From 6f668c918bdf1a4b9501db497c2388b1a75347f0 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Fri, 21 Aug 2009 18:24:15 +0000 Subject: [PATCH 01/92] Initialize branch EL-5 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..42f697a --- /dev/null +++ b/branch @@ -0,0 +1 @@ +EL-5 From 4e0394a358112533479354e8cb28e7383d752c3b Mon Sep 17 00:00:00 2001 From: Timothy Fenn Date: Fri, 21 Aug 2009 20:52:12 +0000 Subject: [PATCH 02/92] - 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..cf5a334 --- /dev/null +++ b/import.log @@ -0,0 +1 @@ +apbs-1_1_0-7_fc10:EL-5:apbs-1.1.0-7.fc10.src.rpm:1250887920 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 206eaaeab85aceb256f69e0f2a704e239338bf9b Mon Sep 17 00:00:00 2001 From: Timothy Fenn Date: Wed, 25 Nov 2009 01:34:32 +0000 Subject: [PATCH 03/92] - update to 1.2.0 --- .cvsignore | 2 +- apbs-configure.ac.patch | 10 ++-- apbs-makefile.am.patch | 114 +++++++++++++++++++++------------------- apbs.spec | 11 ++-- sources | 2 +- 5 files changed, 74 insertions(+), 65 deletions(-) diff --git a/.cvsignore b/.cvsignore index dad4ed2..3a2cdda 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1 +1 @@ -apbs-1.1.0-source.tar.gz +apbs-1.2.0-1.fc12.src.rpm diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch index 162d141..16e4b8d 100644 --- a/apbs-configure.ac.patch +++ b/apbs-configure.ac.patch @@ -1,5 +1,5 @@ ---- configure.ac_orig 2009-07-10 11:37:12.000000000 -0700 -+++ configure.ac 2009-07-10 16:02:33.000000000 -0700 +--- configure.ac_orig 2009-11-05 18:36:35.897587445 -0800 ++++ configure.ac 2009-11-05 18:36:42.545586937 -0800 @@ -390,7 +390,7 @@ if test -n "${USE_FETK_LIBRARY}"; then @@ -9,7 +9,7 @@ if test -z "${maloc_lib}"; then AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified]) fi -@@ -806,7 +806,7 @@ +@@ -810,7 +810,7 @@ fi LDFLAGS=${LDFLAGS_SAVE}; CPPFLAGS=${CPPFLAGS_SAVE}; @@ -18,7 +18,7 @@ dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK dnl # ----------------------- -@@ -1028,6 +1028,7 @@ +@@ -1032,6 +1032,7 @@ blas_lib=${contrib_path}/blas/.libs/libapbsblas.a fi AC_SUBST(apbs_do_blas) @@ -26,7 +26,7 @@ dnl # ----------------------- dnl # If using Portland compilers, do not compile -@@ -1206,7 +1207,9 @@ +@@ -1258,7 +1259,9 @@ else apbs_build_libraries="${top_apbsdir}/bin/libapbsmainroutines.la \ ${top_apbsdir}/src/aaa_lib/libapbs.la \ diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch index 9f8bda0..ce0cbbf 100644 --- a/apbs-makefile.am.patch +++ b/apbs-makefile.am.patch @@ -1,24 +1,33 @@ ---- ./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 +--- ./contrib/opal/Makefile.am_orig 2009-11-05 18:40:35.770586544 -0800 ++++ ./contrib/opal/Makefile.am 2009-11-05 18:42:37.360586985 -0800 +@@ -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) . + +--- ./src/aaa_lib/Makefile.am_orig 2009-11-05 18:40:23.482586423 -0800 ++++ ./src/aaa_lib/Makefile.am 2009-11-05 18:42:37.359585990 -0800 +@@ -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@ +--- ./tools/arpack/Makefile.am_orig 2009-11-05 18:39:26.560836859 -0800 ++++ ./tools/arpack/Makefile.am 2009-11-05 18:42:37.356586914 -0800 @@ -12,7 +12,7 @@ noinst_PROGRAMS = driver @@ -27,10 +36,29 @@ +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 @@ + AM_LDFLAGS = @LDFLAGS@ +--- ./tools/python/vgrid/Makefile.am_orig 2009-11-05 18:39:11.427586298 -0800 ++++ ./tools/python/vgrid/Makefile.am 2009-11-05 18:42:37.356586914 -0800 +@@ -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/python/Makefile.am_orig 2009-11-05 18:39:02.257587290 -0800 ++++ ./tools/python/Makefile.am 2009-11-05 18:42:37.354586041 -0800 +@@ -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 +--- ./bin/Makefile.am_orig 2009-11-05 18:39:54.336586267 -0800 ++++ ./bin/Makefile.am 2009-11-05 18:44:45.550587035 -0800 +@@ -12,10 +12,10 @@ build_libraries = @apbs_build_libraries@ @@ -41,6 +69,12 @@ -apbs_LDADD = ${build_libraries} +apbs_LDADD = ${build_libraries} ./libapbsmainroutines.la + # This is a hack I suspect, but needed to force apbs to be + # rebuilt anytime the make command is issued +@@ -27,19 +27,19 @@ + rm.apbs: Makefile + -rm -f apbs + -libdir = ${prefix}/lib +# libdir = ${prefix}/lib lib_LTLIBRARIES = libapbsmainroutines.la @@ -56,7 +90,7 @@ -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 @@ -66,31 +100,3 @@ +# -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 index 46a0a17..b80fa41 100644 --- a/apbs.spec +++ b/apbs.spec @@ -2,13 +2,13 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.1.0 -Release: 7%{?dist} +Version: 1.2.0 +Release: 1%{?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 +Source0: http://downloads.sourceforge.net/apbs/%{name}-1.2-source.tar.gz Source1: LGPL_V2 # adds blas_lib to AC_SUBST so Makefiles are complete Patch0: apbs-configure.ac.patch @@ -69,7 +69,7 @@ development using the adaptive poisson boltzmann (APBS) solver library. %prep -%setup -q -n %{name}-%{version}-source +%setup -q -n %{name}-1.2-source %patch0 -p0 %patch1 -p0 libtoolize --automake @@ -172,6 +172,9 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Thu Nov 04 2009 Tim Fenn - 1.2.0-1 +- update to 1.2.0 + * Mon Jul 27 2009 Tim Fenn - 1.1.0-7 - remove python byte compiled files in bindir - loop to add tools diff --git a/sources b/sources index ca113f8..66a18f7 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -ca31ba09714e4fc9acce91e7961569cd apbs-1.1.0-source.tar.gz +fdbdff5fe49ba6192a6d77d8afce8f2d apbs-1.2.0-1.fc12.src.rpm From e13a9f45ec30a424f3335a5021b212c0ad4ccc88 Mon Sep 17 00:00:00 2001 From: Timothy Fenn Date: Wed, 25 Nov 2009 01:41:02 +0000 Subject: [PATCH 04/92] - fix broken source --- .cvsignore | 2 +- apbs.spec | 5 ++++- sources | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.cvsignore b/.cvsignore index 3a2cdda..bce7d98 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1 +1 @@ -apbs-1.2.0-1.fc12.src.rpm +apbs-1.2-source.tar.gz diff --git a/apbs.spec b/apbs.spec index b80fa41..42b38cc 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.2.0 -Release: 1%{?dist} +Release: 2%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -172,6 +172,9 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Tue Nov 24 2009 Tim Fenn - 1.2.0-2 +- fix broken source + * Thu Nov 04 2009 Tim Fenn - 1.2.0-1 - update to 1.2.0 diff --git a/sources b/sources index 66a18f7..dcafcc1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -fdbdff5fe49ba6192a6d77d8afce8f2d apbs-1.2.0-1.fc12.src.rpm +ba32bb323b25307204436eaac1ff877b apbs-1.2-source.tar.gz From f19088600d6b8b9eb4be1296d8848d9c831c368a Mon Sep 17 00:00:00 2001 From: Bill Nottingham Date: Wed, 25 Nov 2009 22:40:09 +0000 Subject: [PATCH 05/92] 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 83e161292bee450b6b83c2d56c7d41cab1174ff4 Mon Sep 17 00:00:00 2001 From: Bill Nottingham Date: Thu, 26 Nov 2009 01:28:13 +0000 Subject: [PATCH 06/92] 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 63a0b4f60a911a35c3736254139dfa0e4b06bb9a Mon Sep 17 00:00:00 2001 From: Bill Nottingham Date: Thu, 26 Nov 2009 01:28:14 +0000 Subject: [PATCH 07/92] 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 1ab947bd1d205a911b534f36c2fd592842f02e30 Mon Sep 17 00:00:00 2001 From: Timothy Fenn Date: Mon, 30 Nov 2009 07:24:42 +0000 Subject: [PATCH 08/92] - update to 1.2.1 --- .cvsignore | 2 +- apbs-configure.ac.patch | 43 +++++++++++++++++++++++++++++++++++------ apbs-makefile.am.patch | 40 +++++++++++++++++++++++--------------- apbs.spec | 14 +++++++++----- sources | 2 +- 5 files changed, 72 insertions(+), 29 deletions(-) diff --git a/.cvsignore b/.cvsignore index bce7d98..0682ff7 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1 +1 @@ -apbs-1.2-source.tar.gz +apbs-1.2.1-source.tar.gz diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch index 16e4b8d..7f882f7 100644 --- a/apbs-configure.ac.patch +++ b/apbs-configure.ac.patch @@ -1,6 +1,37 @@ ---- configure.ac_orig 2009-11-05 18:36:35.897587445 -0800 -+++ configure.ac 2009-11-05 18:36:42.545586937 -0800 -@@ -390,7 +390,7 @@ +--- configure.ac_orig 2009-11-25 12:23:02.275659561 -0800 ++++ configure.ac 2009-11-29 23:16:42.319661207 -0800 +@@ -230,14 +230,16 @@ + CXXFLAGS=`echo ${CXXFLAGS} | sed 's/-g//g'`; + fi + fi +-AC_F77_NOFORMAIN ++# AC_F77_NOFORMAIN + FFLAGS="${FLIBS} ${FFLAGS}" +-if test "${CC}" != "icl"; then +- AC_F77_FCN_MANGLE() +-fi ++# this macro is broken, so be sure to set -DVF77_ONEUNDERSCORE ++# if test "${CC}" != "icl"; then ++# AC_F77_FCN_MANGLE() ++# fi + AC_LANG_C + AC_PROG_CPP +-AC_DISABLE_SHARED ++# AC_DISABLE_SHARED ++AC_DISABLE_STATIC + AM_PROG_LIBTOOL + + dnl ########################################################################## +@@ -308,7 +310,7 @@ + dnl # HANDLE COMPILER FLOATING POINT ERROR + dnl # ------------------------------------ + +-AC_FPERROR ++# AC_FPERROR + + dnl ########################################################################## + dnl 8. checks for library functions +@@ -390,7 +392,7 @@ if test -n "${USE_FETK_LIBRARY}"; then maloc_lib_path="${fetk_library_path}" @@ -9,7 +40,7 @@ if test -z "${maloc_lib}"; then AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified]) fi -@@ -810,7 +810,7 @@ +@@ -810,7 +812,7 @@ fi LDFLAGS=${LDFLAGS_SAVE}; CPPFLAGS=${CPPFLAGS_SAVE}; @@ -18,7 +49,7 @@ dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK dnl # ----------------------- -@@ -1032,6 +1032,7 @@ +@@ -1032,6 +1034,7 @@ blas_lib=${contrib_path}/blas/.libs/libapbsblas.a fi AC_SUBST(apbs_do_blas) @@ -26,7 +57,7 @@ dnl # ----------------------- dnl # If using Portland compilers, do not compile -@@ -1258,7 +1259,9 @@ +@@ -1258,7 +1261,9 @@ else apbs_build_libraries="${top_apbsdir}/bin/libapbsmainroutines.la \ ${top_apbsdir}/src/aaa_lib/libapbs.la \ diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch index ce0cbbf..16463fc 100644 --- a/apbs-makefile.am.patch +++ b/apbs-makefile.am.patch @@ -1,5 +1,5 @@ ---- ./contrib/opal/Makefile.am_orig 2009-11-05 18:40:35.770586544 -0800 -+++ ./contrib/opal/Makefile.am 2009-11-05 18:42:37.360586985 -0800 +--- ./contrib/opal/Makefile.am_orig 2009-11-24 18:56:20.564534299 -0800 ++++ ./contrib/opal/Makefile.am 2009-11-24 18:59:57.836534326 -0800 @@ -9,7 +9,7 @@ AUTOMAKE_OPTIONS = no-dependencies SUFFIXES = .H .h .C .c .f .o @@ -9,8 +9,8 @@ SUBDIRS = $(always_built_SUBDIRS) . ---- ./src/aaa_lib/Makefile.am_orig 2009-11-05 18:40:23.482586423 -0800 -+++ ./src/aaa_lib/Makefile.am 2009-11-05 18:42:37.359585990 -0800 +--- ./src/aaa_lib/Makefile.am_orig 2009-11-24 18:57:31.108534078 -0800 ++++ ./src/aaa_lib/Makefile.am 2009-11-29 22:09:14.931662428 -0800 @@ -18,12 +18,12 @@ AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la BLAS_LIBS = @blas_lib@ @@ -26,8 +26,8 @@ INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@ AM_CFLAGS = @wall_pedantic@ ---- ./tools/arpack/Makefile.am_orig 2009-11-05 18:39:26.560836859 -0800 -+++ ./tools/arpack/Makefile.am 2009-11-05 18:42:37.356586914 -0800 +--- ./tools/arpack/Makefile.am_orig 2009-11-24 18:57:41.564534258 -0800 ++++ ./tools/arpack/Makefile.am 2009-11-24 18:59:57.837534477 -0800 @@ -12,7 +12,7 @@ noinst_PROGRAMS = driver @@ -37,8 +37,8 @@ INCLUDES = @inc_list@ AM_CFLAGS = @CFLAGS@ AM_LDFLAGS = @LDFLAGS@ ---- ./tools/python/vgrid/Makefile.am_orig 2009-11-05 18:39:11.427586298 -0800 -+++ ./tools/python/vgrid/Makefile.am 2009-11-05 18:42:37.356586914 -0800 +--- ./tools/python/vgrid/Makefile.am_orig 2009-11-24 18:57:54.604534072 -0800 ++++ ./tools/python/vgrid/Makefile.am 2009-11-24 18:59:57.837534477 -0800 @@ -16,5 +16,6 @@ noinst_PROGRAMS = _vgrid.so _vgrid_so_SOURCES = vgridlib.c @@ -47,8 +47,8 @@ + _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/python/Makefile.am_orig 2009-11-05 18:39:02.257587290 -0800 -+++ ./tools/python/Makefile.am 2009-11-05 18:42:37.354586041 -0800 +--- ./tools/python/Makefile.am_orig 2009-11-24 18:58:01.740534012 -0800 ++++ ./tools/python/Makefile.am 2009-11-24 18:59:57.838534348 -0800 @@ -16,4 +16,5 @@ noinst_PROGRAMS = _apbslib.so _apbslib_so_SOURCES = apbslib.c @@ -56,9 +56,9 @@ -_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 ---- ./bin/Makefile.am_orig 2009-11-05 18:39:54.336586267 -0800 -+++ ./bin/Makefile.am 2009-11-05 18:44:45.550587035 -0800 -@@ -12,10 +12,10 @@ +--- ./bin/Makefile.am_orig 2009-11-24 18:58:07.772534219 -0800 ++++ ./bin/Makefile.am 2009-11-24 19:09:09.452534035 -0800 +@@ -12,34 +12,35 @@ build_libraries = @apbs_build_libraries@ @@ -71,11 +71,19 @@ # This is a hack I suspect, but needed to force apbs to be # rebuilt anytime the make command is issued -@@ -27,19 +27,19 @@ - rm.apbs: Makefile - -rm -f apbs + # Problem before is that there is no dependency between source file + # recompilation and relinking the binary. There is probably + # a cleaner way to do this, I can't find it, however. +-BUILT_SOURCES = rm.apbs + +-rm.apbs: Makefile +- -rm -f apbs ++# BUILT_SOURCES = rm.apbs -libdir = ${prefix}/lib ++# rm.apbs: Makefile ++# -rm -f apbs ++ +# libdir = ${prefix}/lib lib_LTLIBRARIES = libapbsmainroutines.la libapbsmainroutines_la_SOURCES = routines.c diff --git a/apbs.spec b/apbs.spec index 42b38cc..291904a 100644 --- a/apbs.spec +++ b/apbs.spec @@ -2,13 +2,13 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.2.0 -Release: 2%{?dist} +Version: 1.2.1 +Release: 1%{?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}-1.2-source.tar.gz +Source0: http://downloads.sourceforge.net/apbs/%{name}-1.2.1-source.tar.gz Source1: LGPL_V2 # adds blas_lib to AC_SUBST so Makefiles are complete Patch0: apbs-configure.ac.patch @@ -69,9 +69,10 @@ development using the adaptive poisson boltzmann (APBS) solver library. %prep -%setup -q -n %{name}-1.2-source +%setup -q -n %{name}-1.2.1-source %patch0 -p0 %patch1 -p0 +rm acinclude.m4 libtoolize --automake aclocal autoheader @@ -91,7 +92,7 @@ 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" +%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 FFLAGS="-I/usr/include/atlas" CFLAGS="-DVF77_ONEUNDERSCORE" # 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 @@ -172,6 +173,9 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Wed Nov 25 2009 Tim Fenn - 1.2.1-1 +- update to 1.2.1 + * Tue Nov 24 2009 Tim Fenn - 1.2.0-2 - fix broken source diff --git a/sources b/sources index dcafcc1..a83d832 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -ba32bb323b25307204436eaac1ff877b apbs-1.2-source.tar.gz +831d85e90083ec639451657195ff90da apbs-1.2.1-source.tar.gz From 89e76a04b5d48efe491885ac1f538dfcf493100f Mon Sep 17 00:00:00 2001 From: Timothy Fenn Date: Tue, 1 Dec 2009 19:17:12 +0000 Subject: [PATCH 09/92] - add RPM_OPT_FLAGS --- apbs.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 291904a..c3cf1d7 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.2.1 -Release: 1%{?dist} +Release: 2%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -92,7 +92,7 @@ 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 FFLAGS="-I/usr/include/atlas" CFLAGS="-DVF77_ONEUNDERSCORE" +%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 FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" # 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 @@ -173,6 +173,9 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Tue Dec 01 2009 Tim Fenn - 1.2.1-2 +- add RPM_OPT_FLAGS + * Wed Nov 25 2009 Tim Fenn - 1.2.1-1 - update to 1.2.1 From 4daad0a9c52f59928d69250f655567e6a6eb72a4 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Sat, 8 May 2010 01:42:52 +0000 Subject: [PATCH 10/92] Initialize branch EL-6 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..46381b9 --- /dev/null +++ b/branch @@ -0,0 +1 @@ +EL-6 From be3da3ac96e03fd4f48d7ce2abbf5fe0394c625a Mon Sep 17 00:00:00 2001 From: dmalcolm Date: Thu, 22 Jul 2010 00:35:46 +0000 Subject: [PATCH 11/92] - Rebuilt for https://fedoraproject.org/wiki/Features/Python_2.7/MassRebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index c3cf1d7..24bdeb6 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.2.1 -Release: 2%{?dist} +Release: 3%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -173,6 +173,9 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Wed Jul 21 2010 David Malcolm - 1.2.1-3 +- Rebuilt for https://fedoraproject.org/wiki/Features/Python_2.7/MassRebuild + * Tue Dec 01 2009 Tim Fenn - 1.2.1-2 - add RPM_OPT_FLAGS From 7e09a2552a5133fa14c8947fd4a483d3df927e4d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 28 Jul 2010 10:04:18 +0000 Subject: [PATCH 12/92] dist-git conversion --- .cvsignore => .gitignore | 0 Makefile | 21 --------------------- import.log | 1 - 3 files changed, 22 deletions(-) rename .cvsignore => .gitignore (100%) delete mode 100644 Makefile 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/import.log b/import.log deleted file mode 100644 index 4304fcb..0000000 --- a/import.log +++ /dev/null @@ -1 +0,0 @@ -apbs-1_1_0-7_fc10:HEAD:apbs-1.1.0-7.fc10.src.rpm:1250887770 From 8a856cc3b8274e2fa32c0988f436bfe4b326334d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 28 Jul 2010 10:04:18 +0000 Subject: [PATCH 13/92] 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 42f697a..0000000 --- a/branch +++ /dev/null @@ -1 +0,0 @@ -EL-5 diff --git a/import.log b/import.log deleted file mode 100644 index cf5a334..0000000 --- a/import.log +++ /dev/null @@ -1 +0,0 @@ -apbs-1_1_0-7_fc10:EL-5:apbs-1.1.0-7.fc10.src.rpm:1250887920 From a6e6310216a8fe0b4ae2c7c98c748181e108974a Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 28 Jul 2010 10:04:19 +0000 Subject: [PATCH 14/92] 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 46381b9..0000000 --- a/branch +++ /dev/null @@ -1 +0,0 @@ -EL-6 diff --git a/import.log b/import.log deleted file mode 100644 index 4304fcb..0000000 --- a/import.log +++ /dev/null @@ -1 +0,0 @@ -apbs-1_1_0-7_fc10:HEAD:apbs-1.1.0-7.fc10.src.rpm:1250887770 From 7de5b913893874060648b14ef0c5343ef2f90aa4 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 26 Aug 2010 13:36:49 -0700 Subject: [PATCH 15/92] update to 1.2.1 --- .gitignore | 1 + apbs-configure.ac.patch | 43 +++++++++-- apbs-makefile.am.patch | 164 ++++++++++++++++++++++------------------ apbs.spec | 23 ++++-- sources | 2 +- 5 files changed, 146 insertions(+), 87 deletions(-) diff --git a/.gitignore b/.gitignore index dad4ed2..fe06b17 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ apbs-1.1.0-source.tar.gz +/apbs-1.2.1-source.tar.gz diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch index 162d141..7f882f7 100644 --- a/apbs-configure.ac.patch +++ b/apbs-configure.ac.patch @@ -1,6 +1,37 @@ ---- 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 @@ +--- configure.ac_orig 2009-11-25 12:23:02.275659561 -0800 ++++ configure.ac 2009-11-29 23:16:42.319661207 -0800 +@@ -230,14 +230,16 @@ + CXXFLAGS=`echo ${CXXFLAGS} | sed 's/-g//g'`; + fi + fi +-AC_F77_NOFORMAIN ++# AC_F77_NOFORMAIN + FFLAGS="${FLIBS} ${FFLAGS}" +-if test "${CC}" != "icl"; then +- AC_F77_FCN_MANGLE() +-fi ++# this macro is broken, so be sure to set -DVF77_ONEUNDERSCORE ++# if test "${CC}" != "icl"; then ++# AC_F77_FCN_MANGLE() ++# fi + AC_LANG_C + AC_PROG_CPP +-AC_DISABLE_SHARED ++# AC_DISABLE_SHARED ++AC_DISABLE_STATIC + AM_PROG_LIBTOOL + + dnl ########################################################################## +@@ -308,7 +310,7 @@ + dnl # HANDLE COMPILER FLOATING POINT ERROR + dnl # ------------------------------------ + +-AC_FPERROR ++# AC_FPERROR + + dnl ########################################################################## + dnl 8. checks for library functions +@@ -390,7 +392,7 @@ if test -n "${USE_FETK_LIBRARY}"; then maloc_lib_path="${fetk_library_path}" @@ -9,7 +40,7 @@ if test -z "${maloc_lib}"; then AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified]) fi -@@ -806,7 +806,7 @@ +@@ -810,7 +812,7 @@ fi LDFLAGS=${LDFLAGS_SAVE}; CPPFLAGS=${CPPFLAGS_SAVE}; @@ -18,7 +49,7 @@ dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK dnl # ----------------------- -@@ -1028,6 +1028,7 @@ +@@ -1032,6 +1034,7 @@ blas_lib=${contrib_path}/blas/.libs/libapbsblas.a fi AC_SUBST(apbs_do_blas) @@ -26,7 +57,7 @@ dnl # ----------------------- dnl # If using Portland compilers, do not compile -@@ -1206,7 +1207,9 @@ +@@ -1258,7 +1261,9 @@ else apbs_build_libraries="${top_apbsdir}/bin/libapbsmainroutines.la \ ${top_apbsdir}/src/aaa_lib/libapbs.la \ diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch index 9f8bda0..16463fc 100644 --- a/apbs-makefile.am.patch +++ b/apbs-makefile.am.patch @@ -1,73 +1,16 @@ ---- ./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 @@ +--- ./contrib/opal/Makefile.am_orig 2009-11-24 18:56:20.564534299 -0800 ++++ ./contrib/opal/Makefile.am 2009-11-24 18:59:57.836534326 -0800 +@@ -9,7 +9,7 @@ + AUTOMAKE_OPTIONS = no-dependencies + SUFFIXES = .H .h .C .c .f .o - 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 @@ +-always_built_SUBDIRS = ZSI ++# always_built_SUBDIRS = ZSI - build_libraries = @apbs_build_libraries@ + SUBDIRS = $(always_built_SUBDIRS) . --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 +--- ./src/aaa_lib/Makefile.am_orig 2009-11-24 18:57:31.108534078 -0800 ++++ ./src/aaa_lib/Makefile.am 2009-11-29 22:09:14.931662428 -0800 @@ -18,12 +18,12 @@ AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la BLAS_LIBS = @blas_lib@ @@ -83,14 +26,85 @@ INCLUDES = -I${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 +--- ./tools/arpack/Makefile.am_orig 2009-11-24 18:57:41.564534258 -0800 ++++ ./tools/arpack/Makefile.am 2009-11-24 18:59:57.837534477 -0800 +@@ -12,7 +12,7 @@ --always_built_SUBDIRS = ZSI -+# always_built_SUBDIRS = ZSI + 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@ +--- ./tools/python/vgrid/Makefile.am_orig 2009-11-24 18:57:54.604534072 -0800 ++++ ./tools/python/vgrid/Makefile.am 2009-11-24 18:59:57.837534477 -0800 +@@ -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/python/Makefile.am_orig 2009-11-24 18:58:01.740534012 -0800 ++++ ./tools/python/Makefile.am 2009-11-24 18:59:57.838534348 -0800 +@@ -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 +--- ./bin/Makefile.am_orig 2009-11-24 18:58:07.772534219 -0800 ++++ ./bin/Makefile.am 2009-11-24 19:09:09.452534035 -0800 +@@ -12,34 +12,35 @@ - SUBDIRS = $(always_built_SUBDIRS) . + 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 + + # This is a hack I suspect, but needed to force apbs to be + # rebuilt anytime the make command is issued + # Problem before is that there is no dependency between source file + # recompilation and relinking the binary. There is probably + # a cleaner way to do this, I can't find it, however. +-BUILT_SOURCES = rm.apbs + +-rm.apbs: Makefile +- -rm -f apbs ++# BUILT_SOURCES = rm.apbs + +-libdir = ${prefix}/lib ++# rm.apbs: Makefile ++# -rm -f apbs ++ ++# 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 ${prefix}/bin/wsdl2py diff --git a/apbs.spec b/apbs.spec index 46a0a17..c3cf1d7 100644 --- a/apbs.spec +++ b/apbs.spec @@ -2,13 +2,13 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.1.0 -Release: 7%{?dist} +Version: 1.2.1 +Release: 2%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering URL: http://apbs.sourceforge.net/ -Source0: http://downloads.sourceforge.net/apbs/%{name}-%{version}-source.tar.gz +Source0: http://downloads.sourceforge.net/apbs/%{name}-1.2.1-source.tar.gz Source1: LGPL_V2 # adds blas_lib to AC_SUBST so Makefiles are complete Patch0: apbs-configure.ac.patch @@ -69,9 +69,10 @@ development using the adaptive poisson boltzmann (APBS) solver library. %prep -%setup -q -n %{name}-%{version}-source +%setup -q -n %{name}-1.2.1-source %patch0 -p0 %patch1 -p0 +rm acinclude.m4 libtoolize --automake aclocal autoheader @@ -91,7 +92,7 @@ rm doc/programmer/html/vpee_8h__incl.map rm doc/programmer/html/dummy_8c__incl.map %build -%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared --disable-static FFLAGS="-I/usr/include/atlas" +%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" # 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 @@ -172,6 +173,18 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Tue Dec 01 2009 Tim Fenn - 1.2.1-2 +- add RPM_OPT_FLAGS + +* Wed Nov 25 2009 Tim Fenn - 1.2.1-1 +- update to 1.2.1 + +* Tue Nov 24 2009 Tim Fenn - 1.2.0-2 +- fix broken source + +* Thu Nov 04 2009 Tim Fenn - 1.2.0-1 +- update to 1.2.0 + * Mon Jul 27 2009 Tim Fenn - 1.1.0-7 - remove python byte compiled files in bindir - loop to add tools diff --git a/sources b/sources index ca113f8..a83d832 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -ca31ba09714e4fc9acce91e7961569cd apbs-1.1.0-source.tar.gz +831d85e90083ec639451657195ff90da apbs-1.2.1-source.tar.gz From ea47b7a3e4e57811a93268818e3ac00f258b4231 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Mon, 15 Nov 2010 17:53:00 -0800 Subject: [PATCH 16/92] Update to 1.3 --- .gitignore | 1 + apbs-configure.ac.patch | 35 ++++++----- apbs-makefile.am.patch | 129 ++++++++++++++++++++-------------------- apbs.spec | 25 ++++---- sources | 2 +- 5 files changed, 97 insertions(+), 95 deletions(-) diff --git a/.gitignore b/.gitignore index 0682ff7..70de2bf 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ apbs-1.2.1-source.tar.gz +/apbs-1.3-source.tar.gz diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch index 7f882f7..e595ea7 100644 --- a/apbs-configure.ac.patch +++ b/apbs-configure.ac.patch @@ -1,6 +1,6 @@ ---- configure.ac_orig 2009-11-25 12:23:02.275659561 -0800 -+++ configure.ac 2009-11-29 23:16:42.319661207 -0800 -@@ -230,14 +230,16 @@ +--- configure.ac_orig 2010-11-15 11:54:58.428167033 -0800 ++++ configure.ac 2010-11-15 14:26:50.556166647 -0800 +@@ -229,14 +229,15 @@ CXXFLAGS=`echo ${CXXFLAGS} | sed 's/-g//g'`; fi fi @@ -11,18 +11,17 @@ - AC_F77_FCN_MANGLE() -fi +# this macro is broken, so be sure to set -DVF77_ONEUNDERSCORE -+# if test "${CC}" != "icl"; then ++#if test "${CC}" != "icl"; then +# AC_F77_FCN_MANGLE() -+# fi ++#fi AC_LANG_C AC_PROG_CPP -AC_DISABLE_SHARED +# AC_DISABLE_SHARED -+AC_DISABLE_STATIC AM_PROG_LIBTOOL + FFLAGS="${FFLAGS}" - dnl ########################################################################## -@@ -308,7 +310,7 @@ +@@ -308,7 +309,7 @@ dnl # HANDLE COMPILER FLOATING POINT ERROR dnl # ------------------------------------ @@ -31,7 +30,7 @@ dnl ########################################################################## dnl 8. checks for library functions -@@ -390,7 +392,7 @@ +@@ -390,7 +391,7 @@ if test -n "${USE_FETK_LIBRARY}"; then maloc_lib_path="${fetk_library_path}" @@ -40,7 +39,7 @@ if test -z "${maloc_lib}"; then AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified]) fi -@@ -810,7 +812,7 @@ +@@ -816,7 +817,7 @@ fi LDFLAGS=${LDFLAGS_SAVE}; CPPFLAGS=${CPPFLAGS_SAVE}; @@ -49,15 +48,15 @@ dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK dnl # ----------------------- -@@ -1032,6 +1034,7 @@ +@@ -1038,6 +1039,7 @@ blas_lib=${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 -@@ -1258,7 +1261,9 @@ + dnl # -------------------------------- + dnl # HANDLE ZLIB COMPILATION +@@ -1280,7 +1282,9 @@ else apbs_build_libraries="${top_apbsdir}/bin/libapbsmainroutines.la \ ${top_apbsdir}/src/aaa_lib/libapbs.la \ @@ -68,3 +67,11 @@ fi AC_SUBST(apbs_build_libraries) +@@ -1297,7 +1301,6 @@ + contrib/aqua/Makefile + contrib/opal/Makefile + contrib/opal/ZSI/Makefile +- contrib/zlib/Makefile + + tools/Makefile + tools/mesh/Makefile diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch index 16463fc..ddf2963 100644 --- a/apbs-makefile.am.patch +++ b/apbs-makefile.am.patch @@ -1,64 +1,6 @@ ---- ./contrib/opal/Makefile.am_orig 2009-11-24 18:56:20.564534299 -0800 -+++ ./contrib/opal/Makefile.am 2009-11-24 18:59:57.836534326 -0800 -@@ -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) . - ---- ./src/aaa_lib/Makefile.am_orig 2009-11-24 18:57:31.108534078 -0800 -+++ ./src/aaa_lib/Makefile.am 2009-11-29 22:09:14.931662428 -0800 -@@ -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@ ---- ./tools/arpack/Makefile.am_orig 2009-11-24 18:57:41.564534258 -0800 -+++ ./tools/arpack/Makefile.am 2009-11-24 18:59:57.837534477 -0800 -@@ -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@ ---- ./tools/python/vgrid/Makefile.am_orig 2009-11-24 18:57:54.604534072 -0800 -+++ ./tools/python/vgrid/Makefile.am 2009-11-24 18:59:57.837534477 -0800 -@@ -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/python/Makefile.am_orig 2009-11-24 18:58:01.740534012 -0800 -+++ ./tools/python/Makefile.am 2009-11-24 18:59:57.838534348 -0800 -@@ -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 ---- ./bin/Makefile.am_orig 2009-11-24 18:58:07.772534219 -0800 -+++ ./bin/Makefile.am 2009-11-24 19:09:09.452534035 -0800 -@@ -12,34 +12,35 @@ +--- ./bin/Makefile.am_orig 2010-11-15 12:07:02.487166613 -0800 ++++ ./bin/Makefile.am 2010-11-15 12:10:49.109166514 -0800 +@@ -12,34 +12,31 @@ build_libraries = @apbs_build_libraries@ @@ -75,15 +17,12 @@ # recompilation and relinking the binary. There is probably # a cleaner way to do this, I can't find it, however. -BUILT_SOURCES = rm.apbs ++# BUILT_SOURCES = rm.apbs -rm.apbs: Makefile - -rm -f apbs -+# BUILT_SOURCES = rm.apbs - +- -libdir = ${prefix}/lib -+# rm.apbs: Makefile -+# -rm -f apbs -+ +# libdir = ${prefix}/lib lib_LTLIBRARIES = libapbsmainroutines.la libapbsmainroutines_la_SOURCES = routines.c @@ -108,3 +47,61 @@ +# -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 2010-11-15 12:01:13.975197621 -0800 ++++ ./src/aaa_lib/Makefile.am 2010-11-15 12:01:54.567274233 -0800 +@@ -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@ +--- ./tools/python/vgrid/Makefile.am_orig 2010-11-15 12:02:55.717416873 -0800 ++++ ./tools/python/vgrid/Makefile.am 2010-11-15 12:04:33.565198239 -0800 +@@ -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/python/Makefile.am_orig 2010-11-15 12:04:54.918478810 -0800 ++++ ./tools/python/Makefile.am 2010-11-15 14:22:08.880166492 -0800 +@@ -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) ${z_lib} ++_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/arpack/Makefile.am_orig 2010-11-15 12:02:08.657198191 -0800 ++++ ./tools/arpack/Makefile.am 2010-11-15 12:02:26.559231032 -0800 +@@ -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@ +--- ./contrib/opal/Makefile.am_orig 2010-11-15 12:00:27.148447572 -0800 ++++ ./contrib/opal/Makefile.am 2010-11-15 12:00:51.998166490 -0800 +@@ -9,7 +9,7 @@ + AUTOMAKE_OPTIONS = no-dependencies + SUFFIXES = .H .h .C .c .f .o + +-always_built_SUBDIRS = ZSI ++# always_built_SUBDIRS = ZSI + + SUBDIRS = $(always_built_SUBDIRS) . + diff --git a/apbs.spec b/apbs.spec index 24bdeb6..2584e72 100644 --- a/apbs.spec +++ b/apbs.spec @@ -2,13 +2,13 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.2.1 -Release: 3%{?dist} +Version: 1.3 +Release: 1%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering URL: http://apbs.sourceforge.net/ -Source0: http://downloads.sourceforge.net/apbs/%{name}-1.2.1-source.tar.gz +Source0: http://downloads.sourceforge.net/apbs/%{name}-%{version}-source.tar.gz Source1: LGPL_V2 # adds blas_lib to AC_SUBST so Makefiles are complete Patch0: apbs-configure.ac.patch @@ -69,7 +69,7 @@ development using the adaptive poisson boltzmann (APBS) solver library. %prep -%setup -q -n %{name}-1.2.1-source +%setup -q -n %{name}-%{version}-source %patch0 -p0 %patch1 -p0 rm acinclude.m4 @@ -81,18 +81,12 @@ autoconf install -p -m 644 %{SOURCE1} . -# ensure maloc isn't built +# ensure maloc/zlib aren't built rm -rf contrib/maloc - -rm doc/programmer/cooc-filter.sh -rm doc/programmer/apbs.css -rm doc/programmer/html/apbs.css -rm doc/programmer/html/vcap_8h__incl.map -rm doc/programmer/html/vpee_8h__incl.map -rm doc/programmer/html/dummy_8c__incl.map +rm -rf contrib/zlib %build -%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" +%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --disable-zlib --disable-static --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" # 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 @@ -170,9 +164,12 @@ rm -rf %{buildroot} %files doc %defattr(-,root,root,-) -%doc doc/programmer/ +%doc doc/programmer/programmer.pdf %changelog +* Mon Nov 15 2010 Tim Fenn - 1.3-1 +- update to 1.3 + * Wed Jul 21 2010 David Malcolm - 1.2.1-3 - Rebuilt for https://fedoraproject.org/wiki/Features/Python_2.7/MassRebuild diff --git a/sources b/sources index a83d832..4646d30 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -831d85e90083ec639451657195ff90da apbs-1.2.1-source.tar.gz +f99a505365f07f6853979cfe2ef23365 apbs-1.3-source.tar.gz From 22f7484f25d93f851bf3ece5bf6124da17b58bcd Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Mon, 7 Feb 2011 19:42:15 -0600 Subject: [PATCH 17/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 2584e72..5628a41 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 1%{?dist} +Release: 2%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -167,6 +167,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Mon Feb 07 2011 Fedora Release Engineering - 1.3-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild + * Mon Nov 15 2010 Tim Fenn - 1.3-1 - update to 1.3 From b5662b32b568da77245439ccf32ce8ae2ad86ba4 Mon Sep 17 00:00:00 2001 From: Dominik Mierzejewski Date: Wed, 16 Mar 2011 16:22:30 +0100 Subject: [PATCH 18/92] - fix build on EL-5 (add missing BR: gcc-gfortran, run libtoolize with --force) - link only to atlas-provided blas for performance --- apbs.spec | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/apbs.spec b/apbs.spec index 7c82072..276724c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.2.1 -Release: 2%{?dist} +Release: 3%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -15,12 +15,10 @@ 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: gcc-gfotran BuildRequires: libtool BuildRequires: arpack-devel BuildRequires: atlas-devel -BuildRequires: blas-devel BuildRequires: maloc-devel BuildRequires: python-devel Requires: python-ZSI @@ -72,7 +70,7 @@ library. %setup -q -n %{name}-%{version}-source %patch0 -p0 %patch1 -p0 -libtoolize --automake +libtoolize --automake --force aclocal autoheader automake --gnu @@ -91,7 +89,7 @@ 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 FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" +%configure --with-blas-name=cblas --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lcblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" # 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 @@ -172,6 +170,10 @@ rm -rf %{buildroot} %doc doc/programmer/ %changelog +* Wed Mar 16 2011 Dominik Mierzejewski - 1.2.1-3 +- fix build on EL-5 (add missing BR: gcc-gfortran, run libtoolize with --force) +- link only to atlas-provided blas for performance + * Tue Dec 01 2009 Tim Fenn - 1.2.1-2 - add RPM_OPT_FLAGS From 05f576f1a2f6cc5140c83db92abffe3439b4724d Mon Sep 17 00:00:00 2001 From: Dominik Mierzejewski Date: Thu, 17 Mar 2011 07:54:13 +0100 Subject: [PATCH 19/92] Fix typo in BR: gcc-gfortran. --- apbs.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 276724c..2da13b4 100644 --- a/apbs.spec +++ b/apbs.spec @@ -15,7 +15,7 @@ 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: gcc-gfotran +BuildRequires: gcc-gfortran BuildRequires: libtool BuildRequires: arpack-devel BuildRequires: atlas-devel From 1e7a7a70a209a64751c5cf8513e3b484a2cdc07d Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Thu, 12 Jan 2012 15:38:44 -0600 Subject: [PATCH 20/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 5628a41..57a042c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 2%{?dist} +Release: 3%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -167,6 +167,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Thu Jan 12 2012 Fedora Release Engineering - 1.3-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild + * Mon Feb 07 2011 Fedora Release Engineering - 1.3-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild From c080187741d1a324474b1838c2a85ee3109305f3 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 18 Jul 2012 11:23:26 -0500 Subject: [PATCH 21/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 57a042c..a9be565 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 3%{?dist} +Release: 4%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -167,6 +167,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Wed Jul 18 2012 Fedora Release Engineering - 1.3-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild + * Thu Jan 12 2012 Fedora Release Engineering - 1.3-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild From 14a2c91180fb445d5902cf5a5b4b889a419e1bd7 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 13 Feb 2013 10:51:37 -0600 Subject: [PATCH 22/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index a9be565..82398ac 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 4%{?dist} +Release: 5%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -167,6 +167,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Wed Feb 13 2013 Fedora Release Engineering - 1.3-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild + * Wed Jul 18 2012 Fedora Release Engineering - 1.3-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild From 4e01c39bb8467bc656f5b4877c30792567ccd076 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Fri, 2 Aug 2013 20:29:01 -0500 Subject: [PATCH 23/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 82398ac..1678bbd 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 5%{?dist} +Release: 6%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -167,6 +167,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Sat Aug 03 2013 Fedora Release Engineering - 1.3-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild + * Wed Feb 13 2013 Fedora Release Engineering - 1.3-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild From fdbeff6d29fd023be630a6a28509ea4e661a4349 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 31 Oct 2013 00:40:49 -0700 Subject: [PATCH 24/92] * Wed Oct 30 2013 Tim Fenn - 1.3-7 - rebuild for atlas 3.10.1 (consolidates lapack and blas) --- apbs-makefile.am.patch | 2 +- apbs.spec | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch index ddf2963..4b37a48 100644 --- a/apbs-makefile.am.patch +++ b/apbs-makefile.am.patch @@ -90,7 +90,7 @@ 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 ++driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ -ltatlas INCLUDES = @inc_list@ AM_CFLAGS = @CFLAGS@ AM_LDFLAGS = @LDFLAGS@ diff --git a/apbs.spec b/apbs.spec index 1678bbd..4a0ac76 