diff --git a/README.md b/README.md
index 0f62079b354e65626eb906c822c551f75485334f..319f19e0393cbaca858aec3bd1ff65ff9a395088 100644
--- a/README.md
+++ b/README.md
@@ -76,4 +76,4 @@ MOOSE can also read .swc files from NeuroMorpho.org.
# Documentation
-Complete MOOSE Documentation can be found at - http://moose.ncbs.res.in/content/view/5/6/
+Complete MOOSE Documentation can be found at - https://moose.ncbs.res.in/?q=documentation
diff --git a/docs/introduction/install/index.rst b/docs/introduction/install/index.rst
index 430ed780435930d8f739a55f4423a333355313fe..b53e792779a74b1f71b337ca51613e01d7a90a10 100644
--- a/docs/introduction/install/index.rst
+++ b/docs/introduction/install/index.rst
@@ -78,21 +78,9 @@ Next, you need to install required dependencies.
- cmake (version 2.8 or higher)
- gsl-1.16 or higher `download <ftp://ftp.gnu.org/gnu/gsl/>`_.
- libhdf5 development package.
-- libsbml (5.9.0, optional). `download <https://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/>`_
- python development package
- numpy
-.. note::
- `libsml` needs to be compiled with ``zlib`` and ``lxml`` (requires ``libxml2-dev`` or ``libxml2-devel```
- package) support without which, you might face link time errors. Following instructions are known to
- work::
- $ wget http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/libSBML-5.9.0-core-src.tar.gz
- $ tar -xzvf libSBML-5.9.0-core-src.tar.gz
- $ cd libsbml-5.9.0
- $ ./configure --with-zlib --with-libxml
- $ make
- $ sudo make install
-
Most of the dependencies can be installed using package manager.
On ``Debian/Ubuntu``
@@ -175,7 +163,7 @@ Now you can fire up the GUI
.. note::
If you have installed ``moose`` using the package, then GUI is launched by
running following commnad::
- $ moosegui
+ $ moose
Building moogli
---------------
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index d9233825d0eeb7e1251db30af60756e003c7a624..1948958bec32f8bb981ed91d9c751e45252ba473 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -159,6 +159,8 @@ set_target_properties(libmoose PROPERTIES PREFIX "")
## Variable to collect all static libraries.
set(STATIC_LIBRARIES "" )
+# Collect all shared libraries here.
+set(SYSTEM_SHARED_LIBS ${LibXML2_LIBRARIES})
if(WITH_GSL)
find_package(GSL 1.16)
@@ -218,12 +220,16 @@ endif(NOT HDF5_FOUND)
if(HDF5_FOUND)
add_definitions( -DUSE_HDF5 )
include_directories( ${HDF5_INCLUDE_DIRS} )
- foreach(HDF5_LIB ${HDF5_LIBRARIES})
- get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
- if( ${HDF5_LIB_EXT} STREQUAL ".a" )
- list(APPEND STATIC_LIBRARIES ${HDF5_LIB} )
- else( )
- list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIB} )
+ foreach(HDF5_LIB ${HDF5_LIBRARIES} )
+ if(HDF5_LIB)
+ get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
+ if(HDF5_LIB_EXT)
+ if(${HDF5_LIB_EXT} STREQUAL ".a")
+ list(APPEND STATIC_LIBRARIES ${HDF5_LIB} )
+ else( )
+ list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIB} )
+ endif( )
+ endif()
endif( )
endforeach( )
endif( HDF5_FOUND )
@@ -258,27 +264,26 @@ if(WITH_MPI)
endif()
endif(WITH_MPI)
-# These are always shared libraries.
-set(SYSTEM_SHARED_LIBS ${LibXML2_LIBRARIES})
if(WITH_BOOST)
list(APPEND SYSTEM_SHARED_LIBS ${LAPACK_LIBRARIES})
list(APPEND SYSTEM_SHARED_LIBS ${Boost_LIBRARIES})
endif(WITH_BOOST)
-# These libraries could be static of dynamic.
-# When building packages on OBS or launchpad, we build static library of a
-# dependencies if a correct version is not found.
-# Here we make sure that the correct static version is linked; if a correct
-# shared version is found then link the shared version in SYSTEM_SHARED_LIBS.
