From 2364902bc8757bb6759d2415025440d95a0bdb6c Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Fri, 21 Aug 2009 18:24:14 +0000 Subject: [PATCH 1/4] Initialize branch F-11 for apbs --- branch | 1 + 1 file changed, 1 insertion(+) create mode 100644 branch diff --git a/branch b/branch new file mode 100644 index 0000000..25c7708 --- /dev/null +++ b/branch @@ -0,0 +1 @@ +F-11 From 6125d0b9edb56850d62e885a7d7bd39c2a83ccba Mon Sep 17 00:00:00 2001 From: Timothy Fenn Date: Fri, 21 Aug 2009 20:51:31 +0000 Subject: [PATCH 2/4] - initial CVS commit --- .cvsignore | 1 + LGPL_V2 | 482 ++++++++++++++++++++++++++++++++++++++++ apbs-configure.ac.patch | 39 ++++ apbs-makefile.am.patch | 96 ++++++++ apbs.spec | 205 +++++++++++++++++ import.log | 1 + sources | 1 + 7 files changed, 825 insertions(+) create mode 100644 LGPL_V2 create mode 100644 apbs-configure.ac.patch create mode 100644 apbs-makefile.am.patch create mode 100644 apbs.spec create mode 100644 import.log diff --git a/.cvsignore b/.cvsignore index e69de29..dad4ed2 100644 --- a/.cvsignore +++ b/.cvsignore @@ -0,0 +1 @@ +apbs-1.1.0-source.tar.gz diff --git a/LGPL_V2 b/LGPL_V2 new file mode 100644 index 0000000..a96b573 --- /dev/null +++ b/LGPL_V2 @@ -0,0 +1,482 @@ + GNU LIBRARY GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1991 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor + Boston, MA 02110-1301, USA. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +[This is the first released version of the library GPL. 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See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +Also add information on how to contact you by electronic and paper mail. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the library, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random Hacker. + + , 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch new file mode 100644 index 0000000..162d141 --- /dev/null +++ b/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) + diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch new file mode 100644 index 0000000..9f8bda0 --- /dev/null +++ b/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) . + diff --git a/apbs.spec b/apbs.spec new file mode 100644 index 0000000..46a0a17 --- /dev/null +++ b/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 - 1.1.0-7 +- remove python byte compiled files in bindir +- loop to add tools + +* Sun Jul 26 2009 Tim Fenn - 1.1.0-6 +- remove check macro + +* Fri Jul 24 2009 Tim Fenn - 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 - 1.1.0-4 +- merge aqua and pmgZ into libapbs + +* Fri Jul 10 2009 Tim Fenn - 1.1.0-3 +- separate aqua and pmgZ into separate libraries/packages +- add maloc BuildRequires + +* Mon May 04 2009 Tim Fenn - 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 - 1.1.0-1 +- initial build diff --git a/import.log b/import.log new file mode 100644 index 0000000..d2ca69d --- /dev/null +++ b/import.log @@ -0,0 +1 @@ +apbs-1_1_0-7_fc10:F-11:apbs-1.1.0-7.fc10.src.rpm:1250887853 diff --git a/sources b/sources index e69de29..ca113f8 100644 --- a/sources +++ b/sources @@ -0,0 +1 @@ +ca31ba09714e4fc9acce91e7961569cd apbs-1.1.0-source.tar.gz From 9ba303e593022b6af0494cdeadd9442425025a20 Mon Sep 17 00:00:00 2001 From: Bill Nottingham Date: Thu, 26 Nov 2009 01:28:14 +0000 Subject: [PATCH 3/4] Fix typo that causes a failure to update the common directory. (releng #2781) --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 623b8bf..a10ea52 100644 --- a/Makefile +++ b/Makefile @@ -1,10 +1,10 @@ # Makefile for source rpm: apbs -# $Id$ +# $Id: Makefile,v 1.1 2009/08/21 18:24:12 ausil Exp $ 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 "$$d/Makefile.common" ; break ; fi ; done +for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$d/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done endef MAKEFILE_COMMON := $(shell $(find-makefile-common)) From c1938e4227e99a2d499e9b53f6d7a7bf241b9ed3 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 28 Jul 2010 10:04:19 +0000 Subject: [PATCH 4/4] dist-git conversion --- .cvsignore => .gitignore | 0 Makefile | 21 --------------------- branch | 1 - import.log | 1 - 4 files changed, 23 deletions(-) rename .cvsignore => .gitignore (100%) delete mode 100644 Makefile delete mode 100644 branch delete mode 100644 import.log diff --git a/.cvsignore b/.gitignore similarity index 100% rename from .cvsignore rename to .gitignore diff --git a/Makefile b/Makefile deleted file mode 100644 index a10ea52..0000000 --- a/Makefile +++ /dev/null @@ -1,21 +0,0 @@ -# Makefile for source rpm: apbs -# $Id: Makefile,v 1.1 2009/08/21 18:24:12 ausil Exp $ -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 $$d/Makefile.common ] ; then cd $$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) diff --git a/branch b/branch deleted file mode 100644 index 25c7708..0000000 --- a/branch +++ /dev/null @@ -1 +0,0 @@ -F-11 diff --git a/import.log b/import.log deleted file mode 100644 index d2ca69d..0000000 --- a/import.log +++ /dev/null @@ -1 +0,0 @@ -apbs-1_1_0-7_fc10:F-11:apbs-1.1.0-7.fc10.src.rpm:1250887853