sci-chemistry/pymol: adopt to current HEAD

Package-Manager: portage-2.2.0_alpha163

7 files changed, 27 insertions, 300 deletions

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 a2b09bb9e..000000000
--- 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 9bdba45f3..528e220b0 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 b296285e8..000000000
--- 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 9b0bad342..0334845ca 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 076d6907a..000000000
--- 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 cf47082ef..000000000
--- 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 2293670e1..000000000
--- 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", [