diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index 068c20b2316d6bc32641955441f1b9d82dad7de0..4b4fe8f1a63212e8957cc6b6567d54a03fbb0ac6 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -5,7 +5,7 @@ project(pymoose)
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
- cmake_policy(SET CMP0004 OLD)
+ cmake_policy(SET CMP0004 NEW)
if(POLICY CMP0050)
cmake_policy(SET CMP0050 OLD)
endif(POLICY CMP0050)
@@ -18,28 +18,7 @@ include(FindPkgConfig)
# 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(VERSION_FILE ${CMAKE_CURRENT_SOURCE_DIR}/VERSION)
-find_program(GIT_EXEC "git")
-message( STATUS "Looking for git ${GIT_EXEC}" )
-if( (NOT MOOSE_VERSION) AND GIT_EXEC)
- execute_process(
- COMMAND ${GIT_EXEC} describe --tags --long
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
- OUTPUT_VARIABLE MOOSE_VERSION
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
- message(STATUS "+ Writing ${MOOSE_VERSION} to ${VERSION_FILE}" )
- file(WRITE ${VERSION_FILE} ${MOOSE_VERSION})
-elseif( (NOT MOOSE_VERSION) AND (NOT GIT_EXEC) )
- message(STATUS "+ Reading ${VERSION_FILE}" )
- file(READ ${VERSION_FILE} GIT_VERSION_OUTPUT )
-elseif(MOOSE_VERSION)
- message(STATUS "+ Using user specified VERSION = ${MOOSE_VERSION}" )
- file(WRITE ${VERSION_FILE} ${MOOSE_VERSION})
-else()
- message(FATAL_ERROR "Could not determine MOOSE_VERSION" )
-endif( )
-
+set(MOOSE_VERSION 3.2-git)
add_definitions( -DMOOSE_VERSION="${MOOSE_VERSION}")
message( STATUS "MOOSE Version ${MOOSE_VERSION}" )
@@ -89,7 +68,6 @@ endif()
option(DEBUG "Build with debug support" OFF)
option(GPROF "Build for profiling using gprof" OFF)
option(ENABLE_UNIT_TESTS "Enable unit tests (DEBUG should also be ON)" OFF)
-option(WITH_PYTHON "Build native python extension" ON)
option(WITH_MPI "Enable Openmpi support" OFF)
option(WITH_BOOST "Use boost library instead of GSL" OFF)
option(WITH_GSL "Use gsl-library. Alternative is WITH_BOOST" ON)
@@ -129,7 +107,10 @@ endif()
################################### TARGETS ####################################
add_library(libmoose SHARED basecode/main.cpp)
-add_executable(moose.bin basecode/main.cpp)
+
+if(DEBUG)
+ add_executable(moose.bin basecode/main.cpp)
+endif( )
################################### SETUP BUILD ################################
@@ -387,32 +368,32 @@ ELSE(MACOSX)
)
endif(MACOSX)
-add_dependencies(moose.bin libmoose)
-
-target_link_libraries(moose.bin moose ${CMAKE_DL_LIBS})
-if( WITH_BOOST )
- target_link_libraries( moose.bin ${Boost_LIBRARIES} )
-endif( WITH_BOOST )
+if(DEBUG)
+ add_dependencies(moose.bin libmoose)
+ target_link_libraries(moose.bin moose ${CMAKE_DL_LIBS})
+ if( WITH_BOOST )
+ target_link_libraries( moose.bin ${Boost_LIBRARIES} )
+ endif( WITH_BOOST )
+endif()
######################### BUILD PYMOOSE ########################################
-# Root of all python module.
-if(WITH_PYTHON)
- add_subdirectory( pymoose )
-endif(WITH_PYTHON)
+add_subdirectory( pymoose )
######################### INSTALL ##############################################
-install(TARGETS moose.bin
- DESTINATION bin
- )
+if(DEBUG)
+ install(TARGETS moose.bin
+ DESTINATION bin
+ )
-install(TARGETS libmoose
- DESTINATION lib
- )
+ install(TARGETS libmoose
+ DESTINATION lib
+ )
-install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/scripts/moose
- DESTINATION bin
- )
+ install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/scripts/moose
+ DESTINATION bin
+ )
+endif( )
# INSTALL python module.
# This target is built by pymoose/CMakeLists.txt file. Using the --prefix option
@@ -425,19 +406,21 @@ execute_process(
)
message( STATUS "Platform ${_platform_desc}" )
-if(WITH_PYTHON)
- set(EXTRA_ARGS "--prefix ${CMAKE_INSTALL_PREFIX}")
- if( ${_platform_desc} MATCHES ".*(Ubuntu|Debian).*" )
- list( APPEND EXTRA_ARGS "--install-layout=deb" )
- endif( )
-
- install(CODE
- "execute_process(
- COMMAND ${PYTHON_EXECUTABLE} setup.py install ${EXTRA_ARGS}
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/python
- )"
- )
-endif(WITH_PYTHON)
+
+set(EXTRA_ARGS "--prefix ${CMAKE_INSTALL_PREFIX}")
+
+if( ${_platform_desc} MATCHES ".*(Ubuntu|Debian).*" )
+ list( APPEND EXTRA_ARGS "--install-layout=deb" )
+endif( )
+
+# If make is called with sudo, install in system directories. Otherwise use
+# --user to install in user home.
