Squashed 'moose-core/' changes from 1318029..a15a538

a15a538 Merge pull request #131 from dilawar/master
1800283 Merge branch 'master' of github.com:dilawar/moose-core
2ad812f Rdesigeur by sarthak,
8e87707 Fixed the streamer test.
e62ec09 Merge remote-tracking branch 'bhallalab/master'
002edb6 Fix to BhallaLab/moose-core#130.
d7ebbe7 No need to have header name in inverted commas.
414a8d9 stimulustable is check and some more correction
343a08a First version of model merging pools and reaction are done
943f96f  clean up in notes field
f2b71f5 Merge branch 'master' of http://github.com/BhallaLab/moose-core
c742934 kkitUtil: check to see if the color goes beyond genesis color Sequence, _main.py: eliminated enzyme cplx pool to genesis under compartment
9aca1c1 Merge pull request #128 from dilawar/master
322093e Streamer uses name of the table whenever possible.
5be9eb4 Added getName, setName to table. If these are set, use them in Streamer class to write the header of csv file.
f9178d2 Merge branch 'master' of github.com:BhallaLab/moose-core
3d420b0 species concentration/amount is calculated depending on the hasOnlySubstanceUnit flag
9188681 Merge branch 'master' of github.com:BhallaLab/moose-core
cf3d4f8 Merge branch 'master' of github.com:dilawar/moose-core
4d98756 Write path without [0] in streamer numpy table instead of table name.
9b143e4 reaction and enzyme are added with the ratelaw
b2fbc15 Merge branch 'master' of http://github.com/BhallaLab/moose-core
0a765fb Rules are added
07a68b9 If -Wno-unused-but-set-variable is supported by compiler, enable it.
d98241c Merge branch 'master' of github.com:BhallaLab/moose-core
d22bfea Moved Doc from here to BhallaLab/moose . In docs folder.
9f18f0a Merge pull request #125 from dilawar/master
a942a4c Fixed the failed build on travis https://travis-ci.org/BhallaLab/moose-core/jobs/134133078
3d6a8cc Added support to float and double to numpy format. Fixed some documentation about Streamer, correct dt is docstring. More assert statements in streamer test script.
aada8c4 Merge branch 'master' of github.com:BhallaLab/moose-core
303ad71 Changes for gcc4.4. on nargis.
1af4a69 Temporary change before switching to another branch.
0018c55 notes are written for species
895766a species added
a7e9509 paremeter and compartment info is read back to moose
2b9076e  update with more details
170739f Put some more utility inside namespace moose. When writing numpy format, do not write whole path in header. Just name would do.
f01727c Merge remote-tracking branch 'bhallalab/master'
7e95a6d A fix to failing unit-tests. When user writes /compt/a/b, inside MOOSE it is represented as /compt[0]/a[0]/b[0] which could be annoying for Streamer user. Just remove [0]. For other [n], don't do anything.
21fe695 Bringing back some changed undone by bad merge strategy. This should now pass on travis.
ca8d55b Merge branch 'master' of https://github.com/BhallaLab/moose-core
c165976 Fixes issue dilawar/pymoose-community#3  (#123)
c17df70 clean up in filename while writing into SBML
db701fc Enzyme's are written
320b0c3 Function and reaction are written
a8bfc7c compartment and species are written
008e25e moose Annotation like runtime,dts and plots are written
3ba5e33 units are written
bcfa3c7 Merge branch 'master' of http://github.com/BhallaLab/moose-core
d3b3789 firstphase of write file
4418691 For cmake, enable the c++11 support on compiler which supports it. This should fix ">>" to "> >" error in template parameters in boost code which is only supported in cmake build system.
dc9d0c3 Merge branch 'master' of http://github.com/BhallaLab/moose-core
156e762 python readSBML file
2786757 Fixed #124. Not using gsl_rng in global rng. It is not working as expected in class RNG. Using Subha's mtrand() when boost or c++11 is not available.
