[78203] trunk/dports/science/pymol
ryandesign at macports.org
ryandesign at macports.org
Thu Apr 28 03:32:29 PDT 2011
Revision: 78203
http://trac.macports.org/changeset/78203
Author: ryandesign at macports.org
Date: 2011-04-28 03:32:28 -0700 (Thu, 28 Apr 2011)
Log Message:
-----------
pymol: maintainer update to 1.4; see #29242
Modified Paths:
--------------
trunk/dports/science/pymol/Portfile
Added Paths:
-----------
trunk/dports/science/pymol/files/pymol_shell.diff
trunk/dports/science/pymol/files/setup_py.diff
Removed Paths:
-------------
trunk/dports/science/pymol/files/pymol-build.patch
trunk/dports/science/pymol/files/pymol-build.patch2
Modified: trunk/dports/science/pymol/Portfile
===================================================================
--- trunk/dports/science/pymol/Portfile 2011-04-28 10:17:33 UTC (rev 78202)
+++ trunk/dports/science/pymol/Portfile 2011-04-28 10:32:28 UTC (rev 78203)
@@ -2,10 +2,10 @@
# $Id$
PortSystem 1.0
+PortGroup python26 1.0
name pymol
-version 1.3
-revision 3
+version 1.4
categories science
maintainers bromo.med.uc.edu:howarth
description Molecular graphics system
@@ -20,37 +20,21 @@
master_sites sourceforge
fetch.type svn
svn.url https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
-svn.revision 3930
+svn.revision 3945
worksrcdir pymol
-depends_lib port:freetype port:libpng port:python26 port:py26-pmw port:py26-numeric port:mesa port:py26-tkinter
+depends_lib port:freetype port:libpng port:python26 port:py26-pmw port:py26-numeric port:mesa port:glew port:py26-tkinter
depends_run port:xdpyinfo
-patchfiles pymol-build.patch pymol-build.patch2
-use_configure no
+patchfiles setup_py.diff pymol_shell.diff
post-patch {
- reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/contrib/modules/Makefile.pre.in.src
- reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/setup/Rules.osx-fink
- reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/setup/pymol.com.osx-fink
- reinplace "s|-Wno-long-double||g" ${worksrcpath}/setup/Rules.osx-fink
- reinplace "s|/usr/X11R6|${prefix}|g" ${worksrcpath}/setup/Rules.osx-fink
- reinplace "s|/usr/X11R6|${prefix}|g" ${worksrcpath}/modules/pymol/__init__.py
+ reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/setup.py
+ reinplace "s|@@PYTHON_PKGDIR@@|${python.pkgd}|g" ${worksrcpath}/setup/pymol_macports
+ reinplace "s|@@PYTHON_BINARY@@|${python.bin}|g" ${worksrcpath}/setup/pymol_macports
}
-post-configure {
- copy ${worksrcpath}/setup/Rules.osx-fink ${worksrcpath}/Rules.delsci
- if { [variant_isset gcc43] || [variant_isset gcc44] || [variant_isset gcc45] } {
- reinplace "s| -no-cpp-precomp||g" ${worksrcpath}/Rules.delsci
- reinplace "s|^BUILD = |BUILD = -lstdc++ |" ${worksrcpath}/Rules.delsci
- }
-}
-
use_parallel_build no
-pre-build {
- build.args -f Makefile.delsci \
- CC="${configure.cc}" CXX="${configure.cxx}"
-}
variant gcc43 description conflicts gcc44 gcc45 description {build using macports-gcc-4.3} {
depends_lib-append port:gcc43
@@ -76,15 +60,10 @@
configure.compiler macports-gcc-4.5
}
-destroot {
- file mkdir ${destroot}${prefix}/lib/pymol/bin
- copy ${worksrcpath}/setup/pymol.com.osx-fink ${destroot}${prefix}/lib/pymol/bin/pymol
- ln -s ${prefix}/lib/pymol/bin/pymol ${destroot}${prefix}/bin
- foreach d {data modules examples test scripts} {
- copy ${worksrcpath}/${d} ${destroot}${prefix}/lib/pymol
+post-destroot {
