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Dilawar Singh
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Perfecto. Create works.
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‎pymoose/CMakeLists.txt‎

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@@ -4,7 +4,7 @@ include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
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set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../cmake_modules/")
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pybind11_add_module(_moose pymoose.cpp)
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target_link_libraries(_moose moose)
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target_link_libraries(_moose PRIVATE moose)
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enable_testing()
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add_test(NAME sanity

‎pymoose/pymoose.cpp‎

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// =====================================================================================
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//
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// Filename: pymoose.cpp
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//
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// Description:
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//
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// Version: 1.0
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// Created: 03/15/2020 04:03:58 PM
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// Revision: none
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// Compiler: g++
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//
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// Author: Dilawar Singh (), [email protected]
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// Organization: NCBS Bangalore
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//
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// =====================================================================================
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#include <vector>
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#include <typeinfo>
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#include <utility>
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#include "../basecode/header.h"
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#include "../shell/Shell.h"
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#include "../scheduling/Clock.h"
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#include "../utility/print_function.hpp"
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#include "../utility/utility.h"
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#include "../utility/strutil.h"
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#include "../mpi/PostMaster.h"
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#include "pymoose.h"
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class Pool;
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class BufPool;
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#include "../external/pybind11/include/pybind11/pybind11.h"
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using namespace std;
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namespace py = pybind11;
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const vector<const char*> classMap { "AdExIF", "AdThreshIF", "Adaptor",
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"Annotator", "Arith", "BufPool", "CaConc", "Cell", "ChemCompt", "Cinfo",
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"Clock", "Compartment", "ConcChan", "CubeMesh", "CylMesh", "DestField",
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"DiagonalMsg", "DifBuffer", "DifShell", "DiffAmp", "Dsolve",
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"ElementField", "EndoMesh", "Enz", "ExIF", "Finfo", "Function",
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"GapJunction", "GraupnerBrunel2012CaPlasticitySynHandler", "Group",
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"Gsolve", "HHChannel", "HHChannel2D", "HHGate", "HHGate2D", "HSolve",
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"INFINITE", "IntFire", "Interpol", "Interpol2D", "IzhIF", "IzhikevichNrn",
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"Ksolve", "LIF", "Leakage", "LookupField", "MMPump", "MMenz",
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"MarkovChannel", "MarkovGslSolver", "MarkovRateTable", "MarkovSolver",
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"MeshEntry", "MgBlock", "Msg", "Mstring", "NMDAChan", "Nernst",
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"NeuroMesh", "Neuron", "Neutral", "OneToAllMsg", "OneToOneDataIndexMsg",
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"OneToOneMsg", "PIDController", "Pool", "PostMaster", "PsdMesh",
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"PulseGen", "PyRun", "QIF", "RC", "RandSpike", "Reac", "STDPSynHandler",
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"STDPSynapse", "SeqSynHandler", "Shell", "SimpleSynHandler", "SingleMsg",
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"SocketStreamer", "SparseMsg", "Species", "SpikeGen", "SpikeStats",
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"Spine", "SpineMesh", "Stats", "SteadyState", "StimulusTable", "Stoich",
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"Streamer", "SymCompartment", "SynChan", "Synapse", "Table", "Table2",
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"TimeTable", "VClamp" };
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Id initShell(void)
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{
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Cinfo::rebuildOpIndex();
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Id shellId;
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Element* shelle = new GlobalDataElement( shellId, Shell::initCinfo(), "root", 1 );
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Id clockId = Id::nextId();
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assert( clockId.value() == 1 );
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Id classMasterId = Id::nextId();
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Id postMasterId = Id::nextId();
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Shell* s = reinterpret_cast< Shell* >( shellId.eref().data() );
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s->setHardware(1, 1, 0);
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s->setShellElement( shelle );
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/// Sets up the Elements that represent each class of Msg.
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auto numMsg = Msg::initMsgManagers();
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new GlobalDataElement( clockId, Clock::initCinfo(), "clock", 1 );
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new GlobalDataElement( classMasterId, Neutral::initCinfo(), "classes", 1);
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new GlobalDataElement( postMasterId, PostMaster::initCinfo(), "postmaster", 1 );
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assert ( shellId == Id() );
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assert( clockId == Id( 1 ) );
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assert( classMasterId == Id( 2 ) );
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assert( postMasterId == Id( 3 ) );
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Shell::adopt( shellId, clockId, numMsg++ );
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Shell::adopt( shellId, classMasterId, numMsg++ );
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Shell::adopt( shellId, postMasterId, numMsg++ );
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assert( numMsg == 10 ); // Must be the same on all nodes.
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Cinfo::makeCinfoElements( classMasterId );
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return shellId;
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}
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/* --------------------------------------------------------------------------*/
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/**
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* @Synopsis getShell.
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*
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* @Param argc
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* @Param argv
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*
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* @Returns
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*/
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/* ----------------------------------------------------------------------------*/
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Id getShell(int argc, char ** argv)
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{
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static int inited = 0;
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if (inited)
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return Id(0);
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Id shellId = initShell();
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inited = 1;
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Shell * shellPtr = reinterpret_cast<Shell*>(shellId.eref().data());
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if ( shellPtr->myNode() == 0 )
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{
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if ( Shell::numNodes() > 1 )
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{
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// Use the last clock for the postmaster, so that it is called
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// after everything else has been processed and all messages