+install(CODE
+ "execute_process(
+ COMMAND ${PYTHON_EXECUTABLE} setup.cmake.py install ${EXTRA_ARGS}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/python
+ )"
+ )
# Print message to start build process
if(${CMAKE_BUILD_TOOL} MATCHES "make")
@@ -450,16 +433,19 @@ if(${CMAKE_BUILD_TOOL} MATCHES "make")
endif()
+
+
############################ CTEST ######################################
include( CTest )
# If CTEST_OUTPUT_ON_FAILURE environment variable is set, the output is printed
# onto the console if a test fails.
set(ENV{CTEST_OUTPUT_ON_FAILURE} ON)
-# Run this test in debug mode. In Release mode, this does not do anything.
-set(MOOSE_BIN_LOCATION $<TARGET_FILE:moose.bin>)
-message(STATUS "Executable moose.bin will be at ${MOOSE_BIN_LOCATION}" )
if(DEBUG)
+ # Run this test in debug mode. In Release mode, this does not do anything.
+ set(MOOSE_BIN_LOCATION $<TARGET_FILE:moose.bin>)
+ message(STATUS "Executable moose.bin will be at ${MOOSE_BIN_LOCATION}" )
+
add_test(NAME moose.bin-raw-run COMMAND moose.bin -u -q)
endif(DEBUG)
diff --git a/moose-core/biophysics/Neuron.cpp b/moose-core/biophysics/Neuron.cpp
index 4ae85145ffa04acc1521e7bfa8c9319fa809f44a..265635734f0cdc1e94456022614e5a7314321ff3 100644
--- a/moose-core/biophysics/Neuron.cpp
+++ b/moose-core/biophysics/Neuron.cpp
@@ -619,8 +619,8 @@ static void doClassSpecificMessaging( Shell* shell, Id obj, ObjId compt )
if ( obj.element()->cinfo()->isA( "ChanBase" ) )
{
shell->doAddMsg( "Single", compt, "channel", obj, "channel" );
- // Add the message to the Ca pool if not defined
- if ( obj.element()->getName().find_first_of( "Ca" ) != string::npos )
+ // Add the message to the Ca pool if our obj has 'Ca' in its name.
+ if ( obj.element()->getName().find( "Ca" ) != string::npos )
{
// Don't do it if we have the legacy GENESIS format
if ( Neutral::child( obj.eref(), "addmsg1" ) == Id() )
@@ -631,9 +631,9 @@ static void doClassSpecificMessaging( Shell* shell, Id obj, ObjId compt )
wildcardFind( path, elist );
if ( elist.size() > 0 )
{
- // cout << "Added Ca Msg for " << obj.path() << endl;
+ // cout << "Added Ca Msg for " << obj.path() << ", name = " << obj.element()->getName() << endl;
ObjId mid = shell->doAddMsg(
- "single", obj, "IkOut", elist[0], "current" );
+ "single", obj, "IkOut", elist[0], "current" );
assert( !mid.bad());
}
}
diff --git a/moose-core/builtins/TableBase.cpp b/moose-core/builtins/TableBase.cpp
index 4ed17b6904f5b83c40d4c9a61c12fb4eb969eeb5..f5c11e754d02f955b779e7611bf8ef30d2aec35d 100644
--- a/moose-core/builtins/TableBase.cpp
+++ b/moose-core/builtins/TableBase.cpp
@@ -24,6 +24,13 @@ const Cinfo* TableBase::initCinfo()
&TableBase::getVec
);
+ static ValueFinfo< TableBase, string > plotDump(
+ "plotDump",
+ "'File plotname' for dumpling an xplot, as a workaround for an error in the xplot python interface. Note separator is a space. The return value is a dummy.",
+ &TableBase::setPlotDump,
+ &TableBase::getPlotDump
+ );
+
static ReadOnlyValueFinfo< TableBase, double > outputValue(
"outputValue",
"Output value holding current table entry or output of a calculation",
@@ -115,6 +122,7 @@ const Cinfo* TableBase::initCinfo()
static Finfo* tableBaseFinfos[] = {
&vec, // Value
+ &plotDump, // Value, used for debugging xplot function.
