From af3c29a4cff12f8572527cd79095d50d16c5da84 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed, 21 Jun 2017 10:48:03 +0530
Subject: [PATCH] Squashed 'moose-core/' changes from ef066f704..b3b597f41
b3b597f41 Removed legacy Makefile based build flow. CMake is only build-system now. #180.
20dc0a598 a warning message is sent out \n 1.if function is not connected to output and \n 2.yet to write back StimulusTable is to genesis. \n No more transformation with y axis as it has already taken care in kkit.py file
9373d1bc1 python Counter function removed, just to give backward compatibility for Centos6 for python 2.6
e8300d7e9 added to ask User if merged model to be saved
933b25971 Made ReadSwc less verbose. Fixed bug in SeqSynHandler in application of sequencePower.
662eaa2e1 Added sequencePower term to SeqSynHandler to achieve greater specificity for sequences vs all inputs on at once.
7ccc8a2b1 Merge branch 'master' of https://github.com/BhallaLab/moose-core
fe5765ca7 More fixes to plot_utils
6a9a618e7 Fixed the error in plot_tables utility.
658af76a4 Fix for Table.vector bug (#179)
423dc9dc6 Merge branch 'master' of https://github.com/BhallaLab/moose-core
200871a9f Added in hack for rmoogli to display time
157c501b9 reaction or enzyme name is empty then id is taken as name while reading files from SBML
43a235040 color and textcolor inchanged for enzyme
02de4c37e Bugfix for SparseMsg, corrects allocation of synapses when setting connectionList
git-subtree-dir: moose-core
git-subtree-split: b3b597f411500f5956976349f4d56b1cbc94f734
---
Makefile | 512 -----------------------
basecode/Makefile | 99 -----
benchmarks/Makefile | 31 --
biophysics/Makefile | 123 ------
biophysics/ReadSwc.cpp | 4 +-
builtins/Makefile | 68 ---
device/Makefile | 26 --
diffusion/Makefile | 36 --
examples/Makefile | 32 --
external/muparser/Makefile | 42 --
external/tinyxml/Makefile | 25 --
hsolve/Makefile | 52 ---
intfire/Makefile | 50 ---
kinetics/Makefile | 58 ---
ksolve/Makefile | 100 -----
mesh/Makefile | 55 ---
mpi/Makefile | 34 --
msg/Makefile | 44 --
msg/SparseMsg.cpp | 11 +-
pymoose/Makefile | 22 -
pymoose/mfield.cpp | 2 +-
python/moose/SBML/readSBML.py | 3 +-
python/moose/SBML/writeSBML.py | 6 +-
python/moose/chemUtil/chemConnectUtil.py | 5 +-
python/moose/genesis/writeKkit.py | 56 ++-
python/moose/merge/merge.py | 59 ++-
python/moose/plot_utils.py | 6 +-
python/rdesigneur/rmoogli.py | 25 +-
randnum/Makefile | 51 ---
scheduling/Makefile | 34 --
shell/Makefile | 49 ---
signeur/Makefile | 36 --
synapse/Makefile | 50 ---
synapse/SeqSynHandler.cpp | 27 +-
synapse/SeqSynHandler.h | 11 +
utility/Makefile | 45 --
36 files changed, 181 insertions(+), 1708 deletions(-)
delete mode 100644 Makefile
delete mode 100644 basecode/Makefile
delete mode 100644 benchmarks/Makefile
delete mode 100644 biophysics/Makefile
delete mode 100644 builtins/Makefile
delete mode 100644 device/Makefile
delete mode 100644 diffusion/Makefile
delete mode 100644 examples/Makefile
delete mode 100644 external/muparser/Makefile
delete mode 100644 external/tinyxml/Makefile
delete mode 100644 hsolve/Makefile
delete mode 100644 intfire/Makefile
delete mode 100644 kinetics/Makefile
delete mode 100644 ksolve/Makefile
delete mode 100644 mesh/Makefile
delete mode 100644 mpi/Makefile
delete mode 100644 msg/Makefile
delete mode 100644 pymoose/Makefile
delete mode 100644 randnum/Makefile
delete mode 100644 scheduling/Makefile
delete mode 100644 shell/Makefile
delete mode 100644 signeur/Makefile
delete mode 100644 synapse/Makefile
delete mode 100644 utility/Makefile
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 3df49b3d..00000000
--- a/Makefile
+++ /dev/null
@@ -1,512 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment,
-#** also known as GENESIS 3 base code.
-#** copyright (C) 2003- 2006 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-#######################################################################
-# NOTE:
-# This Makefile is compatible with _GNU Make_.
-# This does not work with nmake or borland make.
-# You may have to specify some variables when calling gnu make as
-# described in the comments below. The defaults should work on most
-# Unix clones.
-########################################################################
-
-# Linux compilation:
-# We recommend two levels of compilation: either full debug, with gdb,
-# unit tests and all the rest, or an optimized version for production
-# simulations, without any unit tests or assertions. If you want some
-# intermediate levels, edit the flags.
-######################################################################
-#
-# ADDITIONAL COMMANDLINE VARIABLES FOR MAKE
-#
-######################################################################
-# The variable BUILD determines if it should be optimized (release)
-# or a debug version (default).
-# make can be run with a command line parameter like below:
-# make clean BUILD=debug
-# make BUILD=debug
-# another option is to define BUILD as an environment variable:
-# export BUILD=debug
-# make clean
-# make
-#
-# There are some more variables which just need to be defined for
-# controlling the compilation and the value does not matter. These are:
-#
-# USE_GSL - use GNU Scientific Library for integration in kinetic simulations
-#
-# USE_READLINE - use the readline library which provides command history and
-# better command line editing capabilities
-#
-# GENERATE_WRAPPERS - useful for python interface developers. The binary created
-# with this option looks for a directory named 'generated' in the
-# working directory and creates a wrapper class ( one .h file
-# and a .cpp file ) and partial code for the swig interface file
-# (pymoose.i). These files with some modification can be used for
-# generating the python interface using swig.
-#
-# USE_MPI - compile with support for parallel computing through MPICH library
-
-
-# Default values for flags. The operator ?= assigns the given value only if the
-# variable is not already defined.
-
-USE_HDF5?=1
-USE_CUDA?=0
-USE_NEUROKIT?=0
-PYTHON?=2
-# BUILD (= debug, release)
-ifndef BUILD
-BUILD=release
-endif
-
-#If using mac uncomment the following lines
-# PLATFORM=mac
-#export PLATFORM
-
-# Get the processor architecture - i686 or x86_64
-# All these should be taken care of in a script, not in the
-# Makefile. But we are
-ifndef MACHINE
-MACHINE=i686
-endif
-# We are assuming all non-win32 systems to be POSIX compliant
-# and thus have the command uname for getting Unix system name
-ifneq ($(OSTYPE),win32)
-MACHINE=$(shell uname -m)
-PLATFORM := $(shell uname -s)
-endif
-
-USE_NUMPY=1
-# Debug mode:
-
-ifeq ($(BUILD),debug)
-CXXFLAGS = -g -O0 -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-# Optimized mode:
-ifeq ($(BUILD),release)
-CXXFLAGS = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-# Profiling mode:
-ifeq ($(BUILD),profile)
-CXXFLAGS = -O3 -pg -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-# Profiling mode with gperftoools
-ifeq ($(BUILD),gperf)
-CXXFLAGS = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-LDFLAGS += -lprofiler -ltcmalloc
-USE_GSL = true
-endif
-# Threading mode:
-ifeq ($(BUILD),thread)
-CXXFLAGS = -O3 -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-
-# MPI mode:
-ifeq ($(BUILD),mpi)
-CXXFLAGS = -g -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_MPI = 1
-USE_GSL = true
-endif
-
-# optimized MPI mode:
-ifeq ($(BUILD),ompi)
-CXXFLAGS = -O3 -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
-USE_MPI = 1
-USE_GSL = true
-endif
-
-# optimised mode but with unit tests.
-ifeq ($(BUILD),odebug)
-CXXFLAGS = -O3 -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-
-# including SMOLDYN
-ifdef USE_SMOLDYN
-CXXFLAGS = -g -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER
-USE_GSL = true
-endif
-
-# Use a strict compilation
-ifeq ($(BUILD),developer)
- CXXFLAGS=-g \
- -Wall -Werror -Wno-unused-variable -Wno-unused-function \
- -DDO_UNIT_TESTS -DDEVELOPER -DDEBUG
- USE_GSL = true
-endif
-##########################################################################
-#
-# MAC OS X compilation, Debug mode:
-ifeq ($(PLATFORM),Darwin)
-CXXFLAGS += -DMACOSX # GCC compiler also sets __APPLE__ for Mac OS X which can be used instead
-CXXFLAGS += -Wno-deprecated -force_cpusubtype_ALL -mmacosx-version-min=10.4
-endif
-# Use the options below for compiling on GCC4.1
-# GNU C++ 4.1 and newer might need -ffriend-injection
-#
-#CXXFLAGS = -g -Wall -pedantic -DDO_UNIT_TESTS -ffriend-injection -DUSE_GENESIS_PARSER
-
-# Insert the svn revision no. into the code as a preprocessor macro.
-# Only for release versions we want to pass SVN=0 to make.
-# No more SVN so pass zero
-SVN=0
-ifndef SVN
-SVN?=1
-endif
-empty :=
-space := $(empty) $(empty)
-ifneq ($(SVN),0)
-# Some versions of svnrevision return "Unversioned directory" which causes confusion to gcc
-SVN_REVISION := $(shell svnversion)
-SVN_REVISION := $(subst $(space),_,$(SVN_REVISION))
-# SVN_REVISION := $(subst :,_,$(SVN_REVISION))
-ifneq ($(SVN_REVISION),export)
-CXXFLAGS+=-DSVN_REVISION=\"$(SVN_REVISION)\"
-endif
-endif
-
-
-# Libraries are defined below.
-SUBLIBS =
-# Notice that pthread is no more included
-LIBS = -L/usr/lib -L/usr/local/lib
-
-#LIBS = -lm
-
-# For 64 bit Linux systems add paths to 64 bit libraries
-ifeq ($(PLATFORM),Linux)
-CXXFLAGS += -DLINUX
-ifeq ($(MACHINE),x86_64)
-LIBS+= -L/lib64 -L/usr/lib64
-endif
-endif
-
-##########################################################################
-#
-# Developer options (Don't try these unless you are writing new code!)
-##########################################################################
-# For parallel (MPI) version:
-ifdef USE_MUSIC
-USE_MPI = 1 # Automatically enable MPI if USE_MUSIC is on
-CXXFLAGS += -DUSE_MUSIC
-LIBS += -lmusic
-endif
-
-# The -DMPICH_IGNORE_CXX_SEEK flag is because of a bug in the
-# MPI-2 standard. Enabled by default because it use crops up
-# often enough. You won't need if if you are not using MPICH, or
-# if your version of MPICH has fixed the issue.
-ifdef USE_MPI
-# CXXFLAGS += -DUSE_MPI
-CXXFLAGS += -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK
-endif
-
-#use this for readline library
-#CXXFLAGS = -g -Wall -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DUSE_READLINE
-
-
-# To use GSL, pass USE_GSL=true ( anything on the right will do) in make command line
-ifdef USE_GSL
-LIBS+= $(shell gsl-config --libs)
-#LIBS+= -L/usr/lib -Wl,--no-as-needed -lgsl -lgslcblas -lm
-#LIBS+= -L/usr/lib -lgsl -lgslcblas -lm
-CXXFLAGS+= -DUSE_GSL
-else
-LIBS+= -lm
-endif
-
-#Saeed
-# To use CUDA, pass USE_CUDA=1 in make command line
-ifeq ($(USE_CUDA),1)
-LIBS+= -L/usr/local/cuda/lib64 -LhsolveCuda/cudaLibrary -lcuda -lcudart -lm -lmooseCudaLibrary
-HCUDA_DIR = hsolveCuda
-HCUDA_LIB = hsolveCuda/_hsolveCuda.o
-endif
-
-# To disable numpy pass USE_NUMPY=0
-ifeq ($(USE_NUMPY),1)
-CXXFLAGS+=-DUSE_NUMPY
-endif
-
-# To compile examples, pass EXAMPLES=true ( anything on the right will do) in make command line
-ifdef EXAMPLES
-EXAMPLES_DIR = examples
-EXAMPLES_LIB = examples/_trials.o
-endif
-
-# To use Smoldyn, pass USE_SMOLDYN=true ( anything on the right will do) in make command line
-ifdef USE_SMOLDYN
-#LIBS+= -L/usr/local/lib -lsmoldyn
-CXXFLAGS+= -DUSE_SMOLDYN
-SMOLDYN_DIR = smol
-SMOLDYN_LIB = smol/_smol.o /usr/local/lib/libsmoldyn.a
-LIBS += -lsmoldyn
-endif
-
-# To compile with readline support pass USE_READLINE=true in make command line
-ifdef USE_READLINE
-LIBS+= -lreadline
-CXXFLAGS+= -DUSE_READLINE
-endif
-
-# To compile with curses support (terminal aware printing) pass USE_CURSES=true in make command line
-ifdef USE_CURSES
-LIBS += -lcurses
-CXXFLAGS+= -DUSE_CURSES
-endif
-
-ifdef USE_MUSIC
- MUSIC_DIR = music
- MUSIC_LIB = music/music.o
-endif
-
-# Here we automagically change compilers to deal with MPI.
-ifdef USE_MPI
- CXX = mpicxx --std=c++11
-# CXX = /usr/local/mvapich2/bin/mpicxx
-# PARALLEL_DIR = parallel
-# PARALLEL_LIB = parallel/parallel.o
-else
- CXX = g++ --std=c++11
-# CXX = CC # Choose between Solaris CC and g++ on a Solaris machine
-endif
-
-ifeq ($(USE_HDF5),1)
- CXXFLAGS+= -DUSE_HDF5 -DH5_NO_DEPRECATED_SYMBOLS -I/usr/local/hdf5/include -I/usr/include/hdf5/serial
- LIBS+= -lhdf5 -lhdf5_hl -L/usr/local/hdf5/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial/
-endif
-
-LD = ld
-
-SUBDIR = \
- basecode \
- msg \
- shell \
- randnum\
- scheduling\
- mpi \
- builtins\
- utility \
- external/muparser \
- biophysics \
- synapse \
- intfire \
- kinetics \
- ksolve \
- mesh \
- hsolve \
- diffusion \
- device \
- signeur \
- benchmarks \
- $(SMOLDYN_DIR) \
- $(SBML_DIR) \
- $(HCUDA_DIR) \
- $(EXAMPLES_DIR) \
-
-# Used for 'make clean'
-CLEANSUBDIR = $(SUBDIR) $(PARALLEL_DIR) pymoose
-
-OBJLIBS = \
- basecode/_basecode.o \
- msg/_msg.o \
- shell/_shell.o \
- randnum/_randnum.o \
- scheduling/_scheduling.o \
- mpi/_mpi.o \
- builtins/_builtins.o \
- utility/_utility.o \
- external/muparser/_muparser.o \
- biophysics/_biophysics.o \
- synapse/_synapse.o \
- intfire/_intfire.o \
- kinetics/_kinetics.o \
- ksolve/_ksolve.o \
- hsolve/_hsolve.o \
- mesh/_mesh.o \
- diffusion/_diffusion.o \
- device/_device.o \
- signeur/_signeur.o \
- benchmarks/_benchmarks.o \
- $(SMOLDYN_LIB) \
- $(SBML_LIB) \
- $(HCUDA_LIB) \
- $(EXAMPLES_LIB) \
-
-
-ifeq ($(USE_NEUROKIT),1)
- NEUROKIT_COMMAND = cd ./python/moogli; python setup.py build; cd ../../; cp ./python/moogli/build/*/_moogli.so ./python/moogli/;
-# else
-# NEUROKIT_COMMAND = ""
-endif
-
-
-export CXX
-export CXXFLAGS
-export LD
-export LIBS
-export USE_GSL
-#export USE_SBML
-
-all: moose pymoose
-
-neurokit: ./python/moogli/setup.py
- $(NEUROKIT_COMMAND)
-
-moose: libs $(OBJLIBS) $(PARALLEL_LIB)
- $(CXX) $(CXXFLAGS) $(OBJLIBS) $(PARALLEL_LIB) $(LIBS) -o moose
- @echo "Moose compilation finished"
-
-libmoose.so: libs
- $(CXX) -G $(LIBS) -o libmoose.so
- @echo "Created dynamic library"
-
-# Get the python version
-ifneq ($(OSTYPE),win32)
-ifeq ($(PYTHON),3)
-PYTHON_VERSION := $(subst ., ,$(lastword $(shell python3 --version 2>&1)))
-PYTHON_CFLAGS := $(shell python3-config --cflags)
-PYTHON_LDFLAGS := $(shell python3-config --ldflags)
-else # Python 2.x
-PYTHON_VERSION := $(subst ., ,$(lastword $(shell python --version 2>&1)))
-ifneq ($(BUILD),debug)
-PYTHON_CFLAGS := $(shell python-config --cflags)
-PYTHON_LDFLAGS := $(shell python-config --ldflags)
-else
-PYTHON_CFLAGS := $(shell python-config --includes) \
- -fno-strict-aliasing -fwrapv \
- -Wstrict-prototypes \
- -Wformat -Wformat-security -Werror=format-security \
- -fstack-protector --param=ssp-buffer-size=4
-
-PYTHON_LDFLAGS := -L/usr/lib/$(INSTALLED_PYTHON) \
- -Xlinker -export-dynamic -Wl,-O0 -Wl,-Bsymbolic-functions
-endif # ifneq ($(BUILD),debug)
-endif # ifeq ($(PYTHON),3)
-PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION})
-PYTHON_VERSION_MINOR := $(word 2,${PYTHON_VERSION})
-INSTALLED_PYTHON := python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-endif
-
-# For developer build and strict checking
-ifeq ($(BUILD),developer)
- PYTHON_CFLAGS := $(PYTHON_CFLAGS) -Wall -Werror -Wno-unused-function -Wno-unused-variable
-endif # ifeq(${BUILD},developer)
-
-ifndef PYTHON_CFLAGS
-PYTHON_CFLAGS := -I/usr/include/$(INSTALLED_PYTHON) -fno-strict-aliasing \
- -fwrapv \
- -fstack-protector \
- #-Wstrict-prototypes \ # This option is obsolete for g++-4.8
- --param=ssp-buffer-size=4 \
- -Wformat -Wformat-security -Werror=format-security
-
-PYTHON_LDFLAGS := -L/usr/lib/$(INSTALLED_PYTHON) -Xlinker -export-dynamic -Wl,-O0 -Wl,-Bsymbolic-functions
-endif
-# There are some unix/gcc specific paths here. Should be cleaned up in future.
-pymoose: python/moose/_moose.so
-pymoose: CXXFLAGS += -DPYMOOSE $(PYTHON_CFLAGS)
-# fix: add include dir for numpy headers required by pymoose/moosemodule.cpp
-pymoose: CXXFLAGS += -I$(shell /usr/bin/python -c 'from numpy import get_include; print get_include()')
-pymoose: OBJLIBS += pymoose/_pymoose.o
-pymoose: LDFLAGS += $(PYTHON_LDFLAGS)
-export CXXFLAGS
-python/moose/_moose.so: libs $(OBJLIBS)
- $(MAKE) -C pymoose
- $(CXX) -shared $(LDFLAGS) $(CXXFLAGS) -o $@ $(OBJLIBS) $(LIBS)
- @echo "pymoose module built."
-
-# This will generate an object file without main
-libs:
- @for i in $(SUBDIR) $(PARALLEL_DIR); do \
- $(MAKE) -C $$i || exit $$?; \
- done
- @echo "All Libs compiled"
-
-clean:
- @(for i in $(CLEANSUBDIR) ; do $(MAKE) -C $$i clean; done)
- -rm -rf moose core.* DOCS/html python/moose/*.so python/moose/*.pyc
-
-############ INSTALL (works for sudo make install and deb packaging using dpkg-buildpackage)
-## get the default python module install location
-## no need to know this, the default for public modules is /usr/share/pyshared
-pydir_cmd := python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"
-pydistpkg_dir := $(shell $(pydir_cmd))
-## /usr/share/pyshared/ is a directory which is independent of python version,
-## but modules need to be registered with update-python-modules, giving a list of files
-## debhelper (dpkg-buildpackage) will also copy to this location and do the registration.
-## For make install, I stick to the default python .../dist-packages directory.
-pydistpkg_dirB := /usr/share/pyshared/
-
-username=$(shell basename $(HOME))
-
-install_prefix=/usr
-## Note that $(DESTDIR) is provided by dpkg-buildpackage to specify the local install for deb packaging
-## if doing sudo make install, $(DESTDIR) will be undefined and will cause no trouble
-install:
- ## discard symbols from object files
- strip python/moose/_moose.so
-
- ## delete older .../share/moose, - before rm means ignore errors (eg not found)
- -rm -rf $(DESTDIR)$(install_prefix)/share/moose
- ## -p creates parent directories also if they don't exist
- mkdir -p $(DESTDIR)$(install_prefix)/share/moose
- ## copy filtering out the .svn (hidden) files
- rsync -r --exclude=.svn Demos/* $(DESTDIR)$(install_prefix)/share/moose/Demos
- rsync -r --exclude=.svn gui/* $(DESTDIR)$(install_prefix)/share/moose/gui
- test -d $(DESTDIR)$(install_prefix)/share/doc || mkdir -p $(DESTDIR)$(install_prefix)/share/doc
- rsync -r --exclude=.svn Docs/* $(DESTDIR)$(install_prefix)/share/doc/moose
- # rsync -r --exclude=.svn Demos/* $(DESTDIR)$(install_prefix)/share/moose/
- ## pymoose module goes to python's dist-packages
- ## delete older .../dist-packages/moose, - before rm means ignore errors (eg not found)
- -rm -rf $(DESTDIR)$(pydistpkg_dir)/moose
- -rm -rf $(DESTDIR)$(pydistpkg_dirB)/moose
- ## make directory in case non-existent (needed for deb pkg building)
- mkdir -p $(DESTDIR)$(pydistpkg_dir)
- rsync -r --exclude=.svn --exclude=moose_py3k.py python/* $(DESTDIR)$(pydistpkg_dir)/
-
- ## shell command moosegui for the moose GUI.
- chmod a+x $(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py
- ## -rm instructs make to ignore errors from make eg. file not found
- -rm -f $(DESTDIR)$(install_prefix)/bin/moosegui
- mkdir -p $(DESTDIR)$(install_prefix)/bin
- ln -s $(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py $(DESTDIR)$(install_prefix)/bin/moosegui
-
- ## byte compile the module, gui, Demos (since, later running as user cannot create .pyc in root-owned dirs)
- python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(pydistpkg_dir)/moose',force=1)"
- python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(install_prefix)/share/moose/gui',force=1)"
- python -c "import compileall; compileall.compile_dir('$(DESTDIR)$(install_prefix)/share/moose/Demos',force=1)"
-
- ## see standards.freedesktop.org for specifications for where to put menu entries and icons
- ## copy the .desktop files to /usr/share/applications for link to show up in main menu
- mkdir -p $(DESTDIR)$(install_prefix)/share/applications
- cp gui/MooseGUI.desktop $(DESTDIR)$(install_prefix)/share/applications/
- cp gui/MooseSquidAxon.desktop $(DESTDIR)$(install_prefix)/share/applications/
- ## copy the .desktop files to the desktop too to get icons
- cp gui/MooseGUI.desktop $$HOME/Desktop/
- chmod a+x $$HOME/Desktop/MooseGUI.desktop
- chown $(username) $(HOME)/Desktop/MooseGUI.desktop
- chgrp $(username) $(HOME)/Desktop/MooseGUI.desktop
- cp gui/MooseSquidAxon.desktop $$HOME/Desktop/
- chmod a+x $$HOME/Desktop/MooseSquidAxon.desktop
- chgrp $(username) $(HOME)/Desktop/MooseSquidAxon.desktop
- chown $(username) $(HOME)/Desktop/MooseSquidAxon.desktop
- ## copy icon to /usr/share/icons/hicolor/<size>/apps (hicolor is the fallback theme)
- mkdir -p $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps
- cp gui/icons/moose_icon.png $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps/
- cp gui/icons/squid.png $(DESTDIR)$(install_prefix)/share/icons/hicolor/scalable/apps/
- ## need to update the icon cache to show the icon
- update-icon-caches $(DESTDIR)$(install_prefix)/share/icons/hicolor/
-
-.PHONY: install
diff --git a/basecode/Makefile b/basecode/Makefile
deleted file mode 100644
index 0639a32c..00000000
--- a/basecode/Makefile
+++ /dev/null
@@ -1,99 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment,
-#** also known as GENESIS 3 base code.
-#** copyright (C) 2004 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-# $Id: $
-#
-# $Log: $
-#
-
-TARGET = _basecode.o
-
-
-# CXXFLAGS += -I.. -I../kinetics -I../biophysics
-
-OBJ = \
- consts.o \
- Element.o \
- DataElement.o \
- GlobalDataElement.o \
- LocalDataElement.o \
- Eref.o \
- Finfo.o \
- DestFinfo.o \
- Cinfo.o \
- SrcFinfo.o \
- ValueFinfo.o \
- SharedFinfo.o \
- FieldElementFinfo.o \
- FieldElement.o \
- Id.o \
- ObjId.o \
- global.o \
- SetGet.o \
- OpFuncBase.o \
- EpFunc.o \
- HopFunc.o \
- SparseMatrix.o \
- doubleEq.o \
- testAsync.o \
- main.o \
-
-HEADERS = \
- header.h \
- Cinfo.h \
- Conv.h \
- Dinfo.h \
- MsgDigest.h \
- Element.h \
- DataElement.h \
- GlobalDataElement.h \
- LocalDataElement.h \
- Eref.h \
- global.h \
- Finfo.h \
- DestFinfo.h \
- Id.h \
- ObjId.h \
- ../msg/Msg.h \
- OpFuncBase.h \
- OpFunc.h \
- EpFunc.h \
- HopFunc.h \
- ProcInfo.h \
- SrcFinfo.h \
- ValueFinfo.h \
- LookupValueFinfo.h \
- LookupElementValueFinfo.h \
- SharedFinfo.h \
- FieldElementFinfo.h \
- FieldElement.h \
- MsgFuncBinding.h \
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS) ../shell/Shell.h
-Element.o: FuncOrder.h
-testAsync.o: SparseMatrix.h SetGet.h ../scheduling/Clock.h ../biophysics/IntFire.h ../synapse/SynEvent.h ../synapse/SynHandlerBase.h ../synapse/SimpleSynHandler.h ../synapse/Synapse.h ../randnum/RNG.h
-SparseMsg.o: SparseMatrix.h
-SetGet.o: SetGet.h ../shell/Neutral.h
-HopFunc.o: HopFunc.h ../mpi/PostMaster.h
-global.o: global.h ../randnum/RNG.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) -I../msg -I.. $< -c
-
-.PHONY: pymoose
-
-pymoose: CXXFLAGS += -DPYMOOSE
-
-$(TARGET): $(OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/benchmarks/Makefile b/benchmarks/Makefile
deleted file mode 100644
index 0eb5aef3..00000000
--- a/benchmarks/Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _benchmarks.o
-
-OBJ = \
- benchmarks.o \
- kineticMarks.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-kineticMarks.o: ../shell/Shell.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/biophysics/Makefile b/biophysics/Makefile
deleted file mode 100644
index 6659630c..00000000
--- a/biophysics/Makefile
+++ /dev/null
@@ -1,123 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _biophysics.o
-
-OBJ = \
- IntFire.o \
- SpikeGen.o \
- RandSpike.o \
- CompartmentDataHolder.o \
- CompartmentBase.o \
- Compartment.o \
- SymCompartment.o \
- GapJunction.o \
- ChanBase.o \
- ChanCommon.o \
- HHChannelBase.o \
- HHChannel.o \
- HHGate.o \
- HHGate2D.o \
- HHChannel2D.o \
- CaConcBase.o \
- CaConc.o \
- MgBlock.o \
- Nernst.o \
- Neuron.o \
- Spine.o \
- ReadCell.o \
- SwcSegment.o \
- ReadSwc.o \
- SynChan.o \
- NMDAChan.o \
- testBiophysics.o \
- IzhikevichNrn.o \
- DifShellBase.o \
- DifShell.o \
- DifBufferBase.o \
- DifBuffer.o \
- Leakage.o \
- VectorTable.o \
- MarkovRateTable.o \
- MarkovChannel.o \
- MarkovGslSolver.o \
- MatrixOps.o \
- MarkovSolverBase.o \
- MarkovSolver.o \
- VClamp.o \
-
-
- # MMpump.o \
- # LeakyIaF.o \
- # GapJunction.o \
- # Nernst.o \
- # GHK.o \
- # NMDAChan.o \
-
-# GSL_LIBS = -L/usr/lib -lgsl
-
-HEADERS = \
- ../basecode/header.h \
- ../utility/numutil.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-IntFire.o: IntFire.h
-SpikeGen.o: SpikeGen.h
-RandSpike.o: RandSpike.h ../randnum/randnum.h
-CompartmentDataHolder.o: CompartmentDataHolder.h
-CompartmentBase.o: CompartmentBase.h CompartmentDataHolder.h
-Compartment.o: CompartmentBase.h Compartment.h
-SymCompartment.o: CompartmentBase.h Compartment.h SymCompartment.h
-ChanBase.o: ChanBase.h
-ChanCommon.o: ChanBase.h ChanCommon.h
-SynChan.o: SynChan.h ChanBase.h ChanCommon.h
-NMDAChan.o: NMDAChan.h SynChan.h ChanBase.h ChanCommon.h
-Leakage.o: Leakage.h ChanBase.h ChanCommon.h
-GapJunction.o: GapJunction.h
-HHChannelBase.o: ChanBase.h HHChannelBase.h HHGate.h
-HHChannel.o: ChanBase.h HHChannel.h HHGate.h
-HHGate.o: HHGate.h
-HHChannel2D.o: ChanBase.h HHChannel2D.h HHGate2D.h
-HHGate2D.o: HHGate2D.h
-CaConcBase.o: CaConcBase.h
-CaConc.o: CaConcBase.h CaConc.h
-MgBlock.o: MgBlock.h ChanBase.h
-Nernst.o: Nernst.h
-Neuron.o: Neuron.h SwcSegment.h Spine.h
-Spine.o: Neuron.h SwcSegment.h Spine.h
-ReadCell.o: CompartmentBase.h Compartment.h SymCompartment.h ReadCell.h ../shell/Shell.h ../utility/utility.h
-SwcSegment.o: SwcSegment.h ../utility/Vec.h
-ReadSwc.o: CompartmentBase.h Compartment.h SymCompartment.h SwcSegment.h ReadSwc.h ../shell/Shell.h ../utility/Vec.h
-IzhikevichNrn.o: IzhikevichNrn.h
-DifShellBase.o: DifShellBase.h
-DifShell.o: DifShellBase.h DifShell.h
-DifBufferBase.o: DifBufferBase.h
-DifBuffer.o: DifBufferBase.h DifBuffer.h
-MMPump.o: MMPump.h
-testBiophysics.o: IntFire.h CompartmentBase.h Compartment.h HHChannel.h HHGate.h
-VectorTable.o : VectorTable.h
-MarkovGslSolver.o : MarkovGslSolver.h
-MatrixOps.o : MatrixOps.h
-MarkovRateTable.o : VectorTable.h ../builtins/Interpol2D.h MarkovRateTable.h
-MarkovSolverBase.o : MarkovSolver.h MatrixOps.h MarkovRateTable.h
-MarkovSolver.o : MarkovSolverBase.h MarkovSolver.h
-MarkovChannel.o : VectorTable.h ../builtins/Interpol2D.h MarkovRateTable.h ChanBase.h MarkovChannel.h
-VClamp.o: VClamp.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../external/muparser/include -I .. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
- rm -f *.o $(TARGET) core core.*
diff --git a/biophysics/ReadSwc.cpp b/biophysics/ReadSwc.cpp
index 3fde18ec..69ca680a 100644
--- a/biophysics/ReadSwc.cpp
+++ b/biophysics/ReadSwc.cpp
@@ -53,7 +53,9 @@ ReadSwc::ReadSwc( const string& fname )
cleanZeroLength();
parseBranches();
}
- cout << "ReadSwc: " << fname << " : " << (valid ? "OK" : "FAILED" )<<
+ if ( verbose || !valid || (badSegs > 0) )
+ cout << "ReadSwc: " << fname <<
+ " : " << (valid ? "OK" : "FAILED" )<<
", # Branches = " << branches_.size() <<
". # Segs = " << segs_.size() <<
", bad = " << badSegs <<
diff --git a/builtins/Makefile b/builtins/Makefile
deleted file mode 100644
index 7ff1cebe..00000000
--- a/builtins/Makefile
+++ /dev/null
@@ -1,68 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _builtins.o
-
-OBJ = \
- Arith.o \
- Group.o \
- Mstring.o \
- Func.o \
- Function.o \
- Variable.o \
- InputVariable.o \
- TableBase.o \
- Table.o \
- Interpol.o \
- StimulusTable.o \
- TimeTable.o \
- Stats.o \
- SpikeStats.o \
- Interpol2D.o \
- HDF5WriterBase.o \
- HDF5DataWriter.o \
- StreamerBase.o \
- Streamer.o \
- NSDFWriter.o \
- testNSDF.o \
- testBuiltins.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-Arith.o: Arith.h
-Group.o: Group.h
-Mstring.o: Mstring.h
-Func.o: Func.h
-Function.o: Function.h
-Variable.o: Variable.h
-TableBase.o: TableBase.h
-Table.o: TableBase.h Table.h
-Interpol.o: TableBase.h Interpol.h
-StimulusTable.o: TableBase.h StimulusTable.h
-TimeTable.o: TimeTable.h TableBase.h
-Stats.o: Stats.h
-SpikeStats.o: Stats.h SpikeStats.h
-Interpol2D.o: Interpol2D.h
-HDF5WriterBase.o: HDF5WriterBase.h
-HDF5DataWriter.o: HDF5DataWriter.h HDF5WriterBase.h
-testBuiltins.o: Group.h Arith.h Stats.h ../msg/DiagonalMsg.h ../basecode/SetGet.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../scheduling -I../basecode -I../msg -I../external/muparser/include $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/device/Makefile b/device/Makefile
deleted file mode 100644
index 159d8805..00000000
--- a/device/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-TARGET = _device.o
-
-OBJ = PulseGen.o \
- DiffAmp.o \
- PIDController.o \
- RC.o
-
-HEADERS = \
- ../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ): $(HEADERS)
-PulseGen.o: PulseGen.h
-DiffAmp.o: DiffAmp.h
-PIDController.o: PIDController.h
-RC.o: RC.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
- rm -f *.o $(TARGET) core core.*
diff --git a/diffusion/Makefile b/diffusion/Makefile
deleted file mode 100644
index 458a5ba9..00000000
--- a/diffusion/Makefile
+++ /dev/null
@@ -1,36 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _diffusion.o
-
-OBJ = \
- FastMatrixElim.o \
- DiffPoolVec.o \
- Dsolve.o \
- testDiffusion.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-FastMatrixElim.o: ../basecode/SparseMatrix.h FastMatrixElim.h
-Dsolve.o: ../basecode/SparseMatrix.h ../kinetics/PoolBase.h ../kinetics/lookupVolumeFromMesh.h ../mesh/ChemCompt.h ../ksolve/XferInfo.h ../ksolve/ZombiePoolInterface.h
-DiffPoolVec.o: DiffPoolVec.h ../ksolve/ZombiePoolInterface.h
-testDiffusion.o: Dsolve.h ../ksolve/ZombiePoolInterface.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(GSL_FLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../ksolve $< -c
-
-$(TARGET): $(OBJ) $(GSL_OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(GSL_OBJ) $(GSL_LIBS) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/examples/Makefile b/examples/Makefile
deleted file mode 100644
index 1e7f10ab..00000000
--- a/examples/Makefile
+++ /dev/null
@@ -1,32 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _trials.o
-
-OBJ = \
- Example.o \
- Ex.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-Example.o: Example.h ../basecode/ElementValueFinfo.h
-Ex.o: Ex.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/external/muparser/Makefile b/external/muparser/Makefile
deleted file mode 100644
index 6b8bb423..00000000
--- a/external/muparser/Makefile
+++ /dev/null
@@ -1,42 +0,0 @@
-# Makefile for including muParser into moose.
-# Author: Subhasis Ray
-#
-TARGET = _muparser.o
-
-OBJ = \
- src/muParserBase.o \
- src/muParserBytecode.o \
- src/muParserCallback.o \
- src/muParser.o \
- src/muParserDLL.o \
- src/muParserError.o \
- src/muParserInt.o \
- src/muParserTokenReader.o \
-
-HEADERS = \
- include/muParser.h \
- include/muParserBase.h \
- include/muParserBytecode.h \
- include/muParserCallback.h \
- include/muParserDef.h \
- include/muParserError.h \
- include/muParserFixes.h \
- include/muParserStack.h \
- include/muParserToken.h \
- include/muParserTokenReader.h \
- include/muParserTemplateMagic.h \
-
-
-default: $(TARGET)
-
-$(OBJ): $(HEADERS)
-
-%.o: %.cpp
- $(CXX) $(CXXFLAGS) -I. -I../../ -Iinclude $< -c -o $@
-
-$(TARGET): $(OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
-
diff --git a/external/tinyxml/Makefile b/external/tinyxml/Makefile
deleted file mode 100644
index 45639837..00000000
--- a/external/tinyxml/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-# Makefile for including muParser into moose.
-# Author: Subhasis Ray
-#
-TARGET = _tinyxml2.o
-
-OBJ = \
- tinyxml2.o
-
-HEADERS = \
- tinyxml2.h \
-
-
-default: $(TARGET)
-
-$(OBJ): $(HEADERS)
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) -I. $< -c
-
-$(TARGET): $(OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
-
diff --git a/hsolve/Makefile b/hsolve/Makefile
deleted file mode 100644
index da4e33a3..00000000
--- a/hsolve/Makefile
+++ /dev/null
@@ -1,52 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment,
-#** also known as GENESIS 3 base code.
-#** copyright (C) 2004 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU General Public License version 2
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _hsolve.o
-
-OBJ = \
- HSolveStruct.o \
- HinesMatrix.o \
- HSolvePassive.o \
- RateLookup.o \
- HSolveActive.o \
- HSolveActiveSetup.o \
- HSolveInterface.o \
- HSolve.o \
- HSolveUtils.o \
- testHSolve.o \
- ZombieCompartment.o \
- ZombieCaConc.o \
- ZombieHHChannel.o \
-
-HEADERS = \
- ../basecode/header.h
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-HSolveStruct.o: HSolveStruct.h
-HinesMatrix.o: HinesMatrix.h TestHSolve.h
-HSolvePassive.o: HSolvePassive.h HinesMatrix.h HSolveStruct.h HSolveUtils.h TestHSolve.h ../biophysics/Compartment.h
-RateLookup.o: RateLookup.h
-HSolveActive.o: HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h
-HSolveActiveSetup.o: HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h HSolveUtils.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHGate.h ../biophysics/CaConc.h
-HSolveInterface.o: HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h
-HSolve.o: ../biophysics/Compartment.h ZombieCompartment.h ../biophysics/CaConc.h ZombieCaConc.h ../biophysics/HHGate.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ZombieHHChannel.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-ZombieCompartment.o: ../biophysics/CompartmentBase.h ZombieCompartment.h ../biophysics/Compartment.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-ZombieCaConc.o: ZombieCaConc.h ../biophysics/CaConc.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-ZombieHHChannel.o: ZombieHHChannel.h ../biophysics/HHChannelBase.h ../biophysics/HHChannel.h ../biophysics/ChanBase.h ../biophysics/ChanCommon.h ../biophysics/HHGate.h HSolve.h HSolveActive.h RateLookup.h HSolvePassive.h HinesMatrix.h HSolveStruct.h ../basecode/ElementValueFinfo.h
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
- rm -f *.o $(TARGET) core core.*
diff --git a/intfire/Makefile b/intfire/Makefile
deleted file mode 100644
index 22261ff9..00000000
--- a/intfire/Makefile
+++ /dev/null
@@ -1,50 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _intfire.o
-
-OBJ = \
- IntFireBase.o \
- LIF.o \
- QIF.o \
- ExIF.o \
- AdExIF.o \
- AdThreshIF.o \
- IzhIF.o \
- testIntFire.o \
-
-# GSL_LIBS = -L/usr/lib -lgsl
-
-HEADERS = \
- ../basecode/header.h \
- ../utility/numutil.h \
- IntFireBase.h \
- ../biophysics/CompartmentBase.h \
- ../biophysics/Compartment.h
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-LIF.o: LIF.h
-QIF.o: QIF.h
-ExIF.o: ExIF.h
-AdExIF.o: AdExIF.h
-AdThreshIF.o: AdThreshIF.h
-IzhIF.o: IzhIF.h
-testIntFire.o: LIF.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
- rm -f *.o $(TARGET) core core.*
diff --git a/kinetics/Makefile b/kinetics/Makefile
deleted file mode 100644
index 9b1f6375..00000000
--- a/kinetics/Makefile
+++ /dev/null
@@ -1,58 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _kinetics.o
-
-OBJ = \
- PoolBase.o \
- Pool.o \
- BufPool.o \
- ReacBase.o \
- Reac.o \
- EnzBase.o \
- CplxEnzBase.o \
- Enz.o \
- MMenz.o \
- Species.o \
- ReadKkit.o \
- WriteKkit.o \
- ReadCspace.o \
- lookupVolumeFromMesh.o \
- testKinetics.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-Pool.o: PoolBase.h Pool.h lookupVolumeFromMesh.h
-BufPool.o: PoolBase.h Pool.h BufPool.h lookupVolumeFromMesh.h
-ReacBase.o: ReacBase.h lookupVolumeFromMesh.h
-Reac.o: ReacBase.h Reac.h lookupVolumeFromMesh.h
-EnzBase.o: EnzBase.h lookupVolumeFromMesh.h
-CplxEnzBase.o: EnzBase.h CplxEnzBase.h lookupVolumeFromMesh.h
-Enz.o: EnzBase.h CplxEnzBase.h Enz.h lookupVolumeFromMesh.h
-MMenz.o: EnzBase.h MMenz.h lookupVolumeFromMesh.h
-Boundary.o: Boundary.h
-Species.o: Species.h
-ReadKkit.o: lookupVolumeFromMesh.h ReadKkit.h PoolBase.h Pool.h ../shell/Shell.h
-WriteKkit.o: lookupVolumeFromMesh.h PoolBase.h
-ReadCspace.o: lookupVolumeFromMesh.h ReadCspace.h ../shell/Shell.h
-lookupVolumeFromMesh.o: lookupVolumeFromMesh.h
-testKinetics.o: ReadKkit.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/ksolve/Makefile b/ksolve/Makefile
deleted file mode 100644
index 49b51df4..00000000
--- a/ksolve/Makefile
+++ /dev/null
@@ -1,100 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _ksolve.o
-
-OBJ = \
- KinSparseMatrix.o \
- ZombiePool.o \
- ZombieBufPool.o \
- ZombieReac.o \
- ZombieEnz.o \
- ZombieMMenz.o \
- ZombieFunction.o \
- VoxelPoolsBase.o \
- VoxelPools.o \
- GssaVoxelPools.o \
- RateTerm.o \
- FuncTerm.o \
- Stoich.o \
- Ksolve.o \
- SteadyStateGsl.o \
- Gsolve.o \
- ZombiePoolInterface.o \
- testKsolve.o \
-
-HEADERS = \
- ../basecode/header.h \
- ../basecode/SparseMatrix.h \
- ../basecode/ElementValueFinfo.h \
- RateTerm.h \
- ../external/muparser/include/muParser.h \
- FuncTerm.h \
- KinSparseMatrix.h \
- XferInfo.h \
- ZombiePoolInterface.h \
- Stoich.h \
- ../kinetics/Pool.h \
- ../kinetics/lookupVolumeFromMesh.h \
-
-
-# The GSL library (GNU Scientific Library) provides a range of
-# numerical functions, which allow us to use various advanced integration
-# methods. The GslIntegrator accesses these. This library is licenced
-# under the GPL, so only GPL-compliant uses of MOOSE will be able to
-# use it. Should be fine for academic use.
-# Optional: Comment out the following three items if not using GSL
-ifeq ($(USE_GSL),1)
-GSL_OBJ = \
-
-
-GSL_LIBS = -L/usr/lib -lgsl -lgslcblas
-GSL_FLAGS = -DUSE_GSL
-endif
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-KinSparseMatrix.o: KinSparseMatrix.h ../basecode/SparseMatrix.h
-ZombiePool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ../kinetics/lookupVolumeFromMesh.h
-ZombieBufPool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ZombieBufPool.h ../kinetics/lookupVolumeFromMesh.h
-ZombieBufPool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h
-VoxelPoolsBase.o: VoxelPoolsBase.h ../randnum/RNG.h
-VoxelPools.o: VoxelPoolsBase.h VoxelPools.h OdeSystem.h RateTerm.h Stoich.h
-GssaVoxelPools.o: VoxelPoolsBase.h GssaVoxelPools.h ../basecode/SparseMatrix.h \
- ../randnum/RNG.h KinSparseMatrix.h GssaSystem.h RateTerm.h Stoich.h
-RateTerm.o: RateTerm.h
-FuncTerm.o: FuncTerm.h
-Stoich.o: RateTerm.h FuncTerm.h FuncRateTerm.h Stoich.h ../kinetics/PoolBase.h ../kinetics/ReacBase.h ../kinetics/EnzBase.h ../kinetics/CplxEnzBase.h ../basecode/SparseMatrix.h KinSparseMatrix.h ../scheduling/Clock.h ZombiePoolInterface.h
-ZombieReac.o: RateTerm.h FuncTerm.h Stoich.h ../kinetics/ReacBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieReac.h
-ZombieEnz.o: RateTerm.h FuncTerm.h Stoich.h ../kinetics/EnzBase.h ../kinetics/CplxEnzBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieEnz.h
-ZombieMMenz.o: RateTerm.h FuncTerm.h Stoich.h ../kinetics/EnzBase.h ../kinetics/lookupVolumeFromMesh.h ../basecode/SparseMatrix.h KinSparseMatrix.h ZombieMMenz.h
-ZombieFunction.o: RateTerm.h FuncTerm.h Stoich.h ../builtins/Function.h ZombieFunction.h
-Ksolve.o: RateTerm.h Stoich.h Ksolve.h VoxelPoolsBase.h VoxelPools.h OdeSystem.h ZombiePoolInterface.h
-SteadyStateGsl.o: SteadyStateGsl.h ../basecode/SparseMatrix.h KinSparseMatrix.h RateTerm.h FuncTerm.h Stoich.h ../randnum/randnum.h
-Gsolve.o: RateTerm.h FuncTerm.h FuncRateTerm.h Stoich.h Gsolve.h VoxelPoolsBase.h VoxelPools.h GssaSystem.h ZombiePoolInterface.h ../basecode/SparseMatrix.h KinSparseMatrix.h
-ZombiePoolInterface.o: VoxelPoolsBase.h ZombiePoolInterface.h ../mesh/VoxelJunction.h Stoich.h ../shell/Shell.h
-testKsolve.o: ../shell/Shell.h
-
-#KineticHub.o: KineticHub.h
-
-ifeq ($(USE_GSL),1)
-#Optional: Comment out the following two items if not using GSL.
-$(GSL_OBJ) : $(HEADERS)
-#StateScanner.o: StateScanner.h
-endif # !USE_GSL
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(GSL_FLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode -I../msg -I../kinetics -I../mesh -I../external/muparser/include -I../builtins $< -c
-
-$(TARGET): $(OBJ) $(GSL_OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(GSL_OBJ) $(GSL_LIBS) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/mesh/Makefile b/mesh/Makefile
deleted file mode 100644
index 9e211655..00000000
--- a/mesh/Makefile
+++ /dev/null
@@ -1,55 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _mesh.o
-
-OBJ = \
- ChemCompt.o \
- MeshCompt.o \
- MeshEntry.o \
- CubeMesh.o \
- CylBase.o \
- CylMesh.o \
- NeuroNode.o \
- NeuroMesh.o \
- SpineEntry.o \
- SpineMesh.o \
- PsdMesh.o \
- testMesh.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-MeshEntry.o: MeshEntry.h
-Boundary.o: Boundary.h
-ChemCompt.o: VoxelJunction.h ChemCompt.h MeshEntry.h Boundary.h
-MeshCompt.o: VoxelJunction.h ChemCompt.h MeshCompt.h MeshEntry.h Boundary.h
-CylBase.o: ../utility/Vec.h CylBase.h
-CylMesh.o: ../utility/Vec.h VoxelJunction.h ChemCompt.h CylBase.h CylMesh.h MeshEntry.h Boundary.h
-CubeMesh.o: VoxelJunction.h ChemCompt.h CubeMesh.h MeshEntry.h Boundary.h
-NeuroNode.o: CylBase.h NeuroNode.h
-NeuroMesh.o: ../basecode/SparseMatrix.h ChemCompt.h CylBase.h NeuroNode.h NeuroMesh.h
-SpineMesh.o: ../basecode/SparseMatrix.h VoxelJunction.h ChemCompt.h CylBase.h NeuroNode.h NeuroMesh.h ../utility/Vec.h SpineEntry.h SpineMesh.h
-SpineEntry.o: VoxelJunction.h ChemCompt.h CylBase.h ../utility/Vec.h SpineEntry.h
-PsdMesh.o: ../basecode/SparseMatrix.h VoxelJunction.h ChemCompt.h CylBase.h ../utility/Vec.h SpineEntry.h SpineMesh.h
-testMesh.o: ../basecode/SparseMatrix.h CylBase.h NeuroNode.h MeshEntry.h ChemCompt.h CylMesh.h Boundary.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I.. -I../basecode $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
-
diff --git a/mpi/Makefile b/mpi/Makefile
deleted file mode 100644
index a127fb78..00000000
--- a/mpi/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2013 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _mpi.o
-
-OBJ = \
- PostMaster.o \
- testMpi.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-Postmaster.o: PostMaster.h
-testMpi.o: PostMaster.h
-
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/msg/Makefile b/msg/Makefile
deleted file mode 100644
index 1a373925..00000000
--- a/msg/Makefile
+++ /dev/null
@@ -1,44 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _msg.o
-
-OBJ = \
- Msg.o \
- DiagonalMsg.o \
- OneToAllMsg.o \
- OneToOneMsg.o \
- SingleMsg.o \
- SparseMsg.o \
- OneToOneDataIndexMsg.o \
- testMsg.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-DiagonalMsg.o: DiagonalMsg.h
-OneToAll.o: OneToAll.h
-OneToOne.o: OneToOne.h
-OneToOneDataIndex.o: OneToOneDataIndex.h
-SingleMsg.o: SingleMsg.h
-SparseMsg.o: SparseMsg.h
-testMsg.o: DiagonalMsg.h OneToAllMsg.h OneToOneMsg.h SingleMsg.h SparseMsg.h OneToOneDataIndexMsg.h ../basecode/SetGet.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/msg/SparseMsg.cpp b/msg/SparseMsg.cpp
index 46d3fb5e..0be80c00 100644
--- a/msg/SparseMsg.cpp
+++ b/msg/SparseMsg.cpp
@@ -301,13 +301,12 @@ void SparseMsg::updateAfterFill()
SparseMatrix< unsigned int > temp( matrix_);
temp.transpose();
for ( unsigned int i = 0; i < temp.nRows(); ++ i ) {
- const unsigned int* colIndex;
- const unsigned int* entry;
- unsigned int num = temp.getRow( i, &entry, &colIndex );
if ( i >= startData && i < endData ) {
- // Inefficient. Better to do it in one pass after getting
- // the max num
- e2_->resizeField( i - startData, num + 1 );
+ const unsigned int* colIndex;
+ const unsigned int* entry;
+ // SparseMatrix::getRow returns # of entries.
+ unsigned int num = temp.getRow( i, &entry, &colIndex );
+ e2_->resizeField( i - startData, num );
}
}
e1()->markRewired();
diff --git a/pymoose/Makefile b/pymoose/Makefile
deleted file mode 100644
index 1c8abeca..00000000
--- a/pymoose/Makefile
+++ /dev/null
@@ -1,22 +0,0 @@
-# Makefile
-#
-# Author: Subhasis Ray
-# Created: 2011-03-10 12:10:32 (+0530)
-TARGET = _pymoose.o
-# CXXFLAGS += -I../basecode -I../msg -I../shell
-CXXFLAGS += -DQUIET_MODE
-NUMPY_WARNING_FLAG = -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
-.PHONY: clean
-
-HEADERS = moosemodule.h ../basecode/global.h PyRun.h
-
-OBJ = moosemodule.o mfield.o vec.o melement.o test_moosemodule.o PyRun.o
-
-$(TARGET): $(OBJ) $(HEADERS) ../basecode/main.cpp ../utility/_utility.o ../basecode/_basecode.o
- $(LD) -r -o $(TARGET) $(OBJ) $(LDFLAGS)
-
-.cpp.o: $(HEADERS)
- $(CXX) $(CXXFLAGS) $(NUMPY_WARNING_FLAG) -I.. -I../basecode $< -c
-clean:
- -rm -f *.o
-
diff --git a/pymoose/mfield.cpp b/pymoose/mfield.cpp
index dd452890..18bd3f73 100644
--- a/pymoose/mfield.cpp
+++ b/pymoose/mfield.cpp
@@ -319,7 +319,7 @@ PyObject * moose_DestField_call(PyObject * self, PyObject * args,
PyObject * arg = PyTuple_GetItem(args, ii);
Py_INCREF(arg);
PyTuple_SetItem(newargs, ii+1, arg);
- Py_DECREF(arg);
+ // Py_DECREF(arg);
}
// Call ObjId._setDestField with the new arguments
PyObject * ret = moose_ObjId_setDestField(((_Field*)self)->owner, newargs);
diff --git a/python/moose/SBML/readSBML.py b/python/moose/SBML/readSBML.py
index 255d9678..4dcc89cc 100644
--- a/python/moose/SBML/readSBML.py
+++ b/python/moose/SBML/readSBML.py
@@ -499,7 +499,8 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue,gro
for ritem in range(0, model.getNumReactions()):
reactionCreated = False
groupName = ""
-
+ rName = ""
+ rId = ""
reac = model.getReaction(ritem)
group = ""
reacAnnoInfo = {}
diff --git a/python/moose/SBML/writeSBML.py b/python/moose/SBML/writeSBML.py
index 1727d6e6..5cdb25bc 100644
--- a/python/moose/SBML/writeSBML.py
+++ b/python/moose/SBML/writeSBML.py
@@ -20,7 +20,7 @@ Last-Updated: Tue Apr 4 14:20:00 2017(+0530)
'''
import sys
import re
-from collections import Counter
+#from collections import Counter
import moose
from moose.SBML.validation import validateModel
from moose.chemUtil.chemConnectUtil import *
@@ -499,11 +499,13 @@ def parmUnit(rct_order, cremodel_):
return unit_stream
+def Counter(items):
+ return dict((i, items.count(i)) for i in items)
+
def getSubprd(cremodel_, mobjEnz, type, neighborslist):
if type == "sub":
reacSub = neighborslist
reacSubCou = Counter(reacSub)
-
# print " reacSubCou ",reacSubCou,"()",len(reacSubCou)
noofSub = len(reacSubCou)
rate_law = " "
diff --git a/python/moose/chemUtil/chemConnectUtil.py b/python/moose/chemUtil/chemConnectUtil.py
index 93d8be9d..a8951683 100644
--- a/python/moose/chemUtil/chemConnectUtil.py
+++ b/python/moose/chemUtil/chemConnectUtil.py
@@ -1,6 +1,6 @@
import moose
import numpy as np
-from collections import Counter
+#from collections import Counter
def xyPosition(objInfo,xory):
try:
@@ -177,5 +177,6 @@ def countitems(mitems,objtype):
items = []
items = moose.element(mitems).neighbors[objtype]
uniqItems = set(items)
- countuniqItems = Counter(items)
+ #countuniqItems = Counter(items)
+ countuniqItems = dict((i, items.count(i)) for i in items)
return(uniqItems,countuniqItems)
\ No newline at end of file
diff --git a/python/moose/genesis/writeKkit.py b/python/moose/genesis/writeKkit.py
index 2bd33e21..1e549601 100644
--- a/python/moose/genesis/writeKkit.py
+++ b/python/moose/genesis/writeKkit.py
@@ -51,7 +51,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
'\n\t sudo apt install python-maplotlib', "")
return False
else:
-
+ error = " "
ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"]
matplotcolor = {}
for name,hexno in matplotlib.colors.cnames.items():
@@ -88,19 +88,21 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
cmin,cmax,xmin1,xmax1,ymin1,ymax1 = findMinMax(sceneitems)
for k,v in list(sceneitems.items()):
anno = moose.element(k.path+'/info')
- x1 = calPrime(v['x'])
- y1 = calPrime(v['y'])
- sceneitems[k]['x'] = x1
- sceneitems[k]['y'] = y1
+ # x1 = calPrime(v['x'])
+ # y1 = calPrime(v['y'])
+ # sceneitems[k]['x'] = x1
+ # sceneitems[k]['y'] = y1
f = open(filename, 'w')
writeHeader (f,maxVol)
gtId_vol = writeCompartment(modelpath,compt,f)
writePool(modelpath,f,gtId_vol,sceneitems)
+ error = ""
reacList = writeReac(modelpath,f,sceneitems)
enzList = writeEnz(modelpath,f,sceneitems)
- writeSumtotal(modelpath,f)
+ error = writeSumtotal(modelpath,f,error)
+ error = writeStimulus(modelpath,f,error)
f.write("simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
"simundump xgraph /graphs/conc2 0 0 100 0 1 0\n")
tgraphs = moose.wildcardFind(modelpath+'/##[ISA=Table2]')
@@ -125,7 +127,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
writeNotes(modelpath,f)
writeFooter2(f)
print('Written to file '+filename)
- return True
+ return error,True
else:
print(("Warning: writeKkit:: No model found on " , modelpath))
return False
@@ -341,15 +343,45 @@ def trimPath(mobj):
s = splitpath.replace("_dash_",'-')
return s
-def writeSumtotal( modelpath,f):
+def writeSumtotal( modelpath,f, error):
funclist = moose.wildcardFind(modelpath+'/##[ISA=Function]')
+ s = ""
for func in funclist:
+ fInfound = True
+ fOutfound = True
funcInputs = moose.element(func.path+'/x[0]')
- s = ""
- for funcInput in funcInputs.neighbors["input"]:
- s = s+ "addmsg /kinetics/" + trimPath(funcInput)+ " /kinetics/" + trimPath(moose.element(func.parent)) + " SUMTOTAL n nInit\n"
- f.write(s)
+ if not len(funcInputs.neighbors["input"]):
+ fInfound = False
+ error = error +'\n/'+ (moose.element(func)).parent.name+ '/'+moose.element(func).name + ' function doesn\'t have input which is not allowed in genesis. \n This function is not written down into genesis file\n'
+
+ if not len(func.neighbors["valueOut"]):
+ error = error +'Function'+func.path+' has not been connected to any output, this function is not written to genesis file'
+ fOutfound = False
+ else:
+ for srcfunc in func.neighbors["valueOut"]:
+ if srcfunc.className in ["ZombiePool","ZombieBufPool","Pool","BufPool"]:
+ functionOut = moose.element(srcfunc)
+ else:
+ error = error +'Function output connected to '+srcfunc.name+ ' which is a '+ srcfunc.className+' which is not allowed in genesis, this function '+(moose.element(func)).path+' is not written to file'
+ fOutfound = False
+
+ if fInfound and fOutfound:
+ srcPool = []
+ for funcInput in funcInputs.neighbors["input"]:
+ if funcInput not in srcPool:
+ srcPool.append(funcInput)
+ s = "addmsg /kinetics/" + trimPath(funcInput)+ " /kinetics/"+ trimPath(functionOut)+ " SUMTOTAL n nInit\n"
+ f.write(s)
+ else:
+ error = error + '\n Genesis doesn\'t allow same moluecule connect to function mutiple times. \n Pool \''+ moose.element(funcInput).name + '\' connected to '+ (moose.element(func)).path
+ return error
+
+def writeStimulus(modelpath,f,error):
+
+ if len(moose.wildcardFind(modelpath+'/##[ISA=StimulusTable]')):
+ error = error +'\n StimulusTable is not written into genesis. This is in Todo List'
+ return error
def storePlotMsgs( tgraphs,f):
s = ""
if tgraphs:
diff --git a/python/moose/merge/merge.py b/python/moose/merge/merge.py
index ee940162..a8507808 100644
--- a/python/moose/merge/merge.py
+++ b/python/moose/merge/merge.py
@@ -46,6 +46,7 @@ import mtypes
from moose.chemUtil.chemConnectUtil import *
from moose.chemUtil.graphUtils import *
+from moose.genesis import mooseWriteKkit
def mergeChemModel(src,des):
@@ -54,9 +55,12 @@ def mergeChemModel(src,des):
B = des
loadedA = False
loadedB = False
+ modelA = moose.element('/')
+ modelB = moose.element('/')
if os.path.isfile(A):
modelA,loadedA = loadModels(A)
+
elif moose.exists(A):
modelA = A
loadedA = True
@@ -122,9 +126,10 @@ def mergeChemModel(src,des):
poolListinb = updatePoolList(dictComptB)
E_Duplicated,E_Notcopiedyet,E_Daggling = enzymeMerge(dictComptB,dictComptA,key,poolListinb)
- path, sfile = os.path.split(src)
- path, dfile = os.path.split(des)
- print("\n %s (src) model is merged to %s (des)" %(sfile, dfile))
+ spath, sfile = os.path.split(src)
+ dpath, dfile = os.path.split(des)
+ print("\nThe content of %s (src) model is merged to %s (des)." %(sfile, dfile))
+ # Here any error or warning during Merge is written it down
if funcExist:
print( "\nIn model \"%s\" pool already has connection from a function, these function from model \"%s\" is not allowed to connect to same pool,\n since no two function are allowed to connect to same pool:"%(dfile, sfile))
for fl in list(funcExist):
@@ -169,7 +174,33 @@ def mergeChemModel(src,des):
if E_Daggling:
print ("Enzyme:")
for ed in list(E_Daggling):
- print ("%s " %str(ed.name))
+ print ("%s " %str(ed.name))
+ ## Model is saved
+ print ("\n ")
+ savemodel = raw_input("Do you want to save the model? \"YES\" \"NO\" ")
+ if savemodel.lower() == 'yes' or savemodel.lower() == 'y':
+ mergeto = raw_input("Enter File name ")
+ if mergeto and mergeto.strip():
+ filenameto = 'merge.g'
+ else:
+ if str(mergeto).rfind('.') != -1:
+ mergeto = mergeto[:str(mergeto).rfind('.')]
+ if str(mergeto).rfind('/'):
+ mergeto = mergeto+'merge'
+
+ filenameto = mergeto+'.g'
+
+ error,written = moose.mooseWriteKkit(modelB, filenameto)
+ if written == False:
+ print('Could not save the Model, check the files')
+ else:
+ if error == "":
+ print(" \n The merged model is saved into \'%s\' " %(filenameto))
+ else:
+ print('Model is saved but these are not written\n %s' %(error))
+ else:
+ print ('\nMerged model is available under moose.element(\'%s\')' %(modelB))
+ print (' If you are in python terminal you could save \n >moose.mooseWriteKkit(\'%s\',\'filename.g\')' %(modelB))
def functionMerge(comptA,comptB,key):
funcNotallowed, funcExist = [], []
@@ -264,6 +295,8 @@ def loadModels(filepath):
subtype = mtypes.getSubtype(filepath, modeltype)
if subtype == 'kkit' or modeltype == "cspace":
+ if moose.exists(modelpath):
+ moose.delete(modelpath)
moose.loadModel(filepath,modelpath)
loaded = True
@@ -636,4 +669,20 @@ if __name__ == "__main__":
if not os.path.exists(src):
print("Filename or path does not exist",des)
exit(0)
- mergered = mergeChemModel(src,des)
\ No newline at end of file
+ else:
+ mergered = mergeChemModel(src,des)
+ '''
+ try:
+ sys.argv[3]
+ except IndexError:
+ print ("Merge to save not specified")
+ mergeto = "merge"
+ else:
+ mergeto = sys.argv[3]
+ if str(mergeto).rfind('.') != -1:
+ mergeto = mergeto[:str(mergeto).rfind('.')]
+ if str(mergeto).rfind('/'):
+ mergeto = mergeto+'merge'
+
+ mergered = mergeChemModel(src,des,mergeto)
+ '''
\ No newline at end of file
diff --git a/python/moose/plot_utils.py b/python/moose/plot_utils.py
index 94c8577e..25346524 100644
--- a/python/moose/plot_utils.py
+++ b/python/moose/plot_utils.py
@@ -310,6 +310,7 @@ def plot_tables(data_dict, xvec = None, **kwargs):
plt.figure(figsize=(10, 1.5*len(data_dict)))
if not subplot:
ax = plt.subplot( 1, 1, 1 )
+ kwargs[ 'ax' ] = ax
for i, k in enumerate(data_dict):
pu.info("+ Plotting for %s" % k)
@@ -325,8 +326,9 @@ def plot_tables(data_dict, xvec = None, **kwargs):
yvec = data_dict[k].vector
plotVector(yvec, xvec, label=k, **kwargs)
else:
- ax = plt.subplot(len(data_dict), 1, i)
- yvec = data_dict[k]
+ ax = plt.subplot(len(data_dict), 1, i+1)
+ kwargs[ 'ax' ] = ax
+ yvec = data_dict[k].vector
plotVector(yvec, xvec, label=k, **kwargs)
if subplot:
try:
diff --git a/python/rdesigneur/rmoogli.py b/python/rdesigneur/rmoogli.py
index c1b0d3aa..e1e34a78 100644
--- a/python/rdesigneur/rmoogli.py
+++ b/python/rdesigneur/rmoogli.py
@@ -65,7 +65,9 @@ def interlude( view ):
view.mooGroup.set("color", val, view.mapper)
view.yaw( rotation )
#print moogliDt, len( val ), runtime
- if moose.element("/clock").currentTime >= runtime:
+ currt = moose.element("/clock").currentTime
+ view.timecb.set_title( 'T = {:.3f} s'.format( currt ) )
+ if currt >= runtime:
view.stop()
# This func is used for later viewers, that don't handle advancing time.
@@ -146,13 +148,34 @@ def makeMoogli( rd, mooObj, moogliEntry, fieldInfo ):
moogliEntry[5],
moogliEntry[6]))
cb.set_num_labels(3)
+
+ # Use the text title on a colorbar to display the current time!!
+ # Spectacularly ugly hack, but I was unable to find other ways to put
+ # text in a predefined place in a moogli view.
+ timecb = moogli.widgets.ColorBar( id="timecb",
+ title = "T = 0 s",
+ text_color=moogli.colors.BLACK,
+ position=moogli.geometry.Vec3f(0.1, -0.01, 0.0),
+ size=moogli.geometry.Vec3f(0.01, 0.02, 0.0),
+ text_font="/usr/share/fonts/truetype/ubuntu-font-family/Ubuntu-R.ttf",
+ orientation=0.0,
+ text_character_size=16,
+ label_formatting_precision=1,
+ colormap=moogli.colors.MatplotlibColorMap(matplotlib.cm.rainbow),
+ color_resolution=2,
+ scalar_range=moogli.geometry.Vec2f( 0.0, 1.0 )
+ )
+ timecb.set_num_labels( 0 )
+
view.attach_color_bar(cb)
+ view.attach_color_bar(timecb)
view.rd = rd
view.mooObj = displayObj
view.mooGroup = updateGroup
view.mooField = mooField
view.mooScale = fieldInfo[2]
view.mapper = mapper
+ view.timecb = timecb
viewer.attach_view(view)
return viewer
diff --git a/randnum/Makefile b/randnum/Makefile
deleted file mode 100644
index 259bbb4c..00000000
--- a/randnum/Makefile
+++ /dev/null
@@ -1,51 +0,0 @@
-CXXFLAGS += -I..
