Merge commit '96580978fd046d82b2545fdac8b72ea52bd4956c'

moose-core/.travis.yml

@@ -20,8 +20,9 @@ env:
     - CTEST_MODEL=Nightly
 cache: apt
 
-matrix:
-    allow_failures:
+#matrix:
+#    allow_failures:
+#        - clang
 
 before_script:
     - sudo apt-get install -qq libxml2-dev libbz2-dev
@@ -31,29 +32,31 @@ before_script:
     - sudo apt-get install -qq  python3-numpy python3-matplotlib python3-dev
     - sudo apt-get install -qq libboost-all-dev
     - sudo apt-get install -qq libgsl0-dev
-
-before_install:
-    - sbmlurl="http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/Linux/64-bit/libSBML-5.9.0-Linux-x64.deb"
-    - wget "$sbmlurl" -O libsbml.deb && sudo dpkg -i libsbml.deb 
-    - sudo apt-get install -f
+    - sudo apt-get install -qq python-pip python3-pip
+    - sudo apt-get install -qq libgraphviz-dev
+    - sudo pip install python-libsbml
+    - sudo pip3 install python-libsbml
+    - sudo pip3 install pygraphviz
 
 install:
     - echo "nothing to do here"
 
 script:
-    - sudo ldconfig /usr/lib64
     - # First test is normal make scripts. (outdated).
     - make 
-    - # Now test the cmake with gsl
+    - ## CMAKE based flow
     - mkdir -p _GSL_BUILD && cd _GSL_BUILD && cmake -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python ..
     - make && ctest --output-on-failure
-    - cd .. # Build with python3.
-    - mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && cmake -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 ..
-    - make && ctest --output-on-failure
     - cd .. # Now with boost.
     - mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python ..
     - make && ctest --output-on-failure
-    - cd .. # Now with boost and python3.
+    - cd .. 
+    - echo "Python3 support. Removed python2-networkx and install python3"
+    - sudo apt-get remove -qq python-networkx
+    - sudo apt-get install -qq python3-networkx
+    - mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && cmake -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 ..
+    - make && ctest --output-on-failure
+    - cd .. # Now with BOOST and python3
     - mkdir -p _BOOST_BUILD2 && cd _BOOST_BUILD2 && cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 ..
     - make && ctest --output-on-failure
     - cd ..

moose-core/CMakeLists.txt

@@ -83,19 +83,11 @@ option(WITH_MPI  "Enable Openmpi support" OFF)
 option(WITH_BOOST "Use boost library instead of GSL" OFF)
 option(WITH_GSL  "Use gsl-library. Alternative is WITH_BOOST" ON)
 
-# If SBML is available, it will automaticall enable the support. If ON, then
-# libSBML must be present.
-option(WITH_SBML  "Enable SBML support. Automatically detected." OFF)
-
 # If GSL_STATIC_HOME is set, we use it to search for static gsl libs.
 option(GSL_STATIC_HOME 
     "Path prefix where static gsl library can be found e.g. /opt/sw/gsl116 " 
     OFF
     )
-option(SBML_STATIC_HOME 
-    "Path prefix where static sbml library can be found e.g. /opt/sbml/"
-    OFF
-    )
 option(HDF5_STATIC_HOME
     "Path prefix where static hdf5 library can be found e.g /opt/sw/hdf5 "
     OFF
@@ -165,57 +157,6 @@ if(WITH_BOOST)
     set(WITH_GSL OFF)
 endif(WITH_BOOST)
 