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 6%{?dist} +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 @@ -86,7 +86,7 @@ rm -rf contrib/maloc rm -rf contrib/zlib %build -%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --disable-zlib --disable-static --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" +%configure --with-blas='-L%{_libdir}/atlas -ltatlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --disable-zlib --disable-static --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" # 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 @@ -167,6 +167,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Wed Oct 30 2013 Tim Fenn - 1.3-7 +- rebuild for atlas 3.10.1 (consolidates lapack and blas) + * Sat Aug 03 2013 Fedora Release Engineering - 1.3-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild From 57a01f7c37855154fa38ae854d08dbf3344132a5 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Fri, 6 Jun 2014 20:07:10 -0500 Subject: [PATCH 25/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 4a0ac76..0d7c3ea 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 7%{?dist} +Release: 8%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -167,6 +167,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Sat Jun 07 2014 Fedora Release Engineering - 1.3-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild + * Wed Oct 30 2013 Tim Fenn - 1.3-7 - rebuild for atlas 3.10.1 (consolidates lapack and blas) From 18398c71f0d6c33ffbd9920133ae8bb95c4c4d86 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Wed, 18 Jun 2014 00:26:36 -0700 Subject: [PATCH 26/92] fix for bug 1105956 (apbslib.c patch for format-security error) --- apbs-apbslib.c.patch | 11 +++++++++++ apbs.spec | 8 +++++++- 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 apbs-apbslib.c.patch diff --git a/apbs-apbslib.c.patch b/apbs-apbslib.c.patch new file mode 100644 index 0000000..e48f162 --- /dev/null +++ b/apbs-apbslib.c.patch @@ -0,0 +1,11 @@ +--- tools/python/apbslib.c_orig 2014-06-17 23:59:13.605698731 -0700 ++++ tools/python/apbslib.c 2014-06-17 23:59:52.713168627 -0700 +@@ -850,7 +850,7 @@ + Py_DECREF(old_str); + Py_DECREF(value); + } else { +- PyErr_Format(PyExc_RuntimeError, mesg); ++ PyErr_Format(PyExc_RuntimeError, "%s", mesg); + } + } + diff --git a/apbs.spec b/apbs.spec index 0d7c3ea..535a677 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.3 -Release: 8%{?dist} +Release: 9%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -14,6 +14,8 @@ Source1: LGPL_V2 Patch0: apbs-configure.ac.patch # removes hardcoded prefix setting so DESTDIR works Patch1: apbs-makefile.am.patch +# fix for bug 1105956 +Patch2: apbs-apbslib.c.patch Buildroot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) BuildRequires: autoconf BuildRequires: automake @@ -72,6 +74,7 @@ library. %setup -q -n %{name}-%{version}-source %patch0 -p0 %patch1 -p0 +%patch2 -p0 rm acinclude.m4 libtoolize --automake aclocal @@ -167,6 +170,9 @@ rm -rf %{buildroot} %doc doc/programmer/programmer.pdf %changelog +* Wed Jun 18 2014 Tim Fenn - 1.3-9 +- fix for bug 1105956 (apbslib.c patch for format-security error) + * Sat Jun 07 2014 Fedora Release Engineering - 1.3-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild From a1c63fe7df80186e2da21ebc7e78d2a85603b8ba Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 26 Jun 2014 21:07:18 -0700 Subject: [PATCH 27/92] update to 1.4 --- .gitignore | 1 + apbs-apbslib.c.patch | 11 -- apbs-cmake.patch | 250 ++++++++++++++++++++++++++++++++++++++++ apbs-configure.ac.patch | 77 ------------- apbs-makefile.am.patch | 107 ----------------- apbs.spec | 91 ++++----------- sources | 2 +- 7 files changed, 277 insertions(+), 262 deletions(-) delete mode 100644 apbs-apbslib.c.patch create mode 100644 apbs-cmake.patch delete mode 100644 apbs-configure.ac.patch delete mode 100644 apbs-makefile.am.patch diff --git a/.gitignore b/.gitignore index 70de2bf..3f7b265 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ apbs-1.2.1-source.tar.gz /apbs-1.3-source.tar.gz +/APBS-1.4-source.tar.gz diff --git a/apbs-apbslib.c.patch b/apbs-apbslib.c.patch deleted file mode 100644 index e48f162..0000000 --- a/apbs-apbslib.c.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- tools/python/apbslib.c_orig 2014-06-17 23:59:13.605698731 -0700 -+++ tools/python/apbslib.c 2014-06-17 23:59:52.713168627 -0700 -@@ -850,7 +850,7 @@ - Py_DECREF(old_str); - Py_DECREF(value); - } else { -- PyErr_Format(PyExc_RuntimeError, mesg); -+ PyErr_Format(PyExc_RuntimeError, "%s", mesg); - } - } - diff --git a/apbs-cmake.patch b/apbs-cmake.patch new file mode 100644 index 0000000..73a7fd3 --- /dev/null +++ b/apbs-cmake.patch @@ -0,0 +1,250 @@ +--- CMakeLists.txt_orig 2014-06-18 01:28:14.361212184 -0700 ++++ CMakeLists.txt 2014-06-23 22:11:12.124786178 -0700 +@@ -1,4 +1,5 @@ + cmake_minimum_required (VERSION 2.6) ++SET(CMAKE_POSITION_INDEPENDENT_CODE ON) + + ################################################################################ + # TODO: Add option to build documentation at compile time +@@ -56,10 +57,10 @@ + set(TOOLS_PATH ${APBS_ROOT}/tools) + set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) + +-set(LIBRARY_INSTALL_PATH lib) +-set(HEADER_INSTALL_PATH include/apbs) ++set(LIBRARY_INSTALL_PATH ${LIB_INSTALL_DIR}) ++set(HEADER_INSTALL_PATH ${INCLUDE_INSTALL_DIR}/apbs) + set(EXECUTABLE_INSTALL_PATH bin) +-set(SHARE_INSTALL_PATH share/apbs) ++set(SHARE_INSTALL_PATH ${SHARE_INSTALL_PREFIX}/apbs) + + find_file( + CONTRIB_PATH +@@ -84,14 +85,14 @@ + + message(STATUS "Setting lookup paths for headers and libraries") + +-set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") +-list(APPEND CMAKE_INCLUDE_PATH /usr/include) +-list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) +- +-set(SYS_LIBPATHS "") +-list(APPEND SYS_LIBPATHS /usr/lib) +-list(APPEND SYS_LIBPATHS /usr/local/lib) +-list(APPEND SYS_LIBPATHS /lib/x86_64-linux-gnu) ++#set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") ++#list(APPEND CMAKE_INCLUDE_PATH /usr/include) ++#list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) ++ ++#set(SYS_LIBPATHS "") ++#list(APPEND SYS_LIBPATHS /usr/lib) ++#list(APPEND SYS_LIBPATHS /usr/local/lib) ++#list(APPEND SYS_LIBPATHS /lib/x86_64-linux-gnu) + + set(APBS_LIBS "") + +@@ -854,29 +855,29 @@ + # Set up additional directories to install # + ################################################################################ + +-install( +- DIRECTORY ${APBS_ROOT}/doc +- DESTINATION ${SHARE_INSTALL_PATH} +-) +- +-install( +- DIRECTORY ${APBS_ROOT}/examples +- DESTINATION ${SHARE_INSTALL_PATH} +-) +- +-install( +- DIRECTORY ${APBS_ROOT}/tests +- DESTINATION ${SHARE_INSTALL_PATH} +- FILES_MATCHING +- PATTERN "*.py" +- PATTERN "README" +-) +- +-install( +- DIRECTORY ${APBS_ROOT}/tools +- DESTINATION ${SHARE_INSTALL_PATH} +- PATTERN "CMakeLists.txt" EXCLUDE +-) ++#install( ++# DIRECTORY ${APBS_ROOT}/doc ++# DESTINATION ${SHARE_INSTALL_PATH} ++#) ++ ++#install( ++# DIRECTORY ${APBS_ROOT}/examples ++# DESTINATION ${SHARE_INSTALL_PATH} ++#) ++ ++#install( ++# DIRECTORY ${APBS_ROOT}/tests ++# DESTINATION ${SHARE_INSTALL_PATH} ++# FILES_MATCHING ++# PATTERN "*.py" ++# PATTERN "README" ++#) ++ ++#install( ++# DIRECTORY ${APBS_ROOT}/tools ++# DESTINATION ${SHARE_INSTALL_PATH} ++# PATTERN "CMakeLists.txt" EXCLUDE ++#) + + + +--- src/CMakeLists.txt_orig 2014-06-23 19:57:35.108270115 -0700 ++++ src/CMakeLists.txt 2014-06-23 22:25:44.469683936 -0700 +@@ -32,10 +32,10 @@ + message(STATUS "With external header files ${EXTERNAL_HEADERS}") + message(STATUS "With internal header files ${INTERNAL_HEADERS}") + message(STATUS "With library dependencies ${LIBRARY_DEPENDENCIES}") +- add_library(${LIBRARY_NAME} SHARED ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) +- target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES}) ++ add_library(${LIBRARY_NAME} OBJECT ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) ++ # target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES}) + INSTALL(FILES ${EXTERNAL_HEADERS} DESTINATION ${HEADER_INSTALL_PATH}/${LIBRARY}) +- INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH}) ++ # INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH}) + list(APPEND APBS_INTERNAL_LIBS ${LIBRARY_NAME}) + set(APBS_INTERNAL_LIBS ${APBS_INTERNAL_LIBS} PARENT_SCOPE) + message(STATUS "Added ${LIBRARY_NAME}") +@@ -46,12 +46,19 @@ + add_subdirectory(generic) + add_subdirectory(pmgc) + add_subdirectory(mg) ++add_library(apbs SHARED $ $ $) ++# set a SOVERSION to keep packager happy ++SET_TARGET_PROPERTIES(apbs PROPERTIES SOVERSION "1") ++target_link_libraries(apbs ${LIBRARY_DEPENDENCIES}) ++INSTALL(TARGETS apbs LIBRARY DESTINATION ${LIBRARY_INSTALL_PATH}) + if(ENABLE_FETK) + add_subdirectory(fem) + endif(ENABLE_FETK) + +-add_executable(apbs main.c apbs.h routines.c routines.h) +-target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS}) ++add_executable(apbs-bin main.c apbs.h routines.c routines.h) ++# target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS)} ++target_link_libraries(apbs-bin ${APBS_LIBS} apbs) ++SET_TARGET_PROPERTIES(apbs-bin PROPERTIES OUTPUT_NAME apbs) + + configure_file( + ${APBS_ROOT}/src/config/apbscfg.h.in +@@ -59,4 +66,4 @@ + ) + + INSTALL(FILES apbs.h routines.h DESTINATION ${HEADER_INSTALL_PATH}) +-INSTALL(TARGETS apbs DESTINATION ${EXECUTABLE_INSTALL_PATH}) ++INSTALL(TARGETS apbs-bin DESTINATION ${EXECUTABLE_INSTALL_PATH}) +--- tools/manip/CMakeLists.txt_orig 2014-06-23 20:06:51.205468128 -0700 ++++ tools/manip/CMakeLists.txt 2014-06-23 22:17:44.103764752 -0700 +@@ -1,9 +1,10 @@ + message(STATUS "Building manip") + + set(LIBS "") +-list(APPEND LIBS "apbs_generic") +-list(APPEND LIBS "apbs_mg") +-list(APPEND LIBS "apbs_pmgc") ++#list(APPEND LIBS "apbs_generic") ++#list(APPEND LIBS "apbs_mg") ++#list(APPEND LIBS "apbs_pmgc") ++list(APPEND LIBS "apbs") + if(FETK_ENALBED) + list(APPEND LIBS "apbs_fem") + endif(FETK_ENALBED) +@@ -11,7 +12,9 @@ + message(STATUS "libraries: ${LIBS}") + + add_executable(coulomb coulomb.c) +-target_link_libraries(coulomb ${LIBS}) ++target_link_libraries(coulomb ${LIBS} ${APBS_LIBS}) + + add_executable(born born.c) +-target_link_libraries(born ${LIBS}) ++target_link_libraries(born ${LIBS} ${APBS_LIBS}) ++ ++INSTALL(TARGETS coulomb born DESTINATION ${EXECUTABLE_INSTALL_PATH}) +--- tools/mesh/CMakeLists.txt_orig 2014-06-23 19:47:12.897442708 -0700 ++++ tools/mesh/CMakeLists.txt 2014-06-23 22:16:27.230896796 -0700 +@@ -1,9 +1,10 @@ + message(STATUS "Building mesh") + + set(LIBS "") +-list(APPEND LIBS "apbs_generic") +-list(APPEND LIBS "apbs_mg") +-list(APPEND LIBS "apbs_pmgc") ++#list(APPEND LIBS "apbs_generic") ++#list(APPEND LIBS "apbs_mg") ++#list(APPEND LIBS "apbs_pmgc") ++list(APPEND LIBS "apbs") + if(FETK_ENALBED) + list(APPEND LIBS "apbs_fem") + endif(FETK_ENALBED) +@@ -11,46 +12,48 @@ + message(STATUS "libraries: ${LIBS}") + + add_executable(mgmesh mgmesh.c) +-target_link_libraries(mgmesh ${LIBS}) ++target_link_libraries(mgmesh ${LIBS} ${APBS_LIBS}) + + add_executable(smooth smooth.c) +-target_link_libraries(smooth ${LIBS}) ++target_link_libraries(smooth ${LIBS} ${APBS_LIBS}) + + add_executable(dxmath dxmath.c) +-target_link_libraries(dxmath ${LIBS}) ++target_link_libraries(dxmath ${LIBS} ${APBS_LIBS}) + + add_executable(mergedx mergedx.c) +-target_link_libraries(mergedx ${LIBS}) ++target_link_libraries(mergedx ${LIBS} ${APBS_LIBS}) + + add_executable(mergedx2 mergedx2.c) +-target_link_libraries(mergedx2 ${LIBS}) ++target_link_libraries(mergedx2 ${LIBS} ${APBS_LIBS}) + + add_executable(value value.c) +-target_link_libraries(value ${LIBS}) ++target_link_libraries(value ${LIBS} ${APBS_LIBS}) + + add_executable(multivalue multivalue.c) +-target_link_libraries(multivalue ${LIBS}) ++target_link_libraries(multivalue ${LIBS} ${APBS_LIBS}) + + add_executable(benchmark benchmark.c) +-target_link_libraries(benchmark ${LIBS}) ++target_link_libraries(benchmark ${LIBS} ${APBS_LIBS}) + + add_executable(similarity similarity.c) +-target_link_libraries(similarity ${LIBS}) ++target_link_libraries(similarity ${LIBS} ${APBS_LIBS}) + + add_executable(analysis analysis.c) +-target_link_libraries(analysis ${LIBS}) ++target_link_libraries(analysis ${LIBS} ${APBS_LIBS}) + + add_executable(dx2mol dx2mol.c) +-target_link_libraries(dx2mol ${LIBS}) ++target_link_libraries(dx2mol ${LIBS} ${APBS_LIBS}) + + add_executable(dx2uhbd dx2uhbd.c) +-target_link_libraries(dx2uhbd ${LIBS}) ++target_link_libraries(dx2uhbd ${LIBS} ${APBS_LIBS}) + + add_executable(del2dx del2dx.c) +-target_link_libraries(del2dx ${LIBS}) ++target_link_libraries(del2dx ${LIBS} ${APBS_LIBS}) + + add_executable(tensor2dx tensor2dx.c) +-target_link_libraries(tensor2dx ${LIBS}) ++target_link_libraries(tensor2dx ${LIBS} ${APBS_LIBS}) + + add_executable(uhbd_asc2bin uhbd_asc2bin.c) +-target_link_libraries(uhbd_asc2bin ${LIBS}) ++target_link_libraries(uhbd_asc2bin ${LIBS} ${APBS_LIBS}) ++ ++INSTALL(TARGETS mgmesh smooth dxmath mergedx mergedx2 value multivalue benchmark similarity analysis dx2mol dx2uhbd del2dx tensor2dx uhbd_asc2bin DESTINATION ${EXECUTABLE_INSTALL_PATH}) diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch deleted file mode 100644 index e595ea7..0000000 --- a/apbs-configure.ac.patch +++ /dev/null @@ -1,77 +0,0 @@ ---- configure.ac_orig 2010-11-15 11:54:58.428167033 -0800 -+++ configure.ac 2010-11-15 14:26:50.556166647 -0800 -@@ -229,14 +229,15 @@ - CXXFLAGS=`echo ${CXXFLAGS} | sed 's/-g//g'`; - fi - fi --AC_F77_NOFORMAIN -+# AC_F77_NOFORMAIN - FFLAGS="${FLIBS} ${FFLAGS}" --if test "${CC}" != "icl"; then -- AC_F77_FCN_MANGLE() --fi -+# this macro is broken, so be sure to set -DVF77_ONEUNDERSCORE -+#if test "${CC}" != "icl"; then -+# AC_F77_FCN_MANGLE() -+#fi - AC_LANG_C - AC_PROG_CPP --AC_DISABLE_SHARED -+# AC_DISABLE_SHARED - AM_PROG_LIBTOOL - FFLAGS="${FFLAGS}" - -@@ -308,7 +309,7 @@ - dnl # HANDLE COMPILER FLOATING POINT ERROR - dnl # ------------------------------------ - --AC_FPERROR -+# AC_FPERROR - - dnl ########################################################################## - dnl 8. checks for library functions -@@ -390,7 +391,7 @@ - - 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 "${maloc_lib}"; then - AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified]) - fi -@@ -816,7 +817,7 @@ - fi - LDFLAGS=${LDFLAGS_SAVE}; - CPPFLAGS=${CPPFLAGS_SAVE}; --AC_SUBST(rl_lib) -+# AC_SUBST(rl_lib) - - dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK - dnl # ----------------------- -@@ -1038,6 +1039,7 @@ - blas_lib=${contrib_path}/blas/.libs/libapbsblas.a - fi - AC_SUBST(apbs_do_blas) -+AC_SUBST(blas_lib) - - dnl # -------------------------------- - dnl # HANDLE ZLIB COMPILATION -@@ -1280,7 +1282,9 @@ - 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) - -@@ -1297,7 +1301,6 @@ - contrib/aqua/Makefile - contrib/opal/Makefile - contrib/opal/ZSI/Makefile -- contrib/zlib/Makefile - - tools/Makefile - tools/mesh/Makefile diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch deleted file mode 100644 index 4b37a48..0000000 --- a/apbs-makefile.am.patch +++ /dev/null @@ -1,107 +0,0 @@ ---- ./bin/Makefile.am_orig 2010-11-15 12:07:02.487166613 -0800 -+++ ./bin/Makefile.am 2010-11-15 12:10:49.109166514 -0800 -@@ -12,34 +12,31 @@ - - 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 - - # This is a hack I suspect, but needed to force apbs to be - # rebuilt anytime the make command is issued - # Problem before is that there is no dependency between source file - # recompilation and relinking the binary. There is probably - # a cleaner way to do this, I can't find it, however. --BUILT_SOURCES = rm.apbs -+# BUILT_SOURCES = rm.apbs - --rm.apbs: Makefile -- -rm -f apbs -- --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 2010-11-15 12:01:13.975197621 -0800 -+++ ./src/aaa_lib/Makefile.am 2010-11-15 12:01:54.567274233 -0800 -@@ -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@ ---- ./tools/python/vgrid/Makefile.am_orig 2010-11-15 12:02:55.717416873 -0800 -+++ ./tools/python/vgrid/Makefile.am 2010-11-15 12:04:33.565198239 -0800 -@@ -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/python/Makefile.am_orig 2010-11-15 12:04:54.918478810 -0800 -+++ ./tools/python/Makefile.am 2010-11-15 14:22:08.880166492 -0800 -@@ -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) ${z_lib} -+_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/arpack/Makefile.am_orig 2010-11-15 12:02:08.657198191 -0800 -+++ ./tools/arpack/Makefile.am 2010-11-15 12:02:26.559231032 -0800 -@@ -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@ -ltatlas - INCLUDES = @inc_list@ - AM_CFLAGS = @CFLAGS@ - AM_LDFLAGS = @LDFLAGS@ ---- ./contrib/opal/Makefile.am_orig 2010-11-15 12:00:27.148447572 -0800 -+++ ./contrib/opal/Makefile.am 2010-11-15 12:00:51.998166490 -0800 -@@ -9,7 +9,7 @@ - AUTOMAKE_OPTIONS = no-dependencies - SUFFIXES = .H .h .C .c .f .o - --always_built_SUBDIRS = ZSI -+# always_built_SUBDIRS = ZSI - - SUBDIRS = $(always_built_SUBDIRS) . - diff --git a/apbs.spec b/apbs.spec index 535a677..82216e5 100644 --- a/apbs.spec +++ b/apbs.spec @@ -2,30 +2,21 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.3 -Release: 9%{?dist} +Version: 1.4 +Release: 1%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering URL: http://apbs.sourceforge.net/ -Source0: http://downloads.sourceforge.net/apbs/%{name}-%{version}-source.tar.gz -Source1: LGPL_V2 -# adds blas_lib to AC_SUBST so Makefiles are complete -Patch0: apbs-configure.ac.patch -# removes hardcoded prefix setting so DESTDIR works -Patch1: apbs-makefile.am.patch -# fix for bug 1105956 -Patch2: apbs-apbslib.c.patch -Buildroot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) -BuildRequires: autoconf -BuildRequires: automake -BuildRequires: libtool +Source0: http://downloads.sourceforge.net/apbs/APBS-%{version}-source.tar.gz +Patch0: apbs-cmake.patch +BuildRequires: cmake +BuildRequires: doxygen BuildRequires: arpack-devel BuildRequires: atlas-devel BuildRequires: blas-devel BuildRequires: maloc-devel -BuildRequires: python-devel -Requires: python-ZSI +BuildRequires: zlib-devel %description APBS is a software package for the numerical solution of the @@ -71,54 +62,26 @@ development using the adaptive poisson boltzmann (APBS) solver library. %prep -%setup -q -n %{name}-%{version}-source +%setup -q -n %{name} %patch0 -p0 -%patch1 -p0 -%patch2 -p0 -rm acinclude.m4 -libtoolize --automake -aclocal -autoheader -automake --gnu -autoconf - -install -p -m 644 %{SOURCE1} . - -# ensure maloc/zlib aren't built -rm -rf contrib/maloc -rm -rf contrib/zlib %build -%configure --with-blas='-L%{_libdir}/atlas -ltatlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --disable-zlib --disable-static --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE" -# 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 - +cd build +%cmake -D BUILD_DOC:BOOL=ON .. 