diff --git a/moose-core/.pre-commit-config.yaml b/moose-core/.pre-commit-config.yaml
index 5eccd7a7ee9cc0f150c876dff4905a98545b0306..f8aa18ad4cd7e81f73c6436ad0071e89de8ddce5 100644
--- a/moose-core/.pre-commit-config.yaml
+++ b/moose-core/.pre-commit-config.yaml
@@ -1,5 +1,6 @@
+repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
- sha: v0.8.0
+ sha: v1.2.1
hooks:
- id: check-added-large-files
- id: check-ast
diff --git a/moose-core/.travis.yml b/moose-core/.travis.yml
index f38c78cc58ebcdb6b26d6b499187f9e0cc48e36a..d1de05b822fc17bd41eb64d523a7a150ee23d96b 100644
--- a/moose-core/.travis.yml
+++ b/moose-core/.travis.yml
@@ -1,31 +1,37 @@
language: cpp
-dist: trusty
sudo: required
group: edge
-os:
- - linux
- - osx
+services:
+ - docker
+os:
+- linux
+- osx
notifications:
- email:
- recipients:
- - bhalla@ncbs.res.in
- - dilawar.s.rajput@gmail.com
- - hrani@ncbs.res.in
- on_success: change
- on_failure: always
-
-before_script :
- - echo "OSX related"
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
- - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
+ email:
+ recipients:
+ - bhalla@ncbs.res.in
+ - dilawar.s.rajput@gmail.com
+ - hrani@ncbs.res.in
+ on_success: change
+ on_failure: always
+before_script:
+- echo "OSX related"
+- if [[ "$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:
- - # checking if any python3 incompatible file is in the source tree.
- - python2 -m compileall -q .
- - if type python3 > /dev/null; then python3 -m compileall -q . ; fi
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
- - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi
- - set +e
+-
+- python2 -m compileall -q .
+- if type python3 > /dev/null; then python3 -m compileall -q . ; fi
+- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
+- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi
+- set +e
+
+deploy:
+ on: tags
+ provider: script
+ script: ./.travis/deploy_pypi.sh
diff --git a/moose-core/.travis/deploy_pypi.sh b/moose-core/.travis/deploy_pypi.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ed7c978d94670761a90d4427abc71ef9c664ba2a
--- /dev/null
+++ b/moose-core/.travis/deploy_pypi.sh
@@ -0,0 +1,22 @@
+#!/bin/bash -
+#===============================================================================
+#
+# FILE: deploy_pypi.sh
+#
+# USAGE: ./deploy_pypi.sh
+#
+# DESCRIPTION: Build docker image and deploy on PyPI.
+#
+# OPTIONS: ---
+# REQUIREMENTS: ---
+# BUGS: ---
+# NOTES: ---
+# AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in
+# ORGANIZATION: NCBS Bangalore
+# CREATED: Sunday 04 February 2018 11:46:32 IST
+# REVISION: ---
+#===============================================================================
+set -o nounset # Treat unset variables as an error
+
+git clone https://github.com/BhallaLab/pymoose-wheels
+cd pymoose-wheels && docker build -t bhallalab/wheels .
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index f91b68e213f79a13762f83b5446734edfa703129..8737681d2a56b3d7eb57a3537f985075dda561b5 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -16,18 +16,28 @@ set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake_modules")
include(CheckCXXCompiler.cmake)
include(CheckIncludeFileCXX)
include(FindPkgConfig)
-include(GetRevision)
+
+# getgit revision number
+find_program( GIT_EXEC git )
+if(GIT_EXEC)
+ execute_process(COMMAND ${GIT_EXEC} rev-parse --short HEAD
+ OUTPUT_VARIABLE GIT_HEAD
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ )
+endif()
# If from command line, version info is not passed, use the git to generate a
# version file. If GIT fails, use the previous known version.
-set(MOOSE_VERSION 3.2-git)
-add_definitions( -DMOOSE_VERSION="${MOOSE_VERSION}")
-message( STATUS "MOOSE Version ${MOOSE_VERSION}" )
+if(NOT VERSION_MOOSE)
+ set(VERSION_MOOSE "3.2.0rc1-${GIT_HEAD}")
+endif( )
+add_definitions( -DMOOSE_VERSION="${VERSION_MOOSE}")
+message( STATUS "MOOSE Version ${VERSION_MOOSE}" )
-# Write VERSION to a file VERSION so that setup.py can use it.
-set(VERSION_FILE ${CMAKE_CURRENT_SOURCE_DIR}/VERSION)
-message(STATUS "+ Writing ${MOOSE_VERSION} to ${VERSION_FILE}" )
-file(WRITE ${VERSION_FILE} ${MOOSE_VERSION} )
+# Write VERSION to a file VERSION so that setup.cmake.py can use it.
+set(VERSION_FILE ${CMAKE_CURRENT_SOURCE_DIR}/python/VERSION)
+message(STATUS "+ Writing ${VERSION_MOOSE} to ${VERSION_FILE}" )
+file(WRITE ${VERSION_FILE} ${VERSION_MOOSE} )
# This snippet is from LLVM project.
# Sanity check our source directory to make sure that we are not trying to
@@ -268,19 +278,24 @@ endif(WITH_BOOST)
# these two types because of --whole-archive option. See
# BhallaLab/moose-core#66,
if(WITH_GSL)
- message(STATUS "Using gsl libraries: ${GSL_LIBRARIES}")
- foreach(GSL_LIB ${GSL_LIBRARIES} )
- 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( )
+ if(GSL_STATIC_LIBRARIES)
+ message( STATUS "Using static libraries ${GSL_STATIC_LIBRARIES}" )
+ list(APPEND STATIC_LIBRARIES ${GSL_STATIC_LIBRARIES})
+ else( )
+ message(STATUS "Using gsl libraries: ${GSL_LIBRARIES}")
+ foreach(GSL_LIB ${GSL_LIBRARIES} )
+ 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 ${GSL_LIB})
+ endif( )
+ endif( )
+ endif( )
+ endforeach( )
+ endif( )
endif()
if(WITH_MPI)
@@ -374,6 +389,7 @@ if(DEBUG)
endif( WITH_BOOST )
endif()
+
######################### BUILD PYMOOSE ########################################
add_subdirectory( pymoose )
@@ -434,8 +450,6 @@ if(${CMAKE_BUILD_TOOL} MATCHES "make")
endif()
-
-
############################ CTEST ######################################
include( CTest )
# If CTEST_OUTPUT_ON_FAILURE environment variable is set, the output is printed
diff --git a/moose-core/Jenkinsfile b/moose-core/Jenkinsfile
deleted file mode 100644
index 2b8f686e173b685a42466d93da4128042eeca188..0000000000000000000000000000000000000000
--- a/moose-core/Jenkinsfile
+++ /dev/null
@@ -1,15 +0,0 @@
-pipeline {
- agent any
- stages {
- stage('Build') {
- steps {
- sh 'mkdir -p _build && cd _build && cmake .. && make -j4'
- }
- }
- stage('Test'){
- steps {
- sh 'cd _build && ctest --output-on-failure'
- }
- }
- }
-}
diff --git a/moose-core/README.md b/moose-core/README.md
index 90d19144aadc5d514300fe7acb7805020739d400..dd8e63621de6d0da31186fdb10fd7f940c15e276 100644
--- a/moose-core/README.md
+++ b/moose-core/README.md
@@ -1,6 +1,18 @@
-[](https://travis-ci.org/BhallaLab/moose-core)
+[](https://travis-ci.org/BhallaLab/moose-core) | [](https://badge.fury.io/py/pymoose)
This is the core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository contains
-C++ codebase and python interface. For more details about MOOSE simulator, see https://github.com/BhallaLab/moose/blob/master/README.md
+C++ codebase and python interface called `pymoose`. For more details about MOOSE simulator, visit https://moose.ncbs.res.in .
-This repository is sufficient for using MOOSE as a python module. If you just want to build moose python module, follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md .
+# Download and Install
+
+This repository is sufficient for using MOOSE as a python module. We provide python package via `pip`.
+
+ $ pip install pymoose --user
+
+`pymoose` is part of [MOOSE simulator](https://github.com/BhallaLab/moose). We also provide linux packages of
+MOOSE simlulator. It can be downloaded from [Open Build Service](https://software.opensuse.org//download.html?project=home%3Amoose&package=moose).
+In addition to `pymoose`, it also contain a `GUI` to create and visualize chemical network, and `moogli`, a visualizer of neural activity.
+
+# Build
+
+To build `pymoose`, follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md
diff --git a/moose-core/builtins/Function.cpp b/moose-core/builtins/Function.cpp
index 54224b27fc2a8c0bc3b04fb961cf3a02703f013d..79413c1bb0fea17bee2ebaff277423c278421456 100644
--- a/moose-core/builtins/Function.cpp
+++ b/moose-core/builtins/Function.cpp
@@ -150,7 +150,7 @@ const Cinfo * Function::initCinfo()
"log2 1 logarithm to the base 2\n"
"log10 1 logarithm to the base 10\n"
"log 1 logarithm to the base 10\n"
- "ln 1 logarithm to base e (2.71828...)\n"
+ "ln 1 logarithm to base e (2.71828...)\n"
"exp 1 e raised to the power of x\n"
"sqrt 1 square root of a value\n"
"sign 1 sign function -1 if x<0; 1 if x>0\n"
@@ -166,32 +166,34 @@ const Cinfo * Function::initCinfo()
" if seed = -1, a 'random' seed is created using either\n"
" by random_device or by reading system clock\n"
"\nOperators\n"
- "Op meaning priority\n"
- "= assignment -1\n"
- "&& logical and 1\n"
- "|| logical or 2\n"
- "<= less or equal 4\n"
- ">= greater or equal 4\n"
- "!= not equal 4\n"
- "== equal 4\n"
- "> greater than 4\n"
- "< less than 4\n"
- "+ addition 5\n"
- "- subtraction 5\n"
- "* multiplication 6\n"
- "/ division 6\n"
- "^ raise x to the power of y 7\n"
- "% floating point modulo 7\n"
+ "Op meaning priority\n"
+ "= assignment -1\n"
+ "&& logical and 1\n"
+ "|| logical or 2\n"
+ "<= less or equal 4\n"
+ ">= greater or equal 4\n"
+ "!= not equal 4\n"
+ "== equal 4\n"
+ "> greater than 4\n"
+ "< less than 4\n"
+ "+ addition 5\n"
+ "- subtraction 5\n"
+ "* multiplication 6\n"
+ "/ division 6\n"
+ "^ raise x to the power of y 7\n"
+ "% floating point modulo 7\n"
"\n"
- "?: if then else operator C++ style syntax\n",
+ "?: if then else operator C++ style syntax\n",
&Function::setExpr,
- &Function::getExpr);
+ &Function::getExpr
+ );
static ValueFinfo< Function, unsigned int > numVars(
"numVars",
"Number of variables used by Function.",
&Function::setNumVar,
- &Function::getNumVar);
+ &Function::getNumVar
+ );
static FieldElementFinfo< Function, Variable > inputs(
"x",
@@ -199,7 +201,8 @@ const Cinfo * Function::initCinfo()
Variable::initCinfo(),
&Function::getVar,
&Function::setNumVar,
- &Function::getNumVar);
+ &Function::getNumVar
+ );
static LookupValueFinfo < Function, string, double > constants(
"c",
@@ -229,10 +232,7 @@ const Cinfo * Function::initCinfo()
static DestFinfo reinit( "reinit",
"Handles reinit call.",
new ProcOpFunc< Function >( &Function::reinit ) );
- static Finfo* processShared[] =
- {
- &process, &reinit
- };
+ static Finfo* processShared[] = { &process, &reinit };
static SharedFinfo proc( "proc",
"This is a shared message to receive Process messages "
@@ -382,7 +382,7 @@ Function::Function(const Function& rhs): _numVar(rhs._numVar),
Function& Function::operator=(const Function rhs)
{
- static Eref er;
+ static Eref er;
_clearBuffer();
_mode = rhs._mode;
_lastValue = rhs._lastValue;
diff --git a/moose-core/cmake_modules/GetGitRevisionDescription.cmake b/moose-core/cmake_modules/GetGitRevisionDescription.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..8ab03bc5f0b766462e05edb6afbe9c20e8115b46
--- /dev/null
+++ b/moose-core/cmake_modules/GetGitRevisionDescription.cmake
@@ -0,0 +1,168 @@
+# - Returns a version string from Git
+#
+# These functions force a re-configure on each git commit so that you can
+# trust the values of the variables in your build system.
+#
+# get_git_head_revision(<refspecvar> <hashvar> [<additional arguments to git describe> ...])
+#
+# Returns the refspec and sha hash of the current head revision
+#
+# git_describe(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe on the source tree, and adjusting
+# the output so that it tests false if an error occurs.
+#
+# git_get_exact_tag(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe --exact-match on the source tree,
+# and adjusting the output so that it tests false if there was no exact
+# matching tag.
+#
+# git_local_changes(<var>)
+#
+# Returns either "CLEAN" or "DIRTY" with respect to uncommitted changes.
+# Uses the return code of "git diff-index --quiet HEAD --".
+# Does not regard untracked files.
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright Iowa State University 2009-2010.
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+if(__get_git_revision_description)
+ return()
+endif()
+set(__get_git_revision_description YES)
+
+# We must run the following at "include" time, not at function call time,
+# to find the path to this module rather than the path to a calling list file
+get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
+
+function(get_git_head_revision _refspecvar _hashvar)
+ set(GIT_PARENT_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+ set(GIT_DIR "${GIT_PARENT_DIR}/.git")
+ while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories
+ set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}")
+ get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH)
+ if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT)
+ # We have reached the root directory, we are not in git
+ set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
+ set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
+ return()
+ endif()
+ set(GIT_DIR "${GIT_PARENT_DIR}/.git")
+ endwhile()
+ # check if this is a submodule
+ if(NOT IS_DIRECTORY ${GIT_DIR})
+ file(READ ${GIT_DIR} submodule)
+ string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule})
+ get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
+ get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE)
+ endif()
+ set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
+ if(NOT EXISTS "${GIT_DATA}")
+ file(MAKE_DIRECTORY "${GIT_DATA}")
+ endif()
+
+ if(NOT EXISTS "${GIT_DIR}/HEAD")
+ return()
+ endif()
+ set(HEAD_FILE "${GIT_DATA}/HEAD")
+ configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
+
+ configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
+ "${GIT_DATA}/grabRef.cmake"
+ @ONLY)
+ include("${GIT_DATA}/grabRef.cmake")
+
+ set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE)
+ set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE)
+endfunction()
+
+function(git_describe _var)
+ if(NOT GIT_FOUND)
+ find_package(Git QUIET)
+ endif()
+ get_git_head_revision(refspec hash)
+ if(NOT GIT_FOUND)
+ set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
+ return()
+ endif()
+ if(NOT hash)
+ set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
+ return()
+ endif()
+
+ # TODO sanitize
+ #if((${ARGN}" MATCHES "&&") OR
+ # (ARGN MATCHES "||") OR
+ # (ARGN MATCHES "\\;"))
+ # message("Please report the following error to the project!")
+ # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
+ #endif()
+
+ #message(STATUS "Arguments to execute_process: ${ARGN}")
+
+ execute_process(COMMAND
+ "${GIT_EXECUTABLE}"
+ describe
+ ${hash}
+ ${ARGN}
+ WORKING_DIRECTORY
+ "${CMAKE_CURRENT_SOURCE_DIR}"
+ RESULT_VARIABLE
+ res
+ OUTPUT_VARIABLE
+ out
+ ERROR_QUIET
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ if(NOT res EQUAL 0)
+ set(out "${out}-${res}-NOTFOUND")
+ endif()
+
+ set(${_var} "${out}" PARENT_SCOPE)
+endfunction()
+
+function(git_get_exact_tag _var)
+ git_describe(out --exact-match ${ARGN})
+ set(${_var} "${out}" PARENT_SCOPE)
+endfunction()
+
+function(git_local_changes _var)
+ if(NOT GIT_FOUND)
+ find_package(Git QUIET)
+ endif()
+ get_git_head_revision(refspec hash)
+ if(NOT GIT_FOUND)
+ set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
+ return()
+ endif()
+ if(NOT hash)
+ set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
+ return()
+ endif()
+
+ execute_process(COMMAND
+ "${GIT_EXECUTABLE}"
+ diff-index --quiet HEAD --
+ WORKING_DIRECTORY
+ "${CMAKE_CURRENT_SOURCE_DIR}"
+ RESULT_VARIABLE
+ res
+ OUTPUT_VARIABLE
+ out
+ ERROR_QUIET
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ if(res EQUAL 0)
+ set(${_var} "CLEAN" PARENT_SCOPE)
+ else()
+ set(${_var} "DIRTY" PARENT_SCOPE)
+ endif()
+endfunction()
diff --git a/moose-core/cmake_modules/GetGitRevisionDescription.cmake.in b/moose-core/cmake_modules/GetGitRevisionDescription.cmake.in
new file mode 100644
index 0000000000000000000000000000000000000000..6d8b708efe56a66852752a7a30ec5c16b51cdc9e
--- /dev/null
+++ b/moose-core/cmake_modules/GetGitRevisionDescription.cmake.in
@@ -0,0 +1,41 @@
+#
+# Internal file for GetGitRevisionDescription.cmake
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright Iowa State University 2009-2010.
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+set(HEAD_HASH)
+
+file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
+
+string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
+if(HEAD_CONTENTS MATCHES "ref")
+ # named branch
+ string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
+ if(EXISTS "@GIT_DIR@/${HEAD_REF}")
+ configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
+ else()
+ configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY)
+ file(READ "@GIT_DATA@/packed-refs" PACKED_REFS)
+ if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}")
+ set(HEAD_HASH "${CMAKE_MATCH_1}")
+ endif()
+ endif()
+else()
+ # detached HEAD
+ configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
+endif()
+
+if(NOT HEAD_HASH)
+ file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
+ string(STRIP "${HEAD_HASH}" HEAD_HASH)
+endif()
diff --git a/moose-core/cmake_moose_cpack.cmake b/moose-core/cmake_moose_cpack.cmake
index 985c3fc40307d6a50c52680e8d9459e5d51b5d83..05e7f11498ea91f8b752601bdf5c4ac723e69199 100644
--- a/moose-core/cmake_moose_cpack.cmake
+++ b/moose-core/cmake_moose_cpack.cmake
@@ -58,7 +58,9 @@ if(APPLE)
SET(BUNDLE_NAME ${CMAKE_PROJECT_NAME})
SET(CPACK_BUNDLE_NAME ${BUNDLE_NAME})
- SET_TARGET_PROPERTIES(moose.bin PROPERTIES MACOSX_BUNDLE TRUE)
+ if(DEBUG)
+ SET_TARGET_PROPERTIES(moose.bin PROPERTIES MACOSX_BUNDLE TRUE)
+ endif(DEBUG)
SET_TARGET_PROPERTIES(_moose PROPERTIES MACOSX_BUNDLE TRUE)
endif(APPLE)
diff --git a/moose-core/pymoose/CMakeLists.txt b/moose-core/pymoose/CMakeLists.txt
index d7c5c3c93f13d06713473e8537397fb9ee64f888..713ade07302e224a9600177fce2952d0a61dc791 100644
--- a/moose-core/pymoose/CMakeLists.txt
+++ b/moose-core/pymoose/CMakeLists.txt
@@ -76,7 +76,7 @@ ELSE(MACOSX)
${MOOSE_LIBRARIES}
${STATIC_LIBRARIES}
"-Wl,--no-whole-archive"
- ${PYTHON_LIBRARIES}
+ # ${PYTHON_LIBRARIES}
${SYSTEM_SHARED_LIBS}
)
endif(MACOSX)
diff --git a/moose-core/python/moose/SBML/readSBML.py b/moose-core/python/moose/SBML/readSBML.py
index ff7b7dbc5d9bcefb3754ba172b17618f51ed396b..06de82bc3a7317fa1d8525be13e86fb1013d3026 100644
--- a/moose-core/python/moose/SBML/readSBML.py
+++ b/moose-core/python/moose/SBML/readSBML.py
@@ -970,7 +970,7 @@ def createRules(model, specInfoMap, globparameterIdValue):
if (rule.isAssignment()):
rule_variable = rule.getVariable()
- if specInfoMap.has_key(rule_variable):
+ if rule_variable in specInfoMap:
#In assignment rule only if pool exist, then that is conveted to moose as
# this can be used as summation of pool's, P1+P2+P3 etc
rule_variable = parentSp = str(idBeginWith(rule_variable))
@@ -993,10 +993,9 @@ def createRules(model, specInfoMap, globparameterIdValue):
if found:
allPools = True
for i in ruleMemlist:
- if specInfoMap.has_key(i):
- pass
- else:
+ if i not in specInfoMap:
allPools = False
+ break
if allPools:
#only if addition then summation works, only then I create a function in moose
# which is need to get the summation's output to a pool
diff --git a/moose-core/python/rdesigneur/rdesigneur.py b/moose-core/python/rdesigneur/rdesigneur.py
index 8665281d89c7954d9828930c5e492c18c59e5930..30906a2502bbe8143afb96d91bd8cc9ff3211af5 100644
--- a/moose-core/python/rdesigneur/rdesigneur.py
+++ b/moose-core/python/rdesigneur/rdesigneur.py
@@ -80,6 +80,8 @@ class rdesigneur:
elecDt= 50e-6, # Same default as from MOOSE
chemPlotDt = 1.0, # Same default as from MOOSE
elecPlotDt = 0.1e-3, # Same default as from MOOSE
+ funcDt = 0.1e-3, # Used when turnOffElec is False.
+ # Otherwise system uses chemDt.
cellProto = [],
spineProto = [],
chanProto = [],
@@ -113,6 +115,7 @@ class rdesigneur:
self.diffDt= diffDt
self.elecDt= elecDt
self.elecPlotDt= elecPlotDt
+ self.funcDt= funcDt
self.chemPlotDt= chemPlotDt
self.cellProtoList = cellProto
@@ -640,8 +643,8 @@ class rdesigneur:
################################################################
# Here we display the plots and moogli
################################################################
- def displayMoogli( self, moogliDt, runtime, rotation = math.pi/500.0):
- rmoogli.displayMoogli( self, moogliDt, runtime, rotation )
+ def displayMoogli( self, moogliDt, runtime, rotation = math.pi/500.0, fullscreen = False):
+ rmoogli.displayMoogli( self, moogliDt, runtime, rotation, fullscreen )
def display( self ):
import matplotlib.pyplot as plt
@@ -925,12 +928,14 @@ class rdesigneur:
elecPlotDt = self.elecPlotDt
diffDt = self.diffDt
chemDt = self.chemDt
- for i in range( 0, 9 ):
+ for i in range( 0, 9 ): # Assign elec family of clocks
moose.setClock( i, elecDt )
- moose.setClock( 8, elecPlotDt )
- moose.setClock( 10, diffDt )
- for i in range( 11, 18 ):
+ moose.setClock( 8, elecPlotDt )
+ moose.setClock( 10, diffDt )# Assign diffusion clock.
+ for i in range( 11, 18 ): # Assign the chem family of clocks.
moose.setClock( i, chemDt )
+ if not self.turnOffElec: # Assign the Function clock
+ moose.setClock( 12, self.funcDt )
moose.setClock( 18, self.chemPlotDt )
hsolve = moose.HSolve( self.elecid.path + '/hsolve' )
hsolve.dt = elecDt
diff --git a/moose-core/python/rdesigneur/rmoogli.py b/moose-core/python/rdesigneur/rmoogli.py
index bd4ad97927876d076fb2c3c3610d80e036b66ed4..fcb1a1209f03b4f542f63b0fee38f169588dabb0 100644
--- a/moose-core/python/rdesigneur/rmoogli.py
+++ b/moose-core/python/rdesigneur/rmoogli.py
@@ -157,7 +157,7 @@ def makeMoogli( rd, mooObj, moogliEntry, fieldInfo ):
viewer.attach_view(view)
return viewer
-def displayMoogli( rd, _dt, _runtime, _rotation ):
+def displayMoogli( rd, _dt, _runtime, _rotation, fullscreen = False ):
if not hasMoogli:
return None
global runtime
@@ -167,7 +167,10 @@ def displayMoogli( rd, _dt, _runtime, _rotation ):
moogliDt = _dt
rotation = _rotation
for i in rd.moogNames:
- i.show()
+ if fullscreen:
+ i.showMaximized()
+ else:
+ i.show()
i.start()
#viewer.showMaximized()
#viewer.show()
diff --git a/moose-core/python/setup.cmake.py b/moose-core/python/setup.cmake.py
index 8cd9faf17329584b8eb251b51428567130a53b7c..ebce90693b110574df448678fab379642e644880 100644
--- a/moose-core/python/setup.cmake.py
+++ b/moose-core/python/setup.cmake.py
@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
"""setup.py:
-Script to install python targets.
+Script to install python targets.
NOTE: This script is to be called by CMake. Not intended to be used standalone.
@@ -19,12 +19,17 @@ __status__ = "Development"
import os
import sys
-from distutils.core import setup
+try:
+ from setuptools import setup
+except Exception as e:
+ from distutils.core import setup
+
script_dir = os.path.dirname( os.path.abspath( __file__ ) )
-version = '3.2.git'
+version = '3.2pre1'
+
try:
- with open( os.path.join( script_dir, '..', '..', 'VERSION'), 'r' ) as f:
+ with open( os.path.join( script_dir, 'VERSION'), 'r' ) as f:
version = f.read( )
except Exception as e:
print( 'Failed to read VERSION %s' % e )
@@ -38,9 +43,9 @@ except Exception as e:
suffix = '.so'
setup(
- name='moose',
+ name='pymoose',
version=version,
- description='MOOSE python scripting module.',
+ description='Python scripting interface of MOOSE Simulator (https://moose.ncbs.res.in)',
author='MOOSERes',
author_email='bhalla@ncbs.res.in',
maintainer='Dilawar Singh',
@@ -56,9 +61,9 @@ setup(
, 'moose.chemUtil'
, 'moose.chemMerge'
],
+ install_requires = [ 'python-libsbml', 'numpy' ],
package_dir = {
- 'moose' : 'moose'
- , 'rdesigneur' : 'rdesigneur'
+ 'moose' : 'moose', 'rdesigneur' : 'rdesigneur'
},
package_data = { 'moose' : ['_moose' + suffix, 'neuroml2/schema/NeuroMLCoreDimensions.xml'] },
)
diff --git a/moose-core/scripts/setup.py b/moose-core/setup.py
similarity index 97%
rename from moose-core/scripts/setup.py
rename to moose-core/setup.py
index 746ba5a078982dc72b6b08f694ee5adcce5bfb62..f7eec4a35346b44bb6c2a30ccf08369c151cfbe2 100755
--- a/moose-core/scripts/setup.py
+++ b/moose-core/setup.py
@@ -95,7 +95,7 @@ class InstallCommand(_install):
self.new_dir = os.path.join(os.path.split(__file__)[0], 'python')
os.chdir(self.new_dir)
try:
- ds.spawn(["python", "setup.py", "install"])
+ ds.spawn(["python", "setup.cmake.py", "install"])
except ds.DistutilsExecError as e:
print("Can't install PyMOOSE")
print(e)
@@ -150,7 +150,7 @@ setup(
, description = description
, license = "LGPL"
, url = url
- , long_description = read('README')
+ , long_description = read('./README.md')
, ext_modules = [
Extension('_moose', [ '*' ])
]
diff --git a/moose-core/setup_/__init__.py b/moose-core/setup_/__init__.py
deleted file mode 100644
index 50aca64a597d87ddbda39b60ac2ed743b7ccb993..0000000000000000000000000000000000000000
--- a/moose-core/setup_/__init__.py
+++ /dev/null
@@ -1,203 +0,0 @@
-# -*- coding: utf-8 -*-
-sources = [
- 'basecode/consts.cpp',
- 'basecode/Element.cpp',
- 'basecode/Qinfo.cpp',
- 'basecode/DataHandler.cpp',
- 'basecode/ZeroDimHandler.cpp',
- 'basecode/ZeroDimParallelHandler.cpp',
- 'basecode/BlockHandler.cpp',
- 'basecode/OneDimHandler.cpp',
- 'basecode/TwoDimHandler.cpp',
- 'basecode/AnyDimHandler.cpp',
- 'basecode/DataHandlerWrapper.cpp',
- 'basecode/FieldDataHandlerBase.cpp',
- 'basecode/MsgDataHandler.cpp',
- 'basecode/ZombieHandler.cpp',
- 'basecode/Eref.cpp',
- 'basecode/Finfo.cpp',
- 'basecode/DestFinfo.cpp',
- 'basecode/Cinfo.cpp',
- 'basecode/SrcFinfo.cpp',
- 'basecode/ValueFinfo.cpp',
- 'basecode/SharedFinfo.cpp',
- 'basecode/FieldElementFinfo.cpp',
- 'basecode/Id.cpp',
- 'basecode/ObjId.cpp',
- 'basecode/DataId.cpp',
- 'basecode/SetGet.cpp',
- 'basecode/OpFunc.cpp',
- 'basecode/FieldOpFunc.cpp',
- 'basecode/SparseMatrix.cpp',
- 'basecode/PrepackedBuffer.cpp',
- 'basecode/FuncBarrier.cpp',
- 'basecode/doubleEq.cpp',
- 'basecode/ReduceBase.cpp',
- 'basecode/main.cpp',
- 'basecode/testAsync.cpp',
-
- 'biophysics/SynBase.cpp',
- 'biophysics/IntFire.cpp',
- 'biophysics/IzhikevichNrn.cpp',
- 'biophysics/LeakyIaF.cpp',
- 'biophysics/Synapse.cpp',
- 'biophysics/Compartment.cpp',
- 'biophysics/SymCompartment.cpp',
- 'biophysics/ChanBase.cpp',
- 'biophysics/SynChanBase.cpp',
- 'biophysics/HHChannel.cpp',
- 'biophysics/HHGate.cpp',
- 'biophysics/SynChan.cpp',
- 'biophysics/SpikeGen.cpp',
- 'biophysics/CaConc.cpp',
- 'biophysics/Nernst.cpp',
- 'biophysics/GHK.cpp',
- 'biophysics/NMDAChan.cpp',
- 'biophysics/HHGate2D.cpp',
- 'biophysics/HHChannel2D.cpp',
- 'biophysics/MgBlock.cpp',
- 'biophysics/VectorTable.cpp',
- 'biophysics/MarkovRateTable.cpp',
- 'biophysics/MarkovChannel.cpp',
- 'biophysics/MarkovGslSolver.cpp',
- 'biophysics/MatrixOps.cpp',
- 'biophysics/MarkovSolverBase.cpp',
- 'biophysics/MarkovSolver.cpp',
- 'biophysics/ReadCell.cpp',
- 'biophysics/testBiophysics.cpp',
-
- 'builtins/Arith.cpp',
- 'builtins/Group.cpp',
- 'builtins/Mdouble.cpp',
- 'builtins/Mstring.cpp',
- 'builtins/TableBase.cpp',
- 'builtins/TableEntry.cpp',
- 'builtins/Table.cpp',
- 'builtins/StimulusTable.cpp',
- 'builtins/Stats.cpp',
- 'builtins/Interpol2D.cpp',
- 'builtins/HDF5WriterBase.cpp',
- 'builtins/HDF5DataWriter.cpp',
- 'builtins/testBuiltins.cpp',
-
- 'device/PulseGen.cpp',
- 'device/DiffAmp.cpp',
- 'device/PIDController.cpp',
- 'device/RC.cpp',
-
- 'geom/Geometry.cpp',
- 'geom/Surface.cpp',
- 'geom/Panel.cpp',
- 'geom/CylPanel.cpp',
- 'geom/SpherePanel.cpp',
- 'geom/HemispherePanel.cpp',
- 'geom/DiskPanel.cpp',
- 'geom/RectPanel.cpp',
- 'geom/TriPanel.cpp',
- 'geom/testGeom.cpp',
-
- 'hsolve/HSolveStruct.cpp',
- 'hsolve/HinesMatrix.cpp',
- 'hsolve/HSolvePassive.cpp',
- 'hsolve/RateLookup.cpp',
- 'hsolve/HSolveActive.cpp',
- 'hsolve/HSolveActiveSetup.cpp',
- 'hsolve/HSolveInterface.cpp',
- 'hsolve/HSolve.cpp',
- 'hsolve/HSolveUtils.cpp',
- 'hsolve/testHSolve.cpp',
- 'hsolve/ZombieCompartment.cpp',
- 'hsolve/ZombieCaConc.cpp',
- 'hsolve/ZombieHHChannel.cpp',
-
- 'kinetics/PoolBase.cpp',
- 'kinetics/Pool.cpp',
- 'kinetics/BufPool.cpp',
- 'kinetics/FuncPool.cpp',
- 'kinetics/Reac.cpp',
- 'kinetics/Enz.cpp',
- 'kinetics/MMenz.cpp',
- 'kinetics/Species.cpp',
- 'kinetics/ReadKkit.cpp',
- 'kinetics/ReadCspace.cpp',
- 'kinetics/MathFunc.cpp',
- 'kinetics/SumFunc.cpp',
- 'kinetics/lookupSizeFromMesh.cpp',
- 'kinetics/testKinetics.cpp',
-
- 'ksolve/Port.cpp',
- 'ksolve/Stoich.cpp',
- 'ksolve/KinSparseMatrix.cpp',
- 'ksolve/ZombiePool.cpp',
- 'ksolve/ZombieBufPool.cpp',
- 'ksolve/ZombieFuncPool.cpp',
- 'ksolve/ZombieReac.cpp',
- 'ksolve/ZombieEnz.cpp',
- 'ksolve/ZombieMMenz.cpp',
- 'ksolve/ZombieSumFunc.cpp',
- 'ksolve/RateTerm.cpp',
- 'ksolve/FuncTerm.cpp',
- 'ksolve/GssaStoich.cpp',
- 'ksolve/testKsolve.cpp',
-
- 'manager/SimManager.cpp',
- 'manager/testSimManager.cpp',
-
- 'mesh/ChemMesh.cpp',
- 'mesh/MeshEntry.cpp',
- 'mesh/CylMesh.cpp',
- 'mesh/CubeMesh.cpp',
- 'mesh/Boundary.cpp',
- 'mesh/Stencil.cpp',
- 'mesh/testMesh.cpp',
-
- 'msg/Msg.cpp',
- 'msg/DiagonalMsg.cpp',
- 'msg/OneToAllMsg.cpp',
- 'msg/OneToOneMsg.cpp',
- 'msg/SingleMsg.cpp',
- 'msg/SparseMsg.cpp',
- 'msg/ReduceMsg.cpp',
- 'msg/testMsg.cpp',
-
- 'pymoose/moosemodule.cpp',
-
- 'randnum/mt19937ar.cpp',
-
- 'regressionTests/regressionTest.cpp',
- 'regressionTests/rtTable.cpp',
- 'regressionTests/rtReadKkit.cpp',
- 'regressionTests/rtHHnetwork.cpp',
- 'regressionTests/rtReacDiff.cpp',
- 'regressionTests/perfTestMarkovSolver.cpp',
- 'regressionTests/benchmarkTests.cpp',
-
- 'scheduling/Clock.cpp',
- 'scheduling/Tick.cpp',
- 'scheduling/TickMgr.cpp',
- 'scheduling/testScheduling.cpp',
-
- 'shell/Shell.cpp',
- 'shell/ShellCopy.cpp',
- 'shell/ShellSetGet.cpp',
- 'shell/ShellThreads.cpp',
- 'shell/ProcessLoop.cpp',
- 'shell/LoadModels.cpp',
- 'shell/Neutral.cpp',
- 'shell/Wildcard.cpp',
- 'shell/testShell.cpp',
-
- #~ 'smol/SmolSim.cpp',
- #~ 'smol/SmolPool.cpp',
- #~ 'smol/SmolMol.cpp',
- #~ 'smol/SmolReac.cpp',
- #~ 'smol/SmolEnz.cpp',
- #~ 'smol/SmolMMenz.cpp',
- #~ 'smol/testSmol.cpp',
-
- 'utility/strutil.cpp',
- 'utility/types.cpp',
- 'utility/setupenv.cpp',
- 'utility/numutil.cpp',
- 'utility/Annotator.cpp',
-]
diff --git a/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp b/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp
index 6734a574b696f169131f02acab90247a8788db69..835dc72b7d31f24c95d585567dee6439a33eb3c2 100644
--- a/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp
+++ b/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.cpp
@@ -305,6 +305,15 @@ void GraupnerBrunel2012CaPlasticitySynHandler::addSpike(
delayDPreEvents_.push( PreSynEvent( index, time+delayD_, weight ) );
}
+double GraupnerBrunel2012CaPlasticitySynHandler::getTopSpike(
+ unsigned int index ) const
+{
+ if ( events_.empty() )
+ return 0.0;
+ return events_.top().time;
+}
+
+
void GraupnerBrunel2012CaPlasticitySynHandler::addPostSpike( const Eref& e, double time )
{
postEvents_.push( PostSynEvent( time ) );
diff --git a/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h b/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h
index 2c3055593acdba3bae06331e45b6a4cb2f5b1f8b..f7888602545b6b9742369e12dca5a4fcbbbb44be 100644
--- a/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h
+++ b/moose-core/synapse/GraupnerBrunel2012CaPlasticitySynHandler.h
@@ -95,6 +95,7 @@ class GraupnerBrunel2012CaPlasticitySynHandler: public SynHandlerBase
unsigned int addSynapse();
void dropSynapse( unsigned int droppedSynNumber );
void addSpike( unsigned int index, double time, double weight );
+ double getTopSpike( unsigned int index ) const;
