From a56eb93a8a83bd8d27e3a24b32c1bbfe4827a2dc Mon Sep 17 00:00:00 2001
From: DeLaVlag <michielvandervlag@gmail.com>
Date: Fri, 6 Jan 2023 14:37:56 +0100
Subject: [PATCH 01/11] minval maxval extension for TVB Rateml

---
 lems/model/component.py | 20 ++++++++++++++++++--
 lems/model/dynamics.py  | 10 +++++++++-
 lems/parser/LEMS.py     | 36 +++++++++++++++++++++++++++++++++---
 3 files changed, 60 insertions(+), 6 deletions(-)

diff --git a/lems/model/component.py b/lems/model/component.py
index 1b5b34f..595b5eb 100644
--- a/lems/model/component.py
+++ b/lems/model/component.py
@@ -21,7 +21,7 @@ class Parameter(LEMSBase):
     Stores a parameter declaration.
     """
 
-    def __init__(self, name, dimension, description=""):
+    def __init__(self, name, dimension, minval, maxval, description=""):
         """
         Constructor.
 
@@ -56,6 +56,14 @@ def __init__(self, name, dimension, description=""):
         """ Description of this parameter.
         :type: str """
 
+        self.minval = minval
+        """ Minimum value of this parameter.
+        :type: str """
+
+        self.maxval = maxval
+        """ Maximum value of this parameter.
+        :type: str """
+
     def toxml(self):
         """
         Exports this object into a LEMS XML object
@@ -309,7 +317,7 @@ class Exposure(LEMSBase):
     Stores a exposure specification.
     """
 
-    def __init__(self, name, dimension, description=""):
+    def __init__(self, name, minval, maxval, dimension, description=""):
         """
         Constructor.
 
@@ -320,6 +328,14 @@ def __init__(self, name, dimension, description=""):
         """ Name of the exposure.
         :type: str """
 
+        self.minval = minval
+        """ Minimum value of this parameter.
+        :type: str """
+
+        self.maxval = maxval
+        """ Maximum value of this parameter.
+        :type: str """
+
         self.dimension = dimension
         """ Physical dimension of the exposure.
         :type: str """
diff --git a/lems/model/dynamics.py b/lems/model/dynamics.py
index 1ad1275..3fe6e59 100644
--- a/lems/model/dynamics.py
+++ b/lems/model/dynamics.py
@@ -16,7 +16,7 @@ class StateVariable(LEMSBase):
     Store the specification of a state variable.
     """
 
-    def __init__(self, name, dimension, exposure=None):
+    def __init__(self, name, minval, maxval, dimension, exposure=None):
         """
         Constructor.
 
@@ -27,6 +27,14 @@ def __init__(self, name, dimension, exposure=None):
         """ Name of the state variable.
         :type: str """
 
+        self.minval = minval
+        """ Minimum value of this parameter.
+        :type: str """
+
+        self.maxval = maxval
+        """ Maximum value of this parameter.
+        :type: str """
+
         self.dimension = dimension
         """ Dimension of the state variable.
         :type: str """
diff --git a/lems/parser/LEMS.py b/lems/parser/LEMS.py
index a48eee9..00a4dca 100644
--- a/lems/parser/LEMS.py
+++ b/lems/parser/LEMS.py
@@ -985,6 +985,16 @@ def parse_exposure(self, node):
         except:
             self.raise_error("<Exposure> must specify a name")
 
+        if "minval" in node.lattrib:
+            minval = node.lattrib["minval"]
+        else:
+            minval = 0.0
+
+        if "maxval" in node.lattrib:
+            maxval = node.lattrib["maxval"]
+        else:
+            maxval = 0.0
+
         try:
             dimension = node.lattrib["dimension"]
         except:
@@ -992,7 +1002,7 @@ def parse_exposure(self, node):
 
         description = node.lattrib.get("description", "")
 
-        self.current_component_type.add_exposure(Exposure(name, dimension, description))
+        self.current_component_type.add_exposure(Exposure(name, minval, maxval, dimension, description))
 
     def parse_fixed(self, node):
         """
@@ -1286,13 +1296,23 @@ def parse_parameter(self, node):
         except:
             self.raise_error("<Parameter> must specify a name")
 
+        if "minval" in node.lattrib:
+            minval = node.lattrib["minval"]
+        else:
+            minval = 0.0
+
+        if "maxval" in node.lattrib:
+            maxval = node.lattrib["maxval"]
+        else:
+            maxval = 0.0
+
         try:
             dimension = node.lattrib["dimension"]
         except:
             self.raise_error("Parameter '{0}' has no dimension", name)
 
         description = node.lattrib.get("description", "")
-        parameter = Parameter(name, dimension, description)
+        parameter = Parameter(name, dimension, minval, maxval, description)
 
         self.current_component_type.add_parameter(parameter)
 
@@ -1638,6 +1658,16 @@ def parse_state_variable(self, node):
         else:
             self.raise_error("<StateVariable> must specify a name")
 
+        if "minval" in node.lattrib:
+            minval = node.lattrib["minval"]
+        else:
+            minval = 0.0
+
+        if "maxval" in node.lattrib:
+            maxval = node.lattrib["maxval"]
+        else:
+            maxval = 0.0
+
         if "dimension" in node.lattrib:
             dimension = node.lattrib["dimension"]
         else:
@@ -1648,7 +1678,7 @@ def parse_state_variable(self, node):
         else:
             exposure = None
 
-        self.current_regime.add_state_variable(StateVariable(name, dimension, exposure))
+        self.current_regime.add_state_variable(StateVariable(name, minval, maxval, dimension, exposure))
 
     def parse_structure(self, node):
         """

From 9b15fae9199c7622055194016ce6dfdf11daafd4 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Tue, 17 Jan 2023 16:36:33 +0000
Subject: [PATCH 02/11] Make minval/maxval optional

---
 examples/apitest_maxmin.py | 35 +++++++++++++++++++++++++++++++++++
 lems/model/component.py    |  4 ++--
 lems/model/dynamics.py     |  2 +-
 3 files changed, 38 insertions(+), 3 deletions(-)
 create mode 100644 examples/apitest_maxmin.py

diff --git a/examples/apitest_maxmin.py b/examples/apitest_maxmin.py
new file mode 100644
index 0000000..8d92574
--- /dev/null
+++ b/examples/apitest_maxmin.py
@@ -0,0 +1,35 @@
+#! /usr/bin/python
+
+import lems.api as lems
+
+model = lems.Model()
+
+model.add(lems.Include("maxmin.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", minval=-44, maxval=55))
+iaf1.add(lems.Parameter("reset", "voltage"))
+
+
+fn = "/tmp/maxmin.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)
diff --git a/lems/model/component.py b/lems/model/component.py
index 595b5eb..ea7b513 100644
--- a/lems/model/component.py
+++ b/lems/model/component.py
@@ -21,7 +21,7 @@ class Parameter(LEMSBase):
     Stores a parameter declaration.
     """
 
-    def __init__(self, name, dimension, minval, maxval, description=""):
+    def __init__(self, name, dimension, minval=None, maxval=None, description=""):
         """
         Constructor.
 
@@ -317,7 +317,7 @@ class Exposure(LEMSBase):
     Stores a exposure specification.
     """
 
-    def __init__(self, name, minval, maxval, dimension, description=""):
+    def __init__(self, name, dimension, minval=None, maxval=None, description=""):
         """
         Constructor.
 
diff --git a/lems/model/dynamics.py b/lems/model/dynamics.py
index 3fe6e59..e085a11 100644
--- a/lems/model/dynamics.py
+++ b/lems/model/dynamics.py
@@ -16,7 +16,7 @@ class StateVariable(LEMSBase):
     Store the specification of a state variable.
     """
 
-    def __init__(self, name, minval, maxval, dimension, exposure=None):
+    def __init__(self, name, dimension, minval=None, maxval=None, exposure=None):
         """
         Constructor.
 

From 4a9b717359563c5a4e4ae6c55f8c75f8d6c558fe Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Fri, 27 Jan 2023 16:33:43 +0000
Subject: [PATCH 03/11] Fixes for arg order

---
 lems/parser/LEMS.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lems/parser/LEMS.py b/lems/parser/LEMS.py
index 00a4dca..425e58d 100644
--- a/lems/parser/LEMS.py
+++ b/lems/parser/LEMS.py
@@ -1002,7 +1002,7 @@ def parse_exposure(self, node):
 
         description = node.lattrib.get("description", "")
 
-        self.current_component_type.add_exposure(Exposure(name, minval, maxval, dimension, description))
+        self.current_component_type.add_exposure(Exposure(name, dimension, minval, maxval, description))
 
     def parse_fixed(self, node):
         """
@@ -1678,7 +1678,7 @@ def parse_state_variable(self, node):
         else:
             exposure = None
 
-        self.current_regime.add_state_variable(StateVariable(name, minval, maxval, dimension, exposure))
+        self.current_regime.add_state_variable(StateVariable(name, dimension, minval, maxval, exposure))
 
     def parse_structure(self, node):
         """

From 470bcfb657c1772b9fb58ba43a0fecdf0bca22e6 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Thu, 11 May 2023 12:19:28 +0100
Subject: [PATCH 04/11] To v0.6.3; make sure case without condition serialises
 correctly

---
 lems/__init__.py       | 2 +-
 lems/model/dynamics.py | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/lems/__init__.py b/lems/__init__.py
index 0a1782d..562f3b8 100644
--- a/lems/__init__.py
+++ b/lems/__init__.py
@@ -7,7 +7,7 @@
 
 logger = logging.getLogger("LEMS")
 
-__version__ = "0.6.2"
+__version__ = "0.6.3"
 
 __schema_version__ = "0.7.6"
 __schema_branch__ = "development"
diff --git a/lems/model/dynamics.py b/lems/model/dynamics.py
index e085a11..2ca7244 100644
--- a/lems/model/dynamics.py
+++ b/lems/model/dynamics.py
@@ -178,9 +178,10 @@ def toxml(self):
         """
         Exports this object into a LEMS XML object
         """
-
+        cond = ' condition="{0}"'.format(self.condition) if self.condition is not None else ''
+        print(cond)
         return (
-            '<Case condition="{0}" value="{1}"'.format(self.condition, self.value)
+            '<Case{0} value="{1}"'.format(cond, self.value)
             + "/>"
         )
 

From 49070b73de511a5deb648119e88a48c39d80bc3e Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Thu, 11 May 2023 12:20:24 +0100
Subject: [PATCH 05/11] Remove print..

