Combined 391+386+337+281

.travis.yml

@@ -32,8 +32,3 @@ before_script:
 script:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.ci/travis_build_osx.sh; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.ci/travis_build_linux.sh; fi
-
-after_success:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then\
-      mkdir _sdist && cd _sdist && cmake .. && make sdist && make upload_test;\
-    fi

CMakeLists.txt

@@ -102,6 +102,14 @@ if(WITH_ASAN AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address")
 endif()
 
+if(WITH_GSL)
+    set(WITH_BOOST OFF)
+    set(WITH_BOOST_ODE OFF)
+elseif(WITH_BOOST)
+    set(WITH_BOOST_ODE ON)
+    set(WITH_GSL OFF)
+endif()
+
 ################################### TARGETS ####################################
 
 link_directories(${CMAKE_BINARY_DIR})
@@ -112,17 +120,6 @@ add_executable(moose.bin basecode/main.cpp)
 ################################### SETUP BUILD ################################
 # default include paths.
 include_directories( ${CMAKE_CURRENT_SOURCE_DIR} )
-
-if(WITH_BOOST)
-    set(WITH_BOOST_ODE ON)
-    set(WITH_GSL       OFF)
-endif(WITH_BOOST)
-
-# If using BOOST ODE2 library to solve ODE system, then don't use GSL.
-if(WITH_BOOST_ODE)
-    set(WITH_GSL OFF)
-endif(WITH_BOOST_ODE)
-
 set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS  "MOOSE_LIB")
 set_target_properties(libmoose PROPERTIES PREFIX "")
 
@@ -235,6 +232,7 @@ add_subdirectory(benchmarks)
 add_subdirectory(kinetics)
 add_subdirectory(synapse)
 add_subdirectory(intfire)
+add_subdirectory(external/libsoda)
 
 ###################################### LINKING #################################
 list(APPEND MOOSE_LIBRARIES
@@ -255,6 +253,7 @@ list(APPEND MOOSE_LIBRARIES
     signeur
     diffusion
     ksolve
+    lsoda
     device
     basecode
     )

basecode/global.cpp

@@ -144,6 +144,22 @@ namespace moose {
         if( p.size() == 0 )
             return true;
 
+#ifdef  USE_BOOST_FILESYSTEM
+        try
+        {
+            boost::filesystem::path pdirs( p );
+            boost::filesystem::create_directories( pdirs );
+            LOG( moose::info, "Created directory " << p );
+            return true;
+        }
+        catch(const boost::filesystem::filesystem_error& e)
+        {
+            LOG( moose::warning, "create_directories(" << p << ") failed with "
+                    << e.code().message()
+               );
+            return false;
+        }
+#else      /* -----  not USE_BOOST_FILESYSTEM  ----- */
         string command( "mkdir -p ");
         command += p;
         int ret = system( command.c_str() );
@@ -163,6 +179,7 @@ namespace moose {
             LOG( moose::warning, p << " is no directory" );
             return false;
         }
+#endif     /* -----  not USE_BOOST_FILESYSTEM  ----- */
         return true;
     }
 

basecode/global.h

@@ -17,7 +17,12 @@
 #include <sstream>
 #include <valarray>
 
-#include "../randnum/RNG.h"                        /* Use inbuilt rng */
+
+#ifdef  USE_BOOST_FILESYSTEM
+#include <boost/filesystem.hpp>
+#endif
+
+#include "randnum/RNG.h"                        /* Use inbuilt rng */
 #include "../utility/print_function.hpp"
 
 using namespace std;

basecode/main.cpp

@@ -35,7 +35,6 @@ int testIndex = 0;
     f; \
     cout << std::right << "  [DONE]" << endl; \
 
-extern void testSync();
 extern void testAsync();
 extern void testSyncArray( unsigned int size, unsigned int method );
 extern void testShell();
@@ -67,9 +66,9 @@ extern void testSigNeurProcess();
 extern unsigned int initMsgManagers();
 extern void destroyMsgManagers();
 // void regressionTests();
-#endif
-extern void speedTestMultiNodeIntFireNetwork(
-    unsigned int size, unsigned int runsteps );
+#endif   // DO_UNIT_TESTS
+
+extern void speedTestMultiNodeIntFireNetwork(unsigned int size, unsigned int runsteps);
 
 #ifdef USE_SMOLDYN
 extern void testSmoldyn();

biophysics/CMakeLists.txt

@@ -2,7 +2,11 @@ cmake_minimum_required(VERSION 2.8)
 include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 
 if(WITH_GSL)
+    find_package(GSL 1.16)
     include_directories(${GSL_INCLUDE_DIRS})
+elseif(WITH_BOOST_ODE)
+    find_package(Boost)
+    include_directories(${Boost_INCLUDE_DIRS})
 endif(WITH_GSL)
 
 set(BIOPHYSICS_SRCS
@@ -32,7 +36,6 @@ set(BIOPHYSICS_SRCS
     ReadSwc.cpp
     SynChan.cpp
     NMDAChan.cpp
-    testBiophysics.cpp
     IzhikevichNrn.cpp
     DifShellBase.cpp
     DifShell.cpp
@@ -48,10 +51,9 @@ set(BIOPHYSICS_SRCS
     MarkovSolver.cpp
     VClamp.cpp
     Spine.cpp
+    MarkovOdeSolver.cpp
+    testBiophysics.cpp
     )
 
-if(WITH_GSL)
-    list(APPEND BIOPHYSICS_SRCS MarkovGslSolver.cpp)
-endif(WITH_GSL)
+add_library(biophysics ${BIOPHYSICS_SRCS})
 
-add_library( biophysics ${BIOPHYSICS_SRCS} )