&outputValue, // ReadOnlyValue
&size, // ReadOnlyValue
&y, // ReadOnlyLookupValue
@@ -491,3 +499,21 @@ const vector< double >& TableBase::data( )
{
return vec_;
}
+
+string TableBase::getPlotDump() const
+{
+ static string ret = "plot.Dump";
+ return ret;
+}
+
+void TableBase::setPlotDump( string v )
+{
+
+ std::size_t pos = v.rfind(" ");
+ string fname = v.substr( 0, pos );
+ string plotname = "plot";
+ if ( pos != string::npos )
+ plotname = v.substr( pos );
+ // cout << "setPlotDump( " << fname << ", " << plotname << " ), " << v << "\n";
+ xplot( fname, plotname );
+}
diff --git a/moose-core/builtins/TableBase.h b/moose-core/builtins/TableBase.h
index 5c497a9ed409339ff9b2c1ad2a81000b23e6fa90..ada46bec7d4a544fd8dde22fbf84891dd101fb2e 100644
--- a/moose-core/builtins/TableBase.h
+++ b/moose-core/builtins/TableBase.h
@@ -32,6 +32,9 @@ public:
double getOutputValue() const;
void setOutputValue( double val );
+ string getPlotDump() const;
+ void setPlotDump( string v );
+
double getY( unsigned int index ) const;
//////////////////////////////////////////////////////////////////
diff --git a/moose-core/cmake_modules/FindNumPy.cmake b/moose-core/cmake_modules/FindNumPy.cmake
index b2813e9cd2c46a747b3ac31ee2c3459c32db59d0..f14142f18652c1081f098319b47bf123329352de 100644
--- a/moose-core/cmake_modules/FindNumPy.cmake
+++ b/moose-core/cmake_modules/FindNumPy.cmake
@@ -39,8 +39,6 @@
#============================================================================
# Finding NumPy involves calling the Python interpreter
-set(Python_ADDITIONAL_VERSIONS "2.6 2.7")
-message(STATUS "DEBUG: Python_ADDITIONAL_VERSIONS ${Python_ADDITIONAL_VERSIONS}")
if(NumPy_FIND_REQUIRED)
find_package(PythonInterp REQUIRED)
else()
diff --git a/moose-core/dependencies_list_script/dependencies b/moose-core/dependencies_list_script/dependencies
deleted file mode 100644
index 798f7bdca84b6f2a2194782ee577696f214e35c0..0000000000000000000000000000000000000000
--- a/moose-core/dependencies_list_script/dependencies
+++ /dev/null
@@ -1,19 +0,0 @@
-# AUTHOR : AVIRAL GOEL
-# EMAIL-ID :
-
-# MOOSE Dependencies
-libgsl0-dev
-libgsl0ldbl
-libhdf5-dev
-libxml2-dev
-
-# GUI Dependencies
-#If one needs MOOSE GUI, install below mentioned libraries else comment
-libqt4-dev
-python-qt4-dev
-
-# MOOGLI Dependencies
-#If one needs MOOGLI, install below mentioned libraries else comment
-libopenscenegraph-dev
-python-sip-dev
-python-qt4-gl
diff --git a/moose-core/dependencies_list_script/ubuntu-dep b/moose-core/dependencies_list_script/ubuntu-dep
deleted file mode 100644
index 021e66850b73dbd6c13d9b1a2f7d058fe0e7cdd9..0000000000000000000000000000000000000000
--- a/moose-core/dependencies_list_script/ubuntu-dep
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env sh
-# AUTHOR : AVIRAL GOEL
-# EMAIL-ID :
-
-echo "Installing dependencies for Ubuntu\n"
-sudo -E apt-get install $(grep -vE "^\s*#" dependencies | tr "\n" " ")
-# if one needs SBML support run the below two lines else comment
-#CURRENTLY libSBML-5.9.0 is supported
-sbmlurl="http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/Linux/64-bit/libSBML-5.9.0-Linux-x64.deb"
-sudo -E wget "$sbmlurl" -O "libsbml.deb" && sudo -E dpkg -i "libsbml.deb" && sudo -E rm -rf "libsbml.deb"
-echo "Installed dependencies for Ubuntu\n"
-
diff --git a/moose-core/pymoose/CMakeLists.txt b/moose-core/pymoose/CMakeLists.txt
index 0468f1acf63df56d323e47e5a24577be6ec425c6..7f08aab1c500d9c01f4417d9ba70d3169026568d 100644
--- a/moose-core/pymoose/CMakeLists.txt
+++ b/moose-core/pymoose/CMakeLists.txt
@@ -90,3 +90,15 @@ add_custom_target(copy_python_files
)
add_dependencies(_moose copy_python_files)
+
+
+# Print message at the end of build process.
+add_custom_command( TARGET _moose POST_BUILD
+ COMMAND ${CMAKE_COMMAND} -E cmake_echo_color --cyan
+ "MOOSE python extention is successfully built. Now "
+ " 1. Run 'make install' to install it single user. "
+ " 2. Run 'sudo make install' to install it system-wide. "
+ " "
+ " After installation, 'pip uninstall moose' will uninstall moose. "
+ VERBATIM
+ )
diff --git a/moose-core/python/moose/SBML/readSBML.py b/moose-core/python/moose/SBML/readSBML.py
index c5b00c528641e20764fec236712e8ea70aa167ff..59caa670774be16183199448d7e61102754c3518 100644
--- a/moose-core/python/moose/SBML/readSBML.py
+++ b/moose-core/python/moose/SBML/readSBML.py
@@ -563,7 +563,7 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue,fun
if (reac.isSetId()):
rId = reac.getId()
- groups = [k for k, v in groupInfo.iteritems() if rId in v]
+ groups = [k for k, v in groupInfo.items() if rId in v]
if groups:
group = groups[0]
if (reac.isSetName()):
@@ -1094,7 +1094,7 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
sName = None
sId = spe.getId()
- groups = [k for k, v in groupInfo.iteritems() if sId in v]
+ groups = [k for k, v in groupInfo.items() if sId in v]
if groups:
group = groups[0]
if spe.isSetName():
diff --git a/moose-core/python/moose/chemMerge/merge.py b/moose-core/python/moose/chemMerge/merge.py
index 5b406a25a99ef8428987ac88ab68cb8b2e9a3368..49d7d7162b9ee6ee4c98d86b5769d6bc68967343 100644
--- a/moose-core/python/moose/chemMerge/merge.py
+++ b/moose-core/python/moose/chemMerge/merge.py
@@ -12,7 +12,7 @@
#** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
#Created : Friday Dec 16 23:19:00 2016(+0530)
#Version
-#Last-Updated: Wed Oct 14 00:25:33 2017(+0530)
+#Last-Updated: Wed Oct 25 16:25:33 2017(+0530)
# By: Harsha
#**********************************************************************/
@@ -39,6 +39,7 @@
#
'''
Change log
+Oct 25: line to load SBML file was commented, which is uncommented now and also while copying MMenz had a problem which also cleaned up
Oct 14: absolute import with mtypes just for python3
Oct 12: clean way of cheking the type of path provided, filepath,moose obj, moose path are taken,
@@ -350,9 +351,10 @@ def loadModels(filepath):
loaded = True
elif subtype == 'sbml':
- #moose.mooseReadSBML(filename,modelpath)
- #loaded = True
- pass
+ if moose.exists(modelpath):
+ moose.delete(modelpath)
+ moose.mooseReadSBML(filepath,modelpath)
+ loaded = True
else:
print("This file is not supported for mergering")
modelpath = moose.Shell('/')
@@ -512,7 +514,7 @@ def enzymeMerge(comptA,comptB,key,poolListina):
if eb.className in ["ZombieMMenz","MMenz"]:
eapath = eb.parent.path.replace(objB,objA)
- enz = moose.copy(eb.name,moose.element(eapath))
+ enz = moose.copy(eb,moose.element(eapath))
enzinfo = moose.Annotator(enz.path+'/info')
moose.connect(moose.element(enz).parent,"nOut",moose.element(enz),"enzDest")
#moose.connect(moose.element(enz),"enz",moose.element(enz).parent,"reac")
diff --git a/moose-core/python/rdesigneur/__init__.py b/moose-core/python/rdesigneur/__init__.py
index 188e877d28b4f897865afd7f15a6332c191559a1..caa67eabfcbe9b8311e36d0f7bcb300bf02d3305 100644
--- a/moose-core/python/rdesigneur/__init__.py
+++ b/moose-core/python/rdesigneur/__init__.py
@@ -3,3 +3,4 @@ from __future__ import print_function, absolute_import
from rdesigneur.rdesigneur import *
from rdesigneur.rdesigneur import rdesigneur
+import rdesigneur.rmoogli as rmoogli
diff --git a/moose-core/python/rdesigneur/rdesigneur.py b/moose-core/python/rdesigneur/rdesigneur.py
index 5d1de41ef95d72dc860cb02fb503c3eae6507048..375fe76dec4b290b0e68c85c65370df6cef148cb 100644
--- a/moose-core/python/rdesigneur/rdesigneur.py
+++ b/moose-core/python/rdesigneur/rdesigneur.py
@@ -22,10 +22,12 @@ import imp
import os
import moose
import numpy as np
-import pylab
import math
+import itertools
+import sys
+import time
-import rdesigneur.rmoogli
+import rdesigneur.rmoogli as rmoogli
from rdesigneur.rdesigneurProtos import *
from moose.neuroml.NeuroML import NeuroML
@@ -497,6 +499,10 @@ class rdesigneur:
j += 1
return ret
+ # Utility function for doing lookups for objects.
+ def _makeUniqueNameStr( self, obj ):
+ return obj.name + " " + str( obj.index )
+
# Returns vector of source objects, and the field to use.
# plotSpec is of the form
# [ region_wildcard, region_expr, path, field, title]
@@ -510,7 +516,6 @@ class rdesigneur:
kf = knownFields[field] # Find the field to decide type.
if ( kf[0] == 'CaConcBase' or kf[0] == 'ChanBase' or kf[0] == 'NMDAChan' ):
objList = self._collapseElistToPathAndClass( comptList, plotSpec[2], kf[0] )
- # print ("objList: ", len(objList), kf[1])
return objList, kf[1]
elif (field == 'n' or field == 'conc' or field == 'volume' ):
path = plotSpec[2]
@@ -521,15 +526,11 @@ class rdesigneur:
chemCompt = path[:pos]
cc = moose.element( self.modelPath + '/chem/' + chemCompt)
voxelVec = []
- if ( chemCompt == 'dend' ):
- for i in comptList:
- voxelVec.extend( cc.dendVoxelsOnCompartment[i] )
- else:
- em = cc.elecComptMap
- elecComptMap = { moose.element(em[i]):i for i in range(len(em)) }
- for i in comptList:
- if i in elecComptMap:
- voxelVec.extend( [ elecComptMap[i] ] )
+ temp = [ self._makeUniqueNameStr( i ) for i in comptList ]
+ comptSet = set( temp )
+ #em = [ moose.element(i) for i in cc.elecComptMap ]
+ em = [ self._makeUniqueNameStr(i) for i in cc.elecComptMap ]
+ voxelVec = [i for i in range(len( em ) ) if em[i] in comptSet ]
# Here we collapse the voxelVec into objects to plot.
allObj = moose.vec( self.modelPath + '/chem/' + plotSpec[2] )
#print "####### allObj=", self.modelPath + '/chem/' + plotSpec[2]
@@ -637,29 +638,31 @@ class rdesigneur:
rmoogli.displayMoogli( self, moogliDt, runtime, rotation )
def display( self ):
+ import matplotlib.pyplot as plt
for i in self.plotNames:
-
- pylab.figure( i[2] )
- pylab.title( i[1] )
- pylab.xlabel( "Time (s)" )
- pylab.ylabel( i[4] )
+ plt.figure( i[2] )
+ plt.title( i[1] )
+ plt.xlabel( "Time (s)" )
+ plt.ylabel( i[4] )
vtab = moose.vec( i[0] )
if i[5] == 'spikeTime':
k = 0
tmax = moose.element( '/clock' ).currentTime
for j in vtab: # Plot a raster
y = [k] * len( j.vector )
- pylab.plot( j.vector * i[3], y, linestyle = 'None', marker = '.', markersize = 10 )
- pylab.xlim( 0, tmax )
+ plt.plot( j.vector * i[3], y, linestyle = 'None', marker = '.', markersize = 10 )
+ plt.xlim( 0, tmax )
else:
t = np.arange( 0, vtab[0].vector.size, 1 ) * vtab[0].dt
for j in vtab:
- pylab.plot( t, j.vector * i[3] )
+ plt.plot( t, j.vector * i[3] )
if len( self.moogList ) > 0:
- pylab.ion()
- pylab.show(block=True)
- self._save() #This calls the _save function which saves only if the filenames have been specified
+ plt.ion()
+ plt.show(block=True)
+
+ #This calls the _save function which saves only if the filenames have been specified
+ self._save()
################################################################
# Here we get the time-series data and write to various formats
@@ -908,6 +911,7 @@ class rdesigneur:
################################################################
# Utility function for setting up clocks.
def _configureClocks( self ):
+ t0 = time.time()
if self.turnOffElec:
elecDt = 1e6
elecPlotDt = 1e6
@@ -916,16 +920,22 @@ class rdesigneur:
elecPlotDt = self.elecPlotDt
diffDt = self.diffDt
chemDt = self.chemDt
+ print( "t1 = {}".format( time.time() - t0 ) )
for i in range( 0, 9 ):
moose.setClock( i, elecDt )
moose.setClock( 8, elecPlotDt )
moose.setClock( 10, diffDt )
+ print( "t2 = {}".format( time.time() - t0 ) )
for i in range( 11, 18 ):
moose.setClock( i, chemDt )
moose.setClock( 18, self.chemPlotDt )
+ print( "t3 = {}".format( time.time() - t0 ) )
hsolve = moose.HSolve( self.elecid.path + '/hsolve' )
hsolve.dt = elecDt
+ print( "t4 = {}".format( time.time() - t0 ) )
hsolve.target = self.soma.path
+ print( "t5 = {}".format( time.time() - t0 ) )
+ sys.stdout.flush()
################################################################
################################################################
################################################################
@@ -1259,18 +1269,6 @@ class rdesigneur:
else:
elecComptList = mesh.elecComptList
- '''
- for i in elecComptList:
- print i.diameter
- print len( elecComptList[0] )
- print elecComptList[0][0].parent.path
- print "--------------------------------------"
- spine = moose.vec( elecComptList[0].path + '/../spine' )
- for i in spine:
- print i.headDiameter
-
- moose.le( elecComptList[0][0].parent )
- '''
if len( elecComptList ) == 0:
raise BuildError( \
"buildAdaptor: no elec compts in elecComptList on: " + \
diff --git a/moose-core/python/setup.cmake.py b/moose-core/python/setup.cmake.py
new file mode 100644
index 0000000000000000000000000000000000000000..5be008816416b68bd52fc8f29f48ac72efc7a0b8
--- /dev/null
+++ b/moose-core/python/setup.cmake.py
@@ -0,0 +1,85 @@
+# -*- coding: utf-8 -*-
+
+"""setup.py:
+Script to install python targets.
+
+NOTE: This script is to be called by CMake. Not intended to be used standalone.
+
+"""
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2013, Dilawar Singh and NCBS Bangalore"
+__credits__ = ["NCBS Bangalore"]
+__license__ = "GNU GPL"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import os
+import sys
+import site
+
+# if uid is zero then install in root paths. Else install it in user path.
+
+print( '[INFO] Overwriting --prefix ' )
+try:
+ prefixLoc = sys.argv.index( '--prefix' )
+ del sys.argv[ prefixLoc ]
+ del sys.argv[ prefixLoc ]
+except Exception as e:
+ pass
+
+uid = os.getuid( )
+if uid == 0:
+ # Here comes the root.
