Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv8691
Modified Files:
pymol-py.info pymol-py.patch apbs.info
Log Message:
fix for startup problem
Index: pymol-py.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -d -r1.20 -r1.21
--- pymol-py.info 26 Feb 2013 03:30:52 -0000 1.20
+++ pymol-py.info 8 Mar 2013 17:43:03 -0000 1.21
@@ -1,9 +1,10 @@
Info2: <<
Package: pymol-py%type_pkg[python]
Version: 1.5
-Revision: 8
+Revision: 9
UseMaxBuildJobs: false
-Maintainer: W. G. Scott <[email protected]>
+# Maintainer: W. G. Scott <[email protected]>
+Maintainer: Jack Howarth <[email protected]>
Type: python (2.6 2.7)
# r4023
#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
@@ -16,7 +17,7 @@
Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
PatchFile: pymol-py.patch
-PatchFile-MD5: 2e287d04ecb51af1eeee3767e658ef5d
+PatchFile-MD5: 8048eb990477ee8a404324c864baed57
PatchFile2: pymol-py-rest.patch
PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
SourceDirectory: pymol-%v
@@ -48,7 +49,7 @@
# setup2.py currently mishandles the creation of the pymol_path symlink
# and the placement of the associated subdirectories.
#%p/bin/python%type_raw[python] setup2.py install --root %d
-ln -s %p/lib/python%type_raw[python]/site-packages/pymol
%i/lib/python%type_raw[python]/site-packages/pymol/pymol_path
+#ln -s %p/lib/python%type_raw[python]/site-packages/pymol
%i/lib/python%type_raw[python]/site-packages/pymol/pymol_path
cp -r data modules examples test scripts
%i/lib/python%type_raw[python]/site-packages/pymol
mkdir -p %i/lib/pymol-py%type_pkg[python]/bin
cp pymol.cmd %i/lib/pymol-py%type_pkg[python]/bin/pymol
Index: pymol-py.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- pymol-py.patch 26 Feb 2013 03:30:52 -0000 1.8
+++ pymol-py.patch 8 Mar 2013 17:43:03 -0000 1.9
@@ -1,6 +1,6 @@
diff -uNr pymol-1.5/modules/pmg_tk/PMGApp.py
pymol-1.5.fink/modules/pmg_tk/PMGApp.py
---- pymol-1.5/modules/pmg_tk/PMGApp.py 2012-05-16 21:39:13.000000000 -0400
-+++ pymol-1.5.fink/modules/pmg_tk/PMGApp.py 2013-02-25 21:01:06.000000000
-0500
+--- pymol-1.5/modules/pmg_tk/PMGApp.py 2013-02-25 22:21:17.000000000 -0500
++++ pymol-1.5.fink/modules/pmg_tk/PMGApp.py 2013-03-08 10:29:35.000000000
-0500
@@ -184,7 +184,7 @@
self.fifo.put(cmmd)
@@ -20,8 +20,8 @@
else:
win.destroy()
diff -uNr pymol-1.5/modules/pmg_tk/skins/normal/__init__.py
pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py
---- pymol-1.5/modules/pmg_tk/skins/normal/__init__.py 2013-02-25
20:51:28.000000000 -0500
-+++ pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py 2013-02-25
21:01:06.000000000 -0500
+--- pymol-1.5/modules/pmg_tk/skins/normal/__init__.py 2013-02-25
22:21:17.000000000 -0500
++++ pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py 2013-03-08
10:29:35.000000000 -0500
@@ -250,7 +250,7 @@
self.buttonArea.destroy()
@@ -57,8 +57,8 @@
else: # autocenter, deiconify, and run mainloop
win.destroy()
diff -uNr pymol-1.5/modules/pmg_tk/startup/apbs_tools.py
pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py
---- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2012-04-28
12:45:52.000000000 -0400
-+++ pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py 2013-02-25
21:01:06.000000000 -0500
+--- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2013-02-25
22:21:16.000000000 -0500
++++ pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py 2013-03-08
10:29:35.000000000 -0500
@@ -141,7 +141,7 @@
# APBS_BINARY_LOCATION = '/opt/bin/apbs'
#
@@ -68,9 +68,21 @@
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None
+diff -uNr pymol-1.5/modules/pymol/__init__.py
pymol-1.5.fink/modules/pymol/__init__.py
