chemistry/pdb2pqr[${PYTHON_USEDEP}]
-		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+		!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
 	)
 	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
 RDEPEND="${DEPEND}"
 
+PATCHES=( "${FILESDIR}"/${P}-tk8.6.patch )
+
 src_unpack() {
 	unpack ${A}
 	subversion_src_unpack
@@ -49,8 +51,6 @@ python_prepare_all() {
 		-e "/import/s:argparse:argparseX:g" \
 		-i setup.py || die
 
-	rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
 	sed \
 		-e "s:/opt/local:${EPREFIX}/usr:g" \
 		-e '/ext_comp_args/s:\[.*\]:[]:g' \
@@ -66,17 +66,28 @@ src_prepare() {
 
 python_install() {
 	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
+
+	sed \
+		-e '1d' \
+		-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
+		-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
+		-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
+		-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
 }
 
 python_install_all() {
 	distutils-r1_python_install_all
 
-	python_export python2_7 EPYTHON
+	sed \
+		-e '1i#!/usr/bin/env python' \
+		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
+
+	python_foreach_impl python_doscript "${T}"/${PN}
 
 	# These environment variables should not go in the wrapper script, or else
 	# it will be impossible to use the PyMOL libraries from Python.
 	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
+		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
 		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
 		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
 	EOF


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