+# These libraries could be static of dynamic. We need to discrimate between
+# these two types because of --whole-archive option. See
+# BhallaLab/moose-core#66,
if(WITH_GSL)
message(STATUS "Using STATIC gsl libraries: ${GSL_LIBRARIES}")
-
foreach(GSL_LIB ${GSL_LIBRARIES} )
- get_filename_component( GSL_LIB_EXT ${GSL_LIB} EXT )
- if( GSL_LIB_EXT STREQUAL ".a" )
- list(APPEND STATIC_LIBRARIES ${GSL_LIB})
- else()
- list(APPEND SYSTEM_SHARED_LIBS ${GSL_LIB})
+ if(GSL_LIB)
+ get_filename_component( GSL_LIB_EXT ${GSL_LIB} EXT )
+ if(GSL_LIB_EXT)
+ if(GSL_LIB_EXT STREQUAL ".a" )
+ list(APPEND STATIC_LIBRARIES ${GSL_LIB})
+ else()
+ list(APPEND SYSTEM_SHARED_LIBS ${GSL_LIB})
+ endif( )
+ endif( )
endif( )
endforeach( )
endif()
@@ -343,6 +348,11 @@ list(APPEND MOOSE_LIBRARIES
basecode
)
+# Make sure to remove duplicates.
+list(REMOVE_DUPLICATES STATIC_LIBRARIES)
+if(SYSTEM_SHARED_LIBS)
+ list(REMOVE_DUPLICATES SYSTEM_SHARED_LIBS)
+endif( )
# MAC linker does not understand many of gnu-ld options.
message( STATUS "Shared libs: ${SYSTEM_SHARED_LIBS}")
diff --git a/moose-core/VERSION b/moose-core/VERSION
index 4225763f8cf3bc6309bd0d3fed4f68dde69ac351..50e47c89cafc3ec95774b3110a3dba45256d0b24 100644
--- a/moose-core/VERSION
+++ b/moose-core/VERSION
@@ -1 +1 @@
-3.1.1-40-g8fe5068
\ No newline at end of file
+3.1.1
\ No newline at end of file
diff --git a/moose-core/cmake_modules/FindGSL.cmake b/moose-core/cmake_modules/FindGSL.cmake
index b33139af67aafb535cbcedd1b24452e85ea6be73..93c2686f78e6fbbdde540e86241d0995934c8813 100644
--- a/moose-core/cmake_modules/FindGSL.cmake
+++ b/moose-core/cmake_modules/FindGSL.cmake
@@ -1,146 +1,107 @@
-##
-## Try to find gnu scientific library GSL
-## (see http://www.gnu.org/software/gsl/)
-## Once run this will define:
-##
-## GSL_FOUND = system has GSL lib
-##
-## GSL_LIBRARIES = full path to the libraries
-## on Unix/Linux with additional linker flags from "gsl-config --libs"
-##
-## CMAKE_GSL_CXX_FLAGS = Unix compiler flags for GSL, essentially "`gsl-config --cxxflags`"
-##
-## GSL_INCLUDE_DIRS = where to find headers
-##
-## GSL_LINK_DIRECTORIES = link directories, useful for rpath on Unix
-## GSL_EXE_LINKER_FLAGS = rpath on Unix
-##
-## Felix Woelk 07/2004
-## minor corrections Jan Woetzel
-##
-## www.mip.informatik.uni-kiel.de
-## --------------------------------
-##
-
-message( STATUS "GSL_ROOT_DIR value $ENV{GSL_ROOT_DIR}")
+# Try to find gnu scientific library GSL
+# (see http://www.gnu.org/software/gsl/)
+# Once run this will define:
+#
+# GSL_FOUND = system has GSL lib
+#
+# GSL_VERSION = gsl version
+#
+# GSL_LIBRARIES = name of the libraries.
+#
+# GSL_INCLUDE_DIRS = where to find headers
+#
+# GSL_USE_STATIC_LIBRARIES = Set it ON if you want to search for static
+# libraries.
+#
+# Felix Woelk 07/2004
+# minor corrections Jan Woetzel
+#
+# www.mip.informatik.uni-kiel.de
+# --------------------------------
+#
+# Friday 18 November 2016 09:05:56 AM IST
+# MODIFICATIONS: ## dilawars@ncbs.res.in, For the MOOSE project.
+# This version does not use gsl-config file.
+#
+
+# Set this envrionment variable to search in this path first.