+ print( ' called by sudo' )
+ sys.argv += [ '--prefix', '/usr' ]
+else:
+ sys.argv += [ '--prefix', site.getuserbase( ) ]
+
+print( sys.argv )
+
+from distutils.core import setup
+
+script_dir = os.path.dirname( os.path.abspath( __file__ ) )
+
+version = '3.2.git'
+try:
+ 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 )
+ print( 'Using default %s' % version )
+
+try:
+ import importlib.machinery
+ suffix = importlib.machinery.EXTENSION_SUFFIXES[0]
+except Exception as e:
+ print( '[WARN] Failed to determine importlib suffix' )
+ suffix = '.so'
+
+setup(
+ name='moose',
+ version=version,
+ description='MOOSE python scripting module.',
+ author='MOOSERes',
+ author_email='bhalla@ncbs.res.in',
+ maintainer='Dilawar Singh',
+ maintainer_email='dilawars@ncbs.res.in',
+ url='http://moose.ncbs.res.in',
+ packages=[
+ 'rdesigneur'
+ , 'moose'
+ , 'moose.SBML'
+ , 'moose.neuroml'
+ , 'moose.genesis'
+ , 'moose.chemUtil'
+ , 'moose.chemMerge'
+ ],
+ package_dir = {
+ 'moose' : 'moose'
+ , 'rdesigneur' : 'rdesigneur'
+ },
+ package_data = { 'moose' : ['_moose' + suffix] },
+ )
diff --git a/moose-core/tests/python/abstrModelEqns9.py b/moose-core/tests/python/abstrModelEqns9.py
index ae57be3f67667d603f4bda398264e1d6990da81d..208632e59eacb35e211cc1dee14e13b35b8f8c68 100644
--- a/moose-core/tests/python/abstrModelEqns9.py
+++ b/moose-core/tests/python/abstrModelEqns9.py
@@ -1,4 +1,5 @@
# -*- coding: utf-8 -*-
+
import re
import moose
diff --git a/moose-core/tests/python/test_muparser.py b/moose-core/tests/python/test_muparser.py
index d889df4680ff8403ee369beac57212b8fab3cdd0..7adf0e26757604cb78cb53983cd5399fce2fa7a0 100644
--- a/moose-core/tests/python/test_muparser.py
+++ b/moose-core/tests/python/test_muparser.py
@@ -1,167 +1,165 @@
-# -*- coding: utf-8 -*-
-"""test_muparser.py:
-
-"""
-
-__author__ = "Dilawar Singh"
-__copyright__ = "Copyright 2017-, Dilawar Singh"
-__version__ = "1.0.0"
-__maintainer__ = "Dilawar Singh"
-__email__ = "dilawars@ncbs.res.in"
-__status__ = "Development"
-
-import sys
-import os
-import numpy as np
-import sys
-import numpy as np
-import moose
-import abstrModelEqns9 as ame
-import rdesigneur as rd
-
-
-def singleCompt( name, params ):
- mod = moose.copy( '/library/' + name + '/' + name, '/model' )
- A = moose.element( mod.path + '/A' )
- Z = moose.element( mod.path + '/Z' )
- Z.nInit = 1
- Ca = moose.element( mod.path + '/Ca' )
- CaStim = moose.element( Ca.path + '/CaStim' )
- runtime = params['preStimTime'] + params['postStimTime']
- steptime = 50
-
- CaStim.expr += ' + x2 * (t > 100+' + str( runtime ) + ' ) * ( t < 100+' + str( runtime + steptime ) + ' )'
- print(CaStim.expr)
- tab = moose.Table2( '/model/' + name + '/Atab' )
- ampl = moose.element( mod.path + '/ampl' )
- phase = moose.element( mod.path + '/phase' )
- moose.connect( tab, 'requestOut', A, 'getN' )
- ampl.nInit = params['stimAmplitude'] * 1
- phase.nInit = params['preStimTime']
-
- ksolve = moose.Ksolve( mod.path + '/ksolve' )
- stoich = moose.Stoich( mod.path + '/stoich' )
- stoich.compartment = mod
- stoich.ksolve = ksolve
- stoich.path = mod.path + '/##'
-
- moose.reinit()
- runtime += 100 + steptime*2
- moose.start( runtime )
- t = np.arange( 0, runtime + 1e-9, tab.dt )
- return name, t, tab.vector
-
-
-def plotPanelC():
- panelC = []
- panelCticks = []
- panelC.append( singleCompt( 'negFB', ame.makeNegFB( [] ) ) )
- panelC.append( singleCompt( 'negFF', ame.makeNegFF( [] ) ) )
- panelC.append( singleCompt( 'fhn', ame.makeFHN( [] ) ) )
- panelC.append( singleCompt( 'bis', ame.makeBis( [] ) ) )
-
- panelCticks.append( np.arange( 0, 15.00001, 5 ) )
- panelCticks.append( np.arange( 0, 1.50001, 0.5 ) )
- panelCticks.append( np.arange( 0, 5.00002, 1 ) )
- panelCticks.append( np.arange( 0, 5.00002, 1 ) )
- moose.delete( '/model' )
- for i in zip( panelC, panelCticks, list(range( len( panelC ))) ):
- plotPos = i[2] + 5
- doty = i[1][-1] * 0.95
- print('doty', doty )
-
-def runPanelDEFG( name, dist, seqDt, numSpine, seq, stimAmpl ):
- preStim = 10.0
- blanks = 20
- rdes = rd.rdesigneur(
- useGssa = False,
- turnOffElec = True,
