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 bcd5618..b3c0c36 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,9 +11,9 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 20%{datecommit}%{shortcommit}%{?dist} +Release: 32%{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 @@ -103,38 +103,36 @@ 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 %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 \ +%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} \ -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 @@ -155,7 +153,7 @@ 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 @@ -169,6 +167,7 @@ done %check pushd tests export LD_LIBRARY_PATH=%{buildroot}%{_libdir} +export PATH=%{buildroot}%{_bindir} %{__python3} ./apbs_tester.py %endif @@ -210,9 +209,45 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %files doc %license LICENSE.md -%doc build/doc +%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 + +* 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 + +* 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 + +* 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 + +* 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 + +* 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 + * Wed Jul 19 2023 Fedora Release Engineering - 3.0.0-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild