# Workaround for GCC-10 %define _legacy_common_support 1 %global commit %{nil} %global shortcommit %{nil} %global datecommit %{nil} # To perform all tests, APBS needs to be compiled together additional sub-modules %bcond_without check Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 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/ 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 # Porting to Python-3.11 Patch2: %{name}-python311.patch BuildRequires: gcc-c++ BuildRequires: cmake3 BuildRequires: chrpath BuildRequires: make BuildRequires: doxygen BuildRequires: graphviz BuildRequires: maloc-devel BuildRequires: zlib-devel Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: python3-%{name} %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 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}-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 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. %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}} Obsoletes: %{name}-libs < 0:3.0.0-11 %description -n python3-apbs Python interface of APBS. %prep %autosetup -n %{name}-%{version} -N %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 %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" 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 \ -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 %make_install -C build # 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 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/ # 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 done %if %{with check} %check pushd tests export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %{__python3} ./apbs_tester.py %endif %files %{_bindir}/apbs %files libs %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 %{_includedir}/iapbs/ %{_includedir}/apbs %files tools %{_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-del2dx %{_bindir}/apbs-tensor2dx %files doc %license LICENSE.md %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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 - 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) * 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 * 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 * 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 * 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 * 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 * 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