+SET(GSL_ROOT_DIR $ENV{GSL_ROOT_DIR})
+if(GSL_ROOT_DIR)
+ message( STATUS "Debug: GSL_ROOT_DIR value ${GSL_ROOT_DIR}")
+endif(GSL_ROOT_DIR)
IF(WIN32)
- SET(GSL_MINGW_PREFIX "c:/msys/local" )
- SET(GSL_MSVC_PREFIX "$ENV{LIB_DIR}")
- FIND_LIBRARY(GSL_LIB gsl PATHS
- ${GSL_MINGW_PREFIX}/lib
- ${GSL_MSVC_PREFIX}/lib
- )
- #MSVC version of the lib is just called 'cblas'
- FIND_LIBRARY(GSLCBLAS_LIB gslcblas cblas PATHS
- ${GSL_MINGW_PREFIX}/lib
- ${GSL_MSVC_PREFIX}/lib
- )
-
- FIND_PATH(GSL_INCLUDE_DIRS gsl/gsl_blas.h
- ${GSL_MINGW_PREFIX}/include
- ${GSL_MSVC_PREFIX}/include
- )
+ SET(GSL_MINGW_PREFIX "c:/msys/local" )
+ SET(GSL_MSVC_PREFIX "$ENV{LIB_DIR}")
+ FIND_LIBRARY(GSL_LIB gsl PATHS
+ ${GSL_MINGW_PREFIX}/lib
+ ${GSL_MSVC_PREFIX}/lib
+ )
+ #MSVC version of the lib is just called 'cblas'
+ FIND_LIBRARY(GSLCBLAS_LIB gslcblas cblas PATHS
+ ${GSL_MINGW_PREFIX}/lib
+ ${GSL_MSVC_PREFIX}/lib
+ )
+
+ FIND_PATH(GSL_INCLUDE_DIRS gsl/gsl_blas.h
+ ${GSL_MINGW_PREFIX}/include
+ ${GSL_MSVC_PREFIX}/include
+ )
+
+ IF (GSL_LIB AND GSLCBLAS_LIB)
+ SET (GSL_LIBRARIES ${GSL_LIB} ${GSLCBLAS_LIB})
+ ENDIF (GSL_LIB AND GSLCBLAS_LIB)
- IF (GSL_LIB AND GSLCBLAS_LIB)
- SET (GSL_LIBRARIES ${GSL_LIB} ${GSLCBLAS_LIB})
- ENDIF (GSL_LIB AND GSLCBLAS_LIB)
-
ELSE(WIN32)
- IF(UNIX)
- SET(GSL_CONFIG_PREFER_PATH "$ENV{GSL_ROOT_DIR}/bin")
- # GSL_CONFIG must be cleared. This script may be called again after installing
- # the proper version of gsl
- if(EXISTS "$ENV{GSL_ROOT_DIR}")
- set(GSL_CONFIG "$ENV{GSL_ROOT_DIR}/bin/gsl-config")
- MESSAGE(STATUS "gsl-config from environment variable: ${GSL_CONFIG}")
- set(GSL_INCLUDE_DIRS)
- set(GSL_LIBRARIES)
- set(GSL_VERSION)
- set(GSL_CONFIG_LIBS)
- else()
- FIND_PROGRAM(GSL_CONFIG gsl-config
- ${GSL_CONFIG_PREFER_PATH}
- $ENV{LIB_DIR}/bin
- /usr/local/bin/
- /usr/bin/
- )
- endif()
- IF (GSL_CONFIG)
- # set CXXFLAGS to be fed into CXX_FLAGS by the user:
- SET(GSL_CXX_FLAGS "`${GSL_CONFIG} --cflags`")
-
- # set INCLUDE_DIRS to prefix+include
- EXEC_PROGRAM(${GSL_CONFIG}
- ARGS --prefix
- OUTPUT_VARIABLE GSL_PREFIX)
- SET(GSL_INCLUDE_DIRS ${GSL_PREFIX}/include CACHE STRING INTERNAL)
-
- # set link libraries and link flags
- EXEC_PROGRAM(${GSL_CONFIG}
- ARGS --libs
- OUTPUT_VARIABLE GSL_LIBRARIES)
-
- ## extract link dirs for rpath
- EXEC_PROGRAM(${GSL_CONFIG}
- ARGS --libs
- OUTPUT_VARIABLE GSL_CONFIG_LIBS )
-
- EXEC_PROGRAM(${GSL_CONFIG}
- ARGS --version
- OUTPUT_VARIABLE GSL_VERSION
- )
-
- ## split off the link dirs (for rpath)
- ## use regular expression to match wildcard equivalent "-L*<endchar>"
- ## with <endchar> is a space or a semicolon
- STRING(REGEX MATCHALL "[-][L]([^ ;])+"
- GSL_LINK_DIRECTORIES_WITH_PREFIX
