BhallaLab
diff --git a/‎.ci/travis_prepare_osx.sh
+1 b/‎.ci/travis_prepare_osx.sh
+1
diff --git a/‎.clang-format
+49 b/‎.clang-format
+49
diff --git a/‎.gitlab-ci.yml
+7-1 b/‎.gitlab-ci.yml
+7-1
diff --git a/‎CMakeLists.txt
+37-145 b/‎CMakeLists.txt
+37-145
diff --git a/‎CheckCXXCompiler.cmake
+3-4 b/‎CheckCXXCompiler.cmake
+3-4
diff --git a/‎MANIFEST.in
+2 b/‎MANIFEST.in
+2
diff --git a/‎basecode/CMakeLists.txt
+6-1 b/‎basecode/CMakeLists.txt
+6-1
@@ -45,3 +45,4 @@ $PYTHON3 -m pip install matplotlib --user --upgrade
 $PYTHON3 -m pip install pyNeuroML libNeuroML --user
 $PYTHON3 -m pip install scipy --user
 $PYTHON3 -m pip install pylint --user
+$PYTHON3 -m pip install pytest --user
@@ -0,0 +1,49 @@
+---
+AccessModifierOffset: -4
+SortIncludes: false
+ConstructorInitializerIndentWidth: 4
+AlignEscapedNewlinesLeft: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortFunctionsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakTemplateDeclarations: true
+AlwaysBreakBeforeMultilineStrings: true
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BinPackParameters: true
+ColumnLimit:     80
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+DerivePointerBinding: true
+ExperimentalAutoDetectBinPacking: false
+IndentCaseLabels: true
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 60
+PenaltyBreakString: 1000
+PenaltyBreakFirstLessLess: 120
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerBindsToType: true
+SpacesBeforeTrailingComments: 2
+Cpp11BracedListStyle: true
+Standard:        Auto
+IndentWidth:     4
+TabWidth:        4
+UseTab:          Never
+BreakBeforeBraces: Stroustrup
+IndentFunctionDeclarationAfterType: true
+SpacesInParentheses: false
+SpacesInAngles:  false
+SpaceInEmptyParentheses: false
+SpacesInCStyleCastParentheses: false
+SpaceAfterControlStatementKeyword: false
+SpaceBeforeAssignmentOperators: true
+ContinuationIndentWidth: 4
+Standard : C++11
+...
+
@@ -17,6 +17,12 @@ build:
     - python3 -m pip install python-libsbml --user --upgrade
     - python3 -m pip install pyneuroml --user --upgrade
     - python3 -m pip install sympy scipy --user --upgrade
+    - python3 -m pip install pytest --user --upgrade
     - python3 setup.py build test 
     - python3 setup.py install --user
-    - python3 -c "import moose; moose.test()"
+    - python3 -c "import moose.tests; moose.tests.test()"
+
+  except:
+      - pybind11
+      - devel
+
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.2.3 FATAL_ERROR)
 
 # Project to build MOOSE's python module.
 project(PyMOOSE)
@@ -18,11 +18,7 @@ if(NOT PYTHONINTERP_FOUND)
   find_package(PythonInterp 2.7)
 endif()
 
-# Disable rpath on OSX.
-if(APPLE)
-  set(CMAKE_MACOSX_RPATH OFF)
-endif()
-
+set(CMAKE_MACOSX_RPATH OFF)
 
 # NOTE: version should be changed in setup.py file.
 # If moose version is not given, use setup.py file to get the default version.
@@ -55,19 +51,20 @@ if( CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_BINARY_DIR AND NOT MSVC_IDE )
 endif()
 
 ################################ CMAKE OPTIONS ##################################
-option(WITH_NSDF            "Enable NSDF support. Requires hdf5" OFF )
-
 option(DEBUG                "Build with debug support" OFF)
 option(GPROF                "Build for profiling using gprof" OFF)
 option(ENABLE_UNIT_TESTS    "Enable unit tests (DEBUG should also be ON)" OFF)
 option(WITH_MPI             "Enable Openmpi support" OFF)
+
 option(WITH_BOOST           "Enable boost. Prefer boost over stl" OFF)
 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)
 
+option(WITH_NSDF            "Enable NSDF support. Requires hdf5" OFF )
+
+option(WITH_LEGACY_BINDING  "Use legacy python-bindings" OFF)
 
 ############################ BUILD CONFIGURATION #################################
 
@@ -102,10 +99,8 @@ 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)
+# Override default GSL solvers when BOOST is enabled.
+if(WITH_BOOST OR WITH_BOOST_ODE)
     set(WITH_BOOST_ODE ON)
     set(WITH_GSL OFF)
 endif()
@@ -114,19 +109,16 @@ endif()
 
 link_directories(${CMAKE_BINARY_DIR})
 add_library(libmoose SHARED basecode/main.cpp)
+set_target_properties(libmoose PROPERTIES PREFIX "")
 add_executable(moose.bin basecode/main.cpp)
 
 
 ################################### SETUP BUILD ################################
-# default include paths.
-include_directories( ${CMAKE_CURRENT_SOURCE_DIR} )
-set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS  "MOOSE_LIB")
-set_target_properties(libmoose PROPERTIES PREFIX "")
 
-## Variable to collect all static libraries.
+# Variable to collect all static libraries.
 set(STATIC_LIBRARIES "" )
 # Collect all shared libraries here.
-set(SYSTEM_SHARED_LIBS ${LibXML2_LIBRARIES})
+set(SYSTEM_SHARED_LIBS "")
 
 # BOOST ode library performs better than GSL and ideally should be made default.
 # Unfortunately Boost does not have a very good matrix library; it has ublas
@@ -231,7 +223,7 @@ add_subdirectory(device)
 add_subdirectory(kinetics)
 add_subdirectory(synapse)
 add_subdirectory(intfire)
-add_subdirectory(external/libsoda)
+add_subdirectory(external)
 
 # development related.
 add_subdirectory(devel)
@@ -271,7 +263,7 @@ endif( )
 # especially section 'Mac OS X and the RPATH'
 # Switching is OFF since all libraries are statically linked in module.
 if(APPLE)
-    set_target_properties( libmoose PROPERTIES MACOSX_RPATH OFF)
+    set_target_properties(libmoose PROPERTIES MACOSX_RPATH OFF)
 endif(APPLE)
 
 # MAC linker does not understand many of gnu-ld options.
@@ -304,12 +296,16 @@ if( WITH_BOOST )
     target_link_libraries( moose.bin ${Boost_LIBRARIES} )
 endif( WITH_BOOST )
 
-
 ######################### BUILD PYMOOSE ########################################
 
+if(NOT WITH_LEGACY_BINDING)
+    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11)
+    add_subdirectory(pybind11)
+else()
+    message(STATUS "Building legacy python binding.")
+    add_subdirectory(pymoose)
+endif()
 
-# This target is built by pymoose/CMakeLists.txt file.
-add_subdirectory(pymoose)
 
 # always override debian default installation directory. It will be installed in
 # site-packages instead of dist-packages.
@@ -338,9 +334,6 @@ endif()
 install(TARGETS moose.bin DESTINATION bin CONFIGURATIONS Debug)
 install(TARGETS libmoose DESTINATION lib CONFIGURATIONS Debug)
 
-# NOTE: Install macro for _moose (pymoose) has been moved to
-# pymoose/CMakeLists.txt file.
-
 # Print message to start build process
 if(${CMAKE_BUILD_TOOL} MATCHES "make")
     message(
@@ -353,123 +346,8 @@ endif()
 
 
 ############################ CTEST ######################################
-include( CTest )
-set(CTEST_NIGHTLY_START_TIME "05:30:00 UTC")
-set(CTEST_SUBMIT_URL "http://my.cdash.org/submit.php?project=moose")
-
-if(DEBUG OR "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
-    # Run this test in debug mode. In Release mode, this does not do anything.
-    set(MOOSE_BIN_LOCATION $<TARGET_FILE:moose.bin>)
-    message(STATUS "Executable moose.bin will be at ${MOOSE_BIN_LOCATION}" )
-
-    add_test(NAME moose.bin-raw-run COMMAND moose.bin -u -q)
-endif()
-
-# Core tests.
-set(PYMOOSE_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/py_moose)
-file(GLOB PY_TEST_SCRIPTS "${PYMOOSE_TEST_DIRECTORY}/test_*.py" )
-foreach(_test_script ${PY_TEST_SCRIPTS} )
-    get_filename_component(_name_we ${_test_script} NAME_WE)
-    set(_test_name "core_${_name_we}")
-    add_test(NAME ${_test_name}
-        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
-        WORKING_DIRECTORY ${PYMOOSE_TEST_DIRECTORY})
-     set_tests_properties(${_test_name}
-         PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
-        )
-endforeach()
-
-# Tests for supported formats such as neuroml, sbml etc.
-set(SUPPORT_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/support)
-file(GLOB PY_TEST_SCRIPTS "${SUPPORT_TEST_DIRECTORY}/test_*.py" )
-foreach(_test_script ${PY_TEST_SCRIPTS} )
-    get_filename_component(_name_we ${_test_script} NAME_WE)
-    set(_test_name "support_${_name_we}")
-    add_test(NAME ${_test_name}
-        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
-        WORKING_DIRECTORY ${SUPPORT_TEST_DIRECTORY})
-     set_tests_properties(${_test_name}
-         PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
-        )
-endforeach()
-
-# rdesigneur tests. These tests require matplotlib.
-set(RDES_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/py_rdesigneur) 
-file(GLOB RDES_TEST_SCRIPTS "${RDES_TEST_DIRECTORY}/test_*.py" )
-foreach(_test_script ${RDES_TEST_SCRIPTS})
-    get_filename_component(_name_we ${_test_script} NAME_WE)
-    set(_test_name "rdes_${_name_we}")
-    add_test(NAME ${_test_name}
-        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
-        WORKING_DIRECTORY ${RDES_TEST_DIRECTORY}
-        )
-    set_tests_properties(${_test_name} PROPERTIES 
-        ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python;MOOSE_NUM_THREADS=4"
-        )
-endforeach()
-
-# FIXME TESTS. These should not run by default. We need to fix them.
-set(PYMOOSE_FIXME_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/devel/fixme)
-file(GLOB PY_FIXME_TEST_SCRIPTS "${PYMOOSE_FIXME_TEST_DIRECTORY}/*.py" )
-foreach( _test_script ${PY_FIXME_TEST_SCRIPTS} )
-    get_filename_component( _name_we ${_test_script} NAME_WE)
-    set(_test_name "alpha_${_name_we}")
-    add_test( NAME ${_test_name}
-        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
-        CONFIGURATIONS alpha
-	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 ${CMAKE_CURRENT_SOURCE_DIR}/devel/issues)
-file(GLOB PY_ISSUES_SCRIPTS "${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()
-
-################################# COVERAGE ###################################
-
-add_custom_target(coverage)
-set(PYTEST_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests)
-file(GLOB_RECURSE PYTEST_TEST_SCRIPTS ${PYTEST_TEST_DIRECTORY}/test_*.py)
-
-foreach(_test_script ${PYTEST_TEST_SCRIPTS})
-    get_filename_component(_name_we ${_test_script} NAME_WE)
-    set(_test_name "pytest_${_name_we}")
-    # message(STATUS "Adding test ${_test_name}")
-    add_custom_target(${_test_name}
-        # We collect coverage data but do not show report during each test.
-        # We show report at the end of all tests. Set `--cov-report=` 
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest 
-            --cov=moose --cov=rdesigneur --cov-append --cov-report= 
-            ${_test_script}
-        DEPENDS _moose
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMENT "Executing ${_test_script} using pytest"
-        VERBATIM)
-    add_dependencies(coverage  ${_test_name})
-endforeach()
-
-# Generate report at the end.
-add_custom_command(TARGET coverage POST_BUILD
-    COMMAND ${PYTHON_EXECUTABLE} -m coverage report 
-    COMMAND ${PYTHON_EXECUTABLE} -m coverage html 
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-    COMMENT "Genearting coverage report"
-    VERBATIM)
-
+include(CTest)
+add_subdirectory(tests)
 
 ########################### RELEASE #########################################
 set(PYMOOSE_SDIST_FILE ${CMAKE_BINARY_DIR}/pymoose-${VERSION_MOOSE}.tar.gz)
@@ -519,3 +397,17 @@ foreach(_py_script ${PY_SCRIPTS})
     add_dependencies(pylint ${TGT_NAME} )
 endforeach( )
 
+########################  DOCS ###############################################
+find_package(Doxygen)
+if(DOXYGEN_FOUND)
+    set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/devel/Doxyfile.in)
+    set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
+    configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
+    add_custom_target(doc
+        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMENT "Generating API documentation using Doxygen."
+        VERBATIM)
+else()
+    message(STATUS "Doxygen needs to be installed to generate API docs")
+endif()
@@ -1,5 +1,5 @@
 # Compiler check.
-# Must support c++11
+# Must support c++14
 # If python2 is supported then we can not use c++17. 
 if(COMPILER_IS_TESTED)
     return()
@@ -20,12 +20,11 @@ add_definitions(-Wall
     )
 
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-    # gcc-4.9.0 has regex supports though moose will compile with 4.8.x;
-    # <regex> won't work.
     if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.9")
         message(FATAL_ERROR "Insufficient gcc version. Minimum requried 4.9")
     endif()
     add_definitions( -Wno-unused-local-typedefs )
+    add_definitions( -fmax-errors=5 )
 elseif(("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang") OR ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang"))
     add_definitions( -Wno-unused-local-typedef )
 endif()
@@ -50,7 +49,7 @@ if(COMPILER_SUPPORTS_CXX11)
     endif(APPLE)
 else(COMPILER_SUPPORTS_CXX11)
     message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} is too old. \n"
-      "Please use a compiler which has c++11 support."
+      "Please use a compiler which has full c++11 support."
       )
 endif(COMPILER_SUPPORTS_CXX11)
 
 
@@ -34,3 +34,5 @@ recursive-include signeur *
 recursive-include synapse *
 recursive-include tests *
 recursive-include utility *
+recursive-include pybind11 *
+recursive-include devel *
@@ -1,7 +1,6 @@
 cmake_minimum_required(VERSION 2.8)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
 add_library(basecode
-	consts.cpp
 	Element.cpp
 	DataElement.cpp
 	GlobalDataElement.cpp
@@ -26,3 +25,9 @@ add_library(basecode
 	doubleEq.cpp
 	testAsync.cpp
     )
+
+add_executable(test_globals testGlobals.cpp global.cpp)
+
+enable_testing()
+add_test(NAME cpp_test_globals  COMMAND $<TARGET_FILE:test_globals>)
+