---
 lems/model/dynamics.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lems/model/dynamics.py b/lems/model/dynamics.py
index 2ca7244..e74d3df 100644
--- a/lems/model/dynamics.py
+++ b/lems/model/dynamics.py
@@ -179,7 +179,6 @@ def toxml(self):
         Exports this object into a LEMS XML object
         """
         cond = ' condition="{0}"'.format(self.condition) if self.condition is not None else ''
-        print(cond)
         return (
             '<Case{0} value="{1}"'.format(cond, self.value)
             + "/>"

From 6ddc7335d113ff1ff55b4737532514cca7b17434 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Wed, 14 Jun 2023 15:18:21 +0100
Subject: [PATCH 06/11] Test on macos

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ef404cc..34dcad1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.7", "3.9", "3.10", "3.11"]
-        runs-on: [ubuntu-latest, windows-latest]
+        runs-on: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
     - uses: actions/checkout@v3

From b2184ce30a79832bed3a1a4ce790a054f546ce52 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Fri, 16 Jun 2023 16:31:58 +0100
Subject: [PATCH 07/11] Fix script for masos

---
 ci/run-apitest.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/ci/run-apitest.sh b/ci/run-apitest.sh
index 7dfa607..8507038 100755
--- a/ci/run-apitest.sh
+++ b/ci/run-apitest.sh
@@ -12,6 +12,10 @@ python examples/loadtest.py
 
 # Update NeuroML2 path for CI
 if [ "$CI" = "true" ]; then
-    sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py
+    if [ "$RUNNER_OS" = "macOS" ]; then
+        sed -i '' 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py;
+    else
+        sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py;
+    fi
 fi
 python lems/dlems/exportdlems.py

From 15290150ce0da763c44bbc3dbff3680ae9887183 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Fri, 16 Jun 2023 16:44:18 +0100
Subject: [PATCH 08/11] To v0.6.3

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index c12cd26..58c8c02 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = PyLEMS
-version = 0.6.2
+version = 0.6.3
 author = PyLEMS authors and contributors
 author_email = gautham@lisphacker.org, p.gleeson@gmail.com
 maintainer_email = p.gleeson@gmail.com

From 446b65e3629532fd442423c5a4dfdeb7e5e79e01 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Tue, 19 Sep 2023 11:40:47 +0100
Subject: [PATCH 09/11] Retesting max/min impl - still need to write max/min to
 XML

---
 ci/run-apitest.sh          | 11 ++++++++---
 examples/apitest_maxmin.py |  4 ++--
 examples/maxmin.xml        | 13 +++++++++++++
 3 files changed, 23 insertions(+), 5 deletions(-)
 create mode 100644 examples/maxmin.xml

diff --git a/ci/run-apitest.sh b/ci/run-apitest.sh
index 48666b1..4e689bb 100755
--- a/ci/run-apitest.sh
+++ b/ci/run-apitest.sh
@@ -6,9 +6,14 @@
 #
 # Run api tests on GitHub actions
 
-python examples/apitest.py
-python examples/apitest2.py
-python examples/loadtest.py
+cd examples
+python apitest.py
+python apitest2.py
+python apitest3.py
+python loadtest.py
+python apitest_maxmin.py
+cd ..
+
 
 # Update NeuroML2 path for CI
 if [ "$CI" = "true" ]; then
diff --git a/examples/apitest_maxmin.py b/examples/apitest_maxmin.py
index 8d92574..ad1ebb4 100644
--- a/examples/apitest_maxmin.py
+++ b/examples/apitest_maxmin.py
@@ -4,7 +4,7 @@
 
 model = lems.Model()
 
-model.add(lems.Include("maxmin.xml"))
+#model.add(lems.Include("maxmin.xml"))
 
 model.add(lems.Dimension("voltage", m=1, l=3, t=-3, i=-1))
 model.add(lems.Dimension("time", t=1))
@@ -21,7 +21,7 @@
 iaf1.add(lems.Parameter("reset", "voltage"))
 
 
-fn = "/tmp/maxmin.xml"
+fn = "maxmin.xml"
 model.export_to_file(fn)
 
 print("----------------------------------------------")
diff --git a/examples/maxmin.xml b/examples/maxmin.xml
new file mode 100644
index 0000000..a4f428d
--- /dev/null
+++ b/examples/maxmin.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" ?>
+<Lems xmlns="http://www.neuroml.org/lems/0.7.6" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/lems/0.7.6 https://raw.githubusercontent.com/LEMS/LEMS/development/Schemas/LEMS/LEMS_v0.7.6.xsd">
+  <Dimension name="voltage" m="1" l="3" t="-3" i="-1"/>
+  <Dimension name="time" t="1"/>
+  <Dimension name="capacitance" m="-1" l="-2" t="4" i="2"/>
+  <Unit symbol="mV" dimension="voltage" power="-3" scale="1.0"/>
+  <Unit symbol="ms" dimension="time" power="-3" scale="1.0"/>
+  <Unit symbol="uF" dimension="capacitance" power="-12" scale="1.0"/>
+  <ComponentType name="iaf1" description="">
+    <Parameter name="threshold" dimension="voltage"/>
+    <Parameter name="reset" dimension="voltage"/>
+  </ComponentType>
+</Lems>

From f19ab2df1fffb4e137225aa5cc1ecf48bb2d0711 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Tue, 20 Feb 2024 18:54:24 +0000
Subject: [PATCH 10/11] Better closing of files

---
 lems/model/model.py | 10 +++++++---
 setup.cfg           |  2 +-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lems/model/model.py b/lems/model/model.py
index 527bd91..cbe2d74 100644
--- a/lems/model/model.py
+++ b/lems/model/model.py
@@ -272,7 +272,8 @@ def include_file(self, path, include_dirs=[]):
             parser = LEMSFileParser(self, inc_dirs, self.include_includes)
             if os.access(path, os.F_OK):
                 if not path in self.included_files:
-                    parser.parse(open(path).read())
+                    with open(path) as f:
+                        parser.parse(f.read())
                     self.included_files.append(path)
                     return
                 else:
@@ -284,7 +285,8 @@ def include_file(self, path, include_dirs=[]):
                     new_path = inc_dir + "/" + path
                     if os.access(new_path, os.F_OK):
                         if not new_path in self.included_files:
-                            parser.parse(open(new_path).read())
+                            with open(new_path) as f:
+                                parser.parse(f.read())
                             self.included_files.append(new_path)
                             return
                         else:
@@ -376,7 +378,9 @@ def export_to_file(self, filepath, level_prefix="  "):
 
         f = open(filepath, "w")
         f.write(xmlstr)
-        f.close()
+        f.flush()
+        os.fsync(f.fileno())
+
 
     def resolve(self) -> lems.model.Model:
         """
diff --git a/setup.cfg b/setup.cfg
index a84acf1..6806b45 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = PyLEMS
-version = 0.6.5
+version = 0.6.6
 author = PyLEMS authors and contributors
 author_email = gautham@lisphacker.org, p.gleeson@gmail.com
 maintainer_email = p.gleeson@gmail.com

From c6a67e12d631c7098497c2ccba027b6d9c4037fa Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Mon, 19 Aug 2024 16:50:06 +0100
Subject: [PATCH 11/11] Update pylems examples to formatted version from lems
 repo

---
 examples/SimpleNetwork.xml    |   9 +-
 examples/SingleSimulation.xml |  25 +--
 examples/elecdims.xml         |   3 +-
 examples/ex2dims.xml          |  10 +-
 examples/example1.xml         | 295 ++++++++++++++--------------------
 examples/example2.xml         |  35 ++--
 examples/example3.xml         |  56 ++-----
 examples/example4.xml         |  63 ++------
 examples/example5.xml         |  69 ++------
 examples/example6.xml         |  33 +---
 examples/example7.xml         |  29 +---
 examples/example8.xml         |  74 +++------
 examples/hhaltgate.xml        |  14 +-
 examples/hhcell.xml           |  14 +-
 examples/hhchannel.xml        |  20 +--
 examples/hhmodels.xml         |   8 +-
 examples/misciaf.xml          |  12 +-
 examples/spikegenerators.xml  |   7 +-
 18 files changed, 233 insertions(+), 543 deletions(-)

diff --git a/examples/SimpleNetwork.xml b/examples/SimpleNetwork.xml
index 507842a..9a55a87 100644
--- a/examples/SimpleNetwork.xml
+++ b/examples/SimpleNetwork.xml
@@ -4,7 +4,6 @@
         <Children name="connectivities" type="EventConnectivity"/>
     </ComponentType>
 
-
     <ComponentType name="Population">
         <ComponentReference name="component" type="Component"/>
         <Parameter name="size" dimension="none"/>
@@ -13,8 +12,6 @@
         </Structure>
     </ComponentType>
 
-
-
     <ComponentType name="EventConnectivity">
         <Link name="source" type="Population"/>
         <Link name="target" type="Population"/>
@@ -23,17 +20,13 @@
 
     <ComponentType name="ConnectionPattern"/>
 
-
-
     <ComponentType name="AllAll" extends="ConnectionPattern">
         <Structure>
             <ForEach instances="../source" as="a">
                 <ForEach instances="../target" as="b">
                     <EventConnection from="a" to="b"/>
                 </ForEach>
-            </ForEach>    
+            </ForEach>
         </Structure>
-       
     </ComponentType>
-
 </Lems>
diff --git a/examples/SingleSimulation.xml b/examples/SingleSimulation.xml
index 1a2319d..e6a7d55 100644
--- a/examples/SingleSimulation.xml
+++ b/examples/SingleSimulation.xml
@@ -1,22 +1,17 @@
 <Lems>
-
-
     <ComponentType name="Display">
-        <Text name="title"/>   
+        <Text name="title"/>
         <Parameter name="xmin" dimension="none"/>
         <Parameter name="xmax" dimension="none"/>
         <Parameter name="ymin" dimension="none"/>
         <Parameter name="ymax" dimension="none"/>
-
         <Parameter name="timeScale" dimension="time"/>
         <Children name="lines" type="Line"/>
-
         <Simulation>
             <DataDisplay title="title" dataRegion="xmin,xmax,ymin,ymax"/>
         </Simulation>
     </ComponentType>
 
-
     <ComponentType name="Line">
         <Parameter name="scale" dimension="*"/>
         <Parameter name="timeScale" dimension="*"/>
@@ -27,20 +22,15 @@
         </Simulation>
     </ComponentType>
 
-
     <ComponentType name="OutputFile">
         <Text name="path"/>
         <Text name="fileName"/>
-	
         <Children name="outputColumn" type="OutputColumn"/>
-	
         <Simulation>
             <DataWriter path="path" fileName="fileName"/>
         </Simulation>
-
     </ComponentType>
 
-
     <ComponentType name="OutputColumn">
         <Path name="quantity"/>
         <Simulation>
@@ -48,28 +38,17 @@
         </Simulation>
     </ComponentType>
 
-
-
     <ComponentType name="Simulation">
         <Parameter name="length" dimension="time"/>
         <Parameter name="step" dimension="time"/>
-    
         <ComponentReference name="target" type="Component"/>
-
-
         <Children name="displays" type="Display"/>
-       
         <Children name="outputs" type="OutputFile"/>
-   
         <Dynamics>
             <StateVariable name="t" dimension="time"/>
         </Dynamics>
-    
         <Simulation>
             <Run component="target" variable="t" increment="step" total="length"/>
         </Simulation>
     </ComponentType>
-
-
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/elecdims.xml b/examples/elecdims.xml
index c81221a..612f2cf 100644
--- a/examples/elecdims.xml
+++ b/examples/elecdims.xml
@@ -4,5 +4,4 @@
     <Dimension name="conductance" m="-1" l="-2" t="3" i="2"/>
     <Dimension name="capacitance" m="-1" l="-2" t="4" i="2"/>
     <Dimension name="current" i="1"/>
-    
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/ex2dims.xml b/examples/ex2dims.xml
index aeb1e22..702c319 100644
--- a/examples/ex2dims.xml
+++ b/examples/ex2dims.xml
@@ -1,5 +1,4 @@
-<Lems> 
-
+<Lems>
     <Dimension name="voltage" m="1" l="2" t="-3" i="-1"/>
     <Dimension name="time" t="1"/>
     <Dimension name="per_time" t="-1"/>
@@ -8,8 +7,8 @@
     <Dimension name="current" i="1"/>
     <Dimension name="temperature" k="1"/>
 
-    <Unit symbol="mV" dimension="voltage" power="-3"/> 
-    <Unit symbol="ms" dimension="time" power="-3"/> 
+    <Unit symbol="mV" dimension="voltage" power="-3"/>
+    <Unit symbol="ms" dimension="time" power="-3"/>
     <Unit symbol="pS" dimension="conductance" power="-12"/>
     <Unit symbol="nS" dimension="conductance" power="-9"/>
     <Unit symbol="uF" dimension="capacitance" power="-6"/>
@@ -19,5 +18,4 @@
     <Unit symbol="pA" dimension="current" power="-12"/>
     <Unit symbol="nA" dimension="current" power="-9"/>
     <Unit symbol="degC" dimension="temperature" offset="273.15"/>
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example1.xml b/examples/example1.xml
index d84c23b..393f3f8 100644
--- a/examples/example1.xml
+++ b/examples/example1.xml
@@ -1,275 +1,220 @@
 <Lems>
+    <Target component="sim1"/>
 
-    <Target component="sim1" />
-
-    <Dimension name="voltage" m="1" l="2" t="-3" i="-1" />
-    <Dimension name="time" t="1" />
-    <Dimension name="per_time" t="-1" />
-    <Dimension name="conductance" m="-1" l="-2" t="3" i="2" />
-    <Dimension name="capacitance" m="-1" l="-2" t="4" i="2" />
-    <Dimension name="current" i="1" />
-
+    <Dimension name="voltage" m="1" l="2" t="-3" i="-1"/>
+    <Dimension name="time" t="1"/>
+    <Dimension name="per_time" t="-1"/>
+    <Dimension name="conductance" m="-1" l="-2" t="3" i="2"/>
+    <Dimension name="capacitance" m="-1" l="-2" t="4" i="2"/>
+    <Dimension name="current" i="1"/>
 
     <ComponentType name="iaf1">
-        <Parameter name="threshold" dimension="voltage" />
-        <Parameter name="refractoryPeriod" dimension="time" />
-        <Parameter name="capacitance" dimension="capacitance" />
+        <Parameter name="threshold" dimension="voltage"/>
+        <Parameter name="refractoryPeriod" dimension="time"/>
+        <Parameter name="capacitance" dimension="capacitance"/>
     </ComponentType>
 
-
-    <Unit symbol="mV" dimension="voltage" power="-3" />
-    <Unit symbol="ms" dimension="time" power="-3" />
-    <Unit symbol="pS" dimension="conductance" power="-12" />
-    <Unit symbol="nS" dimension="conductance" power="-9" />
-    <Unit symbol="uF" dimension="capacitance" power="-6" />
-    <Unit symbol="nF" dimension="capacitance" power="-9" />
-    <Unit symbol="pF" dimension="capacitance" power="-12" />
-    <Unit symbol="per_ms" dimension="per_time" power="3" />
-    <Unit symbol="pA" dimension="current" power="-12" />
-
-    <iaf1 id="celltype_a" threshold="-30 mV" refractoryPeriod="2 ms" capacitance="3uF" />
+    <Unit symbol="mV" dimension="voltage" power="-3"/>
+    <Unit symbol="ms" dimension="time" power="-3"/>
+    <Unit symbol="pS" dimension="conductance" power="-12"/>
+    <Unit symbol="nS" dimension="conductance" power="-9"/>
+    <Unit symbol="uF" dimension="capacitance" power="-6"/>
+    <Unit symbol="nF" dimension="capacitance" power="-9"/>
+    <Unit symbol="pF" dimension="capacitance" power="-12"/>
+    <Unit symbol="per_ms" dimension="per_time" power="3"/>
+    <Unit symbol="pA" dimension="current" power="-12"/>
+
+    <iaf1 id="celltype_a" threshold="-30 mV" refractoryPeriod="2 ms" capacitance="3uF"/>
     <!-- or -->
-    <Component id="ctb" type="iaf1" threshold="-30 mV" refractoryPeriod="2 ms" capacitance="1uF" />
-
+    <Component id="ctb" type="iaf1" threshold="-30 mV" refractoryPeriod="2 ms" capacitance="1uF"/>
 
     <ComponentType name="iaf2" extends="iaf1">
-        <Fixed parameter="threshold" value="-45mV" />
+        <Fixed parameter="threshold" value="-45mV"/>
     </ComponentType>
 
     <ComponentType name="iaf3" extends="iaf1">
-        <Parameter name="leakConductance" dimension="conductance" />
-        <Parameter name="leakReversal" dimension="voltage" />
-        <Parameter name="deltaV" dimension="voltage" />
-
-        <EventPort name="spikes-in" direction="in" />
-        <Exposure name="v" dimension="voltage" />
-
+        <Parameter name="leakConductance" dimension="conductance"/>
+        <Parameter name="leakReversal" dimension="voltage"/>
+        <Parameter name="deltaV" dimension="voltage"/>
+        <EventPort name="spikes-in" direction="in"/>
+        <Exposure name="v" dimension="voltage"/>
         <Dynamics>
-            <StateVariable name="v" exposure="v" dimension="voltage" />
-            <TimeDerivative variable="v" value="leakConductance * (leakReversal - v) / capacitance" />
-
+            <StateVariable name="v" exposure="v" dimension="voltage"/>
+            <TimeDerivative variable="v" value="leakConductance * (leakReversal - v) / capacitance"/>
             <OnEvent port="spikes-in">
-                <StateAssignment variable="v" value="v + deltaV" />
+                <StateAssignment variable="v" value="v + deltaV"/>
             </OnEvent>
         </Dynamics>
-
     </ComponentType>
 
-
     <ComponentType name="spikeGenerator">
-        <Parameter name="period" dimension="time" />
-        <EventPort name="a" direction="out" />
-        <Exposure name="tsince" dimension="time" />
+        <Parameter name="period" dimension="time"/>
+        <EventPort name="a" direction="out"/>
+        <Exposure name="tsince" dimension="time"/>
         <Dynamics>
-            <StateVariable name="tsince" exposure="tsince" dimension="time" />
-            <TimeDerivative variable="tsince" value="1" />
+            <StateVariable name="tsince" exposure="tsince" dimension="time"/>
+            <TimeDerivative variable="tsince" value="1"/>
             <OnCondition test="tsince .gt. period">
-                <StateAssignment variable="tsince" value="0" />
-                <EventOut port="a" />
+                <StateAssignment variable="tsince" value="0"/>
+                <EventOut port="a"/>
             </OnCondition>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="spikeGenerator2" extends="spikeGenerator">
         <Dynamics>
-            <StateVariable name="tlast" dimension="time" />
-            <DerivedVariable name="tsince" dimension="time" exposure="tsince" value="t - tlast" />
+            <StateVariable name="tlast" dimension="time"/>
+            <DerivedVariable name="tsince" dimension="time" exposure="tsince" value="t - tlast"/>
             <OnCondition test="t - tlast .gt. period">
-                <StateAssignment variable="tlast" value="t" />
-                <EventOut port="a" />
+                <StateAssignment variable="tlast" value="t"/>
+                <EventOut port="a"/>
             </OnCondition>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHRate">
-        <Parameter name="rate" dimension="per_time" />
-        <Parameter name="midpoint" dimension="voltage" />
-        <Parameter name="scale" dimension="voltage" />
-        <Requirement name="v" dimension="voltage" />
-        <Exposure name="r" dimension="per_time" />
+        <Parameter name="rate" dimension="per_time"/>
+        <Parameter name="midpoint" dimension="voltage"/>
+        <Parameter name="scale" dimension="voltage"/>
+        <Requirement name="v" dimension="voltage"/>
+        <Exposure name="r" dimension="per_time"/>
     </ComponentType>
 
-
     <ComponentType name="HHExpRate" extends="HHRate">
         <Dynamics>
-            <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate * exp((v - midpoint)/scale)" />
+            <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate * exp((v - midpoint)/scale)"/>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHSigmoidRate" extends="HHRate">
         <Dynamics>
-            <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate / (1 + exp( -(v - midpoint)/scale))" />
+            <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate / (1 + exp( -(v - midpoint)/scale))"/>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHExpLinearRate" extends="HHRate">
         <Dynamics>
-            <DerivedVariable name="x" dimension="none" value="(v - midpoint) / scale" />
-            <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate * x / (1 - exp(-x))" />
+            <DerivedVariable name="x" dimension="none" value="(v - midpoint) / scale"/>
+            <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate * x / (1 - exp(-x))"/>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHGate0">
-        <Parameter name="power" dimension="none" />
-        <Child name="Forward" type="HHRate" />
-        <Child name="Reverse" type="HHRate" />
-        <Requirement name="v" dimension="voltage" />
-        <Exposure name="fcond" dimension="none" />
+        <Parameter name="power" dimension="none"/>
+        <Child name="Forward" type="HHRate"/>
+        <Child name="Reverse" type="HHRate"/>
+        <Requirement name="v" dimension="voltage"/>
+        <Exposure name="fcond" dimension="none"/>
         <Dynamics>
-            <StateVariable name="q" dimension="none" />
-            <DerivedVariable dimension="per_time" name="rf" select="Forward/r" />
-            <DerivedVariable dimension="per_time" name="rr" select="Reverse/r" />
-            <TimeDerivative variable="q" value="rf * (1 - q) - rr * q" />
-            <DerivedVariable name="fcond" dimension="none" exposure="fcond" value="q^power" />
+            <StateVariable name="q" dimension="none"/>
+            <DerivedVariable dimension="per_time" name="rf" select="Forward/r"/>
+            <DerivedVariable dimension="per_time" name="rr" select="Reverse/r"/>
+            <TimeDerivative variable="q" value="rf * (1 - q) - rr * q"/>
+            <DerivedVariable name="fcond" dimension="none" exposure="fcond" value="q^power"/>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHGate">
-        <Parameter name="power" dimension="none" />
-        <Child name="Forward" type="HHRate" />
-        <Child name="Reverse" type="HHRate" />
-        <Requirement name="v" dimension="voltage" />
-        <Exposure name="fcond" dimension="none" />
+        <Parameter name="power" dimension="none"/>
+        <Child name="Forward" type="HHRate"/>
+        <Child name="Reverse" type="HHRate"/>
+        <Requirement name="v" dimension="voltage"/>
+        <Exposure name="fcond" dimension="none"/>
         <Dynamics>
-            <StateVariable name="x" dimension="none" />
-            <DerivedVariable name="ex" dimension="none" value="exp(x)" />
-            <DerivedVariable name="q" dimension="none" value="ex / (1 + ex)" />
-            <DerivedVariable name="rf" dimension="per_time" select="Forward/r" />
-            <DerivedVariable name="rr" dimension="per_time" select="Reverse/r" />
-            <TimeDerivative variable="x" value="(1 + ex)^2 / ex * (rf * (1 - q) - rr * q)" />
-            <DerivedVariable name="fcond" dimension="none" exposure="fcond" value="q^power" />
+            <StateVariable name="x" dimension="none"/>
+            <DerivedVariable name="ex" dimension="none" value="exp(x)"/>
+            <DerivedVariable name="q" dimension="none" value="ex / (1 + ex)"/>
+            <DerivedVariable name="rf" dimension="per_time" select="Forward/r"/>
+            <DerivedVariable name="rr" dimension="per_time" select="Reverse/r"/>
+            <TimeDerivative variable="x" value="(1 + ex)^2 / ex * (rf * (1 - q) - rr * q)"/>
+            <DerivedVariable name="fcond" dimension="none" exposure="fcond" value="q^power"/>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHChannel">
-        <Parameter name="conductance" dimension="conductance" />
-        <Children name="gates" type="HHGate" />
-        <Exposure name="g" dimension="conductance" />
+        <Parameter name="conductance" dimension="conductance"/>
+        <Children name="gates" type="HHGate"/>
+        <Exposure name="g" dimension="conductance"/>
         <Dynamics>
-            <DerivedVariable name="gatefeff" dimension="none"
-                             select="gates[*]/fcond" reduce="multiply" />
-            <DerivedVariable name="g" exposure="g"
-                             dimension="conductance" value="conductance * gatefeff" />
+            <DerivedVariable name="gatefeff" dimension="none" select="gates[*]/fcond" reduce="multiply"/>
+            <DerivedVariable name="g" exposure="g" dimension="conductance" value="conductance * gatefeff"/>
         </Dynamics>
     </ComponentType>
 
-
     <HHChannel id="na" conductance="20pS">
         <HHGate id="m" power="3">
-            <Forward type="HHExpLinearRate" rate="1.per_ms"
-                     midpoint="-40mV" scale="10mV" />
-            <Reverse type="HHExpRate" rate="4per_ms" midpoint="-65mV"
-                     scale="-18mV" />
+            <Forward type="HHExpLinearRate" rate="1.per_ms" midpoint="-40mV" scale="10mV"/>
+            <Reverse type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
         </HHGate>
         <HHGate id="h" power="1">
-            <Forward type="HHExpRate" rate="0.07per_ms"
-                     midpoint="-65.mV" scale="-20.mV" />
-            <Reverse type="HHSigmoidRate" rate="1per_ms"
-                     midpoint="-35mV" scale="10mV" />
+            <Forward type="HHExpRate" rate="0.07per_ms" midpoint="-65.mV" scale="-20.mV"/>
+            <Reverse type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
         </HHGate>
     </HHChannel>
 
-
     <HHChannel id="k" conductance="20pS">
         <HHGate id="n" power="4">
-            <Forward type="HHExpLinearRate" rate="0.1per_ms"
-                     midpoint="-55mV" scale="10mV" />
-            <Reverse type="HHExpRate" rate="0.125per_ms"
-                     midpoint="-65mV" scale="-80mV" />
+            <Forward type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
+            <Reverse type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
         </HHGate>
     </HHChannel>
 
-
     <ComponentType name="ChannelPopulation">
-        <ComponentReference name="channel" type="HHChannel" />
-        <Parameter name="number" dimension="none" />
-        <Parameter name="erev" dimension="voltage" />
-        <Requirement name="v" dimension="voltage" />
-        <Exposure name="current" dimension="current" />
-
+        <ComponentReference name="channel" type="HHChannel"/>
+        <Parameter name="number" dimension="none"/>
+        <Parameter name="erev" dimension="voltage"/>
+        <Requirement name="v" dimension="voltage"/>
+        <Exposure name="current" dimension="current"/>
         <Dynamics>
-            <DerivedVariable name="channelg" dimension="conductance" select="channel/g" />
-            <DerivedVariable name="geff" dimension="conductance" value="channelg * number" />
-            <DerivedVariable name="current" dimension="current" exposure="current" value="geff * (erev - v)" />
+            <DerivedVariable name="channelg" dimension="conductance" select="channel/g"/>
+            <DerivedVariable name="geff" dimension="conductance" value="channelg * number"/>
+            <DerivedVariable name="current" dimension="current" exposure="current" value="geff * (erev - v)"/>
         </Dynamics>
-
         <Structure>
-            <ChildInstance component="channel" />
+            <ChildInstance component="channel"/>
         </Structure>
     </ComponentType>
 
-
-
     <ComponentType name="HHCell">
-        <Parameter name="capacitance" dimension="capacitance" />
-        <Children name="populations" type="ChannelPopulation" />
-        <Parameter name="injection" dimension="current" />
-        <Parameter name="v0" dimension="voltage" />
-        <Exposure name="v" dimension="voltage" />
+        <Parameter name="capacitance" dimension="capacitance"/>
+        <Children name="populations" type="ChannelPopulation"/>
+        <Parameter name="injection" dimension="current"/>
+        <Parameter name="v0" dimension="voltage"/>
+        <Exposure name="v" dimension="voltage"/>
         <Dynamics>
             <OnStart>
-                <StateAssignment variable="v" value="v0" />
+                <StateAssignment variable="v" value="v0"/>
             </OnStart>
-
-            <DerivedVariable name="totcurrent"
-                             dimension="current" select="populations[*]/current"
-                             reduce="add" />
-            <StateVariable name="v" exposure="v"
-                           dimension="voltage" />
-            <TimeDerivative variable="v"
-                            value="(totcurrent + injection) / capacitance" />
+            <DerivedVariable name="totcurrent" dimension="current" select="populations[*]/current" reduce="add"/>
+            <StateVariable name="v" exposure="v" dimension="voltage"/>
+            <TimeDerivative variable="v" value="(totcurrent + injection) / capacitance"/>
         </Dynamics>
     </ComponentType>
 
-
-
     <HHCell id="hhcell_1" capacitance="1pF" injection="4pA" v0="-60mV">
-        <ChannelPopulation channel="na" number="6000"  erev="50mV" />
-        <ChannelPopulation channel="k" number="1800" erev="-77mV" />
+        <ChannelPopulation channel="na" number="6000" erev="50mV"/>
+        <ChannelPopulation channel="k" number="1800" erev="-77mV"/>
     </HHCell>
-
-
-    <Component id="celltype_c" type="iaf3" leakConductance="3 pS" refractoryPeriod="3 ms" threshold="45 mV" leakReversal="-50 mV" deltaV="5mV" capacitance="1uF" />
-
-    <Component id="gen1" type="spikeGenerator" period="30ms" />
-
-    <Component id="gen2" type="spikeGenerator2" period="32ms" />
-
-    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS" refractoryPeriod="4ms" capacitance="1pF" />
-
-
-    <Include file="SimpleNetwork.xml" />
-
-
+    <Component id="celltype_c" type="iaf3" leakConductance="3 pS" refractoryPeriod="3 ms" threshold="45 mV" leakReversal="-50 mV" deltaV="5mV" capacitance="1uF"/>
+    <Component id="gen1" type="spikeGenerator" period="30ms"/>
+    <Component id="gen2" type="spikeGenerator2" period="32ms"/>
+    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS" refractoryPeriod="4ms" capacitance="1pF"/>
+    <Include file="SimpleNetwork.xml"/>
     <Network id="net1">
-        <Population id="p1" component="gen1" size="1" />
-        <Population id="p2" component="gen2" size="1" />
-        <Population id="p3" component="iaf3cpt" size="1" />
-
-        <Population id="hhpop" component="hhcell_1" size="1" />
-
+        <Population id="p1" component="gen1" size="1"/>
+        <Population id="p2" component="gen2" size="1"/>
+        <Population id="p3" component="iaf3cpt" size="1"/>
+        <Population id="hhpop" component="hhcell_1" size="1"/>
         <EventConnectivity id="p1-p3" source="p1" target="p3">
-            <Connections type="AllAll" />
+            <Connections type="AllAll"/>
         </EventConnectivity>
     </Network>
-
-
-    <Include file="SingleSimulation.xml" />
-    
+    <Include file="SingleSimulation.xml"/>
     <Simulation id="sim1" length="80ms" step="0.01ms" target="net1">
-        <Display id="d0" title="Example 1: Dimensions, Units, ComponentTypes and Components" 
-                 timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="60">
-            <Line id="tsince" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#00c000" />
-            <Line id="p3v" quantity="p3[0]/v" scale="1mV" timeScale="1ms" color="#0000f0" />
-            <Line id="p0v" quantity="hhpop[0]/v" scale="1mV" timeScale="1ms" color="#ff4040" />
+        <Display id="d0" title="Example 1: Dimensions, Units, ComponentTypes and Components" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="60">
+            <Line id="tsince" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#00c000"/>
+            <Line id="p3v" quantity="p3[0]/v" scale="1mV" timeScale="1ms" color="#0000f0"/>
+            <Line id="p0v" quantity="hhpop[0]/v" scale="1mV" timeScale="1ms" color="#ff4040"/>
         </Display>
     </Simulation>
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example2.xml b/examples/example2.xml
index bdfe1b4..26e3953 100644
--- a/examples/example2.xml
+++ b/examples/example2.xml
@@ -1,51 +1,40 @@
 <Lems>
- 
     <Target component="sim1"/>
- 
+
     <Include file="ex2dims.xml"/>
-    <Include file="hhchannel.xml"/> 
- 
+    <Include file="hhchannel.xml"/>
     <Include file="hhcell.xml"/>
     <Include file="spikegenerators.xml"/>
     <Include file="hhmodels.xml"/>
-    <Include file="misciaf.xml"/> 
-
+    <Include file="misciaf.xml"/>
     <Include file="SimpleNetwork.xml"/>
 
     <HHCell id="hhcell_1" capacitance="1pF" injection="4pA" v0="-60mV">
         <ChannelPopulation channel="na" number="6000" erev="50mV"/>
         <ChannelPopulation channel="k" number="1800" erev="-77mV"/>
     </HHCell>
- 
-    <Component id="gen1" type="spikeGenerator" period="30ms"/>
 
+    <Component id="gen1" type="spikeGenerator" period="30ms"/>
     <Component id="gen2" type="spikeGenerator2" period="32ms"/>
-
-    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS"
-           refractoryPeriod="4ms" capacitance="1pF"/>
-
+    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS" refractoryPeriod="4ms" capacitance="1pF"/>
 