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/ +cd build +make install DESTDIR=%{buildroot} +cd .. # 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` +for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} tools/manip/psize.py; do + mv $bin %{buildroot}%{_bindir}/apbs-`basename $bin` done -# remove unpackaged files from buildroot -rm -f %{buildroot}%{_libdir}/*.la - %clean rm -rf %{buildroot} @@ -128,16 +91,9 @@ rm -rf %{buildroot} %files %defattr(-,root,root,-) -%doc AUTHORS COPYING LGPL_V2 README ChangeLog +%doc doc/license/LICENSE.txt 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/ +%{_libdir}/libapbs*.so.* %files tools %defattr(-,root,root,-) @@ -157,20 +113,23 @@ rm -rf %{buildroot} %{_bindir}/apbs-multivalue %{_bindir}/apbs-benchmark %{_bindir}/apbs-analysis -%{_bindir}/apbs-driver +%{_bindir}/apbs-del2dx +%{_bindir}/apbs-tensor2dx %files devel %defattr(-,root,root,-) -%{_libdir}/libapbs.so -%{_libdir}/libapbsmainroutines.so +%{_libdir}/libapbs*.so %{_includedir}/apbs %files doc %defattr(-,root,root,-) -%doc doc/programmer/programmer.pdf +%doc doc/programmer/html %changelog -* Wed Jun 18 2014 Tim Fenn - 1.3-9 +* Thu Jun 19 2014 Tim Fenn - 1.4-1 +- update to 1.4 + +* Wed Jun 18 2014 Tim Fenn - 1.3-8 - fix for bug 1105956 (apbslib.c patch for format-security error) * Sat Jun 07 2014 Fedora Release Engineering - 1.3-8 diff --git a/sources b/sources index 4646d30..f659863 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -f99a505365f07f6853979cfe2ef23365 apbs-1.3-source.tar.gz +e0281bd44ffecb651e40687cdaa26361 APBS-1.4-source.tar.gz From 4599b4003a8419760aa011def2a636fb88cc4614 Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Fri, 15 Aug 2014 20:41:52 +0000 Subject: [PATCH 28/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 82216e5..aa5539d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.4 -Release: 1%{?dist} +Release: 2%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -126,6 +126,9 @@ rm -rf %{buildroot} %doc doc/programmer/html %changelog +* Fri Aug 15 2014 Fedora Release Engineering - 1.4-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild + * Thu Jun 19 2014 Tim Fenn - 1.4-1 - update to 1.4 From 1b4c686daef95ef64e8d032b9d47d42168488045 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 17 Jun 2015 00:08:16 +0000 Subject: [PATCH 29/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index aa5539d..f59f1b3 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.4 -Release: 2%{?dist} +Release: 3%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -126,6 +126,9 @@ rm -rf %{buildroot} %doc doc/programmer/html %changelog +* Wed Jun 17 2015 Fedora Release Engineering - 1.4-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild + * Fri Aug 15 2014 Fedora Release Engineering - 1.4-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild From 955998c47f7119e2f1713a3c79c62213e9ed7b46 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 3 Feb 2016 16:21:19 +0000 Subject: [PATCH 30/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index f59f1b3..570306a 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.4 -Release: 3%{?dist} +Release: 4%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -126,6 +126,9 @@ rm -rf %{buildroot} %doc doc/programmer/html %changelog +* Wed Feb 03 2016 Fedora Release Engineering - 1.4-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + * Wed Jun 17 2015 Fedora Release Engineering - 1.4-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild From 55e6a65915ee86bf81270c70f388083105bcd540 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 10 Feb 2017 06:07:42 +0000 Subject: [PATCH 31/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 570306a..30795d8 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.4 -Release: 4%{?dist} +Release: 5%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -126,6 +126,9 @@ rm -rf %{buildroot} %doc doc/programmer/html %changelog +* Fri Feb 10 2017 Fedora Release Engineering - 1.4-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild + * Wed Feb 03 2016 Fedora Release Engineering - 1.4-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild From 83699ef143ead03ecc4dcbbec8e78eb3a688025f Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 26 Jul 2017 03:04:25 +0000 Subject: [PATCH 32/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 30795d8..46990f1 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.4 -Release: 5%{?dist} +Release: 6%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -126,6 +126,9 @@ rm -rf %{buildroot} %doc doc/programmer/html %changelog +* Wed Jul 26 2017 Fedora Release Engineering - 1.4-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + * Fri Feb 10 2017 Fedora Release Engineering - 1.4-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild From 1c58882adb9d4c172e8219864dab37f9560cf873 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 2 Aug 2017 17:37:34 +0000 Subject: [PATCH 33/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 46990f1..7df3d20 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.4 -Release: 6%{?dist} +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 @@ -126,6 +126,9 @@ rm -rf %{buildroot} %doc doc/programmer/html %changelog +* Wed Aug 02 2017 Fedora Release Engineering - 1.4-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + * Wed Jul 26 2017 Fedora Release Engineering - 1.4-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild From 78f572531c6e1150fa585df405c0500346b0fe87 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 7 Feb 2018 02:35:29 +0000 Subject: [PATCH 34/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 7df3d20..00a5153 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.4 -Release: 7%{?dist} +Release: 8%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -126,6 +126,9 @@ rm -rf %{buildroot} %doc doc/programmer/html %changelog +* Wed Feb 07 2018 Fedora Release Engineering - 1.4-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild + * Wed Aug 02 2017 Fedora Release Engineering - 1.4-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild From 7889fc27a172335e67bf90f73a24f0094074bed8 Mon Sep 17 00:00:00 2001 From: Igor Gnatenko Date: Wed, 14 Feb 2018 07:01:46 +0100 Subject: [PATCH 35/92] Remove %clean section None of currently supported distributions need that. Last one was EL5 which is EOL for a while. Signed-off-by: Igor Gnatenko --- apbs.spec | 3 --- 1 file changed, 3 deletions(-) diff --git a/apbs.spec b/apbs.spec index 00a5153..bdc7ef6 100644 --- a/apbs.spec +++ b/apbs.spec @@ -82,9 +82,6 @@ for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,v mv $bin %{buildroot}%{_bindir}/apbs-`basename $bin` done -%clean -rm -rf %{buildroot} - %post -p /sbin/ldconfig %postun -p /sbin/ldconfig From 178230c85c4e8b25f7c531101c5c80dab6daff67 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sun, 27 May 2018 14:04:42 -0400 Subject: [PATCH 36/92] update to 1.5 --- .gitignore | 1 + apbs-cmake.patch | 135 ++++++++++++++++++++++++++++++----------------- apbs.spec | 28 ++++++---- sources | 2 +- 4 files changed, 106 insertions(+), 60 deletions(-) diff --git a/.gitignore b/.gitignore index 3f7b265..f5c581c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ apbs-1.2.1-source.tar.gz /apbs-1.3-source.tar.gz /APBS-1.4-source.tar.gz +/apbs-1.5.tar.gz diff --git a/apbs-cmake.patch b/apbs-cmake.patch index 73a7fd3..c801f77 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -1,13 +1,13 @@ ---- CMakeLists.txt_orig 2014-06-18 01:28:14.361212184 -0700 -+++ CMakeLists.txt 2014-06-23 22:11:12.124786178 -0700 +--- CMakeLists.txt_orig 2018-05-20 13:00:17.451341064 -0400 ++++ CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -1,4 +1,5 @@ - cmake_minimum_required (VERSION 2.6) -+SET(CMAKE_POSITION_INDEPENDENT_CODE ON) + cmake_minimum_required (VERSION 2.8.7) ++set(CMAKE_POSITION_INDEPENDENT_CODE ON) ################################################################################ - # TODO: Add option to build documentation at compile time -@@ -56,10 +57,10 @@ - set(TOOLS_PATH ${APBS_ROOT}/tools) + # TODO: Add licensing and authorship information +@@ -63,10 +64,10 @@ + set(TOOLS_PATH ${APBS_BUILD}/tools) set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) -set(LIBRARY_INSTALL_PATH lib) @@ -18,40 +18,70 @@ -set(SHARE_INSTALL_PATH share/apbs) +set(SHARE_INSTALL_PATH ${SHARE_INSTALL_PREFIX}/apbs) - find_file( - CONTRIB_PATH -@@ -84,14 +85,14 @@ + set(APBS_LIBS) + set(APBS_LIB_DIRS) +@@ -78,7 +79,7 @@ + DOC "The path to the external git submodules" + ) + +-set(SYS_LIBPATHS /usr/lib64) ++#set(SYS_LIBPATHS /usr/lib64) + #list(APPEND SYS_LIBPATHS /usr/lib64) + + ################################################################################ +@@ -105,9 +106,9 @@ message(STATUS "Setting lookup paths for headers and libraries") -set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") -list(APPEND CMAKE_INCLUDE_PATH /usr/include) -list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) -- --set(SYS_LIBPATHS "") --list(APPEND SYS_LIBPATHS /usr/lib) --list(APPEND SYS_LIBPATHS /usr/local/lib) --list(APPEND SYS_LIBPATHS /lib/x86_64-linux-gnu) +#set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") +#list(APPEND CMAKE_INCLUDE_PATH /usr/include) +#list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) -+ -+#set(SYS_LIBPATHS "") -+#list(APPEND SYS_LIBPATHS /usr/lib) -+#list(APPEND SYS_LIBPATHS /usr/local/lib) -+#list(APPEND SYS_LIBPATHS /lib/x86_64-linux-gnu) - set(APBS_LIBS "") -@@ -854,29 +855,29 @@ + +@@ -259,11 +260,11 @@ + + if(NOT ENABLE_FETK) + # We'll use autotools to build MALOC if FETK is enabled. +- set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc) +- add_subdirectory(${MALOC_ROOT}) +- include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys +- ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh) +- list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) ++ #set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc) ++ # add_subdirectory(${MALOC_ROOT}) ++ #include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys ++ # ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh) ++ #list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) + list(APPEND APBS_LIBS maloc) + endif() + +@@ -736,12 +737,12 @@ # Set up additional directories to install # ################################################################################ -install( - DIRECTORY ${APBS_ROOT}/doc - DESTINATION ${SHARE_INSTALL_PATH} +- PATTERN "programmer" EXCLUDE +- PATTERN "CMakeLists.txt" EXCLUDE -) -- ++#install( ++# DIRECTORY ${APBS_ROOT}/doc ++# DESTINATION ${SHARE_INSTALL_PATH} ++# PATTERN "programmer" EXCLUDE ++# PATTERN "CMakeLists.txt" EXCLUDE ++#) + + if(BUILD_DOC) + install( +@@ -753,24 +754,24 @@ + ) + endif() + -install( - DIRECTORY ${APBS_ROOT}/examples - DESTINATION ${SHARE_INSTALL_PATH} @@ -71,11 +101,6 @@ - PATTERN "CMakeLists.txt" EXCLUDE -) +#install( -+# DIRECTORY ${APBS_ROOT}/doc -+# DESTINATION ${SHARE_INSTALL_PATH} -+#) -+ -+#install( +# DIRECTORY ${APBS_ROOT}/examples +# DESTINATION ${SHARE_INSTALL_PATH} +#) @@ -94,25 +119,26 @@ +# PATTERN "CMakeLists.txt" EXCLUDE +#) - - ---- src/CMakeLists.txt_orig 2014-06-23 19:57:35.108270115 -0700 -+++ src/CMakeLists.txt 2014-06-23 22:25:44.469683936 -0700 -@@ -32,10 +32,10 @@ + if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}") + install( +--- src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400 ++++ src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 +@@ -32,11 +32,11 @@ message(STATUS "With external header files ${EXTERNAL_HEADERS}") message(STATUS "With internal header files ${INTERNAL_HEADERS}") message(STATUS "With library dependencies ${LIBRARY_DEPENDENCIES}") -- add_library(${LIBRARY_NAME} SHARED ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) +- add_library(${LIBRARY_NAME} ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) - target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES}) + add_library(${LIBRARY_NAME} OBJECT ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) + # target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES}) + #add_dependencies(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES}) INSTALL(FILES ${EXTERNAL_HEADERS} DESTINATION ${HEADER_INSTALL_PATH}/${LIBRARY}) - INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH}) + # INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH}) list(APPEND APBS_INTERNAL_LIBS ${LIBRARY_NAME}) set(APBS_INTERNAL_LIBS ${APBS_INTERNAL_LIBS} PARENT_SCOPE) message(STATUS "Added ${LIBRARY_NAME}") -@@ -46,12 +46,19 @@ +@@ -47,6 +47,11 @@ add_subdirectory(generic) add_subdirectory(pmgc) add_subdirectory(mg) @@ -121,27 +147,38 @@ +SET_TARGET_PROPERTIES(apbs PROPERTIES SOVERSION "1") +target_link_libraries(apbs ${LIBRARY_DEPENDENCIES}) +INSTALL(TARGETS apbs LIBRARY DESTINATION ${LIBRARY_INSTALL_PATH}) + if(ENABLE_FETK) add_subdirectory(fem) - endif(ENABLE_FETK) +@@ -57,7 +62,7 @@ + + message(STATUS ${EXTERNAL_HEADERS}) -add_executable(apbs main.c apbs.h routines.c routines.h) --target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS}) +add_executable(apbs-bin main.c apbs.h routines.c routines.h) -+# target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS)} + message(***************************) + message(STATUS " ") + message(STATUS "APBS Libraries: ${APBS_LIBS}") +@@ -66,7 +71,8 @@ + message(***************************) + + #add_dependencies(apbs ${BEM_LIB}) +-target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS}) +target_link_libraries(apbs-bin ${APBS_LIBS} apbs) +SET_TARGET_PROPERTIES(apbs-bin PROPERTIES OUTPUT_NAME apbs) + #add_dependencies(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS}) configure_file( - ${APBS_ROOT}/src/config/apbscfg.h.in -@@ -59,4 +66,4 @@ - ) +@@ -81,6 +87,6 @@ + endif() INSTALL(FILES apbs.h routines.h DESTINATION ${HEADER_INSTALL_PATH}) -INSTALL(TARGETS apbs DESTINATION ${EXECUTABLE_INSTALL_PATH}) +INSTALL(TARGETS apbs-bin DESTINATION ${EXECUTABLE_INSTALL_PATH}) ---- tools/manip/CMakeLists.txt_orig 2014-06-23 20:06:51.205468128 -0700 -+++ tools/manip/CMakeLists.txt 2014-06-23 22:17:44.103764752 -0700 + + message(STATUS ${CMAKE_C_FLAGS}) +--- tools/manip/CMakeLists.txt_orig 2018-05-20 13:00:31.831387880 -0400 ++++ tools/manip/CMakeLists.txt 2018-05-20 13:07:07.742714938 -0400 @@ -1,9 +1,10 @@ message(STATUS "Building manip") @@ -153,9 +190,9 @@ +#list(APPEND LIBS "apbs_mg") +#list(APPEND LIBS "apbs_pmgc") +list(APPEND LIBS "apbs") - if(FETK_ENALBED) + if(FETK_ENABLED) list(APPEND LIBS "apbs_fem") - endif(FETK_ENALBED) + endif(FETK_ENABLED) @@ -11,7 +12,9 @@ message(STATUS "libraries: ${LIBS}") @@ -168,8 +205,8 @@ +target_link_libraries(born ${LIBS} ${APBS_LIBS}) + +INSTALL(TARGETS coulomb born DESTINATION ${EXECUTABLE_INSTALL_PATH}) ---- tools/mesh/CMakeLists.txt_orig 2014-06-23 19:47:12.897442708 -0700 -+++ tools/mesh/CMakeLists.txt 2014-06-23 22:16:27.230896796 -0700 +--- tools/mesh/CMakeLists.txt_orig 2018-05-20 13:00:26.966372042 -0400 ++++ tools/mesh/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -1,9 +1,10 @@ message(STATUS "Building mesh") @@ -181,9 +218,9 @@ +#list(APPEND LIBS "apbs_mg") +#list(APPEND LIBS "apbs_pmgc") +list(APPEND LIBS "apbs") - if(FETK_ENALBED) + if(FETK_ENABLED) list(APPEND LIBS "apbs_fem") - endif(FETK_ENALBED) + endif(FETK_ENABLED) @@ -11,46 +12,48 @@ message(STATUS "libraries: ${LIBS}") diff --git a/apbs.spec b/apbs.spec index bdc7ef6..1b3600d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -2,20 +2,22 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.4 -Release: 8%{?dist} +Version: 1.5 +Release: 1%{?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/APBS-%{version}-source.tar.gz +Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/apbs-%{version}.tar.gz Patch0: apbs-cmake.patch BuildRequires: cmake BuildRequires: doxygen +BuildRequires: graphviz BuildRequires: arpack-devel BuildRequires: atlas-devel BuildRequires: blas-devel BuildRequires: maloc-devel +BuildRequires: tex(latex) BuildRequires: zlib-devel %description @@ -62,20 +64,23 @@ development using the adaptive poisson boltzmann (APBS) solver library. %prep -%setup -q -n %{name} +%setup -q -n %{name}-pdb2pqr-apbs-%{version} +cd apbs %patch0 -p0 %build -cd build -%cmake -D BUILD_DOC:BOOL=ON .. +cd apbs +# %cmake -D BUILD_DOC:BOOL=ON . +%cmake -D BUILD_DOC:BOOL=OFF . make %{?_smp_mflags} +cd doc/programmer +doxygen %install rm -rf %{buildroot} -cd build +cd apbs make install DESTDIR=%{buildroot} -cd .. # tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} tools/manip/psize.py; do @@ -88,7 +93,7 @@ done %files %defattr(-,root,root,-) -%doc doc/license/LICENSE.txt README ChangeLog +%doc apbs/doc/license/LICENSE.txt apbs/doc/README apbs/doc/ChangeLog.md %{_bindir}/apbs %{_libdir}/libapbs*.so.* @@ -120,9 +125,12 @@ done %files doc %defattr(-,root,root,-) -%doc doc/programmer/html +%doc apbs/doc/programmer/html %changelog +* Sat May 19 2018 Tim Fenn - 1.5-1 +- update to 1.5 + * Wed Feb 07 2018 Fedora Release Engineering - 1.4-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild diff --git a/sources b/sources index f659863..5010b5a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -e0281bd44ffecb651e40687cdaa26361 APBS-1.4-source.tar.gz +SHA512 (apbs-1.5.tar.gz) = 4a117054653a738082f9a25a35c5a0605a1f225e682ff57ed4393689aefe1beffe4fe2364c164d07eb524a26add002b50e29eb297d690494448dac1cef72634d From b39ee134c6894969e6129a05df1b9dc657ec110b Mon Sep 17 00:00:00 2001 From: Igor Gnatenko Date: Mon, 9 Jul 2018 19:06:42 +0200 Subject: [PATCH 37/92] add BuildRequires: gcc-c++ Reference: https://fedoraproject.org/wiki/Changes/Remove_GCC_from_BuildRoot --- apbs.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/apbs.spec b/apbs.spec index 1b3600d..624971c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -10,6 +10,7 @@ Group: Applications/Engineering URL: http://apbs.sourceforge.net/ Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/apbs-%{version}.tar.gz Patch0: apbs-cmake.patch +BuildRequires: gcc-c++ BuildRequires: cmake BuildRequires: doxygen BuildRequires: graphviz From 77b29ba5157a06dd03db9dcea538315817a39fe8 Mon Sep 17 00:00:00 2001 From: Jason Tibbitts Date: Tue, 10 Jul 2018 00:10:51 -0500 Subject: [PATCH 38/92] Remove needless use of %defattr --- apbs.spec | 4 ---- 1 file changed, 4 deletions(-) diff --git a/apbs.spec b/apbs.spec index 624971c..059d207 100644 --- a/apbs.spec +++ b/apbs.spec @@ -93,13 +93,11 @@ done %postun -p /sbin/ldconfig %files -%defattr(-,root,root,-) %doc apbs/doc/license/LICENSE.txt apbs/doc/README apbs/doc/ChangeLog.md %{_bindir}/apbs %{_libdir}/libapbs*.so.