-# the line below are for easy inclusion of libxml++
-#CXXFLAGS += $(shell pkg-config libxml++-2.6 --CXXFLAGS)
-
-TARGET = _randnum.o
-
-OBJ = \
- mt19937ar.o \
- RandGenerator.o \
- UniformRng.o \
- Uniform.o \
- Exponential.o \
- ExponentialRng.o \
- Binomial.o \
- Normal.o \
- Poisson.o \
- Gamma.o \
- PoissonRng.o \
- NormalRng.o \
- BinomialRng.o \
- GammaRng.o \
-
-HEADERS = \
- ../basecode/header.h \
- randnum.h \
- Probability.h \
- RandGenerator.h \
- UniformRng.h \
- Uniform.h \
- Exponential.h \
- ExponentialRng.h \
- Binomial.h \
- Gamma.h \
- Poisson.h \
- PoissonRng.h \
- Normal.h \
- NormalRng.h \
- BinomialRng.h \
- GammaRng.h \
-
-default: $(TARGET)
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $< -c
-# $(CXX) $(CXXFLAGS) $(shell pkg-config libxml++-2.6 --CXXFLAGS) $< -c
-
-$(TARGET): $(OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/scheduling/Makefile b/scheduling/Makefile
deleted file mode 100644
index 2061a090..00000000
--- a/scheduling/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2009 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _scheduling.o
-
-OBJ = \
- Clock.o \
- testScheduling.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-Clock.o: Clock.h
-testScheduling.o: Clock.h
-
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/shell/Makefile b/shell/Makefile
deleted file mode 100644
index 54330143..00000000
--- a/shell/Makefile
+++ /dev/null
@@ -1,49 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _shell.o
-
-OBJ = \
- Shell.o \
- ShellCopy.o \
- ShellThreads.o \
- LoadModels.o \
- SaveModels.o \
- Neutral.o \
- Wildcard.o \
- testShell.o \
-
-HEADERS = \
- ../basecode/header.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-#Shell.o: Shell.h Neutral.h ../scheduling/Clock.h ../sbml/MooseSbmlWriter.h ../sbml/MooseSbmlReader.h
-Shell.o: Shell.h Neutral.h ../scheduling/Clock.h
-ShellCopy.o: Shell.h Neutral.h ../scheduling/Clock.h
-ShellSetGet.o: Shell.h
-ShellThreads.o: Shell.h Neutral.h ../scheduling/Clock.h
-LoadModels.o: Shell.h Neutral.h ../biophysics/SwcSegment.h ../biophysics/ReadSwc.h
-SaveModels.o: Shell.h Neutral.h
-Neutral.o: Neutral.h ../basecode/ElementValueFinfo.h
-Wildcard.o: Wildcard.h Shell.h Neutral.h ../basecode/ElementValueFinfo.h
-testShell.o: Wildcard.h Shell.h Neutral.h ../builtins/Arith.h ../basecode/SparseMatrix.h ../msg/SparseMsg.h ../msg/SingleMsg.h ../basecode/SetGet.h ../basecode/HopFunc.h ../basecode/OpFuncBase.h ../basecode/OpFunc.h
-
-#../kinetics/ReadKkit.h ../biophysics/ReadCell.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I.. -I../basecode -I../msg $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS)
-
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/signeur/Makefile b/signeur/Makefile
deleted file mode 100644
index ad8c5074..00000000
--- a/signeur/Makefile
+++ /dev/null
@@ -1,36 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** Copyright (C) 2003-2012 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-CXXFLAGS += -I..
-# the line below are for easy inclusion of libxml++
-#CXXFLAGS += $(shell pkg-config libxml++-2.6 --cflags)
-
-TARGET = _signeur.o
-
-OBJ = \
- Adaptor.o \
- testSigNeur.o
-
-
-HEADERS = \
- ../basecode/header.h \
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-Adaptor.o: Adaptor.h
-testSigNeur.o: Adaptor.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) -I.. -I../basecode $< -c
-
-$(TARGET): $(OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ)
-clean:
- -rm -f *.o $(TARGET) core core.*
diff --git a/synapse/Makefile b/synapse/Makefile
deleted file mode 100644
index bbf82b99..00000000
--- a/synapse/Makefile
+++ /dev/null
@@ -1,50 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** copyright (C) 2007 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-TARGET = _synapse.o
-
-OBJ = \
- SynHandlerBase.o \
- SimpleSynHandler.o \
- STDPSynHandler.o \
- GraupnerBrunel2012CaPlasticitySynHandler.o \
- Synapse.o \
- STDPSynapse.o \
- RollingMatrix.o \
- SeqSynHandler.o \
- testSynapse.o \
-
-# GSL_LIBS = -L/usr/lib -lgsl
-
-HEADERS = \
- ../basecode/header.h \
- ../utility/numutil.h \
-
-
-default: $(TARGET)
-
-$(OBJ) : $(HEADERS)
-SynHandlerBase.o: SynHandlerBase.h Synapse.h
-SimpleSynHandler.o: SynHandlerBase.h Synapse.h SimpleSynHandler.h SynEvent.h
-STDPSynHandler.o: SynHandlerBase.h STDPSynapse.h STDPSynHandler.h SynEvent.h
-GraupnerBrunel2012CaPlasticitySynHandler.o: SynHandlerBase.h Synapse.h GraupnerBrunel2012CaPlasticitySynHandler.h SynEvent.h
-Synapse.o: Synapse.h SynHandlerBase.h
-STDPSynapse.o: STDPSynapse.h SynHandlerBase.h
-RollingMatrix.o: RollingMatrix.h
-SeqSynHandler.o: SynHandlerBase.h Synapse.h SimpleSynHandler.h SeqSynHandler.h RollingMatrix.h SynEvent.h
-testSynapse.o: SynHandlerBase.h Synapse.h SimpleSynHandler.h SeqSynHandler.h RollingMatrix.h SynEvent.h
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) $(SMOLDYN_FLAGS) -I. -I../basecode -I../msg -I .. -I../external/muparser/include $< -c
-
-$(TARGET): $(OBJ) $(SMOLDYN_OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ) $(SMOLDYN_OBJ) $(SMOLDYN_LIB_PATH) $(SMOLDYN_LIBS) $(GSL_LIBS)
-
-clean:
- rm -f *.o $(TARGET) core core.*
diff --git a/synapse/SeqSynHandler.cpp b/synapse/SeqSynHandler.cpp
index f31f9117..dc826cef 100644
--- a/synapse/SeqSynHandler.cpp
+++ b/synapse/SeqSynHandler.cpp
@@ -140,6 +140,19 @@ const Cinfo* SeqSynHandler::initCinfo()
&SeqSynHandler::setPlasticityScale,
&SeqSynHandler::getPlasticityScale
);
+
+ static ValueFinfo< SeqSynHandler, double > sequencePower(
+ "sequencePower",
+ "Exponent for the outcome of the sequential calculations. "
+ "This is needed because linear summation of terms in the kernel"
+ "means that a brief stong sequence match is no better than lots"
+ "of successive low matches. In other words, 12345 is no better"
+ "than 11111. Using an exponent lets us select the former."
+ "Defaults to 1.0.",
+ &SeqSynHandler::setSequencePower,
+ &SeqSynHandler::getSequencePower
+ );
+
static ReadOnlyValueFinfo< SeqSynHandler, vector< double > >
weightScaleVec(
"weightScaleVec",
@@ -169,6 +182,7 @@ const Cinfo* SeqSynHandler::initCinfo()
&synapseOrderOption, // Field
&seqActivation, // ReadOnlyField
&plasticityScale, // Field
+ &sequencePower, // Field
&weightScaleVec, // ReadOnlyField
&kernel, // ReadOnlyField
&history // ReadOnlyField
@@ -201,6 +215,7 @@ SeqSynHandler::SeqSynHandler()
baseScale_( 0.0 ),
sequenceScale_( 1.0 ),
plasticityScale_( 0.0 ),
+ sequencePower_( 1.0 ),
seqActivation_( 0.0 ),
synapseOrderOption_( -1 ) // sequential ordering
{
@@ -421,6 +436,16 @@ void SeqSynHandler::setPlasticityScale( double v )
plasticityScale_ = v;
}
+double SeqSynHandler::getSequencePower() const
+{
+ return sequencePower_;
+}
+
+void SeqSynHandler::setSequencePower( double v )
+{
+ sequencePower_ = v;
+}
+
vector< double >SeqSynHandler::getWeightScaleVec() const
{
return weightScaleVec_;
@@ -525,7 +550,7 @@ void SeqSynHandler::vProcess( const Eref& e, ProcPtr p )
seqActivation_ = 0.0;
for ( vector< double >::iterator y = correlVec.begin();
y != correlVec.end(); ++y )
- seqActivation_ += *y;
+ seqActivation_ += pow( *y, sequencePower_ );
// We'll use the seqActivation_ to send a special msg.
seqActivation_ *= sequenceScale_;
diff --git a/synapse/SeqSynHandler.h b/synapse/SeqSynHandler.h
index 45217ba0..7489da86 100644
--- a/synapse/SeqSynHandler.h
+++ b/synapse/SeqSynHandler.h
@@ -66,6 +66,8 @@ class SeqSynHandler: public SynHandlerBase
double getSeqActivation() const; // summed activation of syn chan
void setPlasticityScale( double v );
double getPlasticityScale() const;
+ void setSequencePower( double v );
+ double getSequencePower() const;
vector< double > getWeightScaleVec() const;
vector< double > getKernel() const;
vector< double > getHistory() const;
@@ -109,6 +111,15 @@ class SeqSynHandler: public SynHandlerBase
*/
double plasticityScale_;
+ /**
+ * Exponent to use for the outcome of the sequential calculations.
+ * This is needed because linear summation of terms in the kernel
+ * means that a brief stong sequence match is no better than lots
+ * of successive low matches. In other words, 12345 is no better
+ * than 11111.
+ */
+ double sequencePower_;
+
///////////////////////////////////////////
// Some readonly fields
double seqActivation_; // global activation if sequence recognized
diff --git a/utility/Makefile b/utility/Makefile
deleted file mode 100644
index 87af0b7d..00000000
--- a/utility/Makefile
+++ /dev/null
@@ -1,45 +0,0 @@
-#/**********************************************************************
-#** This program is part of 'MOOSE', the
-#** Messaging Object Oriented Simulation Environment.
-#** Copyright (C) 2003-2012 Upinder S. Bhalla. and NCBS
-#** It is made available under the terms of the
-#** GNU Lesser General Public License version 2.1
-#** See the file COPYING.LIB for the full notice.
-#**********************************************************************/
-
-CXXFLAGS += -I..
-# the line below are for easy inclusion of libxml++
-#CXXFLAGS += $(shell pkg-config libxml++-2.6 --cflags)
-
-TARGET = _utility.o
-
-OBJ = \
- strutil.o \
- types.o \
- setupenv.o \
- numutil.o \
- Annotator.o \
- cnpy.o \
- Vec.o \
-
-
-HEADERS = \
- strutil.h \
- numutil.h \
- ../basecode/header.h \
- cnpy.hpp \
-
-default: $(TARGET)
-
-strutil.o: strutil.h
-Annotator.o: Annotator.h
-Vec.o: Vec.h ../basecode/doubleEq.h
-cnpy.o : cnpy.hpp
-
-.cpp.o:
- $(CXX) $(CXXFLAGS) -I.. -I../basecode $< -c
-
-$(TARGET): $(OBJ) $(HEADERS)
- $(LD) -r -o $(TARGET) $(OBJ)
-clean:
- -rm -f *.o $(TARGET) core core.*
--
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