     <Network id="net1">
         <Population id="p1" component="gen1" size="1"/>
         <Population id="p2" component="gen2" size="1"/>
         <Population id="p3" component="iaf3cpt" size="1"/>
-   
         <Population id="hhpop" component="hhcell_1" size="1"/>
-    
-   
         <EventConnectivity id="p1-p3" source="p1" target="p3">
             <Connections type="AllAll"/>
         </EventConnectivity>
     </Network>
-    
-    <Include file="SingleSimulation.xml" />
-    
+
+    <Include file="SingleSimulation.xml"/>
+
     <Simulation id="sim1" length="80ms" step="0.01ms" target="net1">
         <Display id="d0" title="Example 2" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="60">
-            <Line id="tsince" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#00c000" />
-            <Line id="p3v" quantity="p3[0]/v" scale="1mV" timeScale="1ms" color="#0000f0" />
-            <Line id="p0v" quantity="hhpop[0]/v" scale="1mV" timeScale="1ms" color="#ff4040" />
+            <Line id="tsince" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#00c000"/>
+            <Line id="p3v" quantity="p3[0]/v" scale="1mV" timeScale="1ms" color="#0000f0"/>
+            <Line id="p0v" quantity="hhpop[0]/v" scale="1mV" timeScale="1ms" color="#ff4040"/>
         </Display>
     </Simulation>
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example3.xml b/examples/example3.xml
index 7e78b8b..bbee903 100644
--- a/examples/example3.xml
+++ b/examples/example3.xml
@@ -1,21 +1,13 @@
 <Lems>
- 
-    <Target component="sim1"/> 
- 
+    <Target component="sim1"/>
     <Include file="ex2dims.xml"/>
-
     <Include file="spikegenerators.xml"/>
-  
     <Include file="misciaf.xml"/>
- 
 
-    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS"
-           refractoryPeriod="4ms" capacitance="1pF"/>
- 
+    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS" refractoryPeriod="4ms" capacitance="1pF"/>
     <Component id="gena" type="spikeGenerator2" period="32ms"/>
     <Component id="genb" type="spikeGenerator2" period="40ms"/>
 
-
     <ComponentType name="Synapse">
         <Parameter name="deltaG" dimension="conductance"/>
         <Parameter name="erev" dimension="voltage"/>
@@ -23,98 +15,75 @@
         <EventPort name="in" direction="in"/>
         <Requirement name="v" dimension="voltage"/>
         <Exposure name="current" dimension="current"/>
-    
         <Dynamics>
             <StateVariable name="geff" dimension="conductance"/>
             <TimeDerivative variable="geff" value="-geff / tfall"/>
-       
             <OnStart>
                 <StateAssignment variable="geff" value="0"/>
             </OnStart>
-
             <OnEvent port="in">
                 <StateAssignment variable="geff" value="geff + deltaG"/>
-            </OnEvent>     
-        
+            </OnEvent>
             <DerivedVariable name="current" exposure="current" dimension="current" value="geff * (erev - v)"/>
         </Dynamics>
     </ComponentType>
 
+    <Synapse id="sy1" deltaG="30pS" erev="50mV" tfall="10ms"/>
 
-    <Synapse id="sy1" deltaG="30pS" erev="50mV"  tfall="10ms"/>
-
-    
     <ComponentType name="Cell"/>
- 
-    
+
     <ComponentType name="synapseCell" extends="Cell">
         <Parameter name="capacitance" dimension="capacitance"/>
         <Parameter name="leakConductance" dimension="conductance"/>
         <Parameter name="leakReversal" dimension="voltage"/>
         <Exposure name="v" dimension="voltage"/>
         <Attachments name="synapses" type="Synapse"/>
-    
         <Dynamics>
             <StateVariable name="v" dimension="voltage" exposure="v"/>
             <DerivedVariable name="synapticCurrent" dimension="current" select="synapses[*]/current" reduce="add"/>
             <TimeDerivative variable="v" value="(leakConductance * (leakReversal - v) + synapticCurrent) / capacitance"/>
         </Dynamics>
-
     </ComponentType>
 
-    <synapseCell id="sycell" leakReversal="-50mV"  leakConductance="50pS"  capacitance="1pF"/>
-
+    <synapseCell id="sycell" leakReversal="-50mV" leakConductance="50pS" capacitance="1pF"/>
 
     <ComponentType name="ExplicitNetwork">
         <Children name="populations" type="Population"/>
         <Children name="connections" type="ExplicitConnection"/>
     </ComponentType>
 
-
     <ComponentType name="Population">
         <ComponentReference name="component" type="Component"/>
         <Parameter name="size" dimension="none"/>
-   
         <Structure>
             <MultiInstantiate number="size" component="component"/>
         </Structure>
-    
     </ComponentType>
-  
-  
+
     <ComponentType name="ExplicitConnection">
         <Path name="from"/>
         <Path name="to"/>
-     
         <ComponentReference name="synapse" type="Synapse"/>
-      
         <Text name="destination"/>
         <Text name="sourcePort"/>
         <Text name="targetPort"/>
         <Structure>
             <With instance="from" as="a"/>
             <With instance="to" as="b"/>
-            <EventConnection from="a" to="b"
-                          receiver="synapse" receiverContainer="destination" 
-                          sourcePort="sourcePort" targetPort="targetPort"/>
-        
+            <EventConnection from="a" to="b" receiver="synapse" receiverContainer="destination" sourcePort="sourcePort" targetPort="targetPort"/>
         </Structure>
     </ComponentType>
 
-
     <ExplicitNetwork id="net1">
         <Population id="p1" component="gena" size="1"/>
         <Population id="p2" component="genb" size="1"/>
         <Population id="p3" component="sycell" size="3"/>
-    
         <ExplicitConnection from="p1[0]" to="p3[0]" synapse="sy1"/>
         <ExplicitConnection from="p2[0]" to="p3[1]" synapse="sy1"/>
     </ExplicitNetwork>
 
-  
- 
-    <Include file="SingleSimulation.xml" />
-    
+    <Include file="SingleSimulation.xml"/>
+
     <Simulation id="sim1" length="80ms" step="0.01ms" target="net1">
         <Display id="d0" title="Example 3: User defined types for networks and populations" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="60">
             <Line id="gen0_tsince" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#a0a000"/>
@@ -123,7 +92,4 @@
             <Line id="c1_v" quantity="p3[1]/v" scale="1mV" timeScale="1ms" color="#0000f0"/>
         </Display>
     </Simulation>
-  
-  
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example4.xml b/examples/example4.xml
index d905399..74660f4 100644
--- a/examples/example4.xml
+++ b/examples/example4.xml
@@ -1,46 +1,35 @@
 <Lems>
-
     <Target component="sim1"/>
 
     <Include file="ex2dims.xml"/>
-   
-    
+
     <ComponentType name="KSChannel">
         <Parameter name="conductance" dimension="conductance"/>
         <Children name="gates" type="KSGate"/>
         <Exposure name="g" dimension="conductance"/>
-    
         <Dynamics>
             <DerivedVariable name="fopen" dimension="none" select="gates[*]/fopen" reduce="multiply"/>
             <DerivedVariable name="g" exposure="g" dimension="conductance" value="fopen * conductance"/>
         </Dynamics>
     </ComponentType>
 
-
-    
     <ComponentType name="KSGate">
         <Parameter name="power" dimension="none"/>
         <Parameter name="deltaV" dimension="voltage"/>
         <Children name="states" type="KSState"/>
         <Children name="transitions" type="KSTransition"/>
         <Exposure name="fopen" dimension="none"/>
-    
         <Dynamics>
-            <KineticScheme name="ks" nodes="states" stateVariable="occupancy"
-                         edges="transitions" edgeSource="from" edgeTarget="to" 
-                         forwardRate="rf" reverseRate="rr"/>
-       
+            <KineticScheme name="ks" nodes="states" stateVariable="occupancy" edges="transitions" edgeSource="from" edgeTarget="to" forwardRate="rf" reverseRate="rr"/>
             <DerivedVariable name="q" dimension="none" select="states[*]/q" reduce="add"/>
             <DerivedVariable name="fopen" exposure="fopen" dimension="none" value="q^power"/>
         </Dynamics>
     </ComponentType>
 
-    
     <ComponentType name="KSState">
         <Parameter name="relativeConductance" dimension="none"/>
         <Exposure name="q" dimension="none"/>
         <Exposure name="occupancy" dimension="none"/>
-    
         <Dynamics>
             <StateVariable name="occupancy" exposure="occupancy" dimension="none"/>
             <DerivedVariable name="q" exposure="q" value="relativeConductance * occupancy"/>
@@ -51,12 +40,10 @@
         <Fixed parameter="relativeConductance" value="0"/>
     </ComponentType>
 
-
     <ComponentType name="KSOpenState" extends="KSState">
         <Fixed parameter="relativeConductance" value="1"/>
     </ComponentType>
 
-
     <ComponentType name="KSTransition">
         <Link name="from" type="KSState"/>
         <Link name="to" type="KSState"/>
@@ -64,7 +51,6 @@
         <Exposure name="rr" dimension="per_time"/>
     </ComponentType>
 
-
     <ComponentType name="VHalfTransition" extends="KSTransition">
         <Parameter name="vHalf" dimension="voltage"/>
         <Parameter name="z" dimension="none"/>
@@ -72,8 +58,7 @@
         <Parameter name="tau" dimension="time"/>
         <Parameter name="tauMin" dimension="time"/>
         <Constant name="kte" dimension="voltage" value="25.3mV"/>
-        <Requirement name="v" dimension="voltage"/>  
-   
+        <Requirement name="v" dimension="voltage"/>
         <Dynamics>
             <DerivedVariable name="rf0" dimension="per_time" value="exp(z * gamma * (v - vHalf) / kte) / tau"/>
             <DerivedVariable name="rr0" dimension="per_time" value="exp(-z * (1 - gamma) * (v - vHalf) / kte) / tau"/>
@@ -82,53 +67,42 @@
         </Dynamics>
     </ComponentType>
 
-
-
     <KSChannel id="na1" conductance="20pS">
         <KSGate id="m" power="1" deltaV="0.1mV">
             <KSClosedState id="c1"/>
             <KSClosedState id="c2"/>
             <KSOpenState id="o1" relativeConductance="1"/>
             <KSClosedState id="c3"/>
-            <VHalfTransition from="c1" to="c2" vHalf = "-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
-            <VHalfTransition from="c2" to="o1" vHalf = "-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
-            <VHalfTransition from="o1" to="c3" vHalf = "-70mV" z="1.1" gamma="0.90" tau="8.0ms" tauMin="0.01ms"/>         
+            <VHalfTransition from="c1" to="c2" vHalf="-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
+            <VHalfTransition from="c2" to="o1" vHalf="-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
+            <VHalfTransition from="o1" to="c3" vHalf="-70mV" z="1.1" gamma="0.90" tau="8.0ms" tauMin="0.01ms"/>
         </KSGate>
     </KSChannel>
 
-
     <KSChannel id="k1" conductance="30pS">
         <KSGate id="n" power="1" deltaV="0.1mV">
             <KSClosedState id="c1"/>
             <KSOpenState id="o1"/>
-            <VHalfTransition from="c1" to="o1" vHalf = "0mV" z="1.5" gamma="0.75" tau="3.2ms" tauMin="0.3ms"/>
+            <VHalfTransition from="c1" to="o1" vHalf="0mV" z="1.5" gamma="0.75" tau="3.2ms" tauMin="0.3ms"/>
         </KSGate>
     </KSChannel>
 
-
-
-
     <ComponentType name="ChannelPopulation">
         <ComponentReference name="channel" type="KSChannel"/>
         <Parameter name="number" dimension="none"/>
         <Parameter name="erev" dimension="voltage"/>
         <Requirement name="v" dimension="voltage"/>
         <Exposure name="current" dimension="current"/>
-    
         <Dynamics>
             <DerivedVariable name="channelg" dimension="conductance" select="channel/g"/>
             <DerivedVariable name="geff" value="channelg * number"/>
             <DerivedVariable name="current" exposure="current" dimension="current" value="geff * (erev - v)"/>
-        </Dynamics>    
-    
-        <Structure>    
-            <ChildInstance component="channel"/>    
+        </Dynamics>
+        <Structure>
+            <ChildInstance component="channel"/>
         </Structure>
     </ComponentType>
 
-
-
-
     <ComponentType name="KSCell">
         <Parameter name="capacitance" dimension="capacitance"/>
         <Children name="populations" type="ChannelPopulation"/>
@@ -139,24 +113,19 @@
             <OnStart>
                 <StateAssignment variable="v" value="v0"/>
             </OnStart>
-  
             <DerivedVariable name="totcurrent" dimension="current" select="populations[*]/current" reduce="add"/>
-            <StateVariable name="v" exposure="v" dimension="voltage"/> 
+            <StateVariable name="v" exposure="v" dimension="voltage"/>
             <TimeDerivative variable="v" value="(totcurrent + injection) / capacitance"/>
         </Dynamics>
     </ComponentType>
 
-
-
     <KSCell id="kscell_1" capacitance="0.5pF" injection="0.1pA" v0="-60mV">
         <ChannelPopulation id="pna" channel="na1" number="400" erev="50mV"/>
         <ChannelPopulation id="pk" channel="k1" number="180" erev="-77mV"/>
     </KSCell>
 
-  
- 
-    <Include file="SingleSimulation.xml" />
-    
+    <Include file="SingleSimulation.xml"/>
+
     <Simulation id="sim1" length="80ms" step="0.05ms" target="kscell_1">
         <Display id="d0" title="Example 4: Kinetic Schemes" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="60">
             <Line id="v" quantity="v" scale="1mV" timeScale="1ms" color="#0000f0"/>
@@ -165,15 +134,11 @@
             <Line id="K channel - c1" quantity="pk/k1/n/c1/occupancy" scale="1" timeScale="1ms" color="#fffff0"/>
             <Line id="K channel - o1 (=n)" quantity="pk/k1/n/o1/occupancy" scale="1" timeScale="1ms" color="#f00000"/>
         </Display>
-            
         <Display id="d2" title="Example 4: Kinetic Schemes: Na channel states" timeScale="1ms" xmin="-10" xmax="90" ymin="-.1" ymax="1.1">
             <Line id="Na channel - c1" quantity="pna/na1/m/c1/occupancy" scale="1" timeScale="1ms" color="#fffff0"/>
             <Line id="Na channel - c2" quantity="pna/na1/m/c2/occupancy" scale="1" timeScale="1ms" color="#f00000"/>
             <Line id="Na channel - c3" quantity="pna/na1/m/c3/occupancy" scale="1" timeScale="1ms" color="#000ff0"/>
             <Line id="Na channel - o1 (=m)" quantity="pna/na1/m/o1/occupancy" scale="1" timeScale="1ms" color="#ffff33"/>
         </Display>
-        
     </Simulation>
-
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example5.xml b/examples/example5.xml
index c574a42..38aa956 100644
--- a/examples/example5.xml
+++ b/examples/example5.xml
@@ -1,5 +1,4 @@
 <Lems>
-
     <Target component="sim1"/>
 
     <Include file="ex2dims.xml"/>
@@ -9,12 +8,10 @@
         <Parameter name="charge" dimension="none"/>
     </ComponentType>
 
-
     <ComponentType name="Environment">
         <Children name="membranePotentials" type="MembranePotential"/>
     </ComponentType>
 
-
     <ComponentType name="MembranePotential">
         <ComponentReference name="species" type="Species"/>
         <Parameter name="reversal" dimension="voltage"/>
@@ -24,50 +21,39 @@
     <Species id="K" name="Potassium" charge="1"/>
     <Species id="Ca" name="Calcium" charge="1"/>
 
-
     <Environment id="env1">
         <MembranePotential species="Na" reversal="50mV"/>
-        <MembranePotential species="K" reversal="-80mV"/>    
+        <MembranePotential species="K" reversal="-80mV"/>
     </Environment>
 
-
     <ComponentType name="KSChannel">
         <Parameter name="conductance" dimension="conductance"/>
         <ComponentReference name="species" type="Species"/>
         <Children name="gates" type="KSGate"/>
         <Exposure name="g" dimension="conductance"/>
-    
         <Dynamics>
             <DerivedVariable name="fopen" dimension="none" select="gates[*]/fopen" reduce="multiply"/>
             <DerivedVariable name="g" exposure="g" dimension="conductance" value="fopen * conductance"/>
         </Dynamics>
     </ComponentType>
 
-
-    
     <ComponentType name="KSGate">
         <Parameter name="power" dimension="none"/>
         <Parameter name="deltaV" dimension="voltage"/>
         <Children name="states" type="KSState"/>
         <Children name="transitions" type="KSTransition"/>
         <Exposure name="fopen" dimension="none"/>
-    
-        <Dynamics>   
-            <KineticScheme name="ks" nodes="states" stateVariable="occupancy"
-                           edges="transitions" edgeSource="from" edgeTarget="to" 
-                           forwardRate="rf" reverseRate="rr" dependency="v" step="deltaV"/>
-    
+        <Dynamics>
+            <KineticScheme name="ks" nodes="states" stateVariable="occupancy" edges="transitions" edgeSource="from" edgeTarget="to" forwardRate="rf" reverseRate="rr" dependency="v" step="deltaV"/>
             <DerivedVariable name="q" dimension="none" select="states[*]/q" reduce="add"/>
             <DerivedVariable name="fopen" exposure="fopen" dimension="none" value="q^power"/>
         </Dynamics>
     </ComponentType>
 
-    
     <ComponentType name="KSState">
         <Parameter name="relativeConductance" dimension="none"/>
         <Exposure name="q" dimension="none"/>
         <Exposure name="occupancy" dimension="none"/>
-   
         <Dynamics>
             <StateVariable name="occupancy" exposure="occupancy" dimension="none"/>
             <DerivedVariable name="q" exposure="q" value="relativeConductance * occupancy"/>
@@ -78,21 +64,17 @@
         <Fixed parameter="relativeConductance" value="0"/>
     </ComponentType>
 
-
     <ComponentType name="KSOpenState" extends="KSState">
         <Fixed parameter="relativeConductance" value="1"/>
     </ComponentType>
 
-
     <ComponentType name="KSTransition">
         <Link name="from" type="KSState"/>
         <Link name="to" type="KSState"/>
         <Exposure name="rf" dimension="per_time"/>
         <Exposure name="rr" dimension="per_time"/>
- 
     </ComponentType>
 
-
     <ComponentType name="VHalfTransition" extends="KSTransition">
         <Parameter name="vHalf" dimension="voltage"/>
         <Parameter name="z" dimension="none"/>
@@ -100,8 +82,7 @@
         <Parameter name="tau" dimension="time"/>
         <Parameter name="tauMin" dimension="time"/>
         <Constant name="kte" dimension="voltage" value="25.3mV"/>
-        <Requirement name="v" dimension="voltage"/>  
-    
+        <Requirement name="v" dimension="voltage"/>
         <Dynamics>
             <DerivedVariable name="rf0" dimension="per_time" value="exp(z * gamma * (v - vHalf) / kte) / tau"/>
             <DerivedVariable name="rr0" dimension="per_time" value="exp(-z * (1 - gamma) * (v - vHalf) / kte) / tau"/>
@@ -110,35 +91,26 @@
         </Dynamics>
     </ComponentType>
 
-
-
-
-
-
     <KSChannel id="na1" conductance="20pS" species="Na">
         <KSGate power="1" deltaV="0.1mV">
             <KSClosedState id="c1"/>
             <KSClosedState id="c2"/>
             <KSOpenState id="o1" relativeConductance="1"/>
             <KSClosedState id="c3"/>
-            <VHalfTransition from="c1" to="c2" vHalf = "-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
-            <VHalfTransition from="c2" to="o1" vHalf = "-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
-            <VHalfTransition from="o1" to="c3" vHalf = "-70mV" z="1.1" gamma="0.90" tau="8.0ms" tauMin="0.01ms"/>         
+            <VHalfTransition from="c1" to="c2" vHalf="-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
+            <VHalfTransition from="c2" to="o1" vHalf="-35mV" z="2.5" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
+            <VHalfTransition from="o1" to="c3" vHalf="-70mV" z="1.1" gamma="0.90" tau="8.0ms" tauMin="0.01ms"/>
         </KSGate>
     </KSChannel>
 
-
     <KSChannel id="k1" conductance="30pS" species="K">
         <KSGate power="1" deltaV="0.1mV">
             <KSClosedState id="c1"/>
             <KSOpenState id="o1"/>
-            <VHalfTransition from="c1" to="o1" vHalf = "0mV" z="1.5" gamma="0.75" tau="3.2ms" tauMin="0.3ms"/>
+            <VHalfTransition from="c1" to="o1" vHalf="0mV" z="1.5" gamma="0.75" tau="3.2ms" tauMin="0.3ms"/>
         </KSGate>
     </KSChannel>
 
-
-
-
     <ComponentType name="ChannelPopulation">
         <ComponentReference name="channel" type="KSChannel"/>
         <Parameter name="number" dimension="none"/>
@@ -146,21 +118,15 @@
         <Exposure name="current" dimension="current"/>
         <DerivedParameter name="erev" dimension="voltage" select="//MembranePotential[species=channel/species]/reversal"/>
         <Dynamics>
-     
             <DerivedVariable name="channelg" dimension="conductance" select="channel/g"/>
             <DerivedVariable name="geff" value="channelg * number"/>
             <DerivedVariable name="current" exposure="current" value="geff * (erev - v)"/>
-        </Dynamics>    
-    
-    
-        <Structure>    
-            <ChildInstance component="channel"/>    
+        </Dynamics>
+        <Structure>
+            <ChildInstance component="channel"/>
         </Structure>
     </ComponentType>
 
-
-
-
     <ComponentType name="KSCell">
         <Parameter name="capacitance" dimension="capacitance"/>
         <ComponentReference name="environment" type="Environment"/>
@@ -172,27 +138,22 @@
             <OnStart>
                 <StateAssignment variable="v" value="v0"/>
             </OnStart>
-  
             <DerivedVariable name="totcurrent" dimension="current" select="populations[*]/current" reduce="add"/>
-            <StateVariable name="v" exposure="v" dimension="voltage"/> 
+            <StateVariable name="v" exposure="v" dimension="voltage"/>
             <TimeDerivative variable="v" value="(totcurrent + injection) / capacitance"/>
         </Dynamics>
     </ComponentType>
 