eecc171 Adding a small print statement about why assert failed in rdesigneur.
6454673 Merge branch 'master' of github.com:BhallaLab/moose-core
270f1d6 Fixed #112. Not using gsl_rng in global rng. It is not working as expected in class RNG. Using Subha's mtrand() when boost or c++11 is not available.
738d9dc Fixed issue #124.  Adding the issue #124 file to repo for reference. Can't reproduce the error with latest commit (this and previous one).
cc85cfb Update README.md
af178bf This fixes the missing time column in streamer. dilawar/pymoose-community#3.
9faf02e Don't rewrite the table path before writing them to csv in header. dilawar/pymoose-community#3.
806f6a1 Checks if not of tables added are more than 0 or not. If zero, then disable the streamer. Notify the user. Issue dilawar/pymoose-community#3
0a93eaa Importing <cstdio> so that it passes with legacy makefiles as well.
4dc2a6c Merge branch 'master' of https://github.com/BhallaLab/moose-core
56fdc36 Fixes to issue #116  (#120)
357b1b5 Fixed the test script. Method rk4 is not good enough when using boost. Use rk5a.
8057a8f Generate h5 name using tmpnam. If tests are run by two different users on the same system, there won't be any issue with permissions. However this makes testing bit harder during development.
b01caf4 Fixes to gcc-5.x on Ubuntu-16.04.
fc98bfc Adding random library to link flags.
ceea4f0 Use RNG object rather than pointer. Can't figure out why pointer did not work well.
ea5529d FIxed -std=c++11 error.
014175d Fixed issue #116. Using real_distribution instead of int_distribution. Let the library take care of scaling to between 0 and 1.
ab91625 Merge branch 'master' of github.com:BhallaLab/moose-core
e23c827 Some temporary changes before merging. I forgot what there are. Probably RNG initialization is changed.
cf73c1f Update of python setup file. (#118)
51bcf63 Disabled part of code which checks for extension . On some platform it reutrns x86_64.so etc, which probably we don't want. In any case, if build fails on open build service, we can bring it back #78.
fb558d8 Modifying SBML_LIBRARY related macros. Since libsbml is now distributed from mosoe repo as well.
487587b test scripts points to directory commited by @Subha #issue #94.
e47a492 Update INSTALL.md
13afeaf Update README.md
8b33ae5 Merge branch 'master' of github.com:BhallaLab/moose-core
1268296 Merge branch 'master' of github.com:BhallaLab/moose-core
808ae94 Update INSTALL.md
6316820 Update INSTALL.md
2522f47 Merge branch 'master' of github.com:dilawar/moose-core
3f13efd Temp commit.
347e5b0 Update INSTALL.md
d14e4e8 moved to appropriate doc folder.
5a48285 CheckMOOSECompiler -> CheckCXXCompiler.
5ecd06e Updated INSTALL.md file.
0c42d28 Merge remote-tracking branch 'bhallalab/master'
87c193d Deleted cymoose from master branch.
e77361c Fixed moose building after moving _moose target to subdirectory.
af97ec3 Cymoose remains only in my personal clone branch cymoose. Removing it from master branch.
b3542f6 Cleaned up Cmakefile.
7fec36b Moved pymoose target to its own directory.
7575c55 Update test_ksolve.py
904e32a Added missing cmake file.
1998e27 Using ptr instead of object of RNG.
1ee1427 Added ksolve test.
fbf9d90 Test script for ksolve is modified. Total 40 pools.
2ea5ed1 Separate file to check compiler macro.
c7d3e15 Removed the copy constrcutor from RNG class.
1acec97 GssaVoxelPools gets its won random number generator. Had to remove constantness of a function to be able to use uniform( ) or rng call.
08fa1ed test display is changed a bit. Removed some hanging c++11 auto .
c6bc8c3 Printing tests name during tests.
4116cc5 More verbose output when tests are runnug. Added a macro which runs test.
d1c77ce Replaced simple assert( doubleEq(a, b) ) with ASSERT_DOUBLE_EQ( "", a, b );

