From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/
Date: Sun, 19 Feb 2012 12:44:09 +0000 (UTC) [thread overview]
Message-ID: <1329171437.b505aeb44d5b3ba28dfb7d949368452d8855ad33.jlec@gentoo> (raw)
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
}
next reply other threads:[~2012-02-19 12:44 UTC|newest]
Thread overview: 15+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-02-19 12:44 Justin Lecher [this message]
-- strict thread matches above, loose matches on Subject: below --
2014-10-30 13:48 [gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/ Justin Lecher
2014-10-20 18:01 Justin Lecher
2013-02-19 19:35 Justin Lecher
2013-02-15 15:52 Justin Lecher
2012-05-02 19:22 Justin Lecher
2012-03-29 9:07 Justin Lecher
2012-02-20 14:30 Justin Lecher
2011-12-06 16:35 Justin Lecher
2011-08-31 10:05 Justin Lecher
2011-08-26 16:01 Justin Lecher
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2011-06-12 10:53 Justin Lecher
2011-04-28 7:58 Justin Lecher
2011-04-04 11:18 Justin Lecher
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