Merge branch 'master' of https://github.com/dilawar/moose-core

Author: Dilawar Singh

.travis.yml

@@ -3,10 +3,10 @@ sudo: required
 
 matrix:
     include:
-        - os : linux
-          dist: xenial
-        - os : osx
-          osx_image: xcode10.1
+    - os: linux
+      dist: xenial
+    - os: osx
+      osx_image: xcode10.2
 
 notifications:
   email:
@@ -26,12 +26,6 @@ before_script:
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
 
-
-before_script:
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
-- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
-
 script:
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi

.travis/travis_build_osx.sh

@@ -26,23 +26,26 @@ set -e
     # Make sure not to pick up python from /opt.
     PATH=/usr/local/bin:/usr/bin:$PATH
 
+    PYTHON3=$(which python3)
+
     # Get pylint
-    python -m pip install pylint --user
-    python -m pip install python-libsbml --user
-    python -m pip install pyneuroml --user
+    $PYTHON3 -m pip install pylint --user
+    $PYTHON3 -m pip install python-libsbml --user
+    $PYTHON3 -m pip install pyneuroml --user
 
     mkdir -p _GSL_BUILD && cd _GSL_BUILD \
         && cmake -DDEBUG=ON \
-        -DPYTHON_EXECUTABLE=`which python` ..
+        -DPYTHON_EXECUTABLE=$PYTHON3 \
+        ..
     make pylint -j3
-    make && ctest --output-on-failure -E ".*socket_streamer.*"
+    make && ctest --output-on-failure 
 
     cd .. # Now with boost.
     mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
         && cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
-        -DPYTHON_EXECUTABLE=`which python` ..
+        -DPYTHON_EXECUTABLE=`which python3` ..
 
-    make && ctest --output-on-failure -E ".*socket_streamer.*"
+    make -j4 && ctest --output-on-failure 
     cd ..
     set +e
 

.travis/travis_prepare_osx.sh

@@ -28,17 +28,20 @@ brew install python
 brew install numpy
 brew install boost
 
+PYTHON3=$(which python3)
+
 #brew outdated python || brew install python
 #brew outdated numpy || brew install homebrew/python/numpy
 brew unlink numpy && brew link numpy || echo "Failed to link numpy"
 # Numpy caveats
-mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
-echo 'import sys; sys.path.insert(1, "/usr/local/lib/python2.7/site-packages")' >> $HOME/Library/Python/2.7/lib/python/site-packages/homebrew.pth
+#mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
+#echo 'import sys; sys.path.insert(1, "/usr/local/lib/python2.7/site-packages")' >> $HOME/Library/Python/2.7/lib/python/site-packages/homebrew.pth
 
 # To make sure that we do not pick python from /opt etc.
 PATH=/usr/local/bin:/usr/bin:$PATH
 # ensurepip
-python -m ensurepip
-python -m pip install matplotlib --user --upgrade
-python -m pip install pyNeuroML libNeuroML --user
-python -m pip install scipy --user
+$PYTHON3 -m ensurepip
+$PYTHON3 -m pip install matplotlib --user --upgrade
+$PYTHON3 -m pip install pyNeuroML libNeuroML --user
+$PYTHON3 -m pip install scipy --user
+$PYTHON3 -m pip install pylint --user

CMakeLists.txt

@@ -4,7 +4,6 @@ project(pymoose)
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules")
 include(CheckCXXCompiler.cmake)
 include(CheckIncludeFileCXX)
-include(FindPkgConfig)
 
 # getgit revision number
 find_program( GIT_EXEC git )
@@ -78,6 +77,7 @@ option(WITH_BOOST_ODE       "Use boost library ode2 library instead of GSL" OFF)
 option(WITH_GSL             "Use gsl-library. Alternative is WITH_BOOST" ON)
 option(PARALLELIZED_CLOCK   "High level parallelization of moose::Clock (alpha)" OFF )
 option(USE_PRIVATE_RNG      "Stochastic Objects use their private RNG" ON)
+option(WITH_ASAN            "Use AddressSanitizer in DEBUG mode." OFF)
 
 
 ############################ BUILD CONFIGURATION #################################
@@ -87,7 +87,7 @@ add_definitions(-DUSE_GENESIS_PARSER)
 
 if(DEBUG OR "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     message(STATUS "Building for Debug/Unit testing")
-    add_definitions(-DDO_UNIT_TESTS)
+    add_definitions(-DDO_UNIT_TESTS -O)
     set(CMAKE_BUILD_TYPE Debug)
 elseif(ENABLE_UNIT_TESTS)
     MESSAGE(STATUS "Enabled Unit tests")
@@ -109,8 +109,14 @@ if(GPROF AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-pg")
 endif()
 
