Added option to add <Include> to generated model

examples/apitest3.py

@@ -0,0 +1,50 @@
+#! /usr/bin/python
+
+import lems.api as lems
+
+model = lems.Model()
+
+model.add(lems.Include("test.xml"))
+
+model.add(lems.Dimension('voltage', m=1, l=3, t=-3, i=-1))
+model.add(lems.Dimension('time', t=1))
+model.add(lems.Dimension('capacitance', m=-1, l=-2, t=4, i=2))
+
+model.add(lems.Unit('milliVolt', 'mV', 'voltage', -3))
+model.add(lems.Unit('milliSecond', 'ms', 'time', -3))
+model.add(lems.Unit('microFarad', 'uF', 'capacitance', -12))
+
+iaf1 = lems.ComponentType('iaf1')
+model.add(iaf1)
+
+iaf1.add(lems.Parameter('threshold', 'voltage'))
+iaf1.add(lems.Parameter('reset', 'voltage'))
+iaf1.add(lems.Parameter('refractoryPeriod', 'time'))
+iaf1.add(lems.Parameter('capacitance', 'capacitance'))
+iaf1.add(lems.Exposure('vexp', 'voltage'))
+dp = lems.DerivedParameter('range', 'threshold - reset', 'voltage')
+iaf1.add(dp)
+
+iaf1.dynamics.add(lems.StateVariable('v','voltage', 'vexp')) 
+iaf1.dynamics.add(lems.DerivedVariable('v2',dimension='voltage', value='v*2'))
+cdv = lems.ConditionalDerivedVariable('v_abs','voltage')
+cdv.add(lems.Case('v .geq. 0','v'))
+cdv.add(lems.Case('v .lt. 0','-1*v'))
+iaf1.dynamics.add(cdv)
+
+
+model.add(lems.Component('celltype_a', iaf1.name))
+model.add(lems.Component('celltype_b', iaf1.name, threshold="20mV"))
+
+fn = '/tmp/model.xml'
+model.export_to_file(fn)
+
+print("----------------------------------------------")
+print(open(fn,'r').read())
+print("----------------------------------------------")
+
+print("Written generated LEMS to %s"%fn)
+
+from lems.base.util import validate_lems
+
+validate_lems(fn)

lems/model/fundamental.py

@@ -8,6 +8,32 @@
 
 from lems.base.base import LEMSBase
 
+class Include(LEMSBase):
+    """
+    Include another LEMS file.
+    """
+
+    def __init__(self, filename):
+        """
+        Constructor.
+
+        @param filename: Name of the file.
+        @type name: str
+
+        """
+
+        self.file = filename
+        """ Name of the file.
+        @type: str """
+
+
+    def toxml(self):
+        """
+        Exports this object into a LEMS XML object
+        """
+
+        return '<Include file="%s"/>'%self.file
+
 class Dimension(LEMSBase):
     """
     Stores a dimension in terms of the seven fundamental SI units.

lems/model/model.py

@@ -16,7 +16,7 @@
 from lems.base.errors import ModelError
 from lems.base.errors import SimBuildError
 
-from lems.model.fundamental import Dimension,Unit
+from lems.model.fundamental import Dimension,Unit,Include
 from lems.model.component import Constant,ComponentType,Component,FatComponent
 from lems.model.simulation import Run,Record,EventRecord,DataDisplay,DataWriter,EventWriter
 from lems.model.structure import With,EventConnection,ChildInstance,MultiInstantiate
@@ -47,6 +47,10 @@ def __init__(self, include_includes='True'):
         """ List of targets to be run on startup.
         @type: list(str) """
 
+        self.includes = Map()
+        """ Dictionary of includes defined in the model.
+        @type: dict(str -> lems.model.fundamental.Include """
+
         self.dimensions = Map()
         """ Dictionary of dimensions defined in the model.
         @type: dict(str -> lems.model.fundamental.Dimension """
@@ -98,6 +102,16 @@ def add_target(self, target):
 
         self.targets.append(target)
 
+    def add_include(self, include):
+        """
+        Adds an include to the model.
+
+        @param include: Include to be added.
+        @type include: lems.model.fundamental.Include
+        """
+
+        self.includes[include.file] = include
+
     def add_dimension(self, dimension):
         """
         Adds a dimension to the model.
@@ -171,7 +185,9 @@ def add(self, child):
         @param child: Child object to be added.
         """
 
-        if isinstance(child, Dimension):
+        if isinstance(child, Include):
+            self.add_include(child)
+        elif isinstance(child, Dimension):
             self.add_dimension(child)
         elif isinstance(child, Unit):
             self.add_unit(child)
@@ -262,6 +278,9 @@ def export_to_file(self, filepath, level_prefix = '  '):
 
         xmlstr = '<Lems %s>'%namespaces
 
+        for include in self.includes:
+            xmlstr += include.toxml()
+
         for target in self.targets:
             xmlstr += '<Target component="{0}"/>'.format(target)