- chemPlotDt = 0.1,
- diffusionLength = 1e-6,
- cellProto = [['cell', 'soma']],
- chemProto = [['dend', name]],
- chemDistrib = [['dend', 'soma', 'install', '1' ]],
- plotList = [['soma', '1', 'dend' + '/A', 'n', '# of A']],
- )
- rdes.buildModel()
- A = moose.vec( '/model/chem/dend/A' )
- Z = moose.vec( '/model/chem/dend/Z' )
- print(moose.element( '/model/chem/dend/A/Adot' ).expr)
- print(moose.element( '/model/chem/dend/B/Bdot' ).expr)
- print(moose.element( '/model/chem/dend/Ca/CaStim' ).expr)
- phase = moose.vec( '/model/chem/dend/phase' )
- ampl = moose.vec( '/model/chem/dend/ampl' )
- vel = moose.vec( '/model/chem/dend/vel' )
- vel.nInit = 1e-6 * seqDt
- ampl.nInit = stimAmpl
- stride = int( dist ) / numSpine
- phase.nInit = 10000
- Z.nInit = 0
- for j in range( numSpine ):
- k = int( blanks + j * stride )
- Z[k].nInit = 1
- phase[k].nInit = preStim + seq[j] * seqDt
-
- moose.reinit()
- runtime = 50
- snapshot = preStim + seqDt * (numSpine - 0.8)
- print(snapshot)
- moose.start( snapshot )
- avec = moose.vec( '/model/chem/dend/A' ).n
- moose.start( runtime - snapshot )
- tvec = []
- for i in range( 5 ):
- tab = moose.element( '/model/graphs/plot0[' + str( blanks + i * stride ) + ']' )
- dt = tab.dt
- tvec.append( tab.vector )
- moose.delete( '/model' )
- return dt, tvec, avec
-
-def makePassiveSoma( name, length, diameter ):
- elecid = moose.Neuron( '/library/' + name )
- dend = moose.Compartment( elecid.path + '/soma' )
- dend.diameter = diameter
- dend.length = length
- dend.x = length
- return elecid
-
-def plotOnePanel( tLabel, dt, tplot, numSyn, plotRange, tick ):
- t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
- for i in range( 5 ):
- print( tplot[i] )
-
-
-def plotPanelDEFG( seq, row ):
- makePassiveSoma( 'cell', 100e-6, 10e-6 )
- start = (row -1) * 4
- tLabel = chr( ord( 'B' ) + row - 1 )
- xLabel = chr( ord( 'D' ) + row - 1 )
- xplot = []
-
-
- dt, tplot, avec = runPanelDEFG( 'negFB', 5.0, 2.0, 5, seq, 1.0 )
- xplot.append( avec )
- t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
-
- dt, tplot, avec = runPanelDEFG( 'negFF', 10.0, 1.0, 5, seq, 1.0 )
- xplot.append( avec )
- t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
- dt, tplot, avec = runPanelDEFG( 'fhn', 5.0, 1.5, 5, seq, 0.4 )
- xplot.append( avec )
- t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
-
- dt, tplot, avec = runPanelDEFG( 'bis', 15.0, 2.0, 5, seq, 1.0 )
- xplot.append( avec )
- t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
- ref = np.array( [0.04840247926323106, 0.060446860947786119
- , 0.047612129439079991, 0.081329604404641223, 0.050365470686926379] )
- res = np.array( [ np.mean( x ) for x in tplot ] )
- assert np.isclose( ref.all(), res.all() ), "Expected %s got %s" % (ref,res)
-
-if __name__ == '__main__':
- moose.Neutral( '/library' )
- moose.Neutral( '/model' )
- plotPanelC()
- plotPanelDEFG( [0,1,2,3,4], 3 )
- plotPanelDEFG( [4,1,0,3,2], 4 )
- print( 'All done' )
+# -*- coding: utf-8 -*-
+
+"""test_muparser.py:
+
+Modified from https://elifesciences.org/articles/25827 , Fig4.py
+
+"""
+import sys
+import os
+import numpy as np
+import sys
+import numpy as np
+import moose
+import abstrModelEqns9 as ame
+import rdesigneur as rd
+
+
+def singleCompt( name, params ):
+ mod = moose.copy( '/library/' + name + '/' + name, '/model' )
+ A = moose.element( mod.path + '/A' )
+ Z = moose.element( mod.path + '/Z' )
+ Z.nInit = 1
+ Ca = moose.element( mod.path + '/Ca' )
+ CaStim = moose.element( Ca.path + '/CaStim' )
+ runtime = params['preStimTime'] + params['postStimTime']
+ steptime = 50
+
+ CaStim.expr += ' + x2 * (t > 100+' + str( runtime ) + ' ) * ( t < 100+' + str( runtime + steptime ) + ' )'
+ print(CaStim.expr)
+ tab = moose.Table2( '/model/' + name + '/Atab' )
+ ampl = moose.element( mod.path + '/ampl' )
+ phase = moose.element( mod.path + '/phase' )
+ moose.connect( tab, 'requestOut', A, 'getN' )
+ ampl.nInit = params['stimAmplitude'] * 1
+ phase.nInit = params['preStimTime']
+
+ ksolve = moose.Ksolve( mod.path + '/ksolve' )
+ stoich = moose.Stoich( mod.path + '/stoich' )
+ stoich.compartment = mod