+ file copy ${worksrcpath}/setup/pymol_macports ${destroot}${prefix}/bin/pymol
+ file attributes ${destroot}${prefix}/bin/pymol -permissions a+x
+ foreach d {data modules examples test scripts} {
+ copy ${worksrcpath}/${d} ${destroot}${python.pkgd}/pymol
}
}
-
-post-destroot {
- system "${prefix}/bin/python2.6 -O ${prefix}/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/compileall.py -d ${prefix}/lib/pymol/modules ${destroot}${prefix}/lib/pymol/modules"
-}
Deleted: trunk/dports/science/pymol/files/pymol-build.patch
===================================================================
--- trunk/dports/science/pymol/files/pymol-build.patch 2011-04-28 10:17:33 UTC (rev 78202)
+++ trunk/dports/science/pymol/files/pymol-build.patch 2011-04-28 10:32:28 UTC (rev 78203)
@@ -1,98 +0,0 @@
---- contrib/modules/Makefile.pre.in.src.org 2008-05-09 19:09:50.000000000 -0400
-+++ contrib/modules/Makefile.pre.in.src 2008-05-09 19:11:25.000000000 -0400
-@@ -88,10 +88,10 @@
- # === Variables that you may want to customize (rarely) ===
-
- # (Static) build target
--TARGET= python
-+TARGET= python2.6
-
- # Installed python binary (used only by boot target)
--#PYTHON=
-+PYTHON= python2.6
-
- # Add more -I and -D options here
- CFLAGS= $(OPT) -I$(INCLUDEPY) -I$(EXECINCLUDEPY) $(DEFS)
-@@ -126,12 +126,13 @@
- MACHDEP= @MACHDEP@
- SO= @SO@
- LDSHARED= @LDSHARED@
-+BLDSHARED= @LDSHARED@
- CCSHARED= @CCSHARED@
- LINKFORSHARED= @LINKFORSHARED@
- #@SET_CCC@
-
- # Install prefix for architecture-independent files
--prefix= /usr/local
-+prefix= @PREFIX@
-
- # Install prefix for architecture-dependent files
- exec_prefix= $(prefix)
-@@ -168,7 +169,7 @@
- MAKEFILE= $(LIBPL)/Makefile
- CONFIGC= $(LIBPL)/config.c
- CONFIGCIN= $(LIBPL)/config.c.in
--SETUP= $(LIBPL)/Setup.thread $(LIBPL)/Setup.local $(LIBPL)/Setup
-+SETUP= $(LIBPL)/Setup.config $(LIBPL)/Setup.local $(LIBPL)/Setup
-
- SYSLIBS= $(LIBM) $(LIBC)
-
---- setup/Rules.osx-fink.org Sat Apr 3 04:05:01 2004
-+++ setup/Rules.osx-fink Mon Apr 5 18:11:02 2004
-@@ -6,7 +6,7 @@
- #
- #- Building ----------------------------------------------------------
- #--- Tell "make" how to get to PyMOL
--PYMOL_PATH = /Users/delwarl/fink/pymol
-+PYMOL_PATH = @PREFIX@/lib/pymol
- #---------------------------------------------------------------------
- #
- #- Dependencies ------------------------------------------------------
-@@ -14,14 +14,13 @@
- XLIB_DIR = -L/usr/X11R6/lib
- XINC_DIR = -I/usr/X11R6/include
- #--- Python
--PYTHON_EXE = /sw/bin/python2.3
-+PYTHON_EXE = @PREFIX@/bin/python2.6
- PYTHON_LIB =
- PYTHON_LIB_DIR =
--PYTHON_INC_DIR = -I/sw/include/python2.3 \
-- -I/sw/include/python2.3/Numeric
-+PYTHON_INC_DIR = `python2.6-config --include`/Numeric
- #--- Other external dependencies
--EXT_INC_DIR = -I/sw/include
--EXT_LIB_DIR = -L/sw/lib
-+EXT_INC_DIR = -I at PREFIX@/include
-+EXT_LIB_DIR = -L at PREFIX@/lib
- #---------------------------------------------------------------------
- #
- #- Build for LINUX as an importable module ---------------------------
-@@ -30,7 +29,7 @@
- #--- PyMOL configuration
- DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_FINK
- #--- How we build shared libraries
--BUILD = -bundle -bundle_loader /sw/bin/python2.3 -flat_namespace -undefined suppress
-+BUILD = -bundle -bundle_loader @PREFIX@/bin/python2.6 -flat_namespace -undefined suppress
- #--- What are we trying to build?
