snippets/savemodel.py is causing problem now.

Author: Dilawar Singh

pybind11/MooseVec.cpp

@@ -105,7 +105,8 @@ vector<py::object> MooseVec::getAttribute(const string& name)
     return res;
 }
 
-// FIXME: Only double is supported here. Not sure if this is enough.
+// FIXME: Only double is supported here. Not sure if this is enough. This
+// should be the API function.
 py::array_t<double> MooseVec::getAttributeNumpy(const string &name)
 {
     auto cinfo = oid_.element()->cinfo();
@@ -128,7 +129,7 @@ py::array_t<double> MooseVec::getAttributeNumpy(const string &name)
         return py::array_t<double>(res.size(), res.data());
     }
 
-    throw runtime_error("getAttributeNumpy::NotImplemented : " + name +
+    throw runtime_error("MooseVec::getAttributeNumpy::NotImplemented : " + name +
                         " with rttType " + finfo->rttiType() + " and type: '" +
                         finfoType + "'");
     return py::array_t<double>();

pybind11/MooseVec.h

@@ -39,10 +39,12 @@ class MooseVec
     ObjId getDataItem(const size_t i) const;
     ObjId getFieldItem(const size_t i) const;
 
+    // Set attribute to vector.
     void setAttrOneToAll(const string& name, const py::object& val);
 
     void setAttrOneToOne(const string& name, const py::sequence& val);
 
+    // Get attributes.
     vector<py::object> getAttribute(const string& name);
     py::array_t<double> getAttributeNumpy(const string& name);
 

pybind11/helper.cpp

@@ -203,6 +203,7 @@ ObjId shellConnect(const ObjId& src, const string& srcField, const ObjId& tgt,
     return getShellPtr()->doAddMsg(msgType, src, srcField, tgt, tgtField);
 }
 
+#if 0
 void mooseMoveId(const Id& a, const ObjId& b)
 {
     getShellPtr()->doMove(a, b);
@@ -213,6 +214,12 @@ void mooseMoveObjId(const ObjId& a, const ObjId& b)
     getShellPtr()->doMove(a.id, b);
 }
 
+void mooseMoveObPath(const string& a, const ObjId& b)
+{
+    getShellPtr()->doMove(a.id, b);
+}
+#endif
+
 void mooseSetClock(const unsigned int clockId, double dt)
 {
     getShellPtr()->doSetClock(clockId, dt);

pybind11/helper.h

@@ -39,8 +39,17 @@ Id initShell();
 
 bool mooseExists(const string& path);
 
+#if 0
 void mooseMoveId(const Id& a, const ObjId& b);
 void mooseMoveObjId(const ObjId& a, const ObjId& b);
+#endif
+
+template<typename P=ObjId, typename Q=ObjId>
+inline void mooseMove(const P& src, const Q& tgt)
+{
+    getShellPtr()->doMove(Id(src), ObjId(tgt));
+}
+
 
 inline MooseVec mooseObjIdPath(const string& p)
 {

pybind11/pymoose.cpp

@@ -315,9 +315,9 @@ PYBIND11_MODULE(_moose, m)
              },
              py::keep_alive<0, 1>())
         .def("__getitem__", &MooseVec::getItem)
-        .def("__setattr__", &MooseVec::setAttrOneToOne)
         .def("__setattr__", &MooseVec::setAttrOneToAll)
-        .def("__getattr__", &MooseVec::getAttributeNumpy)
+        .def("__setattr__", &MooseVec::setAttrOneToOne)
+        .def("__getattr__", &MooseVec::getAttribute)
         .def("__repr__", [](const MooseVec & v)->string {
              return "<moose.vec class=" + v.dtype() + " path=" + v.path() +
                     " id=" + std::to_string(v.id()) + " size=" +
@@ -346,8 +346,10 @@ PYBIND11_MODULE(_moose, m)
     m.def("create", &mooseCreateFromPath);
     m.def("create", &mooseCreateFromObjId);
     m.def("create", &mooseCreateFromId);
-    m.def("move", &mooseMoveId);
-    m.def("move", &mooseMoveObjId);
+    m.def("move", &mooseMove<ObjId, ObjId>);
+    m.def("move", &mooseMove<ObjId, string>);
+    m.def("move", &mooseMove<string, ObjId>);
+    m.def("move", &mooseMove<string, string>);
     m.def("reinit", &mooseReinit);
     m.def("start", &mooseStart, "runtime"_a, "notify"_a = false);
     m.def("stop", &mooseStop);

python/moose/chemUtil/add_Delete_ChemicalSolver.py

@@ -61,12 +61,7 @@ def mooseAddChemSolver(modelRoot, solver):
     Add the solvers only if all are Chemical compartment
     """
     compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
-    print([(x.__metaclass__, x.className) for x in compts] )
-    print(compts, solver, '1111')
-    print([isinstance(x, (moose.CubeMesh, moose.CylMesh)) for x in compts])
-
     if all(isinstance(x, (moose.CubeMesh,moose.CylMesh)) for x in compts):
-        print('111')
         if not compts:
             return ("Atleast one compartment is required ")
         elif ( len(compts) > 3 ):

python/moose/chemUtil/chemConnectUtil.py

@@ -112,8 +112,8 @@ def validColorcheck(color):
 def xyPosition(objInfo,xory):
     try:
         return float(moose.element(objInfo).getField(xory))
-    except ValueError as e:
-        return float(0)
+    except ValueError:
+        return 0.0
 
 def setupMeshObj(modelRoot):
     ''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
@@ -152,10 +152,10 @@ def setupMeshObj(modelRoot):
         tablist  = moose.wildcardFind(meshEnt.path+'/##[ISA=StimulusTable]')
         if mol_cpl or funclist or enzlist or realist or tablist:
             for m in mol_cpl:
-                if isinstance(moose.element(m.parent),moose.CplxEnzBase):
+                if isinstance(moose.element(m.parent), moose.CplxEnzBase):
                     cplxlist.append(m)
                     objInfo = m.parent.path+'/info'
-                elif isinstance(moose.element(m),moose.PoolBase):
+                elif isinstance(moose.element(m), moose.PoolBase):
                     mollist.append(m)
                     objInfo =m.path+'/info'
                 if moose.exists(objInfo):
@@ -277,11 +277,10 @@ def setupItem(modelPath,cntDict):
                     tablist.append((moose.element(tabconnect),'tab',countuniqItem[tabconnect]))
                 cntDict[tab] = tablist
 
-def countitems(mitems,objtype):
+def countitems(mitems, objtype):
     items = []
-    items = moose.element(mitems).neighbors[objtype]
+    items = mitems.neighbors[objtype]
     uniqItems = set(items)
-    #countuniqItems = Counter(items)
     countuniqItems = dict((i, items.count(i)) for i in items)
     return(uniqItems,countuniqItems)
 

python/moose/genesis/writeKkit.py

@@ -60,6 +60,7 @@
 #               --StimulusTable
 
 def mooseWriteKkit( modelpath, filename, sceneitems={}):
+    print('111')
     global foundmatplotlib_
     if not foundmatplotlib_:
         print('No maplotlib found.'
@@ -154,7 +155,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
             writeFooter1(f)
             writeNotes(modelpath,f)
             writeFooter2(f)
-            print('Written to file '+filename)
+            print('kkit model is written to file '+filename)
             return errors, True
         else:
             print("Warning: writeKkit:: No model found on " , modelpath)