dist-git conversion

#2781)

.gitignore

@@ -0,0 +1 @@
+apbs-1.1.0-source.tar.gz

LGPL_V2

@@ -0,0 +1,482 @@
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Makefile

@@ -1,21 +0,0 @@
-# Makefile for source rpm: apbs
-# $Id$
-NAME := apbs
-SPECFILE = $(firstword $(wildcard *.spec))
-
-define find-makefile-common
-for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done
-endef
-
-MAKEFILE_COMMON := $(shell $(find-makefile-common))
-
-ifeq ($(MAKEFILE_COMMON),)
-# attept a checkout
-define checkout-makefile-common
-test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2
-endef
-
-MAKEFILE_COMMON := $(shell $(checkout-makefile-common))
-endif
-
-include $(MAKEFILE_COMMON)

apbs-configure.ac.patch

@@ -0,0 +1,39 @@
+--- configure.ac_orig	2009-07-10 11:37:12.000000000 -0700
++++ configure.ac	2009-07-10 16:02:33.000000000 -0700
+@@ -390,7 +390,7 @@
+ 
+ if test -n "${USE_FETK_LIBRARY}"; then
+ 	maloc_lib_path="${fetk_library_path}"
+-	AC_CHECK_FILE(${maloc_lib_path}/libmaloc.a,[maloc_lib="yes"],[maloc_lib=""])
++	AC_CHECK_FILE(${maloc_lib_path}/libmaloc.so,[maloc_lib="yes"],[maloc_lib=""])
+ 	if test -z "${maloc_lib}"; then
+ 		AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified])
+ 	fi
+@@ -806,7 +806,7 @@
+ fi
+ LDFLAGS=${LDFLAGS_SAVE};
+ CPPFLAGS=${CPPFLAGS_SAVE};
+-AC_SUBST(rl_lib)
++# AC_SUBST(rl_lib)
+ 
+ dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK
+ dnl # -----------------------
+@@ -1028,6 +1028,7 @@
+ 	blas_lib=${contrib_path}/blas/.libs/libapbsblas.a
+ fi
+ AC_SUBST(apbs_do_blas)
++AC_SUBST(blas_lib)
+ 
+ dnl # -----------------------
+ dnl # If using Portland compilers, do not compile
+@@ -1206,7 +1207,9 @@
+ else
+   apbs_build_libraries="${top_apbsdir}/bin/libapbsmainroutines.la \
+ 			${top_apbsdir}/src/aaa_lib/libapbs.la \
+-			${maloc_lib} ${lib_list}"
++			${top_apbsdir}/contrib/pmgZ/libapbspmgz.la \
++			${top_apbsdir}/contrib/aqua/libapbsaqua.la \
++			${maloc_lib} ${blas_lib} ${lib_list}"
+ fi
+ AC_SUBST(apbs_build_libraries)
+ 

apbs-makefile.am.patch

@@ -0,0 +1,96 @@
+--- ./tools/python/Makefile.am_orig	2009-07-23 12:08:49.000000000 -0700
++++ ./tools/python/Makefile.am	2009-07-23 13:20:16.000000000 -0700
+@@ -16,4 +16,5 @@
+ noinst_PROGRAMS       = _apbslib.so
+ _apbslib_so_SOURCES   = apbslib.c
+ _apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+-_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
++_apbslib_so_LDFLAGS   = @maloc_lib@ @blas_lib@ $(PY_LDFLAGS)
++_apbslib_so_LDADD    = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so
+--- ./tools/python/vgrid/Makefile.am_orig	2009-03-05 12:30:03.000000000 -0800
++++ ./tools/python/vgrid/Makefile.am	2009-07-23 13:20:08.000000000 -0700
+@@ -16,5 +16,6 @@
+    noinst_PROGRAMS     = _vgrid.so
+    _vgrid_so_SOURCES   = vgridlib.c
+    _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+-   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
++   _vgrid_so_LDFLAGS   = $(PY_LDFLAGS) @maloc_lib@ @lib_list@
++   _vgrid_so_LDADD    = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so
+ endif
+--- ./tools/arpack/Makefile.am_orig	2009-07-23 13:20:45.000000000 -0700
++++ ./tools/arpack/Makefile.am	2009-07-23 13:20:47.000000000 -0700
+@@ -12,7 +12,7 @@
+ 
+ noinst_PROGRAMS  = driver
+ driver_SOURCES   = driver.c readhb.f ardriv.f
+-driver_LDADD     = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@
++driver_LDADD     = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ -latlas
+ INCLUDES         = @inc_list@
+ AM_CFLAGS           = @CFLAGS@
+ AM_LDFLAGS           = @LDFLAGS@ @FFLAGS@
+--- ./bin/Makefile.am_orig	2009-07-22 22:08:44.000000000 -0700
++++ ./bin/Makefile.am	2009-07-22 22:11:07.000000000 -0700
+@@ -12,24 +12,24 @@
+ 
+ build_libraries = @apbs_build_libraries@
+ 
+-bindir = ${prefix}/bin
++# bindir = ${prefix}/bin
+ bin_PROGRAMS     = apbs
+ apbs_SOURCES     = main.c 
+-apbs_LDADD       = ${build_libraries}
++apbs_LDADD       = ${build_libraries} ./libapbsmainroutines.la
+ 
+-libdir = ${prefix}/lib
++# libdir = ${prefix}/lib
+ lib_LTLIBRARIES = libapbsmainroutines.la
+ libapbsmainroutines_la_SOURCES = routines.c
+-libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION}
++libapbsmainroutines_la_LDFLAGS = @maloc_lib@ ../src/aaa_lib/libapbs.la -version-info ${APBS_VERSION}
+ 
+ INCLUDES = @inc_list@
+ AM_CFLAGS= @wall_pedantic@
+ AM_LDFLAGS       = @LDFLAGS@ @FFLAGS@
+  
+-includedir = ${prefix}/include/apbs
+-include_HEADERS = routines.h
++# includedir = ${prefix}/include/apbs
++# include_HEADERS = routines.h
+ 
+-install-data-local:
+-	-cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
+-	-chmod 755 ${prefix}/bin/ApbsClient.py
+-	-rm -f ${prefix}/bin/wsdl2py 
+\ No newline at end of file
++#install-data-local:
++#	-cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
++#	-chmod 755 ${prefix}/bin/ApbsClient.py
++#	-rm -f ${prefix}/bin/wsdl2py 
+--- ./src/aaa_lib/Makefile.am_orig	2009-07-22 22:08:57.000000000 -0700
++++ ./src/aaa_lib/Makefile.am	2009-07-22 22:12:12.000000000 -0700
+@@ -18,12 +18,12 @@
+ AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la
+ BLAS_LIBS = @blas_lib@
+ 
+-libdir = ${prefix}/lib
++# libdir = ${prefix}/lib
+ lib_LTLIBRARIES = libapbs.la
+ 
+ libapbs_la_SOURCES = apbs_link.c
+ libapbs_la_LIBADD  = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS}
+-libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
++libapbs_la_LDFLAGS = @maloc_lib@ -version-info ${APBS_VERSION}
+ 
+ INCLUDES         = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@
+ AM_CFLAGS        = @wall_pedantic@
+--- ./contrib/opal/Makefile.am_orig	2009-07-23 17:40:40.000000000 -0700
++++ ./contrib/opal/Makefile.am	2009-07-23 17:40:08.000000000 -0700
+@@ -9,7 +9,7 @@
+ AUTOMAKE_OPTIONS = no-dependencies
+ SUFFIXES = .H .h .C .c .f .o
+ 
+-always_built_SUBDIRS = ZSI
++# always_built_SUBDIRS = ZSI
+ 
+ SUBDIRS = $(always_built_SUBDIRS) .
+ 