-# If this variable is used while packaging; we build this project using another
-# cmake script and pass the location of SBML static library using this variable.
-# Otherwise, this is useless. FIXME: This is not a clean solution.
-if(SBML_STATIC_HOME)
-    include_directories(${SBML_STATIC_HOME}/include)
-    find_library(LIBSBML_LIBRARIES
-        NAMES libsbml-static.a libsbml.a
-        PATHS "${SBML_STATIC_HOME}/lib" "${SBML_STATIC_HOME}/lib64"
-        NO_DEFAULT_PATH
-        )
-    message(STATUS "- Using static version of LIBSBML_LIBRARIES: ${LIBSBML_LIBRARIES}")
-    if(LIBSBML_LIBRARIES)
-        message(STATUS "- Successfully located SBML static library: ${LIBSBML_LIBRARIES}")
-    ELSE()
-        message(FATAL_ERROR 
-            "Can't find static libsbml libraries at path ${SBML_STATIC_HOME}"
-            )
-    endif()
-    set(LIBSBML_FOUND ON)
-else(SBML_STATIC_HOME)
-    pkg_check_modules(LIBSBML libsbml)
-    if(NOT LIBSBML_FOUND)
-        message(STATUS "pkg-config could not find sbml. Fallback to default")
-        find_package(LIBSBML)
-    endif()
-endif(SBML_STATIC_HOME)
-
-if(LIBSBML_FOUND)
-    message(STATUS "LIBSBML found ${LIBSBML_LIBRARIES}")
-    include_directories(${LIBSBML_INCLUDE_DIRS})
-    pkg_check_modules(LibXML2 libxml-2.0)
-    if (!LibXML2_FOUND)
-        find_package(LibXML2 REQUIRED)
-    endif()
-    include_directories(${LibXML2_INCLUDE_DIRS})
-else()
-    message(
-        "======================================================================\n"
-        "libsbml NOT found. \n\n"
-        "If you want to compile with SBML support, download and install \n"
-        "libsbml-5.9.0 from: \n"
-        "http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/ and\n"
-        "rerun cmake.\n\n"
-        "If you don't want SBML support then continue with `make`.\n\n"
-        "If you install libsbml to non-standard place, let the cmake know by\n"
-        "exporting environment variable SBML_DIR to the location.\n"
-        "=====================================================================\n"
-        )
-    SET(WITH_SBML OFF)
-endif()
-
 include_directories(msg basecode)
 
 set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS  "MOOSE_LIB")
@@ -366,7 +307,6 @@ add_subdirectory(biophysics)
 add_subdirectory(builtins)
 add_subdirectory(utility)
 add_subdirectory(mesh)
-add_subdirectory(sbml)
 add_subdirectory(mpi)
 add_subdirectory(signeur)
 add_subdirectory(ksolve)
@@ -400,13 +340,6 @@ elseif(HDF5_FOUND)
     list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIBRARIES})
 endif()
 
-LIST(APPEND STATIC_LIBRARIES moose_sbml)
-if(SBML_STATIC_HOME)
-    list(APPEND STATIC_LIBRARIES ${LIBSBML_LIBRARIES})
-elseif(LIBSBML_FOUND)
-    list(APPEND SYSTEM_SHARED_LIBS ${LIBSBML_LIBRARIES})
-endif()
-
 if(WITH_GSL)
     if(GSL_STATIC_HOME)
         message(STATUS "Using STATIC gsl libraries: ${GSL_LIBRARIES}")

moose-core/CheckCXXCompiler.cmake

@@ -5,6 +5,7 @@ CHECK_CXX_COMPILER_FLAG( "-std=c++11" COMPILER_SUPPORTS_CXX11 )
 CHECK_CXX_COMPILER_FLAG( "-std=c++0x" COMPILER_SUPPORTS_CXX0X )
 CHECK_CXX_COMPILER_FLAG( "-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
 
+
 # Turn warning to error: Not all of the options may be supported on all
 # versions of compilers. be careful here.
 add_definitions(-Wall

moose-core/Makefile

@@ -60,7 +60,7 @@
 
 # Default values for flags. The operator ?= assigns the given value only if the
 # variable is not already defined.
-USE_SBML?=0
+#USE_SBML?=0
 USE_HDF5?=1
 USE_CUDA?=0
 USE_NEUROKIT?=0
@@ -230,16 +230,6 @@ else
 LIBS+= -lm
 endif
 