* %files tools -%defattr(-,root,root,-) %{_bindir}/apbs-psize.py %{_bindir}/apbs-coulomb %{_bindir}/apbs-born @@ -120,12 +118,10 @@ done %{_bindir}/apbs-tensor2dx %files devel -%defattr(-,root,root,-) %{_libdir}/libapbs*.so %{_includedir}/apbs %files doc -%defattr(-,root,root,-) %doc apbs/doc/programmer/html %changelog From f7c75d03eab71bcff3d68de20894cc6884f10fef Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 12 Jul 2018 20:23:16 +0000 Subject: [PATCH 39/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 059d207..6d50ac2 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.5 -Release: 1%{?dist} +Release: 2%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD Group: Applications/Engineering @@ -125,6 +125,9 @@ done %doc apbs/doc/programmer/html %changelog +* Thu Jul 12 2018 Fedora Release Engineering - 1.5-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild + * Sat May 19 2018 Tim Fenn - 1.5-1 - update to 1.5 From ededc9c6754fd4b5db9b3a8f2098dcfafdf08be5 Mon Sep 17 00:00:00 2001 From: Igor Gnatenko Date: Tue, 22 Jan 2019 18:38:31 +0100 Subject: [PATCH 40/92] Remove obsolete ldconfig scriptlets References: https://fedoraproject.org/wiki/Changes/RemoveObsoleteScriptlets Signed-off-by: Igor Gnatenko --- apbs.spec | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/apbs.spec b/apbs.spec index 6d50ac2..56795da 100644 --- a/apbs.spec +++ b/apbs.spec @@ -88,9 +88,7 @@ for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,v mv $bin %{buildroot}%{_bindir}/apbs-`basename $bin` done -%post -p /sbin/ldconfig - -%postun -p /sbin/ldconfig +%ldconfig_scriptlets %files %doc apbs/doc/license/LICENSE.txt apbs/doc/README apbs/doc/ChangeLog.md From 13140fb741c7311878562d7df08e21e51f50a7d7 Mon Sep 17 00:00:00 2001 From: Igor Gnatenko Date: Mon, 28 Jan 2019 20:17:38 +0100 Subject: [PATCH 41/92] Remove obsolete Group tag References: https://fedoraproject.org/wiki/Changes/Remove_Group_Tag --- apbs.spec | 4 ---- 1 file changed, 4 deletions(-) diff --git a/apbs.spec b/apbs.spec index 56795da..f7a9526 100644 --- a/apbs.spec +++ b/apbs.spec @@ -6,7 +6,6 @@ Version: 1.5 Release: 2%{?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: https://github.com/Electrostatics/apbs-pdb2pqr/archive/apbs-%{version}.tar.gz Patch0: apbs-cmake.patch @@ -33,7 +32,6 @@ 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 @@ -44,7 +42,6 @@ poisson boltzmann solver library. %package devel Summary: Libraries and header files for the APBS package -Group: Development/Libraries Requires: %{name} = %{version}-%{release} %description devel @@ -55,7 +52,6 @@ necessary for developing programs using the adaptive poisson boltzmann %package doc Summary: Documentation for the APBS package -Group: Applications/Engineering Requires: %{name} = %{version}-%{release} %description doc From 9dda046063121cd8ce329adead1f215f1430a59b Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 31 Jan 2019 13:34:00 +0000 Subject: [PATCH 42/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index f7a9526..76a37dd 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.5 -Release: 2%{?dist} +Release: 3%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD URL: http://apbs.sourceforge.net/ @@ -119,6 +119,9 @@ done %doc apbs/doc/programmer/html %changelog +* Thu Jan 31 2019 Fedora Release Engineering - 1.5-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild + * Thu Jul 12 2018 Fedora Release Engineering - 1.5-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild From b859cbd7646cadeadc19047879d92e68bf5feb92 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 24 Jul 2019 18:11:18 +0000 Subject: [PATCH 43/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 76a37dd..3a435c1 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.5 -Release: 3%{?dist} +Release: 4%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD URL: http://apbs.sourceforge.net/ @@ -119,6 +119,9 @@ done %doc apbs/doc/programmer/html %changelog +* Wed Jul 24 2019 Fedora Release Engineering - 1.5-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild + * Thu Jan 31 2019 Fedora Release Engineering - 1.5-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild From 1c5d1cc4b23860fd321f674ad826a664a9f6334a Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Tue, 28 Jan 2020 11:49:13 +0000 Subject: [PATCH 44/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 3a435c1..e04a0c1 100644 --- a/apbs.spec +++ b/apbs.spec @@ -3,7 +3,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 1.5 -Release: 4%{?dist} +Release: 5%{?dist} # License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. License: LGPLv2+ and BSD URL: http://apbs.sourceforge.net/ @@ -119,6 +119,9 @@ done %doc apbs/doc/programmer/html %changelog +* Tue Jan 28 2020 Fedora Release Engineering - 1.5-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + * Wed Jul 24 2019 Fedora Release Engineering - 1.5-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild From 61f50e7880a47ddfacaae0f4b734023ecffc13c1 Mon Sep 17 00:00:00 2001 From: sagitter Date: Wed, 13 May 2020 11:15:47 +0200 Subject: [PATCH 45/92] Pre-release 3.0.0 (rhbz#1752306, rhbz#1799157) --- .gitignore | 1 + LGPL_V2 => apbs-LGPL_V2 | 0 apbs-cmake.patch | 122 +++++++++++++++++------------------ apbs.spec | 136 ++++++++++++++++++++++++++++------------ sources | 2 +- 5 files changed, 158 insertions(+), 103 deletions(-) rename LGPL_V2 => apbs-LGPL_V2 (100%) diff --git a/.gitignore b/.gitignore index f5c581c..a8be0bc 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ apbs-1.2.1-source.tar.gz /apbs-1.3-source.tar.gz /APBS-1.4-source.tar.gz /apbs-1.5.tar.gz +/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb.tar.gz diff --git a/LGPL_V2 b/apbs-LGPL_V2 similarity index 100% rename from LGPL_V2 rename to apbs-LGPL_V2 diff --git a/apbs-cmake.patch b/apbs-cmake.patch index c801f77..b0b6d9c 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -1,12 +1,12 @@ ---- CMakeLists.txt_orig 2018-05-20 13:00:17.451341064 -0400 -+++ CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 +--- a/apbs/CMakeLists.txt_orig 2018-05-20 13:00:17.451341064 -0400 ++++ b/apbs/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -1,4 +1,5 @@ - cmake_minimum_required (VERSION 2.8.7) + cmake_minimum_required (VERSION 3.12) +set(CMAKE_POSITION_INDEPENDENT_CODE ON) ################################################################################ # TODO: Add licensing and authorship information -@@ -63,10 +64,10 @@ +@@ -61,10 +62,10 @@ set(TOOLS_PATH ${APBS_BUILD}/tools) set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) @@ -20,7 +20,7 @@ set(APBS_LIBS) set(APBS_LIB_DIRS) -@@ -78,7 +79,7 @@ +@@ -76,7 +77,7 @@ DOC "The path to the external git submodules" ) @@ -29,37 +29,40 @@ #list(APPEND SYS_LIBPATHS /usr/lib64) ################################################################################ -@@ -105,9 +106,9 @@ +@@ -102,10 +103,6 @@ message(STATUS "Setting lookup paths for headers and libraries") -set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") -list(APPEND CMAKE_INCLUDE_PATH /usr/include) -list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) -+#set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") -+#list(APPEND CMAKE_INCLUDE_PATH /usr/include) -+#list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) +- - - -@@ -259,11 +260,11 @@ - - if(NOT ENABLE_FETK) + ################################################################################ + # Enable ansi pedantic compiling # +@@ -288,9 +285,9 @@ # We'll use autotools to build MALOC if FETK is enabled. -- set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc) -- add_subdirectory(${MALOC_ROOT}) -- include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys -- ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh) + #set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc) + #add_subdirectory(${MALOC_ROOT}) +- add_subdirectory(${EXTERNALS_PATH}/fetk/maloc) +- include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base ${EXTERNALS_PATH}/fetk/maloc/src/vsys +- ${EXTERNALS_PATH}/fetk/maloc/src/vsh/ ${EXTERNALS_PATH}/fetk/maloc/src/psh) ++ # add_subdirectory(${EXTERNALS_PATH}/fetk/maloc) ++ # include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base ${EXTERNALS_PATH}/fetk/maloc/src/vsys ++ # ${EXTERNALS_PATH}/fetk/maloc/src/vsh/ ${EXTERNALS_PATH}/fetk/maloc/src/psh) + #include_directories( + # ${EXTERNALS_PATH}/fetk/mc/src/aaa_inc + # ${EXTERNALS_PATH}/fetk/mc/src/aprx +@@ -309,7 +306,7 @@ + # ${MALOC_ROOT}/src/vsh + # ${MALOC_ROOT}/src/vsys + #) - list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) -+ #set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc) -+ # add_subdirectory(${MALOC_ROOT}) -+ #include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys -+ # ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh) -+ #list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) ++ # list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) list(APPEND APBS_LIBS maloc) endif() -@@ -736,12 +737,12 @@ +@@ -821,12 +818,12 @@ # Set up additional directories to install # ################################################################################ @@ -78,7 +81,7 @@ if(BUILD_DOC) install( -@@ -753,24 +754,24 @@ +@@ -838,34 +835,12 @@ ) endif() @@ -95,34 +98,31 @@ - PATTERN "README" -) - --install( +-if(BUILD_TOOLS) +- install( - DIRECTORY ${APBS_ROOT}/tools - DESTINATION ${SHARE_INSTALL_PATH} +- USE_SOURCE_PERMISSIONS - PATTERN "CMakeLists.txt" EXCLUDE --) -+#install( -+# DIRECTORY ${APBS_ROOT}/examples -+# DESTINATION ${SHARE_INSTALL_PATH} -+#) -+ -+#install( -+# DIRECTORY ${APBS_ROOT}/tests -+# DESTINATION ${SHARE_INSTALL_PATH} -+# FILES_MATCHING -+# PATTERN "*.py" -+# PATTERN "README" -+#) -+ -+#install( -+# DIRECTORY ${APBS_ROOT}/tools -+# DESTINATION ${SHARE_INSTALL_PATH} -+# PATTERN "CMakeLists.txt" EXCLUDE -+#) - - if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}") +- ) +- +- if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}") ++if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}") install( ---- src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400 -+++ src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 +- DIRECTORY ${APBS_BUILD}/tools/bin +- DESTINATION ${SHARE_INSTALL_PATH}/tools +- USE_SOURCE_PERMISSIONS +- ) +- endif() ++ DIRECTORY ${APBS_BUILD}/tools/bin ++ DESTINATION ${SHARE_INSTALL_PATH}/tools ++ USE_SOURCE_PERMISSIONS ++ ) + endif() + + ################################################################################ +--- a/apbs/src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400 ++++ b/apbs/src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -32,11 +32,11 @@ message(STATUS "With external header files ${EXTERNAL_HEADERS}") message(STATUS "With internal header files ${INTERNAL_HEADERS}") @@ -138,7 +138,7 @@ list(APPEND APBS_INTERNAL_LIBS ${LIBRARY_NAME}) set(APBS_INTERNAL_LIBS ${APBS_INTERNAL_LIBS} PARENT_SCOPE) message(STATUS "Added ${LIBRARY_NAME}") -@@ -47,6 +47,11 @@ +@@ -45,6 +45,11 @@ add_subdirectory(generic) add_subdirectory(pmgc) add_subdirectory(mg) @@ -150,26 +150,26 @@ if(ENABLE_FETK) add_subdirectory(fem) -@@ -57,7 +62,7 @@ - - message(STATUS ${EXTERNAL_HEADERS}) +@@ -56,7 +61,7 @@ + message(STATUS "External Headers: ${EXTERNAL_HEADERS}") + #add_executable(apbs main.c routines.c) -add_executable(apbs main.c apbs.h routines.c routines.h) +add_executable(apbs-bin main.c apbs.h routines.c routines.h) - message(***************************) message(STATUS " ") message(STATUS "APBS Libraries: ${APBS_LIBS}") -@@ -66,7 +71,8 @@ - message(***************************) + message(STATUS "Internal Libraries: ${APBS_INTERNAL_LIBS}") +@@ -64,7 +69,8 @@ #add_dependencies(apbs ${BEM_LIB}) + #target_include_directories(apbs PRIVATE apbs.h routines.h) -target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS}) +target_link_libraries(apbs-bin ${APBS_LIBS} apbs) +SET_TARGET_PROPERTIES(apbs-bin PROPERTIES OUTPUT_NAME apbs) #add_dependencies(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS}) configure_file( -@@ -81,6 +87,6 @@ +@@ -79,6 +85,6 @@ endif() INSTALL(FILES apbs.h routines.h DESTINATION ${HEADER_INSTALL_PATH}) @@ -177,8 +177,8 @@ +INSTALL(TARGETS apbs-bin DESTINATION ${EXECUTABLE_INSTALL_PATH}) message(STATUS ${CMAKE_C_FLAGS}) ---- tools/manip/CMakeLists.txt_orig 2018-05-20 13:00:31.831387880 -0400 -+++ tools/manip/CMakeLists.txt 2018-05-20 13:07:07.742714938 -0400 +--- a/apbs/tools/manip/CMakeLists.txt_orig 2018-05-20 13:00:31.831387880 -0400 ++++ b/apbs/tools/manip/CMakeLists.txt 2018-05-20 13:07:07.742714938 -0400 @@ -1,9 +1,10 @@ message(STATUS "Building manip") @@ -205,8 +205,8 @@ +target_link_libraries(born ${LIBS} ${APBS_LIBS}) + +INSTALL(TARGETS coulomb born DESTINATION ${EXECUTABLE_INSTALL_PATH}) ---- tools/mesh/CMakeLists.txt_orig 2018-05-20 13:00:26.966372042 -0400 -+++ tools/mesh/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 +--- a/apbs/tools/mesh/CMakeLists.txt_orig 2018-05-20 13:00:26.966372042 -0400 ++++ b/apbs/tools/mesh/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -1,9 +1,10 @@ message(STATUS "Building mesh") diff --git a/apbs.spec b/apbs.spec index e04a0c1..30ae72f 100644 --- a/apbs.spec +++ b/apbs.spec @@ -1,24 +1,40 @@ -%{!?python_sitelib: %global python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")} +# Workaround for GCC-10 +%define _legacy_common_support 1 + +%global commit dfb858d32674438fb8c21421acc86e21667eb8cb +%global shortcommit %(c=%{commit}; echo ${c:0:7}) +%global datecommit 20200512 + +%bcond_without python + +# To perform all tests, APBS needs to be compiled together additional sub-modules +%bcond_with check Name: apbs Summary: Adaptive Poisson Boltzmann Solver -Version: 1.5 -Release: 5%{?dist} -# License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD. +Version: 3.0.0 +Release: 0.1.%{datecommit}.git%{shortcommit}%{?dist} +# iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD -URL: http://apbs.sourceforge.net/ -Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/apbs-%{version}.tar.gz +URL: https://www.poissonboltzmann.org/ +Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/%{commit}/%{name}-pdb2pqr-%{commit}.tar.gz +Source1: apbs-LGPL_V2 Patch0: apbs-cmake.patch -BuildRequires: gcc-c++ + +BuildRequires: gcc-c++ BuildRequires: cmake BuildRequires: doxygen BuildRequires: graphviz -BuildRequires: arpack-devel -BuildRequires: atlas-devel -BuildRequires: blas-devel +#BuildRequires: arpack-devel +#BuildRequires: atlas-devel +#BuildRequires: blas-devel BuildRequires: maloc-devel +BuildRequires: python3-devel +BuildRequires: python3-sphinx +BuildRequires: swig BuildRequires: tex(latex) BuildRequires: zlib-devel +Requires: %{name}-libs%{?_isa} = %{version}-%{release} %description APBS is a software package for the numerical solution of the @@ -32,64 +48,99 @@ visualization (in such applications as PyMOL). %package tools Summary: utility programs that utilize the APBS package -Requires: %{name} = %{version}-%{release} - +Requires: %{name}%{?_isa} = %{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 libs +Summary: Libraries for APBS +%description libs +APBS solver libraries. + %package devel Summary: Libraries and header files for the APBS package -Requires: %{name} = %{version}-%{release} - +Requires: %{name}-libs%{?_isa} = %{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 -Requires: %{name} = %{version}-%{release} - +BuildArch: noarch %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}-pdb2pqr-apbs-%{version} -cd apbs -%patch0 -p0 +%autosetup -n %{name}-pdb2pqr-%{commit} -N +%patch0 -p1 -b .apbs-cmake + +cp -p apbs/contrib/iapbs/COPYING apbs/contrib/iapbs/iapbs-COPYING +cp -p %{SOURCE1} apbs/contrib/iapbs/iapbs-LGPLv2 %build -cd apbs -# %cmake -D BUILD_DOC:BOOL=ON . -%cmake -D BUILD_DOC:BOOL=OFF . -make %{?_smp_mflags} -cd doc/programmer -doxygen +pushd apbs +export CFLAGS="%{build_cflags} -fopenmp -lm" +export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" +%cmake -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ + -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ + -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DENABLE_FETK:BOOL=OFF \ +%if %{with python} + -DENABLE_PYTHON:BOOL=ON \ +%endif + . +%make_build +popd + +# Generate HTML documentation +make html -C doc %install -rm -rf %{buildroot} - -cd apbs -make install DESTDIR=%{buildroot} +%make_install -C apbs # tools -for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} tools/manip/psize.py; do - mv $bin %{buildroot}%{_bindir}/apbs-`basename $bin` +for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do + cp -p $bin %{buildroot}%{_bindir}/apbs-`basename $bin` + rm -f $bin done -%ldconfig_scriptlets +# Move Python libraries under Python's tree directories +mkdir -p %{buildroot}%{python3_sitearch}/apbs +install -pm 755 apbs/tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ +pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py +ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py +install -pm 755 apbs/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ + +# Remove static libraries +for i in `find %{buildroot} -type f \( -name "*.a" \)`; do + rm -f $i +done + +%if %{with check} +%check +pushd apbs/tests +export LD_LIBRARY_PATH=%{buildroot}%{_libdir} +sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py +%{__python3} ./apbs_tester.py +%endif %files -%doc apbs/doc/license/LICENSE.txt apbs/doc/README apbs/doc/ChangeLog.md %{_bindir}/apbs + +%files libs +%license apbs/LICENSE.md apbs/COPYING apbs/contrib/iapbs/iapbs-COPYING apbs/contrib/iapbs/iapbs-LGPLv2 +%doc apbs/README.md %{_libdir}/libapbs*.so.* +%{python3_sitearch}/apbs/ + +%files devel +%{_libdir}/libapbs*.so +%{_includedir}/iapbs/ +%{_includedir}/apbs %files tools %{_bindir}/apbs-psize.py @@ -111,14 +162,17 @@ done %{_bindir}/apbs-del2dx %{_bindir}/apbs-tensor2dx -%files devel -%{_libdir}/libapbs*.so -%{_includedir}/apbs - %files doc -%doc apbs/doc/programmer/html +%license doc/apbs/license.rst +%doc doc/_build/html %changelog +* Wed May 13 2020 Antonio Trande - 3.0.0-0.1.20200512.gitdfb858d +- Pre-release 3.0.0 (rhbz#1752306, rhbz#1799157) +- Add libs sub-package +- Add workaround for GCC-10 +- Use Python3 + * Tue Jan 28 2020 Fedora Release Engineering - 1.5-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild diff --git a/sources b/sources index 5010b5a..ed5bc3e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (apbs-1.5.tar.gz) = 4a117054653a738082f9a25a35c5a0605a1f225e682ff57ed4393689aefe1beffe4fe2364c164d07eb524a26add002b50e29eb297d690494448dac1cef72634d +SHA512 (apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb.tar.gz) = 6889b4426480f3d62518062cffcd0ada9d4916b80dd3b184b30e08558d0d0296fecb352035222ae69764cf64fb8d3fd0eefbb6dc927834d63d30fc18aa2a597a From ab29865a0160749ae864407ecb14ea8629b3f363 Mon Sep 17 00:00:00 2001 From: sagitter Date: Wed, 13 May 2020 14:20:47 +0200 Subject: [PATCH 46/92] Fix release tag --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 30ae72f..ee46485 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 0.1.%{datecommit}.git%{shortcommit}%{?dist} +Release: 0.2.%{datecommit}git%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -167,6 +167,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Wed May 13 2020 Antonio Trande - 3.0.0-0.2.20200512gitdfb858d +- Fix release tag + * Wed May 13 2020 Antonio Trande - 3.0.0-0.1.20200512.gitdfb858d - Pre-release 3.0.0 (rhbz#1752306, rhbz#1799157) - Add libs sub-package From 50645d9eedac6f6bcffb9e48fa71b54e7f8e5779 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miro=20Hron=C4=8Dok?= Date: Tue, 26 May 2020 02:40:35 +0200 Subject: [PATCH 47/92] Rebuilt for Python 3.9 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index ee46485..93b3c3a 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 0.2.%{datecommit}git%{shortcommit}%{?dist} +Release: 0.3.