-
-
     <KSCell id="kscell_1" capacitance="0.4pF" injection="1pA" v0="-60mV" environment="env1">
         <ChannelPopulation channel="na1" number="400"/>
         <ChannelPopulation channel="k1" number="180"/>
     </KSCell>
 
-    
-    <Include file="SingleSimulation.xml" />
-    
+    <Include file="SingleSimulation.xml"/>
+
     <Simulation id="sim1" length="80ms" step="0.05ms" target="kscell_1">
         <Display id="d0" title="Example 5: References and paths" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="60">
             <Line id="v" quantity="v" scale="1mV" timeScale="1ms" color="#0000f0"/>
         </Display>
     </Simulation>
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example6.xml b/examples/example6.xml
index 8dd4025..12e3f6d 100644
--- a/examples/example6.xml
+++ b/examples/example6.xml
@@ -1,44 +1,35 @@
 <Lems>
- 
-    <Target component="sim1"/> 
- 
+    <Target component="sim1"/>
+
     <Include file="ex2dims.xml"/>
-    <Include file="hhchannel.xml"/> 
- 
+    <Include file="hhchannel.xml"/>
     <Include file="hhcell.xml"/>
     <Include file="spikegenerators.xml"/>
     <Include file="hhmodels.xml"/>
     <Include file="misciaf.xml"/>
- 
 
     <HHCell id="hhcell_1" capacitance="1pF" injection="4pA" v0="-60mV">
         <ChannelPopulation id="NaPop" channel="na" number="6000" erev="50mV"/>
         <ChannelPopulation id="KPop" channel="k" number="1800" erev="-77mV"/>
     </HHCell>
- 
-    <Component id="gen1" type="spikeGenerator" period="30ms"/>
 
+    <Component id="gen1" type="spikeGenerator" period="30ms"/>
     <Component id="gen2" type="spikeGenerator2" period="32ms"/>
-
-    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS"
-               refractoryPeriod="4ms" capacitance="1pF"/>
+    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS" refractoryPeriod="4ms" capacitance="1pF"/>
 
     <ComponentType name="Display">
-        <Text name="title"/>   
+        <Text name="title"/>
         <Parameter name="xmin" dimension="none"/>
         <Parameter name="xmax" dimension="none"/>
         <Parameter name="ymin" dimension="none"/>
         <Parameter name="ymax" dimension="none"/>
-
         <Parameter name="timeScale" dimension="time"/>
         <Children name="lines" type="Line"/>
-
         <Simulation>
             <DataDisplay title="title" dataRegion="xmin,xmax,ymin,ymax"/>
         </Simulation>
     </ComponentType>
 
-
     <ComponentType name="Line">
         <Parameter name="scale" dimension="*"/>
         <Parameter name="timeScale" dimension="*"/>
@@ -49,25 +40,19 @@
         </Simulation>
     </ComponentType>
 
-
     <ComponentType name="Simulation">
         <Parameter name="length" dimension="time"/>
         <Parameter name="step" dimension="time"/>
-    
         <ComponentReference name="target" type="Component"/>
-
-
         <Children name="displays" type="Display"/>
-        
         <Dynamics>
             <StateVariable name="t" dimension="time"/>
         </Dynamics>
-    
         <Simulation>
             <Run component="target" variable="t" increment="step" total="length"/>
         </Simulation>
     </ComponentType>
-    
+
     <Simulation id="sim1" length="80ms" step="0.01ms" target="hhcell_1">
         <Display id="d0" title="Example 6: User defined types for simulation and display" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="60">
             <Line id="V" quantity="v" scale="1mV" timeScale="1ms" color="#0000f0"/>
@@ -75,6 +60,4 @@
             <Line id="K_q" quantity="KPop/geff" scale="1nS" timeScale="1ms" color="#00f000"/>-->
         </Display>
     </Simulation>
-  
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example7.xml b/examples/example7.xml
index 4e46e4c..89c6311 100644
--- a/examples/example7.xml
+++ b/examples/example7.xml
@@ -1,76 +1,59 @@
 <Lems>
- 
-    <Target component="sim1"/> 
- 
- 
+    <Target component="sim1"/>
+
     <Include file="ex2dims.xml"/>
     <Include file="spikegenerators.xml"/>
     <Include file="misciaf.xml"/>
 
- 
     <Component id="gen1" type="spikeGenerator" period="30ms"/>
-
     <Component id="gen2" type="spikeGenerator2" period="32ms"/>
-
-    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS"
-           refractoryPeriod="4ms" capacitance="1pF"/>
-
+    <Component id="iaf3cpt" type="iaf3" leakReversal="-50mV" deltaV="50mV" threshold="-30mV" leakConductance="50pS" refractoryPeriod="4ms" capacitance="1pF"/>
 
     <ComponentType name="Network">
         <Children name="populations" type="Population"/>
         <Children name="connectivities" type="EventConnectivity"/>
     </ComponentType>
 
-
     <ComponentType name="Population">
         <ComponentReference name="component" type="Component"/>
         <Parameter name="size" dimension="none"/>
-   
         <Structure>
             <MultiInstantiate number="size" component="component"/>
         </Structure>
-  
     </ComponentType>
 
-
     <ComponentType name="EventConnectivity">
         <Link name="source" type="Population"/>
         <Link name="target" type="Population"/>
         <Child name="Connections" type="ConnectionPattern"/>
     </ComponentType>
 
-
     <ComponentType name="ConnectionPattern"/>
 
-
     <ComponentType name="AllAll" extends="ConnectionPattern">
         <Structure>
             <ForEach instances="../source" as="a">
                 <ForEach instances="../target" as="b">
                     <EventConnection from="a" to="b"/>
                 </ForEach>
-            </ForEach>    
+            </ForEach>
         </Structure>
     </ComponentType>
 
-
     <Network id="net1">
         <Population id="p1" component="gen1" size="2"/>
         <Population id="p3" component="iaf3cpt" size="3"/>
-     
         <EventConnectivity id="p1-p3" source="p1" target="p3">
             <Connections type="AllAll"/>
         </EventConnectivity>
     </Network>
 
+    <Include file="SingleSimulation.xml"/>
 
-    <Include file="SingleSimulation.xml" />
-    
     <Simulation id="sim1" length="80ms" step="0.05ms" target="net1">
         <Display id="d0" title="Example 7: User defined types for networks and populations" timeScale="1ms" xmin="-10" xmax="90" ymin="-50" ymax="90">
             <Line id="gen_v" quantity="p3[0]/v" scale="1mV" timeScale="1ms" color="#0000f0"/>
             <Line id="gen_tsince" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#00c000"/>
         </Display>
     </Simulation>
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/example8.xml b/examples/example8.xml
index 43d0b54..b7dbc6f 100644
--- a/examples/example8.xml
+++ b/examples/example8.xml
@@ -1,119 +1,95 @@
 <Lems>
-
-    <Target component="sim1"/> 
-
-
+    <Target component="sim1"/>
     <Include file="ex2dims.xml"/>
     <Include file="spikegenerators.xml"/>
     <Include file="misciaf.xml"/>
 
-
     <ComponentType name="refractiaf">
         <Parameter name="threshold" dimension="voltage"/>
         <Parameter name="refractoryPeriod" dimension="time"/>
         <Parameter name="capacitance" dimension="capacitance"/>
         <Parameter name="vleak" dimension="voltage"/>
         <Parameter name="gleak" dimension="conductance"/>
-
         <Parameter name="current" dimension="current"/>
         <Parameter name="vreset" dimension="voltage"/>
         <Parameter name="deltaV" dimension="voltage"/>
         <Parameter name="v0" dimension="voltage"/>
-
         <EventPort name="out" direction="out"/>
         <EventPort name="in" direction="in"/>
-
         <Exposure name="v" dimension="voltage"/>
-
-        <Dynamics>     
-            <StateVariable name="v" exposure="v" dimension="voltage" /> 
-            <StateVariable name="tin" dimension="time"/>       
-            
+        <Dynamics>
+            <StateVariable name="v" exposure="v" dimension="voltage"/>
+            <StateVariable name="tin" dimension="time"/>
             <OnStart>
                 <StateAssignment variable="v" value="v0"/>
             </OnStart>
-
-            <Regime name="refr">         
-                <OnEntry>             
-                    <StateAssignment variable="tin" value="t" />             
-                    <StateAssignment variable="v" value="vreset" />          
-                </OnEntry>                   
-                <OnCondition test="t .gt. tin + refractoryPeriod">                 
-                    <Transition regime="int" />             
-                </OnCondition>         
-            </Regime>          
-
-            <Regime name="int" initial="true">         
-                <TimeDerivative variable="v" value="(current + gleak * (vleak - v)) / capacitance" />         
-                <OnCondition test="v .gt. threshold">             
-                    <EventOut port="out" />             
-                    <Transition regime="refr" />         
-                </OnCondition>         
+            <Regime name="refr">
+                <OnEntry>
+                    <StateAssignment variable="tin" value="t"/>
+                    <StateAssignment variable="v" value="vreset"/>
+                </OnEntry>
+                <OnCondition test="t .gt. tin + refractoryPeriod">
+                    <Transition regime="int"/>
+                </OnCondition>
+            </Regime>
+            <Regime name="int" initial="true">
+                <TimeDerivative variable="v" value="(current + gleak * (vleak - v)) / capacitance"/>
+                <OnCondition test="v .gt. threshold">
+                    <EventOut port="out"/>
+                    <Transition regime="refr"/>
+                </OnCondition>
                 <OnEvent port="in">
                     <StateAssignment variable="v" value="v + deltaV"/>
                 </OnEvent>
-
             </Regime>
         </Dynamics>
 
     </ComponentType>
 
-
     <Component id="gen1" type="spikeGenerator" period="7ms"/>
 
-    
-    <Component id="multiregime" type="refractiaf" threshold="-50mV" v0="-80mV"
-               refractoryPeriod="20ms" capacitance="1pF" vreset="-80mV" vleak="-90mV" 
-               gleak="5pS" current="0.00001nA" deltaV="5mV"/>
-
+    <Component id="multiregime" type="refractiaf" threshold="-50mV" v0="-80mV" refractoryPeriod="20ms" capacitance="1pF" vreset="-80mV" vleak="-90mV" gleak="5pS" current="0.00001nA" deltaV="5mV"/>
 
     <ComponentType name="Network">
         <Children name="populations" type="Population"/>
         <Children name="connectivities" type="EventConnectivity"/>
     </ComponentType>
 
-
     <ComponentType name="Population">
         <ComponentReference name="component" type="Component"/>
         <Parameter name="size" dimension="none"/>
         <Structure>
-                <MultiInstantiate number="size" component="component"/>
+            <MultiInstantiate number="size" component="component"/>
         </Structure>
     </ComponentType>
 
-
     <ComponentType name="EventConnectivity">
         <Link name="source" type="Population"/>
         <Link name="target" type="Population"/>
         <Child name="Connections" type="ConnectionPattern"/>
     </ComponentType>
 
