Update to 1.0r2.

3 files changed, 19 insertions, 98 deletions

diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make
deleted file mode 100644
index 7091e92ddf73..000000000000
--- a/biology/pymol/files/patch-Rules.make
+++ /dev/null
@@ -1,71 +0,0 @@
---- Rules.make.orig	Sun Sep 17 20:42:52 2006
-+++ Rules.make	Sun Sep 17 20:48:26 2006
-@@ -4,27 +4,27 @@
- #
- #- Building ----------------------------------------------------------
- #--- Tell "make" how to get to PyMOL 
--PYMOL_PATH = ${HOME}/pymol
-+PYMOL_PATH = @LOCALBASE@
- #---------------------------------------------------------------------
- #
- #- Dependencies ------------------------------------------------------
- #--- X-windows
--XLIB_DIR = -L/usr/X11R6/lib
--XINC_DIR = -I/usr/X11R6/include
-+XLIB_DIR = -L@X11BASE@/lib
-+XINC_DIR = -I@X11BASE@/include
- #--- Python
--PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python
-+PYTHON_EXE = $(PYMOL_PATH)/bin/python
- PYTHON_LIB =
- PYTHON_LIB_DIR = 
--PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.3 \
--	-I$(PYMOL_PATH)/ext/include/python2.3/Numeric
-+PYTHON_INC_DIR = -I$(PYMOL_PATH)/include/@PYTHON_VERSION@ \
-+	-I$(PYMOL_PATH)/include/@PYTHON_VERSION@/Numeric
- #--- Other external dependencies
--EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include
--EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib
-+EXT_INC_DIR = -I$(PYMOL_PATH)/include
-+EXT_LIB_DIR = -L$(PYMOL_PATH)/lib
- #---------------------------------------------------------------------
- #
- #- Build for LINUX as an importable module ---------------------------
- #--- System libraries
--LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -ldl -lpng -lXmu $(ZLIB) -lm
-+LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lpng -lXmu $(ZLIB) -lm
- #--- PyMOL configuration
- DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_INLINE
- #--- How we build shared libraries
-@@ -32,19 +32,19 @@
- #--- What are we trying to build?
- DEST = -o modules/pymol/_cmd.so
- #--- Gcc Options for Linux
--CCOPT1 = -march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
-+CCOPT1 = @PICFLAG@ @CFLAGS@ #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
- #--- libraries for PyOpenGL 
- PYOGL_LIB =  -lglut -lGL -lGLU -lXmu -lXi
- #---------------------------------------------------------------------
- #
- #- Choose One --------------------------------------------------------
- #--- GCC Optimized
--CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer -finline-limit=10000 
-+#CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer -finline-limit=10000 
- #--- GCC Profiling
- #CCOPT2 = -pg -O3 -funroll-loops
- #--- Debugging
- #CCOPT2 = -g -D_MemoryDebug_ON
--CCOPT2 = -g
-+CCOPT2 = #-g
- #---------------------------------------------------------------------
- #
- #- Choose One --------------------------------------------------------
-@@ -70,7 +70,7 @@
- # No changes normally required below here
- #---------------------------------------------------------------------
- 
--CC = cc
-+CC = @CC@
- 
- LIB_DIRS = $(EXT_LIB_DIR) $(PYTHON_LIB_DIR) $(XLIB_DIR)
- 
diff --git a/biology/pymol/files/patch-setup+pymol+com+linux-rh7x b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x
deleted file mode 100644
index c1273c309745..000000000000
--- a/biology/pymol/files/patch-setup+pymol+com+linux-rh7x
+++ /dev/null
@@ -1,27 +0,0 @@
---- setup/pymol.com.linux-rh7x	Sun Nov 20 02:46:39 2005
-+++ setup/pymol.com.linux-rh7x	Sat Jul  1 13:28:49 2006
-@@ -5,7 +5,7 @@
- # ==============================================================
- # Set PYMOL_PATH to point at the correct location on your system
- #
--PYMOL_PATH=/usr/local/pymol
-+PYMOL_PATH=@LOCALBASE@/share/pymol
- export PYMOL_PATH
- #
- # ==============================================================
-@@ -13,13 +13,13 @@
- #
- # python modules
- #
--if [ "$PYTHONPATH" == "" ]; then
-+if [ "$PYTHONPATH" = "" ]; then
- PYTHONPATH=${PYMOL_PATH}/modules
- else
- PYTHONPATH=${PYMOL_PATH}/modules:${PYTHONPATH}
- fi
- export PYTHONPATH
- #
--/usr/bin/python $PYMOL_PATH/modules/pymol/__init__.py "$@"
-+@LOCALBASE@/bin/python $PYMOL_PATH/modules/pymol/__init__.py "$@"
- 
- 
diff --git a/biology/pymol/files/patch-setup.py b/biology/pymol/files/patch-setup.py
new file mode 100644
index 000000000000..08bb35418fee
--- /dev/null
+++ b/biology/pymol/files/patch-setup.py
@@ -0,0 +1,19 @@
+--- setup.py.orig	2007-07-03 07:11:15.000000000 +0900
++++ setup.py	2008-03-06 17:59:33.000000000 +0900
+@@ -88,6 +88,8 @@
+              "layer0","layer1","layer2",
+              "layer3","layer4","layer5",
+              "/usr/include/freetype2",
++             "%%LOCALBASE%%/include",
++             "%%LOCALBASE%%/include/freetype2",
+ #             "/users/warren/ext/include",
+ # VMD plugin support
+ #             "contrib/uiuc/plugins/include",
+@@ -98,6 +100,7 @@
+    pyogl_libs = ["GL","GLU","glut"]
+    lib_dirs=[
+       "/usr/X11R6/lib",
++      "%%LOCALBASE%%/lib",
+ #      "/users/warren/pymol/ext/lib"
+       ]
+    def_macros=[("_PYMOL_MODULE",None),