%{datecommit}git%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -167,6 +167,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Tue May 26 2020 Miro Hrončok - 3.0.0-0.3.20200512gitdfb858d +- Rebuilt for Python 3.9 + * Wed May 13 2020 Antonio Trande - 3.0.0-0.2.20200512gitdfb858d - Fix release tag From fa84d5a43e06437c6ba6fc575ed22027621e6b8a Mon Sep 17 00:00:00 2001 From: sagitter Date: Sun, 31 May 2020 14:34:05 +0200 Subject: [PATCH 48/92] Release 3.0.0 --- .gitignore | 1 + apbs-cmake.patch | 127 +++++++++++++++++++++-------------------------- apbs.spec | 18 +++---- sources | 2 +- 4 files changed, 67 insertions(+), 81 deletions(-) diff --git a/.gitignore b/.gitignore index a8be0bc..58dec5a 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ apbs-1.2.1-source.tar.gz /APBS-1.4-source.tar.gz /apbs-1.5.tar.gz /apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb.tar.gz +/apbs-pdb2pqr-vAPBS-3.0.0.tar.gz diff --git a/apbs-cmake.patch b/apbs-cmake.patch index b0b6d9c..df3007a 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -6,7 +6,7 @@ ################################################################################ # TODO: Add licensing and authorship information -@@ -61,10 +62,10 @@ +@@ -70,10 +71,10 @@ set(TOOLS_PATH ${APBS_BUILD}/tools) set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) @@ -20,104 +20,89 @@ set(APBS_LIBS) set(APBS_LIB_DIRS) -@@ -76,7 +77,7 @@ - DOC "The path to the external git submodules" - ) +@@ -85,7 +86,7 @@ + PATHS "${APBS_ROOT}" + DOC "The path to the external git submodules") -set(SYS_LIBPATHS /usr/lib64) +#set(SYS_LIBPATHS /usr/lib64) #list(APPEND SYS_LIBPATHS /usr/lib64) - ################################################################################ -@@ -102,10 +103,6 @@ +@@ -139,11 +140,6 @@ + ################################################################################ message(STATUS "Setting lookup paths for headers and libraries") -set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") -list(APPEND CMAKE_INCLUDE_PATH /usr/include) -list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) - - +- ################################################################################ # Enable ansi pedantic compiling # -@@ -288,9 +285,9 @@ - # We'll use autotools to build MALOC if FETK is enabled. - #set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc) - #add_subdirectory(${MALOC_ROOT}) -- add_subdirectory(${EXTERNALS_PATH}/fetk/maloc) -- include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base ${EXTERNALS_PATH}/fetk/maloc/src/vsys -- ${EXTERNALS_PATH}/fetk/maloc/src/vsh/ ${EXTERNALS_PATH}/fetk/maloc/src/psh) -+ # add_subdirectory(${EXTERNALS_PATH}/fetk/maloc) -+ # include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base ${EXTERNALS_PATH}/fetk/maloc/src/vsys -+ # ${EXTERNALS_PATH}/fetk/maloc/src/vsh/ ${EXTERNALS_PATH}/fetk/maloc/src/psh) - #include_directories( - # ${EXTERNALS_PATH}/fetk/mc/src/aaa_inc - # ${EXTERNALS_PATH}/fetk/mc/src/aprx -@@ -309,7 +306,7 @@ - # ${MALOC_ROOT}/src/vsh - # ${MALOC_ROOT}/src/vsys - #) -- list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) -+ # list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) - list(APPEND APBS_LIBS maloc) + ################################################################################ +@@ -307,12 +303,12 @@ + ################################################################################ + if(NOT ENABLE_FETK) + # We'll use autotools to build MALOC if FETK is enabled. +- add_subdirectory(${EXTERNALS_PATH}/fetk/maloc) +- include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base +- ${EXTERNALS_PATH}/fetk/maloc/src/vsys +- ${EXTERNALS_PATH}/fetk/maloc/src/vsh +- ${EXTERNALS_PATH}/fetk/maloc/src/psh) +- list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) ++ #add_subdirectory(${EXTERNALS_PATH}/fetk/maloc) ++ #include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base ++ # ${EXTERNALS_PATH}/fetk/maloc/src/vsys ++ # ${EXTERNALS_PATH}/fetk/maloc/src/vsh ++ # ${EXTERNALS_PATH}/fetk/maloc/src/psh) ++ #list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib) + list(APPEND APBS_LIBS maloc) endif() -@@ -821,12 +818,12 @@ +@@ -778,10 +774,10 @@ + ################################################################################ # Set up additional directories to install # ################################################################################ - --install( -- DIRECTORY ${APBS_ROOT}/doc -- DESTINATION ${SHARE_INSTALL_PATH} -- PATTERN "programmer" EXCLUDE -- PATTERN "CMakeLists.txt" EXCLUDE --) -+#install( -+# DIRECTORY ${APBS_ROOT}/doc -+# DESTINATION ${SHARE_INSTALL_PATH} -+# PATTERN "programmer" EXCLUDE -+# PATTERN "CMakeLists.txt" EXCLUDE -+#) +-install(DIRECTORY ${APBS_ROOT}/doc +- DESTINATION ${SHARE_INSTALL_PATH} +- PATTERN "programmer" EXCLUDE +- PATTERN "CMakeLists.txt" EXCLUDE) ++#install(DIRECTORY ${APBS_ROOT}/doc ++# DESTINATION ${SHARE_INSTALL_PATH} ++# PATTERN "programmer" EXCLUDE ++# PATTERN "CMakeLists.txt" EXCLUDE) if(BUILD_DOC) - install( -@@ -838,34 +835,12 @@ - ) + install(DIRECTORY ${APBS_BUILD}/doc/programmer +@@ -791,27 +787,11 @@ + PATTERN "mainpage.h" EXCLUDE) endif() --install( -- DIRECTORY ${APBS_ROOT}/examples -- DESTINATION ${SHARE_INSTALL_PATH} --) +-install(DIRECTORY ${APBS_ROOT}/examples +- DESTINATION ${SHARE_INSTALL_PATH}) - --install( -- DIRECTORY ${APBS_ROOT}/tests -- DESTINATION ${SHARE_INSTALL_PATH} -- FILES_MATCHING +-install(DIRECTORY ${APBS_ROOT}/tests +- DESTINATION ${SHARE_INSTALL_PATH} +- FILES_MATCHING - PATTERN "*.py" -- PATTERN "README" --) +- PATTERN "README") - -if(BUILD_TOOLS) -- install( -- DIRECTORY ${APBS_ROOT}/tools -- DESTINATION ${SHARE_INSTALL_PATH} -- USE_SOURCE_PERMISSIONS -- PATTERN "CMakeLists.txt" EXCLUDE -- ) +- install(DIRECTORY ${APBS_ROOT}/tools +- DESTINATION ${SHARE_INSTALL_PATH} +- USE_SOURCE_PERMISSIONS +- PATTERN "CMakeLists.txt" +- PATTERN "matlab" EXCLUDE) - -- if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}") +- if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}") +- install(DIRECTORY ${APBS_BUILD}/tools/bin +if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}") - install( -- DIRECTORY ${APBS_BUILD}/tools/bin -- DESTINATION ${SHARE_INSTALL_PATH}/tools -- USE_SOURCE_PERMISSIONS -- ) -- endif() -+ DIRECTORY ${APBS_BUILD}/tools/bin -+ DESTINATION ${SHARE_INSTALL_PATH}/tools -+ USE_SOURCE_PERMISSIONS -+ ) ++ install( ++ DIRECTORY ${APBS_BUILD}/tools/bin + DESTINATION ${SHARE_INSTALL_PATH}/tools + USE_SOURCE_PERMISSIONS) +- endif() endif() ################################################################################ diff --git a/apbs.spec b/apbs.spec index 93b3c3a..4b383f0 100644 --- a/apbs.spec +++ b/apbs.spec @@ -1,9 +1,9 @@ # Workaround for GCC-10 %define _legacy_common_support 1 -%global commit dfb858d32674438fb8c21421acc86e21667eb8cb -%global shortcommit %(c=%{commit}; echo ${c:0:7}) -%global datecommit 20200512 +%global commit %{nil} +%global shortcommit %{nil} +%global datecommit %{nil} %bcond_without python @@ -13,11 +13,11 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 0.3.%{datecommit}git%{shortcommit}%{?dist} +Release: 1%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ -Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/%{commit}/%{name}-pdb2pqr-%{commit}.tar.gz +Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/%{version}/%{name}-pdb2pqr-vAPBS-%{version}.tar.gz Source1: apbs-LGPL_V2 Patch0: apbs-cmake.patch @@ -76,7 +76,7 @@ development using the adaptive poisson boltzmann (APBS) solver library. %prep -%autosetup -n %{name}-pdb2pqr-%{commit} -N +%autosetup -n %{name}-pdb2pqr-vAPBS-%{version} -N %patch0 -p1 -b .apbs-cmake cp -p apbs/contrib/iapbs/COPYING apbs/contrib/iapbs/iapbs-COPYING @@ -96,9 +96,6 @@ export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" %make_build popd -# Generate HTML documentation -make html -C doc - %install %make_install -C apbs @@ -167,6 +164,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Sun May 31 2020 Antonio Trande - 3.0.0-1 +- Release 3.0.0 + * Tue May 26 2020 Miro Hrončok - 3.0.0-0.3.20200512gitdfb858d - Rebuilt for Python 3.9 diff --git a/sources b/sources index ed5bc3e..715195d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb.tar.gz) = 6889b4426480f3d62518062cffcd0ada9d4916b80dd3b184b30e08558d0d0296fecb352035222ae69764cf64fb8d3fd0eefbb6dc927834d63d30fc18aa2a597a +SHA512 (apbs-pdb2pqr-vAPBS-3.0.0.tar.gz) = 324306eb22346d9ce54b79d311512bdd9968ec63223354e69314c8d5aa3f4c63fa6afa4ebbbdfd84873edc5a75882934cedc2ad037d92f13f56e35e85ff00666 From 32f5cd570b90b013250619714008ce0cac5f4f1d Mon Sep 17 00:00:00 2001 From: sagitter Date: Wed, 17 Jun 2020 12:28:37 +0200 Subject: [PATCH 49/92] Use cmake3 --- apbs.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 4b383f0..f67a5fc 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 1%{datecommit}%{shortcommit}%{?dist} +Release: 2%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -22,7 +22,7 @@ Source1: apbs-LGPL_V2 Patch0: apbs-cmake.patch BuildRequires: gcc-c++ -BuildRequires: cmake +BuildRequires: cmake3 BuildRequires: doxygen BuildRequires: graphviz #BuildRequires: arpack-devel @@ -164,6 +164,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Wed Jun 17 2020 Antonio Trande - 3.0.0-2 +- Use cmake3 + * Sun May 31 2020 Antonio Trande - 3.0.0-1 - Release 3.0.0 From 689bea38cc707362b7b0b11eabd529c78f65667c Mon Sep 17 00:00:00 2001 From: sagitter Date: Wed, 17 Jun 2020 12:39:24 +0200 Subject: [PATCH 50/92] Use cmake3 macro --- apbs.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index f67a5fc..b4db350 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 2%{datecommit}%{shortcommit}%{?dist} +Release: 3%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -86,7 +86,7 @@ cp -p %{SOURCE1} apbs/contrib/iapbs/iapbs-LGPLv2 pushd apbs export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" -%cmake -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ +%cmake3 -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DENABLE_FETK:BOOL=OFF \ %if %{with python} @@ -164,6 +164,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Wed Jun 17 2020 Antonio Trande - 3.0.0-3 +- Use cmake3 macro + * Wed Jun 17 2020 Antonio Trande - 3.0.0-2 - Use cmake3 From 36400a1dbde02270dd12e3582e916a742591ed6d Mon Sep 17 00:00:00 2001 From: Neal Gompa Date: Sat, 18 Jul 2020 16:40:56 -0400 Subject: [PATCH 51/92] Update to new out-of-source build mechanism --- apbs.spec | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/apbs.spec b/apbs.spec index b4db350..1cb8a15 100644 --- a/apbs.spec +++ b/apbs.spec @@ -1,3 +1,6 @@ +# Force out of source build +%undefine __cmake_in_source_build + # Workaround for GCC-10 %define _legacy_common_support 1 @@ -83,7 +86,9 @@ cp -p apbs/contrib/iapbs/COPYING apbs/contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} apbs/contrib/iapbs/iapbs-LGPLv2 %build -pushd apbs +# Set the source directory +%global _vpath_srcdir apbs + export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" %cmake3 -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ @@ -92,12 +97,11 @@ export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" %if %{with python} -DENABLE_PYTHON:BOOL=ON \ %endif - . -%make_build -popd + %{nil} +%cmake_build %install -%make_install -C apbs +%cmake_install # tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do @@ -110,7 +114,7 @@ mkdir -p %{buildroot}%{python3_sitearch}/apbs install -pm 755 apbs/tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py -install -pm 755 apbs/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ +install -pm 755 %{_vpath_builddir}/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ # Remove static libraries for i in `find %{buildroot} -type f \( -name "*.a" \)`; do From 3c177218156c2ac5f6319be7e0bea39f9a51126b Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Mon, 27 Jul 2020 12:13:49 +0000 Subject: [PATCH 52/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 1cb8a15..00b22bd 100644 --- a/apbs.spec +++ b/apbs.spec @@ -16,7 +16,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 3%{datecommit}%{shortcommit}%{?dist} +Release: 4%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -168,6 +168,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Mon Jul 27 2020 Fedora Release Engineering - 3.0.0-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + * Wed Jun 17 2020 Antonio Trande - 3.0.0-3 - Use cmake3 macro From 374bd6c4e24321f7551a776eb70129a2a42ea7c5 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 1 Aug 2020 00:01:29 +0000 Subject: [PATCH 53/92] - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 00b22bd..b486216 100644 --- a/apbs.spec +++ b/apbs.spec @@ -16,7 +16,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 4%{datecommit}%{shortcommit}%{?dist} +Release: 5%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -168,6 +168,10 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Sat Aug 01 2020 Fedora Release Engineering - 3.0.0-5 +- Second attempt - Rebuilt for + https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + * Mon Jul 27 2020 Fedora Release Engineering - 3.0.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild From 20caf3e812874776f1ed553a3e2588d06d724131 Mon Sep 17 00:00:00 2001 From: sagitter Date: Mon, 3 Aug 2020 22:39:11 +0200 Subject: [PATCH 54/92] Remove redundant tools binary files in /usr/share --- apbs.spec | 3 +++ 1 file changed, 3 insertions(+) diff --git a/apbs.spec b/apbs.spec index b486216..8a9f92b 100644 --- a/apbs.spec +++ b/apbs.spec @@ -116,6 +116,9 @@ pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py install -pm 755 %{_vpath_builddir}/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ +# Remove redundant tools binary files in /usr/share +rm -rf %{buildroot}%{_datadir}/apbs + # Remove static libraries for i in `find %{buildroot} -type f \( -name "*.a" \)`; do rm -f $i From d490ddb9c70367c4feed9f4c4d2632a9b998a139 Mon Sep 17 00:00:00 2001 From: Antonio T Date: Fri, 1 Jan 2021 20:23:08 +0100 Subject: [PATCH 55/92] Add CMake build options --- apbs.spec | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/apbs.spec b/apbs.spec index 8a9f92b..c644de9 100644 --- a/apbs.spec +++ b/apbs.spec @@ -1,6 +1,3 @@ -# Force out of source build -%undefine __cmake_in_source_build - # Workaround for GCC-10 %define _legacy_common_support 1 @@ -16,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 5%{datecommit}%{shortcommit}%{?dist} +Release: 6%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -26,6 +23,7 @@ Patch0: apbs-cmake.patch BuildRequires: gcc-c++ BuildRequires: cmake3 +BuildRequires: make BuildRequires: doxygen BuildRequires: graphviz #BuildRequires: arpack-devel @@ -33,6 +31,7 @@ BuildRequires: graphviz #BuildRequires: blas-devel BuildRequires: maloc-devel BuildRequires: python3-devel +BuildRequires: python3-numpy BuildRequires: python3-sphinx BuildRequires: swig BuildRequires: tex(latex) @@ -86,22 +85,18 @@ cp -p apbs/contrib/iapbs/COPYING apbs/contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} apbs/contrib/iapbs/iapbs-LGPLv2 %build -# Set the source directory -%global _vpath_srcdir apbs - export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" -%cmake3 -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ +%cmake3 -S apbs -B . -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DENABLE_FETK:BOOL=OFF \ %if %{with python} - -DENABLE_PYTHON:BOOL=ON \ + -DENABLE_PYTHON:BOOL=ON %endif - %{nil} -%cmake_build +%make_build %install -%cmake_install +%make_install # tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do @@ -171,6 +166,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Fri Jan 01 2021 Antonio Trande - 3.0.0-6 +- Use cmake3 options + * Sat Aug 01 2020 Fedora Release Engineering - 3.0.0-5 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild From 1403c26aaac8a91fa24cbe660bc2341d4b32e1ae Mon Sep 17 00:00:00 2001 From: Antonio T Date: Fri, 1 Jan 2021 20:53:08 +0100 Subject: [PATCH 56/92] Add CMake build options /2 --- apbs.spec | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/apbs.spec b/apbs.spec index c644de9..84b472f 100644 --- a/apbs.spec +++ b/apbs.spec @@ -87,16 +87,16 @@ cp -p %{SOURCE1} apbs/contrib/iapbs/iapbs-LGPLv2 %build export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" -%cmake3 -S apbs -B . -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ +%cmake3 -S apbs -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DENABLE_FETK:BOOL=OFF \ %if %{with python} -DENABLE_PYTHON:BOOL=ON %endif -%make_build +%cmake_build %install -%make_install +%cmake_install # tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do From 1fba1fa0bff884a7f00646ea94d45123aa43299c Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Tue, 26 Jan 2021 00:17:07 +0000 Subject: [PATCH 57/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 84b472f..19afa95 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 6%{datecommit}%{shortcommit}%{?dist} +Release: 7%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -166,6 +166,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Tue Jan 26 2021 Fedora Release Engineering - 3.0.0-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + * Fri Jan 01 2021 Antonio Trande - 3.0.0-6 - Use cmake3 options From 0491bcd7d82d0906e1aa0a91d834909434be7dce Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 4 Jun 2021 19:59:20 +0200 Subject: [PATCH 58/92] Rebuilt for Python 3.10 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 19afa95..b218946 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 7%{datecommit}%{shortcommit}%{?dist} +Release: 8%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -166,6 +166,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Fri Jun 04 2021 Python Maint - 3.0.0-8 +- Rebuilt for Python 3.10 + * Tue Jan 26 2021 Fedora Release Engineering - 3.0.