diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 89ab9c7..1dd19e1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7,3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     env:
       JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML"
       HDF5_DISABLE_VERSION_CHECK: 1
@@ -58,9 +58,9 @@ jobs:
         cd pyNeuroML
         git checkout $pynml_branch
         pip install pandas==1.3.5
-        pip install NEURON==7.8.2 # Specify version of neuron - 8.2.1 fails
+        pip install NEURON==8.2.2 # Specify version of neuron - 8.2.1 fails
         #pip install -r requirements-dev.txt
-        python setup.py install
+        pip install .
         cd -
 
         # Install latest jnml...
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
new file mode 100644
index 0000000..0fe16bc
--- /dev/null
+++ b/.github/workflows/python-publish.yml
@@ -0,0 +1,36 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
index 4afa231..50bcaa0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -202,3 +202,11 @@ docs/_build
 /examples/pyr_4_sym.cell.nml
 *_eden.py
 arm64
+/examples/Example4_PyNN.mdf
+*.mdf.json
+*.mdf.yaml
+/examples/Example6_PyNN.mdf
+/examples/Example7_Brunel2000.mdf
+/examples/Example3_Network.yaml
+/examples/SimExample3.yaml
+/examples/Example4_PyNN.mdf.1
diff --git a/docs/NeuroMLlite_specification.json b/docs/NeuroMLlite_specification.json
index 97948a1..48f192e 100644
--- a/docs/NeuroMLlite_specification.json
+++ b/docs/NeuroMLlite_specification.json
@@ -1,5 +1,5 @@
 {
-    "version": "NeuroMLlite v0.5.3",
+    "version": "NeuroMLlite v0.5.7",
     "specification": {
         "Network": {
             "definition": "A Network containing multiple Population's, connected by Projection's and receiving Input's",
@@ -237,7 +237,7 @@
                     "description": "Unique identifier for this Population"
                 },
                 "size": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "The size of the population."
                 },
                 "component": {
@@ -366,11 +366,11 @@
                     "description": "type of projection: projection (default; standard chemical, event triggered), electricalProjection\n(for gap junctions) or continuousProjection (for analogue/graded synapses)"
                 },
                 "delay": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Delay to use (default: 0)"
                 },
                 "weight": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Weight to use (default: 1)"
                 },
                 "random_connectivity": {
@@ -395,7 +395,7 @@
                     "description": ""
                 },
                 "probability": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Random probability of connection."
                 }
             }
@@ -442,23 +442,23 @@
                     "description": "Population to target"
                 },
                 "cell_ids": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Specific ids of _Cell_s to apply this input to (cannot be used with percentage"
                 },
                 "percentage": {
-                    "type": "float",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Percentage of Cells to apply input to"
                 },
                 "number_per_cell": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Number of individual inputs per selected Cell (default: 1)"
                 },
                 "segment_ids": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Which segments to target (default: [0])"
                 },
                 "weight": {
-                    "type": "Union[EvaluableExpression, T, VT, ndarray, int, float, str]",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Weight to use (default: 1)"
                 }
             }
diff --git a