- DEST = -o modules/pymol/_cmd.so
- #--- Gcc Options for Linux
---- setup/pymol.com.osx-fink.orig 2005-11-19 12:46:39.000000000 -0500
-+++ setup/pymol.com.osx-fink 2006-01-09 20:24:01.000000000 -0500
-@@ -5,7 +5,7 @@
- # ==============================================================
- # Set PYMOL_PATH to point at the correct location on your system
- #
--PYMOL_PATH=/Users/delwarl/pymol
-+PYMOL_PATH=@PREFIX@/lib/pymol
- export PYMOL_PATH
- #
- # ==============================================================
-@@ -20,6 +20,9 @@
- fi
- export PYTHONPATH
- #
--exec /sw/bin/python $PYMOL_PATH/modules/pymol/__init__.py "$@"
-+APBS_PSIZE=@PREFIX@/bin/apbs-psize.py
-+export APBS_PSIZE
-+#
-+exec @PREFIX@/bin/python2.6 $PYMOL_PATH/modules/pymol/__init__.py -d "_ set stereo_double_pump_mono,quiet=1" "$@"
Deleted: trunk/dports/science/pymol/files/pymol-build.patch2
===================================================================
--- trunk/dports/science/pymol/files/pymol-build.patch2 2011-04-28 10:17:33 UTC (rev 78202)
+++ trunk/dports/science/pymol/files/pymol-build.patch2 2011-04-28 10:32:28 UTC (rev 78203)
@@ -1,56 +0,0 @@
---- Makefile.delsci.orig 2010-07-02 17:29:57.000000000 -0400
-+++ Makefile.delsci 2010-07-02 17:35:04.000000000 -0400
-@@ -61,15 +61,15 @@
- /bin/rm -f .update .includes
- cd contrib;$(MAKE) -f Makefile.delsci
- cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci
-- cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I$(PYMOL_PATH)/layer0 -I$(PYMOL_PATH)/ov/src
-- $(CC) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)
-+ cd modules/cealign/src; $(CXX) -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src
-+ $(CC) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)
-
- semistatic: .includes .depends .update
- /bin/rm -f .update .includes
- cd contrib;$(MAKE) -f Makefile.delsci static
- cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci
-- cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I$(PYMOL_PATH)/layer0 -I$(PYMOL_PATH)/ov/src
-- g++ $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)
-+ cd modules/cealign/src; $(CXX) -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src
-+ $(CXX) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)
-
- free:
- /bin/rm -rf freemol
---- layer4/Makefile.delsci.orig 2010-07-02 17:37:56.000000000 -0400
-+++ layer4/Makefile.delsci 2010-07-02 17:38:17.000000000 -0400
-@@ -3,7 +3,7 @@
-
- include ../Rules.delsci
-
--CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src
-+CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src -I../modules/cealign/src
-
- all: layer
-
---- modules/pmg_tk/startup/apbs_tools.py.orig 2010-07-02 18:40:05.000000000 -0400
-+++ modules/pmg_tk/startup/apbs_tools.py 2010-07-02 18:41:40.000000000 -0400
-@@ -183,6 +183,11 @@
- searchDirs.append("/tmp")
- searchDirs.append(".")
-
-+ # This must come before /opt/local/bin (which may also be in PATH) in
-+ # order for our pdb2pqr importing to work
-+ # correctly. /opt/local/bin/pdb2pqr just calls through to this.
