5 files changed, 44 insertions, 11 deletions

diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile
index 968c1995186e..d53214185a48 100644
--- a/biology/pymol/Makefile
+++ b/biology/pymol/Makefile
@@ -5,8 +5,7 @@
 # $FreeBSD$
 
 PORTNAME=	pymol
-PORTVERSION=	0.90
-PORTREVISION=	1
+PORTVERSION=	0.93
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	pymol
@@ -29,6 +28,14 @@ USE_PYTHON=	yes
 
 .include <bsd.port.pre.mk>
 
+.if !defined(PICFLAG)
+.if ${MACHINE_ARCH} == "sparc64"
+PICFLAG=-fPIC
+.else
+PICFLAG=-fpic
+.endif
+.endif
+
 pre-patch:
 	@${INSTALL_DATA} ${WRKSRC}/setup/Rules.linux ${WRKSRC}/Rules.make
 .if ${PYTHON_REL} >= 230
@@ -37,12 +44,13 @@ pre-patch:
 
 post-patch:
 	@${INSTALL_DATA} ${WRKSRC}/setup/pymol.com.linux-rh7x ${WRKSRC}/setup/pymol.com
-	@${REINPLACE_CMD} 's,@PREFIX@,${PREFIX},g' ${WRKSRC}/setup/pymol.com
+	@${REINPLACE_CMD} -e 's,@PREFIX@,${PREFIX},g' -e 's,@LOCALBASE@,${LOCALBASE},g' ${WRKSRC}/setup/pymol.com
 	@${REINPLACE_CMD} -e 's,@PREFIX@,${PREFIX},g' \
 		-e 's,examples\(/devel/cgo03.py\),${EXAMPLESDIR}\1,' \
 		${WRKSRC}/modules/pmg_tk/Demo.py
 	@${RM} -f ${WRKSRC}/modules/pmg_tk/Demo.py.*
-	@${REINPLACE_CMD} 's,@PYTHON_VERSION@,${PYTHON_VERSION},g' ${WRKSRC}/Rules.make
+	${REINPLACE_CMD} -e 's,@PYTHON_VERSION@,${PYTHON_VERSION},g' \
+		-e 's,@PICFLAG@,${PICFLAG},g' ${WRKSRC}/Rules.make
 
 do-install:
 	@${INSTALL_SCRIPT} ${WRKSRC}/setup/pymol.com ${PREFIX}/bin/pymol
diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo
index 5379be65faf0..66d4c7893b26 100644
--- a/biology/pymol/distinfo
+++ b/biology/pymol/distinfo
@@ -1 +1,2 @@
-MD5 (pymol-0_90-src.tgz) = be181d10df622b011725d9541da22070
+MD5 (pymol-0_93-src.tgz) = f3a4e6d7fb25ad97e07a9f2eead304a5
+SIZE (pymol-0_93-src.tgz) = 2352042
diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make
index aa4c69fccdf5..930081bf6e65 100644
--- a/biology/pymol/files/patch-Rules.make
+++ b/biology/pymol/files/patch-Rules.make
@@ -1,11 +1,11 @@
---- Rules.make.orig	Thu Jul 24 15:21:01 2003
-+++ Rules.make	Thu Jul 24 15:27:58 2003
+--- Rules.make.orig	Wed Mar 17 19:40:11 2004
++++ Rules.make	Wed Mar 17 19:40:33 2004
 @@ -4,22 +4,22 @@
  #
  #- Building ----------------------------------------------------------
  #--- Tell "make" how to get to PyMOL 
 -PYMOL_PATH = /users/warren/pymol
-+PYMOL_PATH = ${PREFIX}
++PYMOL_PATH = ${LOCALBASE}
  #---------------------------------------------------------------------
  #
  #- Dependencies ------------------------------------------------------
@@ -31,7 +31,12 @@
  #---------------------------------------------------------------------
  #
  #- Build for LINUX as an importable module ---------------------------
-@@ -32,14 +32,14 @@
+@@ -28,18 +28,18 @@
+ #--- PyMOL configuration
+ DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY 
+ #--- How we build shared libraries
+-BUILD = -shared 
++BUILD = -shared
  #--- What are we trying to build?
  DEST = -o modules/pymol/_cmd.so
  #--- Gcc Options for Linux
@@ -64,7 +69,7 @@
  