-#harsha
-# To use SBML, pass USE_SBML=1 in make command line
-ifeq ($(USE_SBML),1)
-LIBS+= -lsbml
-CXXFLAGS+=-DUSE_SBML
-LDFLAGS += -L/usr/lib64 -Wl,--rpath='/usr/lib64'
-SBML_DIR = sbml
-SBML_LIB = sbml/_sbml.o
-endif
-
 #Saeed
 # To use CUDA, pass USE_CUDA=1 in make command line
 ifeq ($(USE_CUDA),1)
@@ -371,7 +361,7 @@ export CXXFLAGS
 export LD
 export LIBS
 export USE_GSL
-export USE_SBML
+#export USE_SBML
 
 all: moose pymoose
 

moose-core/MooseTests.cmake

@@ -79,14 +79,14 @@ set_tests_properties(pymoose-ksolve-test
     PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/python"
     )
 
-# Test basic SBML support.
-ADD_TEST(NAME pymoose-test-basic-sbml-support
-    COMMAND ${TEST_COMMAND}
-    ${PROJECT_SOURCE_DIR}/tests/python/test_sbml_support.py
-    )
-set_tests_properties(pymoose-test-basic-sbml-support 
-    PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/python"
-    )
+## Test basic SBML support.
+#ADD_TEST(NAME pymoose-test-basic-sbml-support
+    #COMMAND ${TEST_COMMAND}
+    #${PROJECT_SOURCE_DIR}/tests/python/test_sbml_support.py
+    #)
+#set_tests_properties(pymoose-test-basic-sbml-support 
+    #PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/python"
+    #)
 
 # Test basic SBML support.
 ADD_TEST(NAME pymoose-test-rng

moose-core/basecode/Makefile

@@ -79,7 +79,7 @@ default: $(TARGET)
 
 $(OBJ)	: $(HEADERS) ../shell/Shell.h
 Element.o:	FuncOrder.h
-testAsync.o:	SparseMatrix.h SetGet.h ../scheduling/Clock.h ../biophysics/IntFire.h ../synapse/SynHandlerBase.h ../synapse/SimpleSynHandler.h ../synapse/Synapse.h ../randnum/RNG.h
+testAsync.o:	SparseMatrix.h SetGet.h ../scheduling/Clock.h ../biophysics/IntFire.h ../synapse/SynEvent.h ../synapse/SynHandlerBase.h ../synapse/SimpleSynHandler.h ../synapse/Synapse.h ../randnum/RNG.h
 SparseMsg.o:	SparseMatrix.h
 SetGet.o:	SetGet.h ../shell/Neutral.h
 HopFunc.o:	HopFunc.h ../mpi/PostMaster.h

moose-core/basecode/main.cpp

@@ -57,6 +57,7 @@ extern void testShell();
 extern void testScheduling();
 extern void testSchedulingProcess();
 extern void testBuiltins();
+extern void testSynapse();
 extern void testBuiltinsProcess();
 
 extern void testMpiScheduling();
@@ -342,6 +343,7 @@ void nonMpiTests( Shell* s )
         MOOSE_TEST("testHsolve", testHSolve());
         //MOOSE_TEST("testGeom", testGeom());
         MOOSE_TEST("testMesh", testMesh());
+        MOOSE_TEST("testSynapse", testSynapse());
         MOOSE_TEST( "testSigneur", testSigNeur());
 #ifdef USE_SMOLDYN
         //MOOSE_TEST(testSmoldyn());

moose-core/basecode/testAsync.cpp

@@ -18,6 +18,7 @@
 #include <queue>
 #include "../biophysics/IntFire.h"
 #include "../synapse/Synapse.h"
+#include "../synapse/SynEvent.h"
 #include "../synapse/SynHandlerBase.h"
 #include "../synapse/SimpleSynHandler.h"
 #include "SparseMatrix.h"

moose-core/biophysics/Leakage.cpp

@@ -88,14 +88,23 @@ Leakage::~Leakage()
 
 void Leakage::vProcess( const Eref & e, ProcPtr p )
 {
+	ChanCommon::vSetGk( e, this->vGetGbar( e ) * this->vGetModulation( e ));
+	updateIk();
     sendProcessMsgs(e, p);
 }
 
 void Leakage::vReinit( const Eref & e, ProcPtr p )
 {
+	ChanCommon::vSetGk( e, this->vGetGbar( e ) * this->vGetModulation( e ));
+	updateIk();
     sendReinitMsgs(e, p);
 }
 