////////////////////////////////////////////////////////////////
void addPostSpike( const Eref& e, double time );
diff --git a/moose-core/synapse/STDPSynHandler.cpp b/moose-core/synapse/STDPSynHandler.cpp
index 372e6d66dc60267e8f0997afd95fac722f0cb9bb..a414913b23b3d41d605158671d53c2a3fc0b53a6 100644
--- a/moose-core/synapse/STDPSynHandler.cpp
+++ b/moose-core/synapse/STDPSynHandler.cpp
@@ -190,6 +190,13 @@ void STDPSynHandler::addSpike(
events_.push( PreSynEvent( index, time, weight ) );
}
+double STDPSynHandler::getTopSpike( unsigned int index ) const
+{
+ if ( events_.empty() )
+ return 0.0;
+ return events_.top().time;
+}
+
void STDPSynHandler::addPostSpike( const Eref& e, double time )
{
postEvents_.push( PostSynEvent( time ) );
diff --git a/moose-core/synapse/STDPSynHandler.h b/moose-core/synapse/STDPSynHandler.h
index 947db5f13387af002c573e35dfb5affca8dbd672..c0f1446eff724a4f72b0283b9f3640da0fb6e6de 100644
--- a/moose-core/synapse/STDPSynHandler.h
+++ b/moose-core/synapse/STDPSynHandler.h
@@ -77,6 +77,7 @@ class STDPSynHandler: public SynHandlerBase
unsigned int addSynapse();
void dropSynapse( unsigned int droppedSynNumber );
void addSpike( unsigned int index, double time, double weight );
+ double getTopSpike( unsigned int index ) const;
////////////////////////////////////////////////////////////////
void addPostSpike( const Eref& e, double time );
diff --git a/moose-core/synapse/SeqSynHandler.cpp b/moose-core/synapse/SeqSynHandler.cpp
index 0f29f3d4fe21bc6e4cc1930c065b2749f115fdaa..cb8bb0b69f0670f156fb70bf9525cec45590b62b 100644
--- a/moose-core/synapse/SeqSynHandler.cpp
+++ b/moose-core/synapse/SeqSynHandler.cpp
@@ -513,6 +513,13 @@ void SeqSynHandler::addSpike(unsigned int index, double time, double weight)
latestSpikes_[ synapseOrder_[index] ] += weight;
}
+double SeqSynHandler::getTopSpike( unsigned int index ) const
+{
+ if ( events_.empty() )
+ return 0.0;
+ return events_.top().time;
+}
+
unsigned int SeqSynHandler::addSynapse()
{
unsigned int newSynIndex = synapses_.size();
diff --git a/moose-core/synapse/SeqSynHandler.h b/moose-core/synapse/SeqSynHandler.h
index 58ede36a4ef3042c185b803740ed56fb0c644baf..97b4800f507cdf133f91d480983da05e21b28b16 100644
--- a/moose-core/synapse/SeqSynHandler.h
+++ b/moose-core/synapse/SeqSynHandler.h
@@ -44,6 +44,7 @@ class SeqSynHandler: public SynHandlerBase
unsigned int addSynapse();
void dropSynapse( unsigned int droppedSynNumber );
void addSpike( unsigned int index, double time, double weight );
+ double getTopSpike( unsigned int index ) const;
////////////////////////////////////////////////////////////////
// New fields.
////////////////////////////////////////////////////////////////
diff --git a/moose-core/synapse/SimpleSynHandler.cpp b/moose-core/synapse/SimpleSynHandler.cpp
index b1323cb101783a530a8545f25849eb404f36841c..51100cd28bd0a3badb3ca8476356fa5e3ece8cfc 100644
--- a/moose-core/synapse/SimpleSynHandler.cpp
+++ b/moose-core/synapse/SimpleSynHandler.cpp
@@ -104,6 +104,13 @@ void SimpleSynHandler::addSpike(
events_.push( SynEvent( time, weight ) );
}
+double SimpleSynHandler::getTopSpike( unsigned int index ) const
+{
+ if ( events_.empty() )
+ return 0.0;
+ return events_.top().time;
+}
+
void SimpleSynHandler::vProcess( const Eref& e, ProcPtr p )
{
double activation = 0.0;
diff --git a/moose-core/synapse/SimpleSynHandler.h b/moose-core/synapse/SimpleSynHandler.h
index 9b3138bf0337783f9b4bfd95c800ab5aa6991d14..22ee6c90e8eb366da221254d9fc6a82dc0c3d0d2 100644
--- a/moose-core/synapse/SimpleSynHandler.h
+++ b/moose-core/synapse/SimpleSynHandler.h
@@ -61,6 +61,7 @@ class SimpleSynHandler: public SynHandlerBase
unsigned int addSynapse();
void dropSynapse( unsigned int droppedSynNumber );
void addSpike( unsigned int index, double time, double weight );
+ double getTopSpike( unsigned int index ) const;
////////////////////////////////////////////////////////////////
static const Cinfo* initCinfo();
private:
diff --git a/moose-core/synapse/SynHandlerBase.h b/moose-core/synapse/SynHandlerBase.h
index 660da06d6c8b7d63bcd70878b0d05d2c21839099..e3b3a3834c9008cff8e217a75c7580aa51d2f4d7 100644
--- a/moose-core/synapse/SynHandlerBase.h
+++ b/moose-core/synapse/SynHandlerBase.h
@@ -79,6 +79,7 @@ class SynHandlerBase
*/
virtual void addSpike(
unsigned int index, double time, double weight ) = 0;
+ virtual double getTopSpike( unsigned int index ) const = 0;
////////////////////////////////////////////////////////////////
// Virtual func definitions for fields.
