[82956] trunk/dports/science/pymol-devel
adfernandes at macports.org
adfernandes at macports.org
Mon Aug 22 10:25:20 PDT 2011
Revision: 82956
http://trac.macports.org/changeset/82956
Author: adfernandes at macports.org
Date: 2011-08-22 10:25:19 -0700 (Mon, 22 Aug 2011)
Log Message:
-----------
science/pymol-devel ; sync with pymol, update, and change to python27
Added Paths:
-----------
trunk/dports/science/pymol-devel/Portfile
trunk/dports/science/pymol-devel/files/pymol_shell.diff
trunk/dports/science/pymol-devel/files/setup_py.diff
Removed Paths:
-------------
trunk/dports/science/pymol-devel/Portfile
trunk/dports/science/pymol-devel/files/pymol-build.patch
trunk/dports/science/pymol-devel/files/pymol-build.patch2
Deleted: trunk/dports/science/pymol-devel/Portfile
===================================================================
--- trunk/dports/science/pymol-devel/Portfile 2011-08-22 17:15:51 UTC (rev 82955)
+++ trunk/dports/science/pymol-devel/Portfile 2011-08-22 17:25:19 UTC (rev 82956)
@@ -1,93 +0,0 @@
-# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
-# $Id$
-
-PortSystem 1.0
-
-name pymol-devel
-svn.revision 3937
-version 1.3.${svn.revision}
-revision 2
-conflicts pymol
-categories science
-maintainers adfernandes openmaintainer
-description Molecular graphics system
-long_description PyMOL is a molecular graphics system with an embedded Python interpreter \
- designed for real-time visualization and rapid generation of high-quality \
- molecular graphics images and animations.
-
-platforms darwin
-
-homepage http://www.pymol.org/
-
-master_sites sourceforge
-fetch.type svn
-svn.url https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
-worksrcdir pymol
-
-depends_lib port:freetype port:libpng port:python27 port:py27-pmw port:py27-numeric port:mesa
-depends_run port:xdpyinfo
-
-patchfiles pymol-build.patch pymol-build.patch2
-use_configure no
-
-post-patch {
- reinplace "s|@PREFIX@|${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
-}
-
-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="${configure.cxx}"
-}
-
-default_variants +gcc45
-
-variant gcc43 description conflicts gcc44 gcc45 description {build using macports-gcc-4.3} {
- depends_lib-append port:gcc43
- # the current pymol makefile does not honour CC and CXX environment variables
- build.args-delete CC="${configure.cc}" CXX="${configure.cxx}"
- build.args-append CC="${prefix}/bin/gcc-mp-4.3" CXX="${prefix}/bin/g++-mp-4.3"
- configure.compiler macports-gcc-4.3
-}
-
-variant gcc44 description conflicts gcc43 gcc45 description {build using macports-gcc-4.4} {
- depends_lib-append port:gcc44
- # the current pymol makefile does not honour CC and CXX environment variables
- build.args-delete CC="${configure.cc}" CXX="${configure.cxx}"
- build.args-append CC="${prefix}/bin/gcc-mp-4.4" CXX="${prefix}/bin/g++-mp-4.4"
- configure.compiler macports-gcc-4.4
-}
-
-variant gcc45 description conflicts gcc43 gcc44 description {build using macports-gcc-4.5} {
- depends_lib-append port:gcc45
- # the current pymol makefile does not honour CC and CXX environment variables
- build.args-delete CC="${configure.cc}" CXX="${configure.cxx}"
- build.args-append CC="${prefix}/bin/gcc-mp-4.5" CXX="${prefix}/bin/g++-mp-4.5"
- 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 {
- system "${prefix}/bin/python2.7 -O ${prefix}/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/compileall.py -d ${prefix}/lib/pymol/modules ${destroot}${prefix}/lib/pymol/modules"
-}
Copied: trunk/dports/science/pymol-devel/Portfile (from rev 82951, trunk/dports/science/pymol/Portfile)
===================================================================
--- trunk/dports/science/pymol-devel/Portfile (rev 0)
+++ trunk/dports/science/pymol-devel/Portfile 2011-08-22 17:25:19 UTC (rev 82956)
@@ -0,0 +1,77 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem 1.0
+PortGroup python27 1.0
+
+name pymol-devel
+conflicts pymol
+svn.revision 3964
+version 1.4.1.${svn.revision}
+# revision 1
+categories science
+maintainers adfernandes openmaintainer
+description Molecular graphics system
+long_description PyMOL is a molecular graphics system with an embedded Python interpreter \
+ designed for real-time visualization and rapid generation of high-quality \
+ molecular graphics images and animations.