-find_package(Threads)
-
+if(WITH_ASAN AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
+    message(STATUS "Compiling with ASAN")
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} \
+        -fno-omit-frame-pointer -fsanitize=leak -fsanitize=address")
+    set(CMAKE_LINKER_FLAGS_DEBUG "${CMAKE_LINKER_FLAGS_DEBUG} \
+        -fno-omit-frame-pointer -fsanitize=leak -fsanitize=address")
+    set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address")
+endif()
 
 ################################### TARGETS ####################################
 
@@ -132,8 +138,6 @@ if(WITH_BOOST_ODE)
     set(WITH_GSL OFF)
 endif(WITH_BOOST_ODE)
 
-include_directories(msg basecode)
-
 set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS  "MOOSE_LIB")
 set_target_properties(libmoose PROPERTIES PREFIX "")
 
@@ -143,11 +147,10 @@ set(STATIC_LIBRARIES "" )
 set(SYSTEM_SHARED_LIBS ${LibXML2_LIBRARIES})
 
 # BOOST ode library performs better than GSL and ideally should be made default.
-# Making boost default means that we get rid of gsl. Boost does not have a very
-# good matrix library; it has ublas which is not well maintained and emit a lot
+# Unfortunately Boost does not have a very good matrix library; it has ublas
+# which is not well maintained and emit a lot
 # of warning during compilation. Nonetheless, WITH_BOOST_ODE works fine and
-# produce results quicker than GSL. Both boost ode and ublas are in moose source
-# tree ./external/odeint-v2 and ./external/boost-numeric-bindings
+# produce results quicker than GSL. 
 if(WITH_GSL)
     find_package(GSL 1.16 REQUIRED)
     if(NOT GSL_FOUND)
@@ -172,13 +175,14 @@ if(WITH_GSL)
     # top level.
     include_directories( ${GSL_INCLUDE_DIRS} )
 elseif(WITH_BOOST_ODE)
-    find_package(Boost 1.44 REQUIRED)
-    find_package( LAPACK REQUIRED )
+    find_package(Boost 1.53 REQUIRED)
+    find_package(LAPACK REQUIRED)
 endif()
 
 # if boost ode is being used, don't use GSL.
 if(WITH_BOOST_ODE)
     add_definitions(-DUSE_BOOST_ODE -UUSE_GSL)
+    include_directories(${Boost_INCLUDE_DIRS})
 endif()
 
 # Openmpi
@@ -202,6 +206,7 @@ if(WITH_BOOST_ODE)
     list(APPEND SYSTEM_SHARED_LIBS ${Boost_LIBRARIES})
 endif(WITH_BOOST_ODE)
 
+find_package( Threads )
 list(APPEND SYSTEM_SHARED_LIBS ${CMAKE_THREAD_LIBS_INIT})
 
 # These libraries could be static of dynamic. We need to discrimate between
@@ -265,6 +270,7 @@ list(APPEND MOOSE_LIBRARIES
     msg
     benchmarks
     shell
+    randnum
     scheduling
     moose_mpi
     biophysics
@@ -441,6 +447,7 @@ set(PYMOOSE_TEST_DIRECTORY ${CMAKE_SOURCE_DIR}/tests/python)
 # Collect all python script in tests folder and run them.
 file(GLOB PY_TEST_SCRIPTS "${PYMOOSE_TEST_DIRECTORY}/test_*.py" )
 
+
 # Run python tests.
 foreach( _test_script ${PY_TEST_SCRIPTS} )
     get_filename_component( _test_name ${_test_script} NAME_WE)
@@ -453,6 +460,36 @@ foreach( _test_script ${PY_TEST_SCRIPTS} )
         )
 endforeach( )
 
