* [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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