git-subtree-dir: moose-core
git-subtree-split: a15a538e22f0cd62de95532c2932156055d58673

Author: Dilawar Singh

CMakeLists.txt

@@ -72,7 +72,6 @@ endif()
 
 ################################ CMAKE OPTIONS ##################################
 
-option(WITH_DOC "Build documentation using python-sphinx and doxygen" OFF)
 option(VERBOSITY "Set MOOSE verbosity level (deprecated)" 0)
 ## Unit testing and debug mode.
 option(DEBUG "Build with debug support" OFF)
@@ -201,10 +200,6 @@ if(LIBSBML_FOUND)
         find_package(LibXML2 REQUIRED)
     endif()
     include_directories(${LibXML2_INCLUDE_DIRS})
-    if(${LIBSBML_LIBRARY_DIRS})
-        target_link_libraries(libmoose PROPERTIES LINK_FLAGS "-L${LIBSBML_LIBRARY_DIRS}")
-    endif()
-
 else()
     message(
         "======================================================================\n"
@@ -267,23 +262,17 @@ if(WITH_GSL)
     # top level.
     include_directories( ${GSL_INCLUDE_DIRS} )
 elseif(WITH_BOOST)
-    find_package(Boost 1.44 COMPONENTS filesystem REQUIRED)
+    find_package(Boost 1.44 COMPONENTS filesystem random REQUIRED)
     find_package( LAPACK REQUIRED )
     add_definitions( -DUSE_BOOST -UUSE_GSL )
     include_directories( ${Boost_INCLUDE_DIRS} )
-    #    check_include_file_cxx(
-    #        ${Boost_INCLUDE_DIRS}/boost/random/random_device.hpp
-    #        BOOST_RANDOM_DEVICE_EXISTS
-    #        )
-    #    if(BOOST_RANDOM_DEVICE_EXISTS)
-    #        add_definitions(-DBOOST_RANDOM_DEVICE_EXISTS)
-    #    endif(BOOST_RANDOM_DEVICE_EXISTS)
-    #    check_include_file_cxx(
-    #        ${Boost_INCLUDE_DIRS}/boost/filesystem.hpp BOOST_FILESYSTEM_EXISTS
-    #        )
-    #    if(BOOST_FILESYSTEM_EXISTS)
-    #        add_definitions( -DBOOST_FILESYSTEM_EXISTS )
-    #    endif(BOOST_FILESYSTEM_EXISTS)
+    check_include_file_cxx(
+        ${Boost_INCLUDE_DIRS}/boost/random/random_device.hpp
+        BOOST_RANDOM_DEVICE_EXISTS
+        )
+    if(BOOST_RANDOM_DEVICE_EXISTS)
+        add_definitions(-DBOOST_RANDOM_DEVICE_EXISTS)
+    endif(BOOST_RANDOM_DEVICE_EXISTS)
 endif()
 
 ## Setup hdf5
@@ -513,42 +502,14 @@ if(CMAKE_VERSION VERSION_LESS "2.8.0")
     target_link_libraries(moose.bin PUBLIC moose)
 ELSE()
     target_link_libraries(moose.bin LINK_PUBLIC moose)
-    if(LIBSBML_FOUND)
-        target_link_libraries(moose.bin LINK_PUBLIC ${LIBSBML_LIBRARIES})
-    endif(LIBSBML_FOUND)
 ENDIF()
 
-if(WITH_DOC)
-    FIND_PACKAGE(Doxygen REQUIRED)
-    add_custom_command(TARGET libmoose POST_BUILD
-        COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.full
-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-        COMMENT "Building developer documentation"
-        VERBATIM
-        )
-endif(WITH_DOC)
-
 ######################### BUILD PYMOOSE ########################################
 # Root of all python module.
 if(WITH_PYTHON)
     add_subdirectory( pymoose )
 endif(WITH_PYTHON)
 
-## Moose documentation
-option(WITH_DOC "Build documentation using python-sphinx and doxygen" OFF)
-if(WITH_DOC)
-    FIND_PACKAGE(Sphinx REQUIRED)
-    message(STATUS "Build documentation.")
-    set(USER_DOC_OUTPUT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Docs/user/py/_build/html)
-    set(DEVELOPER_DOC_OUTPUT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Docs/developer/html)
-    ADD_CUSTOM_TARGET(docs ALL
-        COMMAND ./docgen
-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-        COMMENT "Generating html doc using sphinx and doxygen"
-        )
-
-endif(WITH_DOC)
-
 ######################### INSTALL ##############################################
 
 install(TARGETS moose.bin
@@ -575,17 +536,6 @@ if(WITH_PYTHON)
 
 endif(WITH_PYTHON)
 
-if(WITH_DOC)
-    message(STATUS "Installing moose doc")
-    install(DIRECTORY ${USER_DOC_OUTPUT_DIR}
-        DESTINATION share/doc/moose
-        )
-
-    install(DIRECTORY ${DEVELOPER_DOC_OUTPUT_DIR}
-        DESTINATION share/doc/moose/developer
-        )
-endif()
-
 # Print message to start build process
 if(${CMAKE_BUILD_TOOL} MATCHES "make")
     message(

CheckCXXCompiler.cmake

@@ -5,6 +5,8 @@ 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
@@ -18,6 +20,13 @@ if(COMPILER_WARNS_STRICT_ALIASING)
     add_definitions( -Wno-strict-aliasing )
 endif(COMPILER_WARNS_STRICT_ALIASING)
 
+# Disable some harmless warnings.
+CHECK_CXX_COMPILER_FLAG( "-Wno-unused-but-set-variable"
+    COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN
+    )
+if(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
+    add_definitions( "-Wno-unused-but-set-variable" )
+endif(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
 
 if(COMPILER_SUPPORTS_CXX11)
     message(STATUS "Your compiler supports c++11 features. Enabling it")