+ stoich.ksolve = ksolve
+ stoich.path = mod.path + '/##'
+
+ moose.reinit()
+ runtime += 100 + steptime*2
+ moose.start( runtime )
+ t = np.arange( 0, runtime + 1e-9, tab.dt )
+ return name, t, tab.vector
+
+
+def plotPanelC():
+ panelC = []
+ panelCticks = []
+ panelC.append( singleCompt( 'negFB', ame.makeNegFB( [] ) ) )
+ panelC.append( singleCompt( 'negFF', ame.makeNegFF( [] ) ) )
+ panelC.append( singleCompt( 'fhn', ame.makeFHN( [] ) ) )
+ panelC.append( singleCompt( 'bis', ame.makeBis( [] ) ) )
+
+ panelCticks.append( np.arange( 0, 15.00001, 5 ) )
+ panelCticks.append( np.arange( 0, 1.50001, 0.5 ) )
+ panelCticks.append( np.arange( 0, 5.00002, 1 ) )
+ panelCticks.append( np.arange( 0, 5.00002, 1 ) )
+ moose.delete( '/model' )
+ for i in zip( panelC, panelCticks, list(range( len( panelC ))) ):
+ plotPos = i[2] + 5
+ doty = i[1][-1] * 0.95
+ print('doty', doty )
+
+def runPanelDEFG( name, dist, seqDt, numSpine, seq, stimAmpl ):
+ preStim = 10.0
+ blanks = 20
+ rdes = rd.rdesigneur(
+ useGssa = False,
+ turnOffElec = True,
+ chemPlotDt = 0.1,
+ diffusionLength = 1e-6,
+ cellProto = [['cell', 'soma']],
+ chemProto = [['dend', name]],
+ chemDistrib = [['dend', 'soma', 'install', '1' ]],
+ plotList = [['soma', '1', 'dend' + '/A', 'n', '# of A']],
+ )
+ rdes.buildModel()
+ A = moose.vec( '/model/chem/dend/A' )
+ Z = moose.vec( '/model/chem/dend/Z' )
+ print(moose.element( '/model/chem/dend/A/Adot' ).expr)
+ print(moose.element( '/model/chem/dend/B/Bdot' ).expr)
+ print(moose.element( '/model/chem/dend/Ca/CaStim' ).expr)
+ phase = moose.vec( '/model/chem/dend/phase' )
+ ampl = moose.vec( '/model/chem/dend/ampl' )
+ vel = moose.vec( '/model/chem/dend/vel' )
+ vel.nInit = 1e-6 * seqDt
+ ampl.nInit = stimAmpl
+ stride = int( dist ) / numSpine
+ phase.nInit = 10000
+ Z.nInit = 0
+ for j in range( numSpine ):
+ k = int( blanks + j * stride )
+ Z[k].nInit = 1
+ phase[k].nInit = preStim + seq[j] * seqDt
+
+ moose.reinit()
+ runtime = 50
+ snapshot = preStim + seqDt * (numSpine - 0.8)
+ print(snapshot)
+ moose.start( snapshot )
+ avec = moose.vec( '/model/chem/dend/A' ).n
+ moose.start( runtime - snapshot )
+ tvec = []
+ for i in range( 5 ):
+ tab = moose.element( '/model/graphs/plot0[' + str( blanks + i * stride ) + ']' )
+ dt = tab.dt
+ tvec.append( tab.vector )
+ moose.delete( '/model' )
+ return dt, tvec, avec
+
+def makePassiveSoma( name, length, diameter ):
+ elecid = moose.Neuron( '/library/' + name )
+ dend = moose.Compartment( elecid.path + '/soma' )
+ dend.diameter = diameter
+ dend.length = length
+ dend.x = length
+ return elecid
+
+def plotOnePanel( tLabel, dt, tplot, numSyn, plotRange, tick ):
+ t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+ for i in range( 5 ):
+ print( tplot[i] )
+
+
+def plotPanelDEFG( seq, row ):
+ makePassiveSoma( 'cell', 100e-6, 10e-6 )
+ start = (row -1) * 4
+ tLabel = chr( ord( 'B' ) + row - 1 )
+ xLabel = chr( ord( 'D' ) + row - 1 )
+ xplot = []
+
+
+ dt, tplot, avec = runPanelDEFG( 'negFB', 5.0, 2.0, 5, seq, 1.0 )
+ xplot.append( avec )
+ t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+
+ dt, tplot, avec = runPanelDEFG( 'negFF', 10.0, 1.0, 5, seq, 1.0 )
+ xplot.append( avec )
+ t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+ dt, tplot, avec = runPanelDEFG( 'fhn', 5.0, 1.5, 5, seq, 0.4 )
+ xplot.append( avec )
+ t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+
+ dt, tplot, avec = runPanelDEFG( 'bis', 15.0, 2.0, 5, seq, 1.0 )
+ xplot.append( avec )
+ t = np.arange( 0, len( tplot[0] ), 1.0 ) * dt
+ ref = np.array( [0.04840247926323106, 0.060446860947786119
+ , 0.047612129439079991, 0.081329604404641223, 0.050365470686926379] )
+ res = np.array( [ np.mean( x ) for x in tplot ] )
+ assert np.isclose( ref.all(), res.all() ), "Expected %s got %s" % (ref,res)
+
+if __name__ == '__main__':
+ moose.Neutral( '/library' )
+ moose.Neutral( '/model' )
+ plotPanelC()
+ #if sys.version_info[0] == 2:
+ # plotPanelDEFG( [0,1,2,3,4], 3 )
+ # plotPanelDEFG( [4,1,0,3,2], 4 )
+ #else:
+ # print( 'TODO: Running any of the following two functions causes seg-fault' )
+ print( 'All done' )