-+ searchDirs.append(os.path.join("/opt", "local", "share", "pdb2pqr"))
-+
- searchDirs.extend(string.split(os.environ["PATH"], ":"))
- searchDirs.append(os.path.join("/usr", "local", "bin"))
- searchDirs.append(os.path.join("/opt", "local", "bin"))
-@@ -787,7 +792,7 @@
- label_pyclass = FileDialogButtonClassFactory.get(self.setPsizeLocation),
- validate = {'validator':quickFileValidation,},
- #value = '/usr/local/apbs-0.3.1/tools/manip/psize.py',
-- value = get_default_location('psize.py'),
-+ value = get_default_location('apbs-psize.py'),
- label_text = 'APBS psize.py location:',
- )
- self.psize.pack(fill = 'x', padx = 20, pady = 10)
Added: trunk/dports/science/pymol/files/pymol_shell.diff
===================================================================
--- trunk/dports/science/pymol/files/pymol_shell.diff (rev 0)
+++ trunk/dports/science/pymol/files/pymol_shell.diff 2011-04-28 10:32:28 UTC (rev 78203)
@@ -0,0 +1,29 @@
+--- /dev/null 2011-04-22 23:16:48.000000000 -0400
++++ setup/pymol_macports 2011-04-22 23:19:48.000000000 -0400
+@@ -0,0 +1,26 @@
++#!/bin/sh
++#
++# PyMOL startup script
++#
++# ==============================================================
++# Set PYMOL_PATH to point at the correct location on your system
++#
++PYMOL_PATH=@@PYTHON_PKGDIR@@/pymol
++export PYMOL_PATH
++#
++# ==============================================================
++# (no changes usually required below here)
++#
++# python modules
++#
++if [ "$PYTHONPATH" == "" ]; then
++PYTHONPATH=${PYMOL_PATH}/modules
++else
++PYTHONPATH=${PYMOL_PATH}/modules:${PYTHONPATH}
++fi
++export PYTHONPATH
++#
++APBS_PSIZE=@PREFIX@/bin/apbs-psize.py
++export APBS_PSIZE
++#
++exec @@PYTHON_BINARY@@ @@PYTHON_PKGDIR@@/pymol/__init__.py -d "_ set stereo_double_pump_mono,quiet=1" "$@"
Added: trunk/dports/science/pymol/files/setup_py.diff
===================================================================
--- trunk/dports/science/pymol/files/setup_py.diff (rev 0)
+++ trunk/dports/science/pymol/files/setup_py.diff 2011-04-28 10:32:28 UTC (rev 78203)
@@ -0,0 +1,43 @@
+--- setup.py.orig 2011-04-22 22:47:12.000000000 -0400
++++ setup.py 2011-04-22 22:48:24.000000000 -0400
+@@ -101,11 +101,10 @@
+ #
+ # REMEMEBER to use "./ext/bin/python ..."
+ #
+- EXT = os.getcwd()+"/ext"
++ EXT = "@PREFIX@"
+ inc_dirs=["ov/src",
+ "layer0","layer1","layer2",
+ "layer3","layer4","layer5",
+- "/usr/X11R6/include",
+ EXT+"/include",
+ EXT+"/include/GL",
+ EXT+"/include/freetype2",
+@@ -116,13 +115,16 @@
+ pyogl_libs = []
+ lib_dirs=[]
+ def_macros=[("_PYMOL_MODULE",None),
++ ("_PYMOL_INLINE",None),
+ ("_PYMOL_LIBPNG",None),
+ ("_PYMOL_FREETYPE",None),
++ ("_PYMOL_NUMPY",None),
++ ("_PYMOL_OPENGL_SHADERS",None),
++ ("NO_MMLIBS",None),
+ ]
+- ext_comp_args=[]
++ ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
+ ext_link_args=[
+- "-L/usr/X11R6/lib", "-lGL", "-lXxf86vm",
+- "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype"
++ "-L"+EXT+"/lib", "-lpng", "-lGL", "-lglut", "-lGLEW", "-lfreetype"
+ ]
+ #============================================================================
+ else: # linux or other unix
+@@ -181,6 +183,7 @@
+ 'pymol/opengl/glu',
+ 'pymol/opengl/glut',
+ 'pymol/wizard',
++ 'pymol2',
+ 'web',
+ 'web/examples',
+ 'web/javascript', ],
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