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// are ready to send out.
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shellPtr->doUseClock( "/postmaster", "process", 9 );
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shellPtr->doSetClock( 9, 1.0 ); // Use a sensible default.
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}
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}
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return shellId;
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}
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/**
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Utility function to create objects from full path, dimensions
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and classname.
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*/
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Id createIdFromPath(string path, string type, size_t numData)
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{
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string parent_path;
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string name;
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string trimmed_path = moose::trim( path );
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size_t pos = trimmed_path.rfind("/");
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if (pos != string::npos)
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{
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name = trimmed_path.substr(pos+1);
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parent_path = trimmed_path.substr(0, pos);
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}
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else
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{
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name = trimmed_path;
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}
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// handle relative path
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if (trimmed_path[0] != '/')
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{
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string current_path = SHELLPTR->getCwe().path();
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if (current_path != "/")
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{
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parent_path = current_path + "/" + parent_path;
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}
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else
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{
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parent_path = current_path + parent_path;
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}
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}
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else if (parent_path.empty())
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{
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parent_path = "/";
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}
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ObjId parent_id(parent_path);
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if (parent_id.bad() )
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{
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string message = "Parent element does not exist: ";
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message += parent_path;
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PyErr_SetString(PyExc_ValueError, message.c_str());
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return Id();
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}
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Id nId = SHELLPTR->doCreate(type,
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parent_id,
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string(name),
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numData,
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MooseGlobal
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);
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if (nId == Id() && trimmed_path != "/" && trimmed_path != "/root")
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{
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string message = "no such moose class : " + type;
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PyErr_SetString(PyExc_TypeError, message.c_str());
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}
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return nId;
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}
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PYBIND11_MODULE(_moose, m)
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{
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m.doc() = R"moosedoc(moose module.
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)moosedoc";
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py::class_<ObjId>(m, "ObjId")
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.def(py::init<>())
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;
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py::class_<Id>(m, "Id")
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.def(py::init<>())
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;
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// Add Shell Class.
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py::class_<Shell>(m, "Shell")
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.def(py::init<>())
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.def("doCreate", &Shell::doCreate)
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.def("doDelete", &Shell::doDelete)
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.def("doAddMsg", &Shell::doAddMsg)
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.def("doQuit", &Shell::doQuit)
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.def("doStart", &Shell::doStart)
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.def("doReinit", &Shell::doReinit)
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.def("doStop", &Shell::doStop)
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.def("doMove", &Shell::doMove)
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.def("doCopy", &Shell::doCopy)
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.def("destroy", &Shell::destroy)
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.def("doFind", &Shell::doFind)
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.def("doLoadModel", &Shell::doLoadModel)
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.def("doSaveModel", &Shell::doSaveModel)
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.def("handleCreate", &Shell::handleCreate)
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.def("handleCopy", &Shell::handleCopy)
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.def("handleQuit", &Shell::handleQuit)
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;
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m.def("create", &createIdFromPath);
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m.attr("__version__") = MOOSE_VERSION;
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}

‎pymoose/pymoose.h‎

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// =====================================================================================
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//
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// Filename: pymoose.h
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//
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// Description: pymoose module.
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//
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// Version: 1.0
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// Created: 03/17/2020 05:32:37 PM
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// Revision: none
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// Compiler: g++
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//
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// Author: Dilawar Singh (), [email protected]
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// Organization: NCBS Bangalore
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//
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// =====================================================================================
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#ifndef PYMOOSE_H
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#define PYMOOSE_H
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Id initShell(void);
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/**
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Return the Id of the Shell object.
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*/
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Id getShell(int argc, char ** argv);
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// Macro to create the Shell * out of shellId
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#define SHELLPTR (reinterpret_cast<Shell*>(getShell(0, NULL).eref().data()))
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Id createIdFromPath(string path, string type, size_t numData=1);
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#endif /* end of include guard: PYMOOSE_H */

‎pymoose/test_pybind_moose.py‎

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@@ -1,4 +1,5 @@
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import _moose as M
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print("Using _moose from %s" % M.__file__)
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print(dir(M))
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print(dir(M.Shell))
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a = M.create('a', 'Neutral', 1)
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print(a)

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