Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild

Signed-off-by: Fedora Release Engineering <releng@fedoraproject.org>

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 <nsoblath@gmail.com>
+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 <process.h>
++#else
++#include <unistd.h>
++#endif
+ 
+ /*! \def MAX_BUF_SIZE
+     \brief Buffer size for internal APBS string input.

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})
+ 

apbs.spec

@@ -11,9 +11,9 @@
 Name: apbs
 Summary: Adaptive Poisson Boltzmann Solver
 Version: 3.0.0
-Release: 16%{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
@@ -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
@@ -80,6 +82,8 @@ BuildRequires: texlive-etoc
 BuildRequires: texlive-tocloft
 BuildRequires: texlive-ulem
 BuildRequires: texlive-newunicodechar
+BuildRequires: texlive-wasy
+BuildRequires: texlive-wasysym
 BuildArch: noarch
 %description doc
 The apbs-doc package contains API reference inforemation for
@@ -99,36 +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
 
+%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
@@ -147,9 +151,9 @@ 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/
+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
@@ -163,6 +167,7 @@ done
 %check
 pushd tests
 export LD_LIBRARY_PATH=%{buildroot}%{_libdir}
+export PATH=%{buildroot}%{_bindir}
 %{__python3} ./apbs_tester.py
 %endif
 
@@ -204,9 +209,57 @@ 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 <releng@fedoraproject.org> - 3.0.0-32
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild
+
+* Fri Sep 19 2025 Python Maint <python-maint@redhat.com> - 3.0.0-31
+- Rebuilt for Python 3.14.0rc3 bytecode
+
+* Fri Aug 15 2025 Python Maint <python-maint@redhat.com> - 3.0.0-30
+- Rebuilt for Python 3.14.0rc2 bytecode
+
+* Thu Jul 24 2025 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-29
+- Fix rhbz#2380463
+
+* Wed Jul 23 2025 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-28
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild
+
+* Tue Jun 03 2025 Python Maint <python-maint@redhat.com> - 3.0.0-27
+- Rebuilt for Python 3.14
+
+* Thu Jan 16 2025 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-26
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild
+
+* Wed Jul 17 2024 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-25
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild
+
+* Sat Jun 08 2024 Python Maint <python-maint@redhat.com> - 3.0.0-24
+- Rebuilt for Python 3.13
+
+* Sat May 25 2024 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-23
+- Fix patch commands
+
+* Mon Jan 22 2024 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-22
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Fri Jan 19 2024 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-21
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Wed Jul 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-20
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
+
+* Wed Jun 14 2023 Python Maint <python-maint@redhat.com> - 3.0.0-19
+- Rebuilt for Python 3.12
+
+* Mon Feb 06 2023 Florian Weimer <fweimer@redhat.com> - 3.0.0-18
+- Fix C99 compatibility issue
+
+* Wed Jan 18 2023 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-17
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
+
 * Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-16
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild