diff --git a/.cvsignore b/.cvsignore deleted file mode 100644 index e69de29..0000000 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..85ecb73 --- /dev/null +++ b/.gitignore @@ -0,0 +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 diff --git a/Makefile b/Makefile deleted file mode 100644 index 623b8bf..0000000 --- a/Makefile +++ /dev/null @@ -1,21 +0,0 @@ -# Makefile for source rpm: apbs -# $Id$ -NAME := apbs -SPECFILE = $(firstword $(wildcard *.spec)) - -define find-makefile-common -for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done -endef - -MAKEFILE_COMMON := $(shell $(find-makefile-common)) - -ifeq ($(MAKEFILE_COMMON),) -# attept a checkout -define checkout-makefile-common -test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2 -endef - -MAKEFILE_COMMON := $(shell $(checkout-makefile-common)) -endif - -include $(MAKEFILE_COMMON) diff --git a/apbs-LGPL_V2 b/apbs-LGPL_V2 new file mode 100644 index 0000000..a96b573 --- /dev/null +++ b/apbs-LGPL_V2 @@ -0,0 +1,482 @@ + GNU LIBRARY GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1991 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor + Boston, MA 02110-1301, USA. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +[This is the first released version of the library GPL. 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See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +Also add information on how to contact you by electronic and paper mail. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the library, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random Hacker. + + , 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! diff --git a/apbs-c99.patch b/apbs-c99.patch new file mode 100644 index 0000000..4a5b282 --- /dev/null +++ b/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 +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 new file mode 100644 index 0000000..c457571 --- /dev/null +++ b/apbs-cmake.patch @@ -0,0 +1,325 @@ +--- 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 3.13...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) + +-set(LIBRARY_INSTALL_PATH lib) +-set(HEADER_INSTALL_PATH include/apbs) ++set(LIBRARY_INSTALL_PATH ${LIB_INSTALL_DIR}) ++set(HEADER_INSTALL_PATH ${INCLUDE_INSTALL_DIR}/apbs) + set(EXECUTABLE_INSTALL_PATH bin) +-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") + +-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() + +@@ -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) + + 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}/tests +- DESTINATION ${SHARE_INSTALL_PATH} +- FILES_MATCHING +- PATTERN "*.py" +- 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 ${SHARE_INSTALL_PATH}/tools + USE_SOURCE_PERMISSIONS) +- endif() + endif() + + ################################################################################ +@@ -880,7 +860,7 @@ + set(CPACK_PACKAGE_NAME "${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 @@ + 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} ${INTERNAL_HEADERS}) +- target_link_libraries(${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 @@ + add_subdirectory(generic) + add_subdirectory(pmgc) + add_subdirectory(mg) ++add_library(apbs SHARED $ $ $) ++# set a SOVERSION to keep packager happy ++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}") + + #add_executable(apbs main.c routines.c) +-add_executable(apbs main.c apbs.h routines.c routines.h) ++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-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() + + 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 +@@ -1,9 +1,10 @@ + message(STATUS "Building manip") + + set(LIBS "") +-list(APPEND LIBS "apbs_generic") +-list(APPEND LIBS "apbs_mg") +-list(APPEND LIBS "apbs_pmgc") ++#list(APPEND LIBS "apbs_generic") ++#list(APPEND LIBS "apbs_mg") ++#list(APPEND LIBS "apbs_pmgc") ++list(APPEND LIBS "apbs") + if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") + endif(FETK_ENABLED) +@@ -11,7 +12,9 @@ + message(STATUS "libraries: ${LIBS}") + + add_executable(coulomb coulomb.c) +-target_link_libraries(coulomb ${LIBS}) ++target_link_libraries(coulomb ${LIBS} ${APBS_LIBS}) + + add_executable(born born.c) +-target_link_libraries(born ${LIBS}) ++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 +@@ -1,9 +1,10 @@ + message(STATUS "Building mesh") + + set(LIBS "") +-list(APPEND LIBS "apbs_generic") +-list(APPEND LIBS "apbs_mg") +-list(APPEND LIBS "apbs_pmgc") ++#list(APPEND LIBS "apbs_generic") ++#list(APPEND LIBS "apbs_mg") ++#list(APPEND LIBS "apbs_pmgc") ++list(APPEND LIBS "apbs") + if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") + endif(FETK_ENABLED) +@@ -11,46 +12,48 @@ + message(STATUS "libraries: ${LIBS}") + + add_executable(mgmesh mgmesh.c) +-target_link_libraries(mgmesh ${LIBS}) ++target_link_libraries(mgmesh ${LIBS} ${APBS_LIBS}) + + add_executable(smooth smooth.c) +-target_link_libraries(smooth ${LIBS}) ++target_link_libraries(smooth ${LIBS} ${APBS_LIBS}) + + add_executable(dxmath dxmath.c) +-target_link_libraries(dxmath ${LIBS}) ++target_link_libraries(dxmath ${LIBS} ${APBS_LIBS}) + + add_executable(mergedx mergedx.c) +-target_link_libraries(mergedx ${LIBS}) ++target_link_libraries(mergedx ${LIBS} ${APBS_LIBS}) + + add_executable(mergedx2 mergedx2.c) +-target_link_libraries(mergedx2 ${LIBS}) ++target_link_libraries(mergedx2 ${LIBS} ${APBS_LIBS}) + + add_executable(value value.c) +-target_link_libraries(value ${LIBS}) ++target_link_libraries(value ${LIBS} ${APBS_LIBS}) + + add_executable(multivalue multivalue.c) +-target_link_libraries(multivalue ${LIBS}) ++target_link_libraries(multivalue ${LIBS} ${APBS_LIBS}) + + add_executable(benchmark benchmark.c) +-target_link_libraries(benchmark ${LIBS}) ++target_link_libraries(benchmark ${LIBS} ${APBS_LIBS}) + + add_executable(similarity similarity.c) +-target_link_libraries(similarity ${LIBS}) ++target_link_libraries(similarity ${LIBS} ${APBS_LIBS}) + + add_executable(analysis analysis.c) +-target_link_libraries(analysis ${LIBS}) ++target_link_libraries(analysis ${LIBS} ${APBS_LIBS}) + + add_executable(dx2mol dx2mol.c) +-target_link_libraries(dx2mol ${LIBS}) ++target_link_libraries(dx2mol ${LIBS} ${APBS_LIBS}) + + add_executable(dx2uhbd dx2uhbd.c) +-target_link_libraries(dx2uhbd ${LIBS}) ++target_link_libraries(dx2uhbd ${LIBS} ${APBS_LIBS}) + + add_executable(del2dx del2dx.c) +-target_link_libraries(del2dx ${LIBS}) ++target_link_libraries(del2dx ${LIBS} ${APBS_LIBS}) + + add_executable(tensor2dx tensor2dx.c) +-target_link_libraries(tensor2dx ${LIBS}) ++target_link_libraries(tensor2dx ${LIBS} ${APBS_LIBS}) + + add_executable(uhbd_asc2bin uhbd_asc2bin.c) +-target_link_libraries(uhbd_asc2bin ${LIBS}) ++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 new file mode 100644 index 0000000..5f64696 --- /dev/null +++ b/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 diff --git a/apbs-python311.patch b/apbs-python311.patch new file mode 100644 index 0000000..adf7420 --- /dev/null +++ b/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() diff --git a/apbs.spec b/apbs.spec new file mode 100644 index 0000000..b3c0c36 --- /dev/null +++ b/apbs.spec @@ -0,0 +1,435 @@ +# 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: 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: 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 +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 +%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 +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 +%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 + 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 %_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 +%{_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 %_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 + +* 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 + +* 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 diff --git a/sources b/sources index e69de29..2e522a3 100644 --- a/sources +++ b/sources @@ -0,0 +1 @@ +SHA512 (apbs-3.0.0.tar.gz) = 9107acf5fb591cd7a822dc3cb0be58b5d3142e85951585749068e748459bceb0c7503ecfd95b6b4370378d619c30aedb04f5e3ca5c1ad15683533171cb7208fb