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

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

.gitignore

@@ -1,3 +1,7 @@
 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
+/apbs-pdb2pqr-vAPBS-3.0.0.tar.gz
+/apbs-3.0.0.tar.gz

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

@@ -1,13 +1,22 @@
---- CMakeLists.txt_orig	2014-06-18 01:28:14.361212184 -0700
-+++ CMakeLists.txt	2014-06-23 22:11:12.124786178 -0700
+--- 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 2.6)
-+SET(CMAKE_POSITION_INDEPENDENT_CODE ON)
+-cmake_minimum_required (VERSION 3.12)
++cmake_minimum_required(VERSION 3.13...4.0)
++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
+@@ -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)
  
 -set(LIBRARY_INSTALL_PATH lib)
@@ -18,101 +27,127 @@
 -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)
+@@ -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)
+ 
+ 
+@@ -139,11 +140,6 @@
+ ################################################################################
  message(STATUS "Setting lookup paths for headers and libraries")
  
 -set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
 -list(APPEND CMAKE_INCLUDE_PATH /usr/include)
 -list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
 -
--set(SYS_LIBPATHS "")
--list(APPEND SYS_LIBPATHS /usr/lib)
--list(APPEND SYS_LIBPATHS /usr/local/lib)
--list(APPEND SYS_LIBPATHS /lib/x86_64-linux-gnu)
-+#set(CMAKE_INCLUDE_PATH "${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)
+-
+ ################################################################################
+ # Enable ansi pedantic compiling                                               #
+ ################################################################################
+@@ -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()
  
- set(APBS_LIBS "")
- 
-@@ -854,29 +855,29 @@
+@@ -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}
--)
+ if(BUILD_DOC)
+     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")
 -
--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
-+#)
+-if(BUILD_TOOLS)
+-    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}")
+-    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()
+ 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")
  
---- 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 @@
+ 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}")
      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 @@
+@@ -45,6 +45,11 @@
  add_subdirectory(generic)
  add_subdirectory(pmgc)
  add_subdirectory(mg)
@@ -121,27 +156,38 @@
 +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)
+@@ -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)
--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(STATUS " ")
+ message(STATUS "APBS Libraries: ${APBS_LIBS}")
+ 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(
-     ${APBS_ROOT}/src/config/apbscfg.h.in
-@@ -59,4 +66,4 @@
-     )
+@@ -79,6 +85,6 @@
+ 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})
+--- 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")
  
@@ -153,9 +199,9 @@
 +#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 +214,8 @@
 +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
+--- 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")
  
@@ -181,9 +227,9 @@
 +#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}")
  
@@ -248,3 +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-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

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()

apbs.spec

@@ -1,22 +1,43 @@
-%{!?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 %{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: 1.4
-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
-URL: http://apbs.sourceforge.net/
-Source0: http://downloads.sourceforge.net/apbs/APBS-%{version}-source.tar.gz
-Patch0: apbs-cmake.patch
-BuildRequires: cmake
+Version: 3.0.0
+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/
+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
+
+Patch3: apbs-c99.patch
+
+BuildRequires: gcc-c++
+BuildRequires: cmake3
+BuildRequires: chrpath
+BuildRequires: make
 BuildRequires: doxygen
-BuildRequires: arpack-devel
-BuildRequires: atlas-devel
-BuildRequires: blas-devel
+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
@@ -29,74 +50,144 @@ 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}
-
+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
-Group: Development/Libraries
-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
-Group: Applications/Engineering
-Requires: %{name} = %{version}-%{release}
-
+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
+BuildRequires: texlive-wasy
+BuildRequires: texlive-wasysym
+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
-%setup -q -n %{name}
-%patch0 -p0
+%autosetup -n %{name}-%{version} -N
+%patch -P 0 -p2 -b .apbs-cmake
+%patch -P 1 -p1 -b .exclude_tests
+
+%if 0%{?python3_version_nodots} >= 311
+%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
-cd build
-%cmake -D BUILD_DOC:BOOL=ON ..
-make %{?_smp_mflags}
+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" \
+ -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}
+
+%cmake_build
 
 %install
-rm -rf %{buildroot}
+%cmake_install
 
-cd build
-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
-    mv $bin %{buildroot}%{_bindir}/apbs-`basename $bin`
+# 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
 
-%clean
-rm -rf %{buildroot}
+# 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
 
-%post -p /sbin/ldconfig
+chrpath -d %{buildroot}%{_libdir}/libapbs.so.1
 
-%postun -p /sbin/ldconfig
+# 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 %_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
+done
+
+%if %{with check}
+%check
+pushd tests
+export LD_LIBRARY_PATH=%{buildroot}%{_libdir}
+export PATH=%{buildroot}%{_bindir}
+%{__python3} ./apbs_tester.py
+%endif
 
 %files
-%defattr(-,root,root,-)
-%doc doc/license/LICENSE.txt README ChangeLog
 %{_bindir}/apbs
-%{_libdir}/libapbs*.so.*
+
+%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
-%defattr(-,root,root,-)
 %{_bindir}/apbs-psize.py
 %{_bindir}/apbs-coulomb
 %{_bindir}/apbs-born
@@ -116,16 +207,147 @@ rm -rf %{buildroot}
 %{_bindir}/apbs-del2dx
 %{_bindir}/apbs-tensor2dx
 
-%files devel
-%defattr(-,root,root,-)
-%{_libdir}/libapbs*.so
-%{_includedir}/apbs
-
 %files doc
-%defattr(-,root,root,-)
-%doc doc/programmer/html
+%license LICENSE.md
+%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
+
+* Mon Jun 13 2022 Python Maint <python-maint@redhat.com> - 3.0.0-15
+- Rebuilt for Python 3.11
+
+* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-14
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Tue Jan 04 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-13
+- Patched for Python-3.11
+
+* Mon Nov 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-12
+- Re-enable tests
+
+* Mon Nov 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-11
+- Fix installation conflict of python package
+
+* Sun Oct 31 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-10
+- Compile from a new source archive
+
+* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-9
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 3.0.0-8
+- Rebuilt for Python 3.10
+
+* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-7
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
+* Fri Jan 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-6
+- Use cmake3 options
+
+* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-5
+- Second attempt - Rebuilt for
+  https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Wed Jun 17 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-3
+- Use cmake3 macro
+
+* Wed Jun 17 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-2
+- Use cmake3
+
+* Sun May 31 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-1
+- Release 3.0.0
+
+* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 3.0.0-0.3.20200512gitdfb858d
+- Rebuilt for Python 3.9
+
+* Wed May 13 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-0.2.20200512gitdfb858d
+- Fix release tag
+
+* Wed May 13 2020 Antonio Trande <sagitter@fedoraproject.org> - 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 <releng@fedoraproject.org> - 1.5-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
+
+* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.5-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
+
+* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.5-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
+
+* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.5-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
+
+* Sat May 19 2018 Tim Fenn <tim.fenn@gmail.com> - 1.5-1
+- update to 1.5
+
+* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-8
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
+
+* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-7
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
+
+* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-6
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
+
+* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
+
 * Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-4
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
 

sources

@@ -1 +1 @@
-e0281bd44ffecb651e40687cdaa26361  APBS-1.4-source.tar.gz
+SHA512 (apbs-3.0.0.tar.gz) = 9107acf5fb591cd7a822dc3cb0be58b5d3142e85951585749068e748459bceb0c7503ecfd95b6b4370378d619c30aedb04f5e3ca5c1ad15683533171cb7208fb