+--- pymol-1.5/modules/pymol/__init__.py 2013-02-25 22:21:15.000000000
-0500
++++ pymol-1.5.fink/modules/pymol/__init__.py 2013-03-08 10:31:16.000000000
-0500
+@@ -142,7 +142,7 @@
+ if (pymol_file[0:1] not in [ '\\', '/' ]) and
pymol_file[1:2]!=':':
+ pymol_file = os.getcwd()+"/"+pymol_file # make path
absolute
+
+- pymol_path =
re.sub(r"[\/\\][^\/\\]*$","/pymol_path",pymol_file)
++ pymol_path = re.sub(r"[\/\\][^\/\\]*$","",pymol_file)
+
+ if os.path.isdir(pymol_path):
+ os.environ['PYMOL_PATH'] = pymol_path
diff -uNr pymol-1.5/pymol.cmd pymol-1.5.fink/pymol.cmd
--- pymol-1.5/pymol.cmd 1969-12-31 19:00:00.000000000 -0500
-+++ pymol-1.5.fink/pymol.cmd 2013-02-25 21:01:06.000000000 -0500
++++ pymol-1.5.fink/pymol.cmd 2013-03-08 10:29:35.000000000 -0500
@@ -0,0 +1,16 @@
+#!/bin/sh
+#
@@ -89,8 +101,8 @@
+ exec @FINKPREFIX@/bin/python2.X
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d "_ set
stereo_double_pump_mono,quiet=1" -M "$@"
+fi
diff -uNr pymol-1.5/setup.py pymol-1.5.fink/setup.py
---- pymol-1.5/setup.py 2013-02-25 20:51:33.000000000 -0500
-+++ pymol-1.5.fink/setup.py 2013-02-25 21:05:43.000000000 -0500
+--- pymol-1.5/setup.py 2013-02-25 22:22:12.000000000 -0500
++++ pymol-1.5.fink/setup.py 2013-03-08 10:29:35.000000000 -0500
@@ -216,7 +216,7 @@
libs += ["png", "freetype"]
Index: apbs.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/apbs.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- apbs.info 11 Jun 2012 14:21:36 -0000 1.2
+++ apbs.info 8 Mar 2013 17:43:03 -0000 1.3
@@ -1,89 +1,52 @@
Package: apbs
-Version: 1.3.0
-Revision: 3
-UseMaxBuildJobs: false
-Source:
http://downloads.sourceforge.net/project/%n/%n/%n-%v/%n-1.3-source.tar.gz
-Source-MD5: f99a505365f07f6853979cfe2ef23365
-Depends: readline5-shlibs, gcc46-shlibs, python27
-BuildDepends: gcc46, python27, fink (>= 0.24.12)
-BuildConflicts: g77, g95, fort77
-Conflicts: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
-Replaces: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
-ConfigureParams: --disable-openmp --build=%m-apple-darwin`uname -r|cut -f1
-d.` --host=%m-apple-darwin`uname -r|cut -f1 -d.`
-SetCFLAGS: -O3
+Version: 1.4.0
+Revision: 1
+Source:
http://downloads.sourceforge.net/project/%n/%n/%n-%v/APBS-1.4-source.tar.gz
+Source-MD5: e0281bd44ffecb651e40687cdaa26361
+Depends: readline6-shlibs, maloc-shlibs, python27
+BuildDepends: readline6, maloc, fink (>= 0.28)
+BuildDependsOnly: true
Description: Adaptive Poisson-Boltzmann Solver
-PatchFile: %n.patch
-PatchFile-MD5: 2662144e3e3508a944902c0a5e29eaf1
-PatchScript: <<
-sed 's|@INSTALL_DIR@|%d|g' < %{PatchFile} | patch -p1
-<<
+SourceDirectory: %n
CompileScript: <<
#!/bin/bash -efv
-PATH=%p/bin:%p/sbin:${PATH} ; export PATH
-source %p/bin/init.sh
-perl -pi -e 's|PY_SHARED="-shared"|PY_SHARED="-bundle"|g' configure
-BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
-py_path=%p/bin/python2.7 F77=gfortran ./configure %c --enable-python
--with-python=%p/bin/python2.7 \
---disable-openmp --with-blas="-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib
-Wl,-undefined -Wl,dynamic_lookup" FFLAGS="-O3"
-perl -pi -e 's|\${prefix}/share|%i/share/%n|g' Makefile
-perl -pi -e 's|\$\(DESTDIR\)\$\(libdir\)|share/apbs/lib|g'
contrib/blas/Makefile
+cd build
+CMAKE_OPTIONS="-DCMAKE_INSTALL_PREFIX=%p \
+ -DCMAKE_VERBOSE_MAKEFILE=ON \
+ -DCMAKE_COLOR_MAKEFILE=ON \
+ -DCMAKE_BUILD_TYPE=Release \
+ -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \
+ -DCMAKE_INSTALL_NAME_DIR=%p/lib \
+ -DCMAKE_SYSTEM_PREFIX_PATH=\"%p;\/usr\" \
+ -DCMAKE_FIND_FRAMEWORK=LAST \
+ -DENABLE_OPENMP:BOOL=OFF \
+ -DENABLE_MPI:BOOL=OFF"
+cmake $CMAKE_OPTIONS -DCMAKE_C_FLAGS="-I%p/include -O3 -ffast-math -g" ..