apbs.spec

@@ -0,0 +1,205 @@
+%{!?python_sitelib: %global python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
+
+Name: apbs
+Summary: Adaptive Poisson Boltzmann Solver
+Version: 1.1.0
+Release: 7%{?dist}
+# License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD.
+License: LGPLv2+ and BSD
+Group: Applications/Engineering
+URL: http://apbs.sourceforge.net/
+Source0: http://downloads.sourceforge.net/apbs/%{name}-%{version}-source.tar.gz
+Source1: LGPL_V2
+# adds blas_lib to AC_SUBST so Makefiles are complete
+Patch0: apbs-configure.ac.patch
+# removes hardcoded prefix setting so DESTDIR works
+Patch1: apbs-makefile.am.patch
+Buildroot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+BuildRequires: autoconf
+BuildRequires: automake
+BuildRequires: libtool
+BuildRequires: arpack-devel
+BuildRequires: atlas-devel
+BuildRequires: blas-devel
+BuildRequires: maloc-devel
+BuildRequires: python-devel
+Requires: python-ZSI
+
+%description
+APBS is a software package for the numerical solution of the
+Poisson-Boltzmann equation (PBE), one of the most popular continuum
+models for describing electrostatic interactions between molecular
+solutes in salty, aqueous media.  APBS was designed to efficiently
+evaluate electrostatic properties for such simulations for a wide
+range of length scales to enable the investigation of molecules with
+tens to millions of atoms. It is also widely used in molecular
+visualization (in such applications as PyMOL).
+
+%package tools
+Summary: utility programs that utilize the APBS package
+Group: Applications/Engineering
+Requires: %{name} = %{version}-%{release}
+
+%description tools
+
+The apbs-tools package contains several utility programs for
+conversion, analysis and preparation of files that use the adaptive
+poisson boltzmann solver library.
+
+%package devel
+Summary: Libraries and header files for the APBS package
+Group: Development/Libraries
+Requires: %{name} = %{version}-%{release}
+
+%description devel
+
+The apbs-devel package contains the header files and libraries
+necessary for developing programs using the adaptive poisson boltzmann
+(APBS) solver library.
+
+%package doc
+Summary: Documentation for the APBS package
+Group: Applications/Engineering
+Requires: %{name} = %{version}-%{release}
+
+%description doc
+
+The apbs-doc package contains API reference inforemation for
+development using the adaptive poisson boltzmann (APBS) solver
+library.
+
+%prep
+%setup -q -n %{name}-%{version}-source
+%patch0 -p0
+%patch1 -p0
+libtoolize --automake
+aclocal
+autoheader
+automake --gnu
+autoconf
+
+install -p -m 644 %{SOURCE1} .
+
+# ensure maloc isn't built
+rm -rf contrib/maloc
+
+rm doc/programmer/cooc-filter.sh
+rm doc/programmer/apbs.css
+rm doc/programmer/html/apbs.css
+rm doc/programmer/html/vcap_8h__incl.map
+rm doc/programmer/html/vpee_8h__incl.map
+rm doc/programmer/html/dummy_8c__incl.map
+
+%build
+%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared --disable-static FFLAGS="-I/usr/include/atlas"
+# die, rpath, die.
+sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
+sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
+
+sed -i 's|\"/usr/local/apbs-1.1.0\"|\"%{python_sitelib}/apbs\"|g' bin/ApbsClient.py
+
+make %{?_smp_mflags}
+
+%install
+rm -rf %{buildroot}
+
+make install DESTDIR=%{buildroot} INSTALL='install -p' CPPROG="cp -p"
+
+install -p -m 755 bin/ApbsClient.py %{buildroot}%{_bindir}/
+
+mkdir -p ${RPM_BUILD_ROOT}%{python_sitelib}/apbs
+cp -p contrib/opal/opal-py-1.9.3/wsdl/*.py ${RPM_BUILD_ROOT}%{python_sitelib}/apbs/
+
+mkdir -p %{buildroot}%{_includedir}/apbs
+install -p -m 644 src/aaa_inc/apbs/*.h %{buildroot}%{_includedir}/apbs/
+
+# tools
+for bin in tools/manip/{psize.py,coulomb,born} tools/mesh/{mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis} tools/arpack/driver; do
+    install -p -m 755 $bin %{buildroot}%{_bindir}/apbs-`basename $bin`
+done
+
+# remove unpackaged files from buildroot
+rm -f %{buildroot}%{_libdir}/*.la
+
+%clean
+rm -rf %{buildroot}
+
+%post -p /sbin/ldconfig
+
+%postun -p /sbin/ldconfig
+
+%files
+%defattr(-,root,root,-)
+%doc AUTHORS COPYING LGPL_V2 README ChangeLog
+%{_bindir}/apbs
+%{_bindir}/ApbsClient.py
+%if 0%{?fedora}<11 || 0%{?rhel} == 4 || 0%{?rhel} == 5
+%exclude %{_bindir}/*.pyc
+%exclude %{_bindir}/*.pyo
+%endif
+%{_libdir}/libapbs.so.*
+%{_libdir}/libapbsmainroutines.so.*
+%{python_sitelib}/apbs/
+
+%files tools
+%defattr(-,root,root,-)
+%{_bindir}/apbs-psize.py
+%{_bindir}/apbs-coulomb
+%{_bindir}/apbs-born
+%{_bindir}/apbs-mgmesh
+%{_bindir}/apbs-dxmath
+%{_bindir}/apbs-mergedx2
+%{_bindir}/apbs-mergedx
+%{_bindir}/apbs-value
+%{_bindir}/apbs-uhbd_asc2bin
+%{_bindir}/apbs-smooth
+%{_bindir}/apbs-dx2mol
+%{_bindir}/apbs-dx2uhbd
+%{_bindir}/apbs-similarity
+%{_bindir}/apbs-multivalue
+%{_bindir}/apbs-benchmark
+%{_bindir}/apbs-analysis
+%{_bindir}/apbs-driver
+
+%files devel
+%defattr(-,root,root,-)
+%{_libdir}/libapbs.so
+%{_libdir}/libapbsmainroutines.so
+%{_includedir}/apbs
+
+%files doc
+%defattr(-,root,root,-)
+%doc doc/programmer/
+
+%changelog
+* Mon Jul 27 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-7
+- remove python byte compiled files in bindir
+- loop to add tools
+
+* Sun Jul 26 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-6
+- remove check macro
+
+* Fri Jul 24 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-5
+- enable and add arpack, python to buildrequires, fix files section accordingly
+- add check macro
+- move tools to a subpackage
+- move doc into subpackage
+- spec cleanup
+
+* Thu Jul 23 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-4
+- merge aqua and pmgZ into libapbs
+
+* Fri Jul 10 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-3
+- separate aqua and pmgZ into separate libraries/packages
+- add maloc BuildRequires
+
+* Mon May 04 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-2
+- fix RPM_BUILD_ROOT
+- rename patches
+- add "-q" to setup
+- add README to doc
+- edit description
+- edit license
+
+* Fri Apr 24 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-1
+- initial build

sources

@@ -0,0 +1 @@
+ca31ba09714e4fc9acce91e7961569cd  apbs-1.1.0-source.tar.gz