Version Bump

(Portage version: 2.2.0_alpha86/cvs/Linux x86_64)

7 files changed, 318 insertions, 0 deletions

diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
new file mode 100644
index 000000000000..e865bfd04174
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
@@ -0,0 +1,147 @@
+ 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
+-                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
+@@ -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-1.5.0.1-flags.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-flags.patch
new file mode 100644
index 000000000000..9bdba45f3b1f
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-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-1.5.0.1-nosplash.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-nosplash.patch
new file mode 100644
index 000000000000..b296285e89ca
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-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-1.5.0.1-prefix.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch
new file mode 100644
index 000000000000..830eb8febbf5
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch
@@ -0,0 +1,43 @@
+ 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':
+                     ]
+         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
+                  "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-1.5.0.1-setup.py.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch
new file mode 100644
index 000000000000..076d6907a183
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch
@@ -0,0 +1,39 @@
+ 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-1.5.0.1-vmd.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-vmd.patch
new file mode 100644
index 000000000000..cf47082efb2b
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-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-1.5.0.1-web.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-web.patch
new file mode 100644
index 000000000000..fe61f0264f0b
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-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",