From 178230c85c4e8b25f7c531101c5c80dab6daff67 Mon Sep 17 00:00:00 2001
From: Tim Fenn <tfenn@localhost.localdomain>
Date: May 27 2018 18:04:42 +0000
Subject: update to 1.5


---

diff --git a/.gitignore b/.gitignore
index 3f7b265..f5c581c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 apbs-1.2.1-source.tar.gz
 /apbs-1.3-source.tar.gz
 /APBS-1.4-source.tar.gz
+/apbs-1.5.tar.gz
diff --git a/apbs-cmake.patch b/apbs-cmake.patch
index 73a7fd3..c801f77 100644
--- a/apbs-cmake.patch
+++ b/apbs-cmake.patch
@@ -1,13 +1,13 @@
---- CMakeLists.txt_orig	2014-06-18 01:28:14.361212184 -0700
-+++ CMakeLists.txt	2014-06-23 22:11:12.124786178 -0700
+--- CMakeLists.txt_orig	2018-05-20 13:00:17.451341064 -0400
++++ 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 2.8.7)
++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
+@@ -63,10 +64,10 @@
+ set(TOOLS_PATH ${APBS_BUILD}/tools)
  set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
  
 -set(LIBRARY_INSTALL_PATH lib)
@@ -18,40 +18,70 @@
 -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)
+@@ -78,7 +79,7 @@
+   DOC "The path to the external git submodules"
+   )
+ 
+-set(SYS_LIBPATHS /usr/lib64)
++#set(SYS_LIBPATHS /usr/lib64)
+ #list(APPEND SYS_LIBPATHS /usr/lib64)
+ 
+ ################################################################################
+@@ -105,9 +106,9 @@
  
  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)
  
- set(APBS_LIBS "")
  
-@@ -854,29 +855,29 @@
+ 
+@@ -259,11 +260,11 @@
+ 
+ if(NOT ENABLE_FETK)
+   # We'll use autotools to build MALOC if FETK is enabled.
+-  set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc)
+-  add_subdirectory(${MALOC_ROOT})
+-  include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys
+-    ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh)
+-  list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
++  #set(MALOC_ROOT ${EXTERNALS_PATH}/fetk/maloc)
++  # add_subdirectory(${MALOC_ROOT})
++  #include_directories(${MALOC_ROOT}/src/base ${MALOC_ROOT}/src/vsys
++  #  ${MALOC_ROOT}/src/vsh ${MALOC_ROOT}/src/psh)
++  #list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
+   list(APPEND APBS_LIBS maloc)
+ endif()
+ 
+@@ -736,12 +737,12 @@
  # 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(
+@@ -753,24 +754,24 @@
+     )
+ endif()
+ 
 -install(
 -    DIRECTORY ${APBS_ROOT}/examples
 -    DESTINATION ${SHARE_INSTALL_PATH}
@@ -71,11 +101,6 @@
 -    PATTERN "CMakeLists.txt" EXCLUDE
 -)
 +#install(
-+#    DIRECTORY ${APBS_ROOT}/doc
-+#    DESTINATION ${SHARE_INSTALL_PATH}
-+#)
-+
-+#install(
 +#    DIRECTORY ${APBS_ROOT}/examples
 +#    DESTINATION ${SHARE_INSTALL_PATH}
 +#)
@@ -94,25 +119,26 @@
 +#    PATTERN "CMakeLists.txt" EXCLUDE
 +#)
  
- 
- 
---- 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 @@
+ if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
+     install(
+--- src/CMakeLists.txt_orig	2018-05-20 13:00:20.518351049 -0400
++++ src/CMakeLists.txt	2018-05-20 13:00:47.917440250 -0400
+@@ -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 @@
+@@ -47,6 +47,11 @@
  add_subdirectory(generic)
  add_subdirectory(pmgc)
  add_subdirectory(mg)
@@ -121,27 +147,38 @@
 +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)
+@@ -57,7 +62,7 @@
+ 
+ message(STATUS ${EXTERNAL_HEADERS})
  
 -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(***************************)
+ message(STATUS " ")
+ message(STATUS "APBS Libraries: ${APBS_LIBS}")
+@@ -66,7 +71,8 @@
+ message(***************************)
+ 
+ #add_dependencies(apbs ${BEM_LIB})
+-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 @@
-     )
+@@ -81,6 +87,6 @@
+ 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})
+--- tools/manip/CMakeLists.txt_orig	2018-05-20 13:00:31.831387880 -0400
++++ tools/manip/CMakeLists.txt	2018-05-20 13:07:07.742714938 -0400
 @@ -1,9 +1,10 @@
  message(STATUS "Building manip")
  
@@ -153,9 +190,9 @@
 +#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 +205,8 @@
 +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
+--- tools/mesh/CMakeLists.txt_orig	2018-05-20 13:00:26.966372042 -0400
++++ tools/mesh/CMakeLists.txt	2018-05-20 13:00:47.917440250 -0400
 @@ -1,9 +1,10 @@
  message(STATUS "Building mesh")
  
@@ -181,9 +218,9 @@
 +#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}")
  
diff --git a/apbs.spec b/apbs.spec
index bdc7ef6..1b3600d 100644
--- a/apbs.spec
+++ b/apbs.spec
@@ -2,20 +2,22 @@
 
 Name: apbs
 Summary: Adaptive Poisson Boltzmann Solver
-Version: 1.4
-Release: 8%{?dist}
+Version: 1.5
+Release: 1%{?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
+Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/apbs-%{version}.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: tex(latex)
 BuildRequires: zlib-devel
 
 %description
@@ -62,20 +64,23 @@ development using the adaptive poisson boltzmann (APBS) solver
 library.
 
 %prep
-%setup -q -n %{name}
+%setup -q -n %{name}-pdb2pqr-apbs-%{version}
+cd apbs
 %patch0 -p0
 
 %build
-cd build
-%cmake -D BUILD_DOC:BOOL=ON ..
+cd apbs
+# %cmake -D BUILD_DOC:BOOL=ON .
+%cmake -D BUILD_DOC:BOOL=OFF .
 make %{?_smp_mflags}
+cd doc/programmer
+doxygen
 
 %install
 rm -rf %{buildroot}
 
-cd build
+cd apbs
 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
@@ -88,7 +93,7 @@ done
 
 %files
 %defattr(-,root,root,-)
-%doc doc/license/LICENSE.txt README ChangeLog
+%doc apbs/doc/license/LICENSE.txt apbs/doc/README apbs/doc/ChangeLog.md
 %{_bindir}/apbs
 %{_libdir}/libapbs*.so.*
 
@@ -120,9 +125,12 @@ done
 
 %files doc
 %defattr(-,root,root,-)
-%doc doc/programmer/html
+%doc apbs/doc/programmer/html
 
 %changelog
+* 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
 
diff --git a/sources b/sources
index f659863..5010b5a 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-e0281bd44ffecb651e40687cdaa26361  APBS-1.4-source.tar.gz
+SHA512 (apbs-1.5.tar.gz) = 4a117054653a738082f9a25a35c5a0605a1f225e682ff57ed4393689aefe1beffe4fe2364c164d07eb524a26add002b50e29eb297d690494448dac1cef72634d