make
<<
InstallScript: <<
#!/bin/zsh -efv
-rm -Rf **/CVS # fink validate complains if this junk is left behind.
-perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' examples/**/*.py
-perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' tools/**/*.py
-rm -f **/*.o
-#
-# make install DESTDIR=%d
-# install it ourselves:
- mkdir -p %i/bin
- /bin/cp bin/apbs bin/ApbsClient.py %i/bin/.
- echo '#!%p/bin/python2.7' >| %i/bin/wsdl2py
- echo "from ZSI.generate.commands import wsdl2py" >> %i/bin/wsdl2py
- echo "wsdl2py()" >> %i/bin/wsdl2py
- chmod a+x %i/bin/wsdl2py
- #
- mkdir -p %i/share/%n
- /bin/cp -r examples %i/share/%n/.
- /bin/cp -r tools %i/share/%n/.
- /bin/cp -r doc %i/share/%n/.
- #
- mkdir -p %i/share/doc
- ln -s %p/share/%n/doc %i/share/doc/%n
- #
- mkdir -p %i/lib/python2.7/site-packages/ZSI
- /bin/cp -r contrib/opal/ZSI/ZSI/*
%i/lib/python2.7/site-packages/ZSI/.
- #
- mkdir -p %i/include/apbs
- /bin/cp **/*.h %i/include/apbs/.
- #
- mkdir -p %i/lib
- /bin/rm -rf contrib
- /bin/cp **/.*/*.a %i/lib/.
- /bin/cp **/*.la %i/lib/.
- ranlib %i/lib/*.a
-#
-<<
-PreRmScript: <<
-/usr/bin/find %p/lib/python2.7/site-packages/ZSI -name '*.pyo' -delete
+cd build
+make install DESTDIR=%d
+perl -pi -e "s|env python|env %p/bin/python2.7|g"
%i/share/%n/tools/manip/psize.py
+perl -pi -e "s|env python|env %p/bin/python2.7|g"
%i/share/apbs/examples/protein-rna/fit.py
+for f in apbs_check_forces apbs_check_results apbs_logger apbs_tester; do
+perl -pi -e "s|env python|env %p/bin/python2.7|g" %i/share/apbs/tests/$f.py
+done
<<
-PostInstScript: <<
-%p/bin/python2.7 -O %p/lib/python2.7/compileall.py -q
%p/lib/python2.7/site-packages/ZSI
+Shlibs: <<
+ !%p/lib/libapbs_generic.dylib
+ !%p/lib/libapbs_mg.dylib
+ !%p/lib/libapbs_pmgc.dylib
<<
-################################################################################
-SplitOff: <<
- Package: %N-dev
- BuildDependsOnly: true
- Description: apbs headers, static libraries and libtool files
- Files:<<
- include/apbs
- lib/*.a
- lib/*.la
- <<
+DescPackaging: <<
+APBS starting at version 1.4.0 now uses cmake for builds. The ABPS python
+support is disabled by default and currently unable to find fink's python.
+The cmake build only supports shared libraries but doesn't soversion them
+yet so these are treated as private, the -dev split-off is dropped and
+the package is BuildDependsOnly: true until upstream gets serious about
+its shared library handling and implements soversioning.
<<
-################################################################################
Homepage: http://apbs.sourceforge.net/
RunTimeVars: <<
APBS_PSIZE:%p/share/%n/tools/manip
------------------------------------------------------------------------------
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