-
     <ComponentType name="ConnectionPattern"/>
 
-
     <ComponentType name="AllAll" extends="ConnectionPattern">
         <Structure>
             <ForEach instances="../source" as="a">
                 <ForEach instances="../target" as="b">
                     <EventConnection from="a" to="b"/>
                 </ForEach>
-            </ForEach>    
+            </ForEach>
         </Structure>
     </ComponentType>
 
-
     <Network id="net1">
         <Population id="p1" component="gen1" size="1"/>
         <Population id="p3" component="multiregime" size="2"/>
-
         <EventConnectivity id="p1-p3" source="p1" target="p3">
             <Connections type="AllAll"/>
         </EventConnectivity>
     </Network>
 
-
-    <Include file="SingleSimulation.xml" />
+    <Include file="SingleSimulation.xml"/>
 
     <Simulation id="sim1" length="80ms" step="0.05ms" target="net1">
         <Display id="d0" title="Example 8: Regimes in dynamics definitions" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="20">
@@ -121,6 +97,4 @@
             <Line id="gen_sv" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#f00000"/>
         </Display>
     </Simulation>
-
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/hhaltgate.xml b/examples/hhaltgate.xml
index 39906ee..64c3f8d 100644
--- a/examples/hhaltgate.xml
+++ b/examples/hhaltgate.xml
@@ -1,24 +1,18 @@
 <Lems>
- 
     <ComponentType name="HHGate">
-        <Parameter name="power" dimension="none"/> 
+        <Parameter name="power" dimension="none"/>
         <Child name="Forward" type="HHRate"/>
         <Child name="Reverse" type="HHRate"/>
         <Requirement name="v" dimension="voltage"/>
         <Exposure name="fcond" dimension="none"/>
-    
-   
         <Dynamics simultaneous="false">
             <StateVariable name="x" dimension="none"/>
             <DerivedVariable name="ex" dimension="none" value="exp(x)"/>
             <DerivedVariable name="q" dimension="none" value="ex / (1 + ex)"/>
             <DerivedVariable name="rf" dimension="per_time" select="Forward/r"/>
-            <DerivedVariable name="rr" dimension="per_time" select="Reverse/r"/> 
-        
+            <DerivedVariable name="rr" dimension="per_time" select="Reverse/r"/>
             <TimeDerivative variable="x" value="(1 + ex)^2 / ex * (rf * (1 - q) - rr * q)"/>
-      
             <DerivedVariable name="fcond" dimension="none" exposure="fcond" value="q^power"/>
-        </Dynamics>    
+        </Dynamics>
     </ComponentType>
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/hhcell.xml b/examples/hhcell.xml
index 90575e1..782f299 100644
--- a/examples/hhcell.xml
+++ b/examples/hhcell.xml
@@ -1,12 +1,9 @@
 <Lems>
-
     <Include file="hhchannel.xml"/>
-
     <Dimension name="voltage" m="1" l="2" t="-3" i="-1"/>
     <Dimension name="capacitance" m="-1" l="-2" t="4" i="2"/>
     <Dimension name="current" i="1"/>
 
-    
     <ComponentType name="ChannelPopulation">
         <ComponentReference name="channel" type="HHChannel"/>
         <Parameter name="number" dimension="none"/>
@@ -14,36 +11,29 @@
         <Requirement name="v" dimension="voltage"/>
         <Exposure name="current" dimension="current"/>
         <Exposure name="geff" dimension="conductance"/>
-  
         <Structure>
             <ChildInstance component="channel"/>
         </Structure>
-  
         <Dynamics simultaneous="false">
             <DerivedVariable name="channelg" dimension="conductance" select="channel/g"/>
             <DerivedVariable name="geff" exposure="geff" value="channelg * number"/>
             <DerivedVariable name="current" exposure="current" value="geff * (erev - v)"/>
         </Dynamics>
-    
     </ComponentType>
 
-
     <ComponentType name="HHCell">
         <Parameter name="capacitance" dimension="capacitance"/>
         <Children name="populations" type="ChannelPopulation"/>
         <Parameter name="injection" dimension="current"/>
         <Parameter name="v0" dimension="voltage"/>
         <Exposure name="v" dimension="voltage"/>
-    
         <Dynamics simultaneous="true">
             <OnStart>
                 <StateAssignment variable="v" value="v0"/>
             </OnStart>
-  
             <DerivedVariable name="totcurrent" dimension="current" select="populations[*]/current" reduce="add"/>
-            <StateVariable name="v" exposure="v" dimension="voltage"/> 
+            <StateVariable name="v" exposure="v" dimension="voltage"/>
             <TimeDerivative variable="v" value="(totcurrent + injection) / capacitance"/>
         </Dynamics>
     </ComponentType>
- 
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/hhchannel.xml b/examples/hhchannel.xml
index 7e7c6b4..debc1cb 100644
--- a/examples/hhchannel.xml
+++ b/examples/hhchannel.xml
@@ -1,5 +1,4 @@
 <Lems>
-
     <Dimension name="voltage" m="1" l="2" t="-3" i="-1"/>
     <Dimension name="time" t="1"/>
     <Dimension name="per_time" t="-1"/>
@@ -7,7 +6,6 @@
     <Dimension name="capacitance" m="-1" l="-2" t="4" i="2"/>
     <Dimension name="current" i="1"/>
 
-    
     <ComponentType name="HHRate">
         <Parameter name="rate" dimension="per_time"/>
         <Parameter name="midpoint" dimension="voltage"/>
@@ -16,49 +14,42 @@
         <Exposure name="r" dimension="per_time"/>
     </ComponentType>
 
-
     <ComponentType name="HHExpRate" extends="HHRate">
         <Dynamics>
-            <DerivedVariable name="r" exposure="r"  dimension="per_time" value="rate * exp((v - midpoint)/scale)"/>
+            <DerivedVariable name="r" exposure="r" dimension="per_time" value="rate * exp((v - midpoint)/scale)"/>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHSigmoidRate" extends="HHRate">
         <Dynamics>
             <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate / (1 + exp( -(v - midpoint)/scale))"/>
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="HHExpLinearRate" extends="HHRate">
         <Dynamics>
             <DerivedVariable name="x" dimension="none" value="(v - midpoint) / scale"/>
             <DerivedVariable name="r" dimension="per_time" exposure="r" value="rate * x / (1 - exp(-x))"/>
         </Dynamics>
     </ComponentType>
- 
 
     <ComponentType name="HHGate0">
-        <Parameter name="power" dimension="none"/> 
+        <Parameter name="power" dimension="none"/>
         <Child name="Forward" type="HHRate"/>
         <Child name="Reverse" type="HHRate"/>
         <Requirement name="v" dimension="voltage"/>
         <Exposure name="fcond" dimension="none"/>
-    
         <Dynamics simultaneous="true">
             <StateVariable name="q" dimension="none"/>
             <DerivedVariable dimension="per_time" name="rf" select="Forward/r"/>
-            <DerivedVariable dimension="per_time" name="rr" select="Reverse/r"/> 
+            <DerivedVariable dimension="per_time" name="rr" select="Reverse/r"/>
             <TimeDerivative variable="q" value="rf * (1 - q) - rr * q"/>
             <DerivedVariable name="fcond" dimension="none" exposure="fcond" value="q^power"/>
-        </Dynamics>    
+        </Dynamics>
     </ComponentType>
 
-
     <Include file="hhaltgate.xml"/>
 
-    
     <ComponentType name="HHChannel">
         <Parameter name="conductance" dimension="conductance"/>
         <Children name="gates" type="HHGate"/>
@@ -68,7 +59,4 @@
             <DerivedVariable name="g" exposure="g" dimension="conductance" value="conductance * gatefeff"/>
         </Dynamics>
     </ComponentType>
-
-
 </Lems>
-
diff --git a/examples/hhmodels.xml b/examples/hhmodels.xml
index 60c3685..770bbe9 100644
--- a/examples/hhmodels.xml
+++ b/examples/hhmodels.xml
@@ -1,29 +1,25 @@
 <Lems>
     <Include file="hhchannel.xml"/>
 
-    <Unit symbol="mV" dimension="voltage" power="-3"/> 
+    <Unit symbol="mV" dimension="voltage" power="-3"/>
     <Unit symbol="per_ms" dimension="per_time" power="3"/>
     <Unit symbol="pS" dimension="conductance" power="-12"/>
 
-    
     <HHChannel id="na" conductance="20pS">
         <HHGate id="m" power="3">
             <Forward type="HHExpLinearRate" rate="1.per_ms" midpoint="-40mV" scale="10mV"/>
             <Reverse type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
         </HHGate>
-    
         <HHGate id="h" power="1">
             <Forward type="HHExpRate" rate="0.07per_ms" midpoint="-65.mV" scale="-20.mV"/>
             <Reverse type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
         </HHGate>
     </HHChannel>
 
-
     <HHChannel id="k" conductance="20pS">
         <HHGate id="n" power="4">
             <Forward type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
             <Reverse type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
         </HHGate>
     </HHChannel>
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/misciaf.xml b/examples/misciaf.xml
index 6899cae..10ea7f2 100644
--- a/examples/misciaf.xml
+++ b/examples/misciaf.xml
@@ -1,7 +1,5 @@
 <Lems>
-    
     <Include file="elecdims.xml"/>
-   
 
     <ComponentType name="iaf1">
         <Parameter name="threshold" dimension="voltage"/>
@@ -9,24 +7,18 @@
         <Parameter name="capacitance" dimension="capacitance"/>
     </ComponentType>
 
-
     <ComponentType name="iaf3" extends="iaf1">
         <Parameter name="leakConductance" dimension="conductance"/>
         <Parameter name="leakReversal" dimension="voltage"/>
         <Parameter name="deltaV" dimension="voltage"/>
         <EventPort name="spikes-in" direction="in"/>
         <Exposure name="v" dimension="voltage"/>
-
         <Dynamics>
             <StateVariable name="v" exposure="v" dimension="voltage"/>
             <TimeDerivative variable="v" value="leakConductance * (leakReversal - v) / capacitance"/>
-             
             <OnEvent port="spikes-in">
                 <StateAssignment variable="v" value="v + deltaV"/>
-            </OnEvent>      
+            </OnEvent>
         </Dynamics>
-
     </ComponentType>
- 
-
-</Lems>
\ No newline at end of file
+</Lems>
diff --git a/examples/spikegenerators.xml b/examples/spikegenerators.xml
index dd8db3f..6c0d8da 100644
--- a/examples/spikegenerators.xml
+++ b/examples/spikegenerators.xml
@@ -1,7 +1,5 @@
 <Lems>
-
     <Dimension name="time" t="1"/>
- 
 
     <ComponentType name="spikeGenerator">
         <Parameter name="period" dimension="time"/>
@@ -17,7 +15,6 @@
         </Dynamics>
     </ComponentType>
 
-
     <ComponentType name="spikeGenerator2" extends="spikeGenerator">
         <Dynamics>
             <DerivedVariable name="tsince" exposure="tsince" value="t - tlast"/>
@@ -28,6 +25,4 @@
             </OnCondition>
         </Dynamics>
     </ComponentType>
- 
-
-</Lems>
\ No newline at end of file
+</Lems>