diff --git a/.gitignore b/.gitignore index 85ecb73..3f7b265 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,3 @@ 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 diff --git a/apbs-LGPL_V2 b/LGPL_V2 similarity index 100% rename from apbs-LGPL_V2 rename to LGPL_V2 diff --git a/apbs-c99.patch b/apbs-c99.patch deleted file mode 100644 index 4a5b282..0000000 --- a/apbs-c99.patch +++ /dev/null @@ -1,23 +0,0 @@ -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-cmake.patch b/apbs-cmake.patch index c457571..73a7fd3 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -1,22 +1,13 @@ ---- 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 +--- 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 3.12) -+cmake_minimum_required(VERSION 3.13...4.0) -+set(CMAKE_POSITION_INDEPENDENT_CODE ON) + cmake_minimum_required (VERSION 2.6) ++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) + # 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) @@ -27,127 +18,101 @@ -set(SHARE_INSTALL_PATH share/apbs) +set(SHARE_INSTALL_PATH ${SHARE_INSTALL_PREFIX}/apbs) - set(APBS_LIBS) - set(APBS_LIB_DIRS) -@@ -85,7 +86,7 @@ - PATHS "${APBS_ROOT}" - DOC "The path to the external git submodules") + find_file( + CONTRIB_PATH +@@ -84,14 +85,14 @@ --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 "${CMAKE_INCLUDE_PATH}") -list(APPEND CMAKE_INCLUDE_PATH /usr/include) -list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) - -- - ################################################################################ - # Enable ansi pedantic compiling # - ################################################################################ -@@ -307,12 +303,12 @@ - ################################################################################ - if(NOT ENABLE_FETK) - # We'll use autotools to build MALOC if FETK is enabled. -- add_subdirectory(${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 ${EXTERNALS_PATH}/fetk/maloc/lib) - list(APPEND APBS_LIBS maloc) - endif() +-set(SYS_LIBPATHS "") +-list(APPEND SYS_LIBPATHS /usr/lib) +-list(APPEND SYS_LIBPATHS /usr/local/lib) +-list(APPEND SYS_LIBPATHS /lib/x86_64-linux-gnu) ++#set(CMAKE_INCLUDE_PATH "${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) -@@ -778,10 +774,10 @@ - ################################################################################ + set(APBS_LIBS "") + +@@ -854,29 +855,29 @@ # 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(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}/doc +- DESTINATION ${SHARE_INSTALL_PATH} +-) - --install(DIRECTORY ${APBS_ROOT}/tests -- DESTINATION ${SHARE_INSTALL_PATH} -- FILES_MATCHING +-install( +- DIRECTORY ${APBS_ROOT}/examples +- DESTINATION ${SHARE_INSTALL_PATH} +-) +- +-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 ${SHARE_INSTALL_PATH} -- USE_SOURCE_PERMISSIONS -- PATTERN "CMakeLists.txt" -- PATTERN "matlab" EXCLUDE) -- -- if(NOT "${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() +-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 ${SHARE_INSTALL_PATH} ++# PATTERN "CMakeLists.txt" EXCLUDE ++#) - ################################################################################ -@@ -880,7 +860,7 @@ - set(CPACK_PACKAGE_NAME "${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 -@@ -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 @@ +--- 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} ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS}) +- add_library(${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} ${LIBRARY_DEPENDENCIES}) - #add_dependencies(${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}") -@@ -45,6 +45,11 @@ +@@ -46,12 +46,19 @@ add_subdirectory(generic) add_subdirectory(pmgc) add_subdirectory(mg) @@ -156,38 +121,27 @@ +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) -@@ -56,7 +61,7 @@ - message(STATUS "External Headers: ${EXTERNAL_HEADERS}") + endif(ENABLE_FETK) - #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) - 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 ${APBS_LIBS} ${APBS_INTERNAL_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( -@@ -79,6 +85,6 @@ - endif() + ${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}) - - 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 +--- 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") @@ -199,9 +153,9 @@ +#list(APPEND LIBS "apbs_mg") +#list(APPEND LIBS "apbs_pmgc") +list(APPEND LIBS "apbs") - if(FETK_ENABLED) + if(FETK_ENALBED) list(APPEND LIBS "apbs_fem") - endif(FETK_ENABLED) + endif(FETK_ENALBED) @@ -11,7 +12,9 @@ message(STATUS "libraries: ${LIBS}") @@ -214,8 +168,8 @@ +target_link_libraries(born ${LIBS} ${APBS_LIBS}) + +INSTALL(TARGETS coulomb born DESTINATION ${EXECUTABLE_INSTALL_PATH}) ---- 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 +--- 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") @@ -227,9 +181,9 @@ +#list(APPEND LIBS "apbs_mg") +#list(APPEND LIBS "apbs_pmgc") +list(APPEND LIBS "apbs") - if(FETK_ENABLED) + if(FETK_ENALBED) list(APPEND LIBS "apbs_fem") - endif(FETK_ENABLED) + endif(FETK_ENALBED) @@ -11,46 +12,48 @@ message(STATUS "libraries: ${LIBS}") @@ -294,32 +248,3 @@ +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-exclude_tests.patch b/apbs-exclude_tests.patch deleted file mode 100644 index 5f64696..0000000 --- a/apbs-exclude_tests.patch +++ /dev/null @@ -1,60 +0,0 @@ ---- 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-python311.patch b/apbs-python311.patch deleted file mode 100644 index adf7420..0000000 --- a/apbs-python311.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- 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() diff --git a/apbs.spec b/apbs.spec index b3c0c36..aa5539d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -1,43 +1,22 @@ -# 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 +%{!?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: 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 +Version: 1.4 +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/APBS-%{version}-source.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: zlib-devel -Requires: %{name}-libs%{?_isa} = %{version}-%{release} -Requires: python3-%{name} %description APBS is a software package for the numerical solution of the @@ -50,144 +29,74 @@ 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} +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 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} +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 -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 +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. -%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 -%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 +%setup -q -n %{name} +%patch0 -p0 %build -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 +cd build +%cmake -D BUILD_DOC:BOOL=ON .. +make %{?_smp_mflags} %install -%cmake_install +rm -rf %{buildroot} -# 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 +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` 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 +%clean +rm -rf %{buildroot} -chrpath -d %{buildroot}%{_libdir}/libapbs.so.1 +%post -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 +%postun -p /sbin/ldconfig %files +%defattr(-,root,root,-) +%doc doc/license/LICENSE.txt README ChangeLog %{_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 +%{_libdir}/libapbs*.so.* %files tools +%defattr(-,root,root,-) %{_bindir}/apbs-psize.py %{_bindir}/apbs-coulomb %{_bindir}/apbs-born @@ -207,153 +116,16 @@ export PATH=%{buildroot}%{_bindir} %{_bindir}/apbs-del2dx %{_bindir}/apbs-tensor2dx +%files devel +%defattr(-,root,root,-) +%{_libdir}/libapbs*.so +%{_includedir}/apbs + %files doc -%license LICENSE.md -%doc %_vpath_builddir/doc +%defattr(-,root,root,-) +%doc doc/programmer/html %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 - -* 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 - -* 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 - -* 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 diff --git a/sources b/sources index 2e522a3..f659863 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (apbs-3.0.0.tar.gz) = 9107acf5fb591cd7a822dc3cb0be58b5d3142e85951585749068e748459bceb0c7503ecfd95b6b4370378d619c30aedb04f5e3ca5c1ad15683533171cb7208fb +e0281bd44ffecb651e40687cdaa26361 APBS-1.4-source.tar.gz