+# Alpha tests. These should not run by default.
+set(MOOSE_ALPHA_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/alpha)
+file(GLOB PY_ALPHA_TEST_SCRIPTS "${PYMOOSE_ALPHA_TEST_DIRECTORY}/*.py" )
+foreach( _test_script ${PY_ALPHA_TEST_SCRIPTS} )
+    get_filename_component( _test_name ${_test_script} NAME_WE)
+    add_test( NAME ${_test_name}
+        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
+	CONFIGURATIONS Devel
+	WORKING_DIRECTORY ${PYMOOSE_ALPHA_TEST_DIRECTORY}
+        )
+     set_tests_properties( ${_test_name}
+         PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
+        )
+endforeach( )
+
+# Regression and github issues. These should not run by default.
+set(PYMOOSE_ISSUES_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/issues)
+file(GLOB PY_ISSUES_SCRIPTS "${PYMOOSE_ISSUES_DIRECTORY}/*.py" )
+foreach( _test_script ${PY_ISSUES_SCRIPTS} )
+    get_filename_component( _test_name ${_test_script} NAME_WE)
+    add_test( NAME ${_test_name}
+        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
+	CONFIGURATIONS Devel
+	WORKING_DIRECTORY ${PYMOOSE_ISSUES_DIRECTORY}
+        )
+     set_tests_properties( ${_test_name}
+         PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
+        )
+endforeach( )
+
 # add pylint target.
 set(PYSCRIPTS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/python )
 file(GLOB_RECURSE PY_SCRIPTS  "python/*.py")
@@ -476,4 +513,5 @@ foreach( _py_script ${PY_SCRIPTS} )
 endforeach( )
 
 ############################ CPACK ######################################
+# This is not maintained anymore since packaging is done using OpenBuildService 
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake_moose_cpack.cmake)

basecode/FuncOrder.h

@@ -13,28 +13,31 @@
 
 class FuncOrder
 {
-    public:
-            FuncOrder()
-                : func_( 0 ), index_( 0 )
-            {;}
+public:
+    FuncOrder()
+        : func_( 0 ), index_( 0 )
+    {;}
 
-            const OpFunc* func() const {
-                    return func_;
-            }
-            unsigned int index() const {
-                    return index_;
-            }
+    const OpFunc* func() const
+    {
+        return func_;
+    }
+    unsigned int index() const
+    {
+        return index_;
+    }
 
-            void set( const OpFunc* func, unsigned int index ) {
-                func_ = func;
-                   index_ = index;
-            }
+    void set( const OpFunc* func, unsigned int index )
+    {
+        func_ = func;
+        index_ = index;
+    }
 
-            bool operator<( const FuncOrder& other ) const
-            {
-                return func_ < other.func_;
-            }
-    private:
-        const OpFunc* func_;
-        unsigned int index_;
+    bool operator<( const FuncOrder& other ) const
+    {
+        return func_ < other.func_;
+    }
+private:
+    const OpFunc* func_;
+    unsigned int index_;
 };

basecode/global.cpp

@@ -49,7 +49,7 @@ namespace moose {
         { "HSolve", {0.0, 0} }
     };
 
-    moose::RNG<double> rng;
+    moose::RNG rng;
 
     /* Check if path is OK */
     int checkPath( const string& path  )
@@ -104,6 +104,11 @@ namespace moose {
         return moose::rng.uniform( );
     }
 
+    double mtrand( double a, double b )
+    {
+        return (b-a) * mtrand() + a; 
+    }
+
     // MOOSE suffixes [0] to all elements to path. Remove [0] with null
     // character whenever possible. For n > 0, [n] should not be touched. Its
     // the user job to take the pain and write the correct path.

basecode/global.h

@@ -56,7 +56,7 @@ extern unsigned int totalTests;
 namespace moose
 {
 
-    extern moose::RNG<double> rng;
+    extern moose::RNG rng;
 
     extern map<string, valarray<double>> solverProfMap;
 
@@ -114,6 +114,18 @@ namespace moose
      */
     double mtrand( void );
 
+    /* --------------------------------------------------------------------------*/
+    /**
+     * @Synopsis  Overloaded function. Random number between a and b
+     *
+     * @Param a lower limit.
+     * @Param b Upper limit.
+     *
+     * @Returns   
+     */
+    /* ----------------------------------------------------------------------------*/
+    double mtrand( double a, double b );
+
     /**
      * @brief Create a POSIX compatible path from a given string.
      * Remove/replace bad characters.

basecode/header.h

@@ -99,7 +99,6 @@ class Neutral;
 #include "SharedFinfo.h"
 #include "FieldElementFinfo.h"
 #include "FieldElement.h"
-#include "../builtins/Streamer.h"
 #include "../shell/Neutral.h"
 
 

biophysics/Compartment.cpp

@@ -268,7 +268,7 @@ void Compartment::vRandInject( const Eref& e, double prob, double current)
 
 #ifdef DO_UNIT_TESTS
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "../shell/Shell.h"
 //#include "../randnum/randnum.h"