- "${GSL_CONFIG_LIBS}" )
- # MESSAGE("DBG GSL_LINK_DIRECTORIES_WITH_PREFIX=${GSL_LINK_DIRECTORIES_WITH_PREFIX}")
- ## remove prefix -L because we need the pure directory for LINK_DIRECTORIES
-
- IF (GSL_LINK_DIRECTORIES_WITH_PREFIX)
- STRING(REGEX REPLACE "[-][L]" "" GSL_LINK_DIRECTORIES ${GSL_LINK_DIRECTORIES_WITH_PREFIX} )
- ENDIF (GSL_LINK_DIRECTORIES_WITH_PREFIX)
- SET(GSL_EXE_LINKER_FLAGS "-Wl,-rpath,${GSL_LINK_DIRECTORIES}" CACHE STRING INTERNAL)
- # MESSAGE("DBG GSL_LINK_DIRECTORIES=${GSL_LINK_DIRECTORIES}")
- # MESSAGE("DBG GSL_EXE_LINKER_FLAGS=${GSL_EXE_LINKER_FLAGS}")
+ IF(GSL_USE_STATIC_LIBRARIES)
+ SET(GSL_LIB_NAMES libgsl.a)
+ SET(GSL_CBLAS_LIB_NAMES libgslcblas.a)
+ ELSE(GSL_USE_STATIC_LIBRARIES)
+ SET(GSL_LIB_NAMES gsl)
+ SET(GSL_CBLAS_LIB_NAMES gslcblas)
+ ENDIF( )
+
+ FIND_LIBRARY(GSL_LIB
+ NAMES ${GSL_LIB_NAMES}
+ PATHS
+ ${GSL_ROOT_DIR}/lib ${GSL_ROOT_DIR}/lib64
+ /opt/lib /opt/lib64
+ )
+
+ FIND_LIBRARY(GSLCBLAS_LIB
+ NAMES ${GSL_CBLAS_LIB_NAMES}
+ PATHS
+ ${GSL_ROOT_DIR}/lib ${GSL_ROOT_DIR}/lib64
+ /opt/lib /opt/lib64
+ )
+ IF (GSL_LIB AND GSLCBLAS_LIB)
+ SET (GSL_LIBRARIES ${GSL_LIB} ${GSLCBLAS_LIB})
+ ENDIF (GSL_LIB AND GSLCBLAS_LIB)
+
+ FIND_PATH(GSL_INCLUDE_DIRS NAMES gsl/gsl_blas.h
+ PATHS ${GSL_ROOT_DIR}/include /opt/include
+ )
- # ADD_DEFINITIONS("-DHAVE_GSL")
- # SET(GSL_DEFINITIONS "-DHAVE_GSL")
- MARK_AS_ADVANCED(
- GSL_CXX_FLAGS
- GSL_INCLUDE_DIRS
- GSL_LIBRARIES
- GSL_LINK_DIRECTORIES
- GSL_DEFINITIONS
- )
-
- ELSE(GSL_CONFIG)
- IF (GSL_FIND_REQUIRED)
- MESSAGE(FATAL_ERROR "Could not find gsl-config. Please set it manually. GSL_CONFIG=${GSL_CONFIG}")
- ELSE (GSL_FIND_REQUIRED)
- MESSAGE(STATUS "Could not find GSL")
- # TODO: Avoid cmake complaints if GSL is not found
- ENDIF (GSL_FIND_REQUIRED)
-
- ENDIF(GSL_CONFIG)
-
- ENDIF(UNIX)
ENDIF(WIN32)
-
-IF(GSL_LIBRARIES)
- IF(GSL_INCLUDE_DIRS OR GSL_CXX_FLAGS)
-
- SET(GSL_FOUND 1)
-
- MESSAGE(STATUS "Using GSL from ${GSL_PREFIX}")
-
- ENDIF(GSL_INCLUDE_DIRS OR GSL_CXX_FLAGS)
-ENDIF(GSL_LIBRARIES)
+# FIND version
+if(GSL_INCLUDE_DIRS)
+ file(READ "${GSL_INCLUDE_DIRS}/gsl/gsl_version.h" GSL_VERSION_TEXT)
+ string(REGEX REPLACE ".*define[ ]+GSL_MAJOR_VERSION[ ]*([0-9]+).*" "\\1"
+ GSL_MAJOR_VERSION "${GSL_VERSION_TEXT}")
+ string(REGEX REPLACE ".*define[ ]+GSL_MINOR_VERSION[ ]*([0-9]+).*" "\\1"
+ GSL_MINOR_VERSION "${GSL_VERSION_TEXT}")
+ set(GSL_VERSION "${GSL_MAJOR_VERSION}.${GSL_MINOR_VERSION}")
+ message(STATUS "GSL version : ${GSL_VERSION}")
+endif(GSL_INCLUDE_DIRS)
+
+IF(GSL_LIBRARIES AND GSL_VERSION)
+ IF(GSL_INCLUDE_DIRS)
+ MESSAGE(STATUS "Found GSL ${GSL_LIBRARIES}")
+ SET(GSL_FOUND 1)
+ ENDIF(GSL_INCLUDE_DIRS)
+ENDIF()