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild From 186611cad67172b7c9d49861f52edc49b28f392c Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 21 Jul 2021 12:49:13 +0000 Subject: [PATCH 59/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering From 0667085b825ed3058613ed90ec839192d4242c5e Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 21 Jul 2021 17:45:17 +0000 Subject: [PATCH 60/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index b218946..3eba357 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 8%{datecommit}%{shortcommit}%{?dist} +Release: 9%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -166,6 +166,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Wed Jul 21 2021 Fedora Release Engineering - 3.0.0-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Fri Jun 04 2021 Python Maint - 3.0.0-8 - Rebuilt for Python 3.10 From a250b716beb23d4f7b211408159411ef8782c7db Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 15:48:11 +0100 Subject: [PATCH 61/92] Compile from a new source archive --- .gitignore | 1 + apbs-cmake.patch | 9 ++++ apbs-exclude_tests.patch | 60 +++++++++++++++++++++ apbs.spec | 114 +++++++++++++++++++++++++-------------- sources | 2 +- 5 files changed, 146 insertions(+), 40 deletions(-) create mode 100644 apbs-exclude_tests.patch diff --git a/.gitignore b/.gitignore index 58dec5a..85ecb73 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ apbs-1.2.1-source.tar.gz /apbs-1.5.tar.gz /apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb.tar.gz /apbs-pdb2pqr-vAPBS-3.0.0.tar.gz +/apbs-3.0.0.tar.gz diff --git a/apbs-cmake.patch b/apbs-cmake.patch index df3007a..dbcb876 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -106,6 +106,15 @@ endif() ################################################################################ +@@ -880,7 +860,7 @@ + set(CPACK_PACKAGE_NAME "${PACKAGE_NAME}") + set(CPACK_PACKAGE_DESCRIPTION "APBS - Adaptive Poisson Boltzmann Solver") + +-set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/../LICENSE.md") ++set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.md") + set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/README.md") + + set(CPACK_SOURCE_IGNORE_FILES "${PROJECT_BINARY_DIR};/.git/;.gitignore;/tools/matlab/") --- a/apbs/src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400 +++ b/apbs/src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -32,11 +32,11 @@ diff --git a/apbs-exclude_tests.patch b/apbs-exclude_tests.patch new file mode 100644 index 0000000..5f64696 --- /dev/null +++ b/apbs-exclude_tests.patch @@ -0,0 +1,60 @@ +--- a/tests/test_cases.orig.cfg 2020-05-30 03:47:30.000000000 +0200 ++++ b/tests/test_cases.cfg 2021-11-01 11:30:08.175043842 +0100 +@@ -74,57 +74,3 @@ + apbs-mol : 1.847663548071E+03 1.883912182952E+03 2.732623683321E+03 3.123035854133E+03 -3.624863445503E+01 -3.904121297757E+02 -3.541635359318E+02 + apbs-smol : 1.847860440020E+03 1.885436377745E+03 2.734040568569E+03 3.125279428954E+03 -3.757593797629E+01 -3.912388198513E+02 -3.536628818750E+02 + +- +-[geoflow] +-input_dir : ../examples/geoflow +-imidazole : -1.030222099963E+01 5.417419E-01 +- +- +-[bem] +-input_dir : ../examples/bem +-451c_order1 : -1.172906546441e+03 +-451c_order5 : -1.175936034727E+03 +- +-[bem-pKa] +-input_dir : ../examples/bem-pKa +-ASH66 : -9.954199102140E-01 +-2LZT-ASH66 : -8.620097356247E+01 +-2LZT-noASH66 : -8.601110775968E+01 +- +-[bem-binding-energy] +-input_dir : ../examples/bem-binding-energy +-1d30 : -5.249027161163E+03 +-1d30_monomer1 : -6.232145066905E+03 +-1d30_monomer2 : -1.821470879387E+02 +- +- +-[pbam] +-input_dir : ../examples/pbam +-toy_energyforce : -4.965018552290E+01 -4.965018552290E+01 +- +-[pbsam] +-input_dir : ../examples/pbsam-gly +-gly_energyforce : 6.176608555569E-05 6.210593742215E-05 +- +- +-[protein-rna] +-input_dir : ../examples/protein-rna +-setup : python apbs_dx.py +-apbs-0.025 : 3.186122223752E+04 3.662855899462E+04 8.477786964834E+03 1.000545153104E+04 2.329205982055E+04 2.653636629928E+04 8.674116429353E+01 +-apbs-0.050 : 3.184763478312E+04 3.661493366846E+04 8.475252516617E+03 1.000292179294E+04 2.327168361816E+04 2.651594350839E+04 9.606836713866E+01 +-apbs-0.075 : 3.184033569905E+04 3.660761530545E+04 8.473669396547E+03 1.000134276339E+04 2.326088212207E+04 2.650511882057E+04 1.011537214883E+02 +-apbs-0.100 : 3.183548000794E+04 3.660274809589E+04 8.472507235893E+03 1.000018407412E+04 2.325372656922E+04 2.649794981016E+04 1.046142116108E+02 +-apbs-0.125 : 3.183190100647E+04 3.659916161996E+04 8.471585837513E+03 9.999265654586E+03 2.324845847155E+04 2.649267328362E+04 1.072226817610E+02 +-apbs-0.150 : 3.182909678356E+04 3.659635228953E+04 8.470821300868E+03 9.998503715551E+03 2.324433086171E+04 2.648854016160E+04 1.093084123761E+02 +-apbs-0.175 : 3.182680817429E+04 3.659406006570E+04 8.470167484600E+03 9.997852199372E+03 2.324096101131E+04 2.648516662194E+04 1.110412443877E+02 +-apbs-0.200 : 3.182488501939E+04 3.659213428941E+04 8.469596195763E+03 9.997282974485E+03 2.323812822097E+04 2.648233134327E+04 1.125199716537E+02 +-apbs-0.225 : 3.182323306491E+04 3.659048040133E+04 8.469088900775E+03 9.996777552566E+03 2.323569434544E+04 2.647989580221E+04 1.138070465620E+02 +-apbs-0.250 : 3.182178954360E+04 3.658903543806E+04 8.468632740499E+03 9.996323108319E+03 2.323356752071E+04 2.647776789284E+04 1.149444369078E+02 +-apbs-0.275 : 3.182051070674E+04 3.658775551975E+04 8.468218414737E+03 9.995910367297E+03 2.323168374787E+04 2.647588345522E+04 1.159616972338E+02 +-apbs-0.300 : 3.181936493519E+04 3.658660893678E+04 8.467838971928E+03 9.995532397856E+03 2.322999676177E+04 2.647419611346E+04 1.168804254687E+02 +-apbs-0.325 : 3.181832869046E+04 3.658557208654E+04 8.467489074881E+03 9.995183878464E+03 2.322847209567E+04 2.647267132259E+04 1.177168854906E+02 +-apbs-0.400 : 3.181571629593E+04 3.658295870300E+04 8.466578740909E+03 9.994277216885E+03 2.322463613929E+04 2.646883588223E+04 1.198456038803E+02 +-apbs-0.500 : 3.181302243781E+04 3.658026461575E+04 8.465598755475E+03 9.993301332440E+03 2.322070101887E+04 2.646490251594E+04 1.220607673699E+02 +-apbs-0.600 : 3.181090090954E+04 3.657814345443E+04 8.464799341688E+03 9.992505379555E+03 2.321762631365E+04 2.646183001839E+04 1.238080564885E+02 +-apbs-0.700 : 3.180915789156E+04 3.657640108752E+04 8.464126109756E+03 9.991835140855E+03 2.321512352191E+04 2.645932953757E+04 1.252364090878E+02 +-apbs-0.800 : 3.180768241803E+04 3.657492640520E+04 8.463546035019E+03 9.991257699113E+03 2.321302636223E+04 2.645723464562E+04 1.264340604647E+02 diff --git a/apbs.spec b/apbs.spec index 3eba357..99082f7 100644 --- a/apbs.spec +++ b/apbs.spec @@ -5,38 +5,34 @@ %global shortcommit %{nil} %global datecommit %{nil} -%bcond_without python - # To perform all tests, APBS needs to be compiled together additional sub-modules -%bcond_with check +%bcond_without check Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 9%{datecommit}%{shortcommit}%{?dist} +Release: 10%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ -Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/%{version}/%{name}-pdb2pqr-vAPBS-%{version}.tar.gz -Source1: apbs-LGPL_V2 -Patch0: apbs-cmake.patch +Source0: https://github.com/Electrostatics/apbs/archive/refs/tags/v%{version}/%{name}-%{version}.tar.gz +Source1: %{name}-LGPL_V2 + +Patch0: %{name}-cmake.patch + +# Exclude tests because they are for features inactivated +Patch1: %{name}-exclude_tests.patch BuildRequires: gcc-c++ BuildRequires: cmake3 +BuildRequires: chrpath BuildRequires: make BuildRequires: doxygen BuildRequires: graphviz -#BuildRequires: arpack-devel -#BuildRequires: atlas-devel -#BuildRequires: blas-devel BuildRequires: maloc-devel -BuildRequires: python3-devel -BuildRequires: python3-numpy -BuildRequires: python3-sphinx -BuildRequires: swig -BuildRequires: tex(latex) BuildRequires: zlib-devel Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: python3-%{name} %description APBS is a software package for the numerical solution of the @@ -49,7 +45,7 @@ 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 +Summary: Utility programs that utilize the APBS package Requires: %{name}%{?_isa} = %{version}-%{release} %description tools The apbs-tools package contains several utility programs for @@ -71,45 +67,81 @@ necessary for developing programs using the adaptive poisson boltzmann %package doc Summary: Documentation for the APBS package +BuildRequires: tex(latex) +BuildRequires: texlive-multirow +BuildRequires: texlive-hanging +BuildRequires: texlive-adjustbox +BuildRequires: texlive-stackengine +BuildRequires: texlive-sectsty +BuildRequires: texlive-etoc +BuildRequires: texlive-tocloft +BuildRequires: texlive-ulem +BuildRequires: texlive-newunicodechar BuildArch: noarch %description doc The apbs-doc package contains API reference inforemation for development using the adaptive poisson boltzmann (APBS) solver library. -%prep -%autosetup -n %{name}-pdb2pqr-vAPBS-%{version} -N -%patch0 -p1 -b .apbs-cmake +%package -n python3-apbs +Summary: Python interface of APBS +BuildRequires: python3-devel +BuildRequires: python3-numpy +BuildRequires: python3-sphinx +BuildRequires: swig +%{?python_provide:%python_provide python3-%{name}} +%description -n python3-apbs +Python interface of APBS. -cp -p apbs/contrib/iapbs/COPYING apbs/contrib/iapbs/iapbs-COPYING -cp -p %{SOURCE1} apbs/contrib/iapbs/iapbs-LGPLv2 +%prep +%autosetup -n %{name}-%{version} -N +%patch0 -p2 -b .apbs-cmake +%patch1 -p1 -b .exclude_tests + +cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING +cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 %build +# CMake needs BUILD_SHARED_LIBS:BOOL=OFF to build Python libraries +# Using CMake rpm macro automatically enables the shared libs building export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" -%cmake3 -S apbs -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ +mkdir -p build +cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ - -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DENABLE_FETK:BOOL=OFF \ -%if %{with python} - -DENABLE_PYTHON:BOOL=ON -%endif -%cmake_build + -DENABLE_FETK:BOOL=OFF -DCMAKE_C_FLAGS:STRING="%{build_cflags} -fopenmp -lm -DNDEBUG" \ + -DCMAKE_CXX_FLAGS:STRING="%{build_cxxflags} -fopenmp -lm -DNDEBUG" \ + -DBUILD_SHARED_LIBS:BOOL=OFF -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON \ + -DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON \ + -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ + -DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \ + -DLIB_INSTALL_DIR:PATH=%{_libdir} \ + -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} +make -O -j1 V=1 -C build %install -%cmake_install +%make_install -C build -# tools +# Tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do cp -p $bin %{buildroot}%{_bindir}/apbs-`basename $bin` rm -f $bin done +# Remove rpaths +for bin in %{buildroot}%{_bindir}/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do + chrpath -d $bin + chrpath -d %{buildroot}%{_bindir}/apbs +done + +chrpath -d %{buildroot}%{_libdir}/libapbs.so.1 + # Move Python libraries under Python's tree directories mkdir -p %{buildroot}%{python3_sitearch}/apbs -install -pm 755 apbs/tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ +install -pm 755 tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py -install -pm 755 %{_vpath_builddir}/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ +install -pm 755 build/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ # Remove redundant tools binary files in /usr/share rm -rf %{buildroot}%{_datadir}/apbs @@ -121,9 +153,8 @@ done %if %{with check} %check -pushd apbs/tests +pushd tests export LD_LIBRARY_PATH=%{buildroot}%{_libdir} -sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %{__python3} ./apbs_tester.py %endif @@ -131,13 +162,15 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %{_bindir}/apbs %files libs -%license apbs/LICENSE.md apbs/COPYING apbs/contrib/iapbs/iapbs-COPYING apbs/contrib/iapbs/iapbs-LGPLv2 -%doc apbs/README.md -%{_libdir}/libapbs*.so.* +%license LICENSE.md COPYING contrib/iapbs/iapbs-COPYING contrib/iapbs/iapbs-LGPLv2 +%doc README.md +%{_libdir}/libapbs.so.1 + +%files -n python3-apbs %{python3_sitearch}/apbs/ %files devel -%{_libdir}/libapbs*.so +%{_libdir}/libapbs.so %{_includedir}/iapbs/ %{_includedir}/apbs @@ -162,10 +195,13 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %{_bindir}/apbs-tensor2dx %files doc -%license doc/apbs/license.rst -%doc doc/_build/html +%license LICENSE.md +%doc build/doc %changelog +* Sun Oct 31 2021 Antonio Trande - 3.0.0-10 +- Compile from a new source archive + * Wed Jul 21 2021 Fedora Release Engineering - 3.0.0-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild diff --git a/sources b/sources index 715195d..2e522a3 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (apbs-pdb2pqr-vAPBS-3.0.0.tar.gz) = 324306eb22346d9ce54b79d311512bdd9968ec63223354e69314c8d5aa3f4c63fa6afa4ebbbdfd84873edc5a75882934cedc2ad037d92f13f56e35e85ff00666 +SHA512 (apbs-3.0.0.tar.gz) = 9107acf5fb591cd7a822dc3cb0be58b5d3142e85951585749068e748459bceb0c7503ecfd95b6b4370378d619c30aedb04f5e3ca5c1ad15683533171cb7208fb From 2d9c28a5d9e8be0b9f2544e311bed5b645e8e3bd Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 17:28:58 +0100 Subject: [PATCH 62/92] Fix installation conflict of python package --- apbs.spec | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 99082f7..12c1b2e 100644 --- a/apbs.spec +++ b/apbs.spec @@ -6,12 +6,12 @@ %global datecommit %{nil} # To perform all tests, APBS needs to be compiled together additional sub-modules -%bcond_without check +%bcond_with check Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 10%{datecommit}%{shortcommit}%{?dist} +Release: 11%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -90,6 +90,7 @@ BuildRequires: python3-numpy BuildRequires: python3-sphinx BuildRequires: swig %{?python_provide:%python_provide python3-%{name}} +Obsoletes: %{name}-libs < 3.0.0-10 %description -n python3-apbs Python interface of APBS. @@ -199,6 +200,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Nov 01 2021 Antonio Trande - 3.0.0-11 +- Fix installation conflict of python package + * Sun Oct 31 2021 Antonio Trande - 3.0.0-10 - Compile from a new source archive From 2714d4da05f4b0d9d3d7bbe978fa307c4f32f664 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 17:30:04 +0100 Subject: [PATCH 63/92] Fix installation conflict of python package /2 --- apbs.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 12c1b2e..5177fc3 100644 --- a/apbs.spec +++ b/apbs.spec @@ -90,7 +90,7 @@ BuildRequires: python3-numpy BuildRequires: python3-sphinx BuildRequires: swig %{?python_provide:%python_provide python3-%{name}} -Obsoletes: %{name}-libs < 3.0.0-10 +Obsoletes: %{name}-libs < 0:3.0.0-11 %description -n python3-apbs Python interface of APBS. From e36cff8ce853f2f1e015918503eac0e5866cd0f6 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 18:13:47 +0100 Subject: [PATCH 64/92] Re-enable tests --- apbs.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 5177fc3..d778cf7 100644 --- a/apbs.spec +++ b/apbs.spec @@ -6,12 +6,12 @@ %global datecommit %{nil} # To perform all tests, APBS needs to be compiled together additional sub-modules -%bcond_with check +%bcond_without check Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 11%{datecommit}%{shortcommit}%{?dist} +Release: 12%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -200,6 +200,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Nov 01 2021 Antonio Trande - 3.0.0-12 +- Re-enable tests + * Mon Nov 01 2021 Antonio Trande - 3.0.0-11 - Fix installation conflict of python package From d8042f16d7d69e8dffff2e9f48afe10f92609517 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 4 Jan 2022 16:01:26 +0100 Subject: [PATCH 65/92] Patched for Python-3.11 --- apbs.spec | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index d778cf7..22e888d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 12%{datecommit}%{shortcommit}%{?dist} +Release: 13%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -23,6 +23,9 @@ Patch0: %{name}-cmake.patch # Exclude tests because they are for features inactivated Patch1: %{name}-exclude_tests.patch +# Porting to Python-3.11 +Patch2: %{name}-python311.patch + BuildRequires: gcc-c++ BuildRequires: cmake3 BuildRequires: chrpath @@ -99,6 +102,10 @@ Python interface of APBS. %patch0 -p2 -b .apbs-cmake %patch1 -p1 -b .exclude_tests +%if 0%{?python3_version_nodots} >= 311 +%patch2 -p1 -b .python311 +%endif + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 @@ -200,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Tue Jan 04 2022 Antonio Trande - 3.0.0-13 +- Patched for Python-3.11 + * Mon Nov 01 2021 Antonio Trande - 3.0.0-12 - Re-enable tests From 797d60a8fa287c009a6c2dc413bd7e2149d432b0 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 4 Jan 2022 16:06:02 +0100 Subject: [PATCH 66/92] Add patch file --- apbs-python311.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 apbs-python311.patch diff --git a/apbs-python311.patch b/apbs-python311.patch new file mode 100644 index 0000000..adf7420 --- /dev/null +++ b/apbs-python311.patch @@ -0,0 +1,11 @@ +--- a/tools/manip/inputgen.orig.py 2020-05-30 03:47:30.000000000 +0200 ++++ b/tools/manip/inputgen.py 2021-12-26 12:13:08.819979543 +0100 +@@ -266,7 +266,7 @@ + file (string) + """ + nproc = 0 +- file = open(filename, 'rU') ++ file = open(filename) + text = "" + while 1: + line = file.readline() From 8ed4dc788eedab34933d0d96b25c3c4b3ff232a7 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 19 Jan 2022 21:27:15 +0000 Subject: [PATCH 67/92] - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 22e888d..c6d3d0c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 13%{datecommit}%{shortcommit}%{?dist} +Release: 14%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jan 19 2022 Fedora Release Engineering - 3.0.0-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + * Tue Jan 04 2022 Antonio Trande - 3.0.0-13 - Patched for Python-3.11 From b1c8820a70ab5542247b81dd8f550808c327e74e Mon Sep 17 00:00:00 2001 From: Python Maint Date: Mon, 13 Jun 2022 18:55:54 +0200 Subject: [PATCH 68/92] Rebuilt for Python 3.11 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index c6d3d0c..8752b6c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 14%{datecommit}%{shortcommit}%{?dist} +Release: 15%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Jun 13 2022 Python Maint - 3.0.0-15 +- Rebuilt for Python 3.11 + * Wed Jan 19 2022 Fedora Release Engineering - 3.0.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild From c9f299b0fc9617a2d0483c44018caa134e4ce439 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 20 Jul 2022 21:02:27 +0000 Subject: [PATCH 69/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 8752b6c..4f4a16e 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 15%{datecommit}%{shortcommit}%{?dist} +Release: 16%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 20 2022 Fedora Release Engineering - 3.0.0-16 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + * Mon Jun 13 2022 Python Maint - 3.0.0-15 - Rebuilt for Python 3.11 From 065b3accf8fea19f16c1dfdf84f0959541a6a258 Mon Sep 17 00:00:00 2001 From: Lumir Balhar Date: Tue, 1 Nov 2022 06:58:32 +0100 Subject: [PATCH 70/92] Change location of pathfix.py For more info see https://fedoraproject.org/wiki/Changes/Python3.12#pathfix.py_tool_will_be_removed --- apbs.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 4f4a16e..9210da1 100644 --- a/apbs.spec +++ b/apbs.spec @@ -147,7 +147,7 @@ chrpath -d %{buildroot}%{_libdir}/libapbs.so.1 # Move Python libraries under Python's tree directories mkdir -p %{buildroot}%{python3_sitearch}/apbs install -pm 755 tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ -pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py +%{__python3} %{_rpmconfigdir}/redhat/pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py install -pm 755 build/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ From 4be9e4746a7a2822a2d587d45c24c04f4ec945f1 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 18 Jan 2023 21:56:56 +0000 Subject: [PATCH 71/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 9210da1..75b4300 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 16%{datecommit}%{shortcommit}%{?dist} +Release: 17%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jan 18 2023 Fedora Release Engineering - 3.0.0-17 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + * Wed Jul 20 2022 Fedora Release Engineering - 3.0.0-16 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild From b0c00fdb38d1e12455b374d2fc1198b4321cb656 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sat, 28 Jan 2023 20:11:24 +0100 Subject: [PATCH 72/92] Add texlive-wasysym --- apbs.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/apbs.spec b/apbs.spec index 75b4300..0933e95 100644 --- a/apbs.spec +++ b/apbs.spec @@ -80,6 +80,7 @@ BuildRequires: texlive-etoc BuildRequires: texlive-tocloft BuildRequires: texlive-ulem BuildRequires: texlive-newunicodechar +BuildRequires: texlive-wasysym BuildArch: noarch %description doc The apbs-doc package contains API reference inforemation for From 3a7a53a8301cd7c68e7614a1f8ddf4644d830f55 Mon Sep 17 00:00:00 2001 From: Florian Weimer Date: Mon, 6 Feb 2023 08:11:37 +0100 Subject: [PATCH 73/92] Add missing BuildRequires: texlive-wasy Otherwise, the build fails with: ! I can't find file `wasy7'. --- apbs.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/apbs.spec b/apbs.spec index 0933e95..a9b34a8 100644 --- a/apbs.spec +++ b/apbs.spec @@ -80,6 +80,7 @@ BuildRequires: texlive-etoc BuildRequires: texlive-tocloft BuildRequires: texlive-ulem BuildRequires: texlive-newunicodechar +BuildRequires: texlive-wasy BuildRequires: texlive-wasysym BuildArch: noarch %description doc From 66636ea5145bc43047ec3393d586e0eb29dcdf63 Mon Sep 17 00:00:00 2001 From: Florian Weimer Date: Mon, 6 Feb 2023 08:21:53 +0100 Subject: [PATCH 74/92] Fix C99 compatibility issue Related to: --- apbs-c99.patch | 23 +++++++++++++++++++++++ apbs.spec | 9 ++++++++- 2 files changed, 31 insertions(+), 1 deletion(-) create mode 100644 apbs-c99.patch diff --git a/apbs-c99.patch b/apbs-c99.patch new file mode 100644 index 0000000..4a5b282 --- /dev/null +++ b/apbs-c99.patch @@ -0,0 +1,23 @@ +Partial backport of this commit, to avoid an implicit declaration of +getpid and future build failures: + +Author: Noah Oblath +Date: Mon Jan 24 15:33:56 2022 -0800 + + Nsoblath/issue 163 (#171) + +diff -ur apbs-3.0.0.orig/contrib/iapbs/src/apbs_driver.c apbs-3.0.0/contrib/iapbs/src/apbs_driver.c +--- apbs-3.0.0.orig/contrib/iapbs/src/apbs_driver.c 2020-05-30 03:47:30.000000000 +0200 ++++ apbs-3.0.0/contrib/iapbs/src/apbs_driver.c 2023-02-06 07:58:46.215007012 +0100 +@@ -18,6 +18,11 @@ + + #include "apbs_driver.h" + ++#ifdef WIN32 ++#include ++#else ++#include ++#endif + + /*! \def MAX_BUF_SIZE + \brief Buffer size for internal APBS string input. diff --git a/apbs.spec b/apbs.spec index a9b34a8..d9085d0 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 17%{datecommit}%{shortcommit}%{?dist} +Release: 18%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -26,6 +26,8 @@ Patch1: %{name}-exclude_tests.patch # Porting to Python-3.11 Patch2: %{name}-python311.patch +Patch3: apbs-c99.patch + BuildRequires: gcc-c++ BuildRequires: cmake3 BuildRequires: chrpath @@ -108,6 +110,8 @@ Python interface of APBS. %patch2 -p1 -b .python311 %endif +%patch3 -p1 + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 @@ -209,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Feb 06 2023 Florian Weimer - 3.0.0-18 +- Fix C99 compatibility issue + * Wed Jan 18 2023 Fedora Release Engineering - 3.0.0-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild From 95dca6667353f7d74e948c1eb87898abb638183c Mon Sep 17 00:00:00 2001 From: Python Maint Date: Wed, 14 Jun 2023 06:13:12 +0200 Subject: [PATCH 75/92] Rebuilt for Python 3.12 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index d9085d0..7e0bb65 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 18%{datecommit}%{shortcommit}%{?dist} +Release: 19%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jun 14 2023 Python Maint - 3.0.0-19 +- Rebuilt for Python 3.12 + * Mon Feb 06 2023 Florian Weimer - 3.0.0-18 - Fix C99 compatibility issue From 6c77a00b14148e0a3ad4ba169e657ecdc8226dc2 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 19 Jul 2023 13:32:10 +0000 Subject: [PATCH 76/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 7e0bb65..bcd5618 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 19%{datecommit}%{shortcommit}%{?dist} +Release: 20%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 19 2023 Fedora Release Engineering - 3.0.0-20 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + * Wed Jun 14 2023 Python Maint - 3.0.0-19 - Rebuilt for Python 3.12 From e1527066ef1036bd18ae72171a3604ddcff570b6 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 19 Jan 2024 13:19:14 +0000 Subject: [PATCH 77/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index bcd5618..327ab9c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 20%{datecommit}%{shortcommit}%{?dist} +Release: 21%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Fri Jan 19 2024 Fedora Release Engineering - 3.0.0-21 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Wed Jul 19 2023 Fedora Release Engineering - 3.0.0-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild From 9c73f66c0ba3217c190b7d4417e7cd530fc20de5 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Mon, 22 Jan 2024 23:16:39 +0000 Subject: [PATCH 78/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 327ab9c..cbb96f6 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 21%{datecommit}%{shortcommit}%{?dist} +Release: 22%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Jan 22 2024 Fedora Release Engineering - 3.0.0-22 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Fri Jan 19 2024 Fedora Release Engineering - 3.0.0-21 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From 5773361a204d3b42a99475c75e82e77a1f1479dd Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sat, 25 May 2024 20:00:26 +0200 Subject: [PATCH 79/92] Fix patch commands --- apbs.spec | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/apbs.spec b/apbs.spec index cbb96f6..ea24cc8 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,9 +11,9 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 22%{datecommit}%{shortcommit}%{?dist} +Release: 23%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. -License: LGPLv2+ and BSD +License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ Source0: https://github.com/Electrostatics/apbs/archive/refs/tags/v%{version}/%{name}-%{version}.tar.gz Source1: %{name}-LGPL_V2 @@ -103,14 +103,14 @@ Python interface of APBS. %prep %autosetup -n %{name}-%{version} -N -%patch0 -p2 -b .apbs-cmake -%patch1 -p1 -b .exclude_tests +%patch -P 0 -p2 -b .apbs-cmake +%patch -P 1 -p1 -b .exclude_tests %if 0%{?python3_version_nodots} >= 311 -%patch2 -p1 -b .python311 +%patch -P 2 -p1 -b .python311 %endif -%patch3 -p1 +%patch -P 3 -p1 cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Sat May 25 2023 Antonio Trande - 3.0.0-23 +- Fix patch commands + * Mon Jan 22 2024 Fedora Release Engineering - 3.0.0-22 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From 0255ed726be519e2596ef7f7ffa57d8576b80840 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sat, 25 May 2024 20:45:53 +0200 Subject: [PATCH 80/92] Fix Changelog --- apbs.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index ea24cc8..b13a491 100644 --- a/apbs.spec +++ b/apbs.spec @@ -213,7 +213,7 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog -* Sat May 25 2023 Antonio Trande - 3.0.0-23 +* Sat May 25 2024 Antonio Trande - 3.0.0-23 - Fix patch commands * Mon Jan 22 2024 Fedora Release Engineering - 3.0.0-22 From acba49821cc83b0680e1626841ac2b798c1ed494 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Sat, 8 Jun 2024 08:08:15 +0200 Subject: [PATCH 81/92] Rebuilt for Python 3.13 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index b13a491..9b50552 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 23%{datecommit}%{shortcommit}%{?dist} +Release: 24%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Sat Jun 08 2024 Python Maint - 3.0.0-24 +- Rebuilt for Python 3.13 + * Sat May 25 2024 Antonio Trande - 3.0.0-23 - Fix patch commands From 12b548c50300ae878da6b3a2c36862a56ad16342 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 17 Jul 2024 17:14:20 +0000 Subject: [PATCH 82/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 9b50552..ed6c2d8 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 24%{datecommit}%{shortcommit}%{?dist} +Release: 25%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 17 2024 Fedora Release Engineering - 3.0.0-25 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild + * Sat Jun 08 2024 Python Maint - 3.0.0-24 - Rebuilt for Python 3.13 From 3172b4fb1b5331cc05868b7451b0201bbd3d3d87 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 16 Jan 2025 11:19:31 +0000 Subject: [PATCH 83/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index ed6c2d8..ddca290 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 25%{datecommit}%{shortcommit}%{?dist} +Release: 26%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Thu Jan 16 2025 Fedora Release Engineering - 3.0.0-26 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild + * Wed Jul 17 2024 Fedora Release Engineering - 3.0.0-25 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild From c815b178467f0a36746241a736889345be82d010 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Tue, 3 Jun 2025 12:29:37 +0200 Subject: [PATCH 84/92] Rebuilt for Python 3.14 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index ddca290..08be658 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 26%{datecommit}%{shortcommit}%{?dist} +Release: 27%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Tue Jun 03 2025 Python Maint - 3.0.0-27 +- Rebuilt for Python 3.14 + * Thu Jan 16 2025 Fedora Release Engineering - 3.0.0-26 - Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild From b3f9fbd6d070fc0b628f3265792b6fd25df9ecd1 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 23 Jul 2025 17:07:38 +0000 Subject: [PATCH 85/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 08be658..5451beb 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 27%{datecommit}%{shortcommit}%{?dist} +Release: 28%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 23 2025 Fedora Release Engineering - 3.0.0-28 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild + * Tue Jun 03 2025 Python Maint - 3.0.0-27 - Rebuilt for Python 3.14 From 08c273025bba250ab243c0c8edd95295a7bf3836 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 19:45:04 +0200 Subject: [PATCH 86/92] Fix rhbz#2380463 --- apbs.spec | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/apbs.spec b/apbs.spec index 5451beb..0232f5d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 28%{datecommit}%{shortcommit}%{?dist} +Release: 29%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -120,8 +120,7 @@ cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 # Using CMake rpm macro automatically enables the shared libs building export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" -mkdir -p build -cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release \ +%cmake -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ -DENABLE_FETK:BOOL=OFF -DCMAKE_C_FLAGS:STRING="%{build_cflags} -fopenmp -lm -DNDEBUG" \ -DCMAKE_CXX_FLAGS:STRING="%{build_cxxflags} -fopenmp -lm -DNDEBUG" \ @@ -131,10 +130,11 @@ cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release \ -DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \ -DLIB_INSTALL_DIR:PATH=%{_libdir} \ -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} -make -O -j1 V=1 -C build + +%cmake_build %install -%make_install -C build +%cmake_install # Tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Thu Jul 24 2025 Antonio Trande - 3.0.0-29 +- Fix rhbz#2380463 + * Wed Jul 23 2025 Fedora Release Engineering - 3.0.0-28 - Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild From b1d95aaa718c0b7f6d6d31102ddbc1d8e0631f16 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 19:57:43 +0200 Subject: [PATCH 87/92] Fix build directory --- apbs.spec | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 0232f5d..f36c2ff 100644 --- a/apbs.spec +++ b/apbs.spec @@ -155,7 +155,7 @@ mkdir -p %{buildroot}%{python3_sitearch}/apbs install -pm 755 tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ %{__python3} %{_rpmconfigdir}/redhat/pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py -install -pm 755 build/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ +install -pm 755 %_vpath_builddir/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ # Remove redundant tools binary files in /usr/share rm -rf %{buildroot}%{_datadir}/apbs @@ -210,7 +210,7 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %files doc %license LICENSE.md -%doc build/doc +%doc %_vpath_builddir/doc %changelog * Thu Jul 24 2025 Antonio Trande - 3.0.0-29 From ba54c74207e39696808b594bd88436b29bcb61d7 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 21:59:51 +0200 Subject: [PATCH 88/92] Update CMake patches --- apbs-cmake.patch | 46 +++++++++++++++++++++++++++++++++++++++++++++- apbs.spec | 4 +--- 2 files changed, 46 insertions(+), 4 deletions(-) diff --git a/apbs-cmake.patch b/apbs-cmake.patch index dbcb876..c457571 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -1,11 +1,20 @@ --- a/apbs/CMakeLists.txt_orig 2018-05-20 13:00:17.451341064 -0400 +++ b/apbs/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -1,4 +1,5 @@ - cmake_minimum_required (VERSION 3.12) +-cmake_minimum_required (VERSION 3.12) ++cmake_minimum_required(VERSION 3.13...4.0) +set(CMAKE_POSITION_INDEPENDENT_CODE ON) ################################################################################ # TODO: Add licensing and authorship information +@@ -7,7 +8,6 @@ + # (configure.ac:1306) + ################################################################################ + set(CMAKE_VERBOSE_MAKEFILE true) +-cmake_policy(SET CMP0054 OLD) + cmake_policy(SET CMP0042 NEW) + set(CMAKE_MACOSX_RPATH 1) + @@ -70,10 +71,10 @@ set(TOOLS_PATH ${APBS_BUILD}/tools) set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) @@ -117,6 +126,12 @@ set(CPACK_SOURCE_IGNORE_FILES "${PROJECT_BINARY_DIR};/.git/;.gitignore;/tools/matlab/") --- a/apbs/src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400 +++ b/apbs/src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 +@@ -1,4 +1,4 @@ +-cmake_minimum_required(VERSION 2.8) ++cmake_minimum_required(VERSION 3.13...4.0) + + macro(add_items TYPE) + @@ -32,11 +32,11 @@ message(STATUS "With external header files ${EXTERNAL_HEADERS}") message(STATUS "With internal header files ${INTERNAL_HEADERS}") @@ -279,3 +294,32 @@ +target_link_libraries(uhbd_asc2bin ${LIBS} ${APBS_LIBS}) + +INSTALL(TARGETS mgmesh smooth dxmath mergedx mergedx2 value multivalue benchmark similarity analysis dx2mol dx2uhbd del2dx tensor2dx uhbd_asc2bin DESTINATION ${EXECUTABLE_INSTALL_PATH}) +--- a/a/tools/python/CMakeLists.orig.txt 2020-05-30 03:47:30.000000000 +0200 ++++ b/b/tools/python/CMakeLists.txt 2025-07-24 20:56:31.152039088 +0200 +@@ -1,3 +1,4 @@ ++cmake_minimum_required(VERSION 3.13...4.0) + if (${CMAKE_VERSION} VERSION_GREATER "3.13") + CMAKE_POLICY(SET CMP0078 OLD) + CMAKE_POLICY(SET CMP0086 OLD) +@@ -23,18 +24,16 @@ + SET(CMAKE_SWIG_FLAGS "") + + SWIG_ADD_LIBRARY(apbslib +- #TYPE USE_BUILD_SHARED_LIBS ++ TYPE USE_BUILD_SHARED_LIBS + TYPE SHARED + LANGUAGE python + SOURCES apbslib.i) + + # Hack to get the correct shared library extensions. Why does Python suck so hard wrt to this? +-if(APPLE) +- set(CMAKE_SHARED_LIBRARY_SUFFIX ".so") +-endif(APPLE) ++set(CMAKE_SHARED_LIBRARY_SUFFIX ".so") + + # Another hack to get SWIG to use the the correct library extension! +-#SET_TARGET_PROPERTIES(${SWIG_MODULE_apbslib_REAL_NAME} PROPERTIES SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX}) ++SET_TARGET_PROPERTIES(${SWIG_MODULE_apbslib_REAL_NAME} PROPERTIES SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX}) + + SWIG_LINK_LIBRARIES(apbslib ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${Python3_LIBRARIES}) + diff --git a/apbs.spec b/apbs.spec index f36c2ff..1c0fe3d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -116,15 +116,13 @@ cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 %build -# CMake needs BUILD_SHARED_LIBS:BOOL=OFF to build Python libraries -# Using CMake rpm macro automatically enables the shared libs building export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" %cmake -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ -DENABLE_FETK:BOOL=OFF -DCMAKE_C_FLAGS:STRING="%{build_cflags} -fopenmp -lm -DNDEBUG" \ -DCMAKE_CXX_FLAGS:STRING="%{build_cxxflags} -fopenmp -lm -DNDEBUG" \ - -DBUILD_SHARED_LIBS:BOOL=OFF -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON \ + -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON \ -DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \ From 602c04ccf301e34299fe80c9b5e0eb26697499f1 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 22:15:14 +0200 Subject: [PATCH 89/92] Exporting binary path --- apbs.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/apbs.spec b/apbs.spec index 1c0fe3d..962309f 100644 --- a/apbs.spec +++ b/apbs.spec @@ -167,6 +167,7 @@ done %check pushd tests export LD_LIBRARY_PATH=%{buildroot}%{_libdir} +export PATH=%{buildroot}%{_bindir} %{__python3} ./apbs_tester.py %endif From 0ab0f837596b3b4593b4fd2378f2ec71b19f8a6c Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 15 Aug 2025 12:38:14 +0200 Subject: [PATCH 90/92] Rebuilt for Python 3.14.0rc2 bytecode --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 962309f..601a19c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 29%{datecommit}%{shortcommit}%{?dist} +Release: 30%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -212,6 +212,9 @@ export PATH=%{buildroot}%{_bindir} %doc %_vpath_builddir/doc %changelog +* Fri Aug 15 2025 Python Maint - 3.0.0-30 +- Rebuilt for Python 3.14.0rc2 bytecode + * Thu Jul 24 2025 Antonio Trande - 3.0.0-29 - Fix rhbz#2380463 From 328dda165355c22bcf785d4135b1befab5df0463 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 19 Sep 2025 12:07:07 +0200 Subject: [PATCH 91/92] Rebuilt for Python 3.14.0rc3 bytecode --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 601a19c..bc582e2 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 30%{datecommit}%{shortcommit}%{?dist} +Release: 31%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -212,6 +212,9 @@ export PATH=%{buildroot}%{_bindir} %doc %_vpath_builddir/doc %changelog +* Fri Sep 19 2025 Python Maint - 3.0.0-31 +- Rebuilt for Python 3.14.0rc3 bytecode + * Fri Aug 15 2025 Python Maint - 3.0.0-30 - Rebuilt for Python 3.14.0rc2 bytecode From 9fa9b189bc58f8cbef17895880ef5619ea08a2a8 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 16 Jan 2026 03:48:49 +0000 Subject: [PATCH 92/92] Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index bc582e2..b3c0c36 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 31%{datecommit}%{shortcommit}%{?dist} +Release: 32%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -212,6 +212,9 @@ export PATH=%{buildroot}%{_bindir} %doc %_vpath_builddir/doc %changelog +* Fri Jan 16 2026 Fedora Release Engineering - 3.0.0-32 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild + * Fri Sep 19 2025 Python Maint - 3.0.0-31 - Rebuilt for Python 3.14.0rc3 bytecode