+void Leakage::vSetGbar( const Eref& e, double gbar )
+{
+		ChanCommon::vSetGk( e, gbar * this->vGetModulation( e ) );
+		ChanCommon::vSetGbar( e, gbar );
+}
 
 // 
 // Leakage.cpp ends here

moose-core/biophysics/Leakage.h

@@ -56,6 +56,7 @@ class Leakage: public ChanCommon
     ~Leakage();
     void vProcess( const Eref & e, ProcPtr p );
     void vReinit( const Eref & e, ProcPtr p );
+    void vSetGbar( const Eref & e, double gbar );
 
     static const Cinfo * initCinfo();
 };

moose-core/biophysics/ReadCell.cpp

@@ -823,7 +823,7 @@ bool ReadCell::addSpikeGen(
 		shell_->doAddMsg(
 			"Single",
 			compt,
-			"VmSrc",
+			"VmOut",
 			chan,
 			"Vm"
 		);

moose-core/biophysics/SynChan.cpp

@@ -199,10 +199,16 @@ void SynChan::normalizeGbar()
 /// Update alpha function terms for synaptic channel.
 double SynChan::calcGk()
 {
+		/*
 	X_ = getModulation() * activation_ * xconst1_ + X_ * xconst2_;
 	Y_ = X_ * yconst1_ + Y_ * yconst2_;
 	activation_ = 0.0;
 	return Y_ * norm_;
+	*/
+	X_ = activation_ * xconst1_ + X_ * xconst2_;
+	Y_ = X_ * yconst1_ + Y_ * yconst2_;
+	activation_ = 0.0;
+	return Y_ * norm_ * getModulation();
 }
 
 void SynChan::vProcess( const Eref& e, ProcPtr info )

moose-core/external/muparser/include/muParser.h

@@ -101,6 +101,7 @@ namespace mu
     static value_type  Rint(value_type);
     static value_type  Sign(value_type);
     static value_type  Fmod(value_type, value_type);
+    static value_type  Quot(value_type, value_type);
 
     // Random between a and b, with fixed seed.
     static value_type  Rand2(value_type, value_type, value_type); 

moose-core/external/muparser/src/muParser.cpp

@@ -110,6 +110,7 @@ namespace mu
   value_type Parser::Exp(value_type v)  { return MathImpl<value_type>::Exp(v);  }
   value_type Parser::Abs(value_type v)  { return MathImpl<value_type>::Abs(v);  }
   value_type Parser::Fmod(value_type v1, value_type v2) { return fmod(v1, v2); }
+  value_type Parser::Quot(value_type v1, value_type v2) { return (int)(v1 / v2); }
 
   // If no seed is given, 
   value_type Parser::Rand( value_type seed ) 
@@ -336,6 +337,7 @@ namespace mu
       DefineFun(_T("avg"), Avg);
       DefineFun(_T("min"), Min);
       DefineFun(_T("max"), Max);
+      DefineFun(_T("quot"), Quot);
     }
   }
 

moose-core/external/muparser/src/muParserTokenReader.cpp

@@ -154,8 +154,10 @@ namespace mu
 #else
     ParserTokenReader* ptr = new ParserTokenReader(*this);
     ptr->SetParent( a_pParent );
-    delete ptr;
-    return NULL;
+	return ptr;
+	// Upi Bhalla 13 June 2016: I think the original two lines below are wrong
+    // delete ptr;
+    // return NULL;
 #endif
 
   }