  C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \
 -   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS)
-+   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) $(PYMOL_INC_DIRS)
++   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) $(PYMOL_INC_DIRS) @PICFLAG@
 +
 +override CFLAGS := $(C_FLAGS) ${CFLAGS}
  
diff --git a/biology/pymol/files/patch-setup+pymol+com+linux-rh7x b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x
index 07ae40a91fc9..3d785f32abc9 100644
--- a/biology/pymol/files/patch-setup+pymol+com+linux-rh7x
+++ b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x
@@ -14,5 +14,5 @@
  #dbx /usr/bin/python 
  #gdb /usr/bin/python 
 -/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
-+@PREFIX@/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
++@LOCALBASE@/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
  
diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index 79ce103ff778..e33133c5c93b 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -215,6 +215,9 @@ share/pymol/modules/pymol/editor.pyo
 share/pymol/modules/pymol/embed/__init__.py
 share/pymol/modules/pymol/embed/__init__.pyc
 share/pymol/modules/pymol/embed/__init__.pyo
+share/pymol/modules/pymol/embed/epymol/__init__.pyo
+share/pymol/modules/pymol/embed/epymol/__init__.pyc    
+share/pymol/modules/pymol/embed/epymol/__init__.py
 share/pymol/modules/pymol/embed/wxpymol/__init__.py
 share/pymol/modules/pymol/embed/wxpymol/__init__.pyc
 share/pymol/modules/pymol/embed/wxpymol/__init__.pyo
@@ -366,6 +369,7 @@ share/pymol/modules/pymol/xwin.pyc
 share/pymol/modules/pymol/xwin.pyo
 share/pymol/test/README
 share/pymol/test/cyg
+share/pymol/test/dat/odd01.pdb
 share/pymol/test/dat/1tii.pdb
 share/pymol/test/dat/3al1.pdb
 share/pymol/test/dat/3al1.r3d
@@ -378,6 +382,10 @@ share/pymol/test/dat/pept.r3d
 share/pymol/test/dat/small01.mol
 share/pymol/test/dat/tiny.pdb
 share/pymol/test/dat/water.pdb
+share/pymol/test/inp/B04.py
+share/pymol/test/inp/B05.py
+share/pymol/test/inp/C0700odd.pml
+share/pymol/test/inp/C1100do.py
 share/pymol/test/inp/B01.py
 share/pymol/test/inp/B02.py
 share/pymol/test/inp/B03.py
@@ -423,6 +431,15 @@ share/pymol/test/inp/T02.py
 share/pymol/test/inp/T03.py
 share/pymol/test/inp/T04.py
 share/pymol/test/inp/U01.pml
+share/pymol/test/ref/C0700odd.1.pdb
+share/pymol/test/ref/C0700odd.2.pdb
+share/pymol/test/ref/C0700odd.3.pdb
+share/pymol/test/ref/C0700odd.4.pdb
+share/pymol/test/ref/C0700odd.5.pdb
+share/pymol/test/ref/C0700odd.6.pdb
+share/pymol/test/ref/C0700odd.7.pdb
+share/pymol/test/ref/C0700odd.log
+share/pymol/test/ref/C1100do.log
 share/pymol/test/ref/C0001quit.log
 share/pymol/test/ref/C0010hello.log
 share/pymol/test/ref/C0020pdb.log
@@ -482,6 +499,7 @@ share/pymol/test/win.py
 @dirrm share/pymol/modules/pymol/opengl/gl
 @dirrm share/pymol/modules/pymol/opengl
 @dirrm share/pymol/modules/pymol/embed/wxpymol
+@dirrm share/pymol/modules/pymol/embed/epymol
 @dirrm share/pymol/modules/pymol/embed
 @dirrm share/pymol/modules/pymol
 @dirrm share/pymol/modules/pmg_wx
@@ -520,6 +538,7 @@ share/pymol/test/win.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/sele_wiz.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/start_pymol.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/pick_wiz.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/launching/README
 %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_demo.py