////////////////////////////////////////////////////////////////
diff --git a/moose-core/synapse/Synapse.cpp b/moose-core/synapse/Synapse.cpp
index 17aa5a0daeb64bdcc31efb1cfc5c5ebc27f88186..30c97b1b8021622966b72b3320602e76dfdeb1dd 100644
--- a/moose-core/synapse/Synapse.cpp
+++ b/moose-core/synapse/Synapse.cpp
@@ -8,6 +8,7 @@
**********************************************************************/
#include "header.h"
+#include "ElementValueFinfo.h"
#include "SynHandlerBase.h"
#include "Synapse.h"
@@ -26,6 +27,13 @@ const Cinfo* Synapse::initCinfo()
&Synapse::setDelay,
&Synapse::getDelay
);
+ static ElementValueFinfo< Synapse, double > spikeTime(
+ "spikeTime",
+ "Value field interface to add spike (by assignment) and to "
+ "read the value of the spike on top of the queue.",
+ &Synapse::addSpike,
+ &Synapse::getTopSpike
+ );
static DestFinfo addSpike( "addSpike",
"Handles arriving spike messages, inserts into event queue.",
@@ -34,6 +42,7 @@ const Cinfo* Synapse::initCinfo()
static Finfo* synapseFinfos[] = {
&weight, // Field
&delay, // Field
+ &spikeTime, // ElementField
&addSpike, // DestFinfo
};
@@ -103,6 +112,11 @@ void Synapse::addSpike( const Eref& e, double time )
handler_->addSpike( e.fieldIndex(), time + delay_, weight_ );
}
+double Synapse::getTopSpike( const Eref& e ) const
+{
+ return handler_->getTopSpike( e.fieldIndex() );
+}
+
/////////////////////////////////////////////////////////////
// Callbacks for message add/drop
/////////////////////////////////////////////////////////////
diff --git a/moose-core/synapse/Synapse.h b/moose-core/synapse/Synapse.h
index 12e5915de832eab23cf8eaa5cb2d3af6c0a8d10b..4ac1593c8fd7a19a205099904a5d1fc9b90b1471 100644
--- a/moose-core/synapse/Synapse.h
+++ b/moose-core/synapse/Synapse.h
@@ -26,6 +26,7 @@ class Synapse
double getDelay() const;
void addSpike( const Eref& e, double time );
+ double getTopSpike( const Eref& e ) const;
void setHandler( SynHandlerBase* h );
diff --git a/moose-core/wheels/Dockerfile b/moose-core/wheels/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..cec973ab7386cb5fb611c360b6f4152ee026359b
--- /dev/null
+++ b/moose-core/wheels/Dockerfile
@@ -0,0 +1,17 @@
+FROM quay.io/pypa/manylinux1_x86_64
+MAINTAINER Dilawar Singh <dilawar.s.rajput@gmail.com>
+
+# If you are behind proxy, uncomment the following lines with appropriate
+# values. Otherwise comment them out.
+ENV http_proxy http://proxy.ncbs.res.in:3128
+ENV https_proxy http://proxy.ncbs.res.in:3128
+ENV PATH=/usr/local/bin:$PATH
+
+RUN yum update
+RUN yum install -y cmake28 && ln -sf /usr/bin/cmake28 /usr/bin/cmake
+RUN yum install -y wget
+RUN if [ ! -f /usr/local/lib/libgsl.a ]; then \
+ wget --no-check-certificate ftp://ftp.gnu.org/gnu/gsl/gsl-2.4.tar.gz && \
+ tar xvf gsl-2.4.tar.gz && cd gsl-2.4 && ./configure && make -j2 && \
+ make install && cd; fi
+RUN ./build_wheels.sh
diff --git a/moose-core/wheels/build_wheels.sh b/moose-core/wheels/build_wheels.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5509ea8530b8a80b009d79fd8db29de334ef8fa4
--- /dev/null
+++ b/moose-core/wheels/build_wheels.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+set -e
+set -x
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+MOOSE_SOURCE_DIR=/tmp/moose-core
+# Clone git or update.
+if [ ! -d $MOOSE_SOURCE_DIR ]; then
+ git clone -b wheels https://github.com/BhallaLab/moose-core --depth 10 $MOOSE_SOURCE_DIR
+else
+ cd $MOOSE_SOURCE_DIR && git pull && git merge master -X theirs && cd -
+fi
+
+# Try to link statically.
+GSL_STATIC_LIBS="/usr/local/lib/libgsl.a;/usr/local/lib/libgslcblas.a"
+CMAKE=/usr/bin/cmake28
+
+WHEELHOUSE=$HOME/wheelhouse
+mkdir -p $WHEELHOUSE
+for PYDIR in /opt/python/cp27-cp27m/ /opt/python/cp34-cp34m/ /opt/python/cp36-cp36m/; do
+ PYVER=$(basename $PYDIR)
+ mkdir -p $PYVER
+ (
+ cd $PYVER
+ echo "Building using $PYDIR in $PYVER"
+ PYTHON=$(ls $PYDIR/bin/python?.?)
+ $PYTHON -m pip install numpy
+ $CMAKE -DPYTHON_EXECUTABLE=$PYTHON \
+ -DGSL_STATIC_LIBRARIES=$GSL_STATIC_LIBS \
+ -DMOOSE_VERSION="3.2rc1" ${MOOSE_SOURCE_DIR}
+ make -j4
+
+ # Now build bdist_wheel
+ cd python
+ cp setup.cmake.py setup.py
+ $PYDIR/bin/pip wheel . -w $WHEELHOUSE
+ )
+done
+
+# now check the wheels.
+for whl in $WHEELHOUSE/*.whl; do
+ #auditwheel repair "$whl" -w $WHEELHOUSE
+ auditwheel show "$whl"
+done
+ls -lh $WHEELHOUSE/*.whl