+
+platforms darwin
+
+homepage http://www.pymol.org/
+
+master_sites sourceforge
+fetch.type svn
+svn.url https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
+worksrcdir pymol
+
+depends_lib port:freetype port:libpng port:python27 port:py27-pmw port:py27-numpy port:py27-scipy port:mesa port:glew port:py27-tkinter
+depends_run port:xdpyinfo
+
+patchfiles setup_py.diff pymol_shell.diff
+
+post-patch {
+ reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/setup.py
+ reinplace "s|@@PYTHON_PKGDIR@@|${python.pkgd}|g" ${worksrcpath}/setup/pymol_macports
+ reinplace "s|@@PYTHON_BINARY@@|${python.bin}|g" ${worksrcpath}/setup/pymol_macports
+}
+
+use_parallel_build yes
+
+platform darwin 11 {
+ python.add_archflags no
+ build.env CC="/usr/bin/clang" CXX="/usr/bin/clang++"
+}
+
+variant gcc43 description conflicts gcc44 gcc45 gcc46 description {build using macports-gcc-4.3} {
+ depends_lib-append port:gcc43
+ python.add_archflags no
+ build.env CC="${prefix}/bin/gcc-mp-4.3" CXX="${prefix}/bin/g++-mp-4.3"
+}
+
+variant gcc44 description conflicts gcc43 gcc45 gcc46 description {build using macports-gcc-4.4} {
+ depends_lib-append port:gcc44
+ python.add_archflags no
+ build.env CC="${prefix}/bin/gcc-mp-4.4" CXX="${prefix}/bin/g++-mp-4.4"
+}
+
+variant gcc45 description conflicts gcc43 gcc44 gcc46 description {build using macports-gcc-4.5} {
+ depends_lib-append port:gcc45
+ python.add_archflags no
+ build.env CC="${prefix}/bin/gcc-mp-4.5" CXX="${prefix}/bin/g++-mp-4.5"
+}
+
+variant gcc46 description conflicts gcc43 gcc44 gcc45 description {build using macports-gcc-4.6} {
+ depends_lib-append port:gcc46
+ python.add_archflags no
+ build.env CC="${prefix}/bin/gcc-mp-4.6" CXX="${prefix}/bin/g++-mp-4.6"
+}
+
+post-destroot {
+ file copy ${worksrcpath}/setup/pymol_macports ${destroot}${prefix}/bin/pymol
+ file attributes ${destroot}${prefix}/bin/pymol -permissions a+x
+ ln -s ${python.pkgd}/pymol ${destroot}${python.pkgd}/pymol/pymol_path
+ foreach d {data modules examples test scripts} {
+ copy ${worksrcpath}/${d} ${destroot}${python.pkgd}/pymol
+ }
+}
Deleted: trunk/dports/science/pymol-devel/files/pymol-build.patch
===================================================================
--- trunk/dports/science/pymol-devel/files/pymol-build.patch 2011-08-22 17:15:51 UTC (rev 82955)
+++ trunk/dports/science/pymol-devel/files/pymol-build.patch 2011-08-22 17:25:19 UTC (rev 82956)
@@ -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= python2.7
-
- # Installed python binary (used only by boot target)
--#PYTHON=
-+PYTHON= python2.7
-
- # 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/python2.7
- PYTHON_LIB =
- PYTHON_LIB_DIR =
--PYTHON_INC_DIR = -I/sw/include/python2.3 \
-- -I/sw/include/python2.3/Numeric
-+PYTHON_INC_DIR = `python2.7-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/python2.7 -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/python2.7 $PYMOL_PATH/modules/pymol/__init__.py -d "_ set stereo_double_pump_mono,quiet=1" "$@"
Deleted: trunk/dports/science/pymol-devel/files/pymol-build.patch2
===================================================================
--- trunk/dports/science/pymol-devel/files/pymol-build.patch2 2011-08-22 17:15:51 UTC (rev 82955)
+++ trunk/dports/science/pymol-devel/files/pymol-build.patch2 2011-08-22 17:25:19 UTC (rev 82956)
@@ -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)
Copied: trunk/dports/science/pymol-devel/files/pymol_shell.diff (from rev 82951, trunk/dports/science/pymol/files/pymol_shell.diff)
===================================================================
--- trunk/dports/science/pymol-devel/files/pymol_shell.diff (rev 0)
+++ trunk/dports/science/pymol-devel/files/pymol_shell.diff 2011-08-22 17:25:19 UTC (rev 82956)
@@ -0,0 +1,22 @@
+--- /dev/null 2011-04-22 23:16:48.000000000 -0400
++++ setup/pymol_macports 2011-04-22 23:19:48.000000000 -0400
+@@ -0,0 +1,19 @@
++#!/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
++#
++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" "$@"
Copied: trunk/dports/science/pymol-devel/files/setup_py.diff (from rev 82951, trunk/dports/science/pymol/files/setup_py.diff)
===================================================================
--- trunk/dports/science/pymol-devel/files/setup_py.diff (rev 0)
+++ trunk/dports/science/pymol-devel/files/setup_py.diff 2011-08-22 17:25:19 UTC (rev 82956)
@@ -0,0 +1,41 @@
+--- setup.py.orig 2011-07-25 16:38:04.000000000 -0400
++++ setup.py 2011-07-26 00:00:37.000000000 -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",
+@@ -118,11 +117,14 @@
+ def_macros=[("_PYMOL_MODULE",None),
+ ("_PYMOL_LIBPNG",None),
+ ("_PYMOL_FREETYPE",None),
++ ("_PYMOL_INLINE",None),
++ ("_PYMOL_NUMPY",None),
++ ("_PYMOL_OPENGL_SHADERS",None),
++ ("NO_MMLIBS",None),
+ ]
+- ext_comp_args=[]
++ ext_comp_args=["-ffast-math","-funroll-loops","-O3","-fcommon"]
+ ext_link_args=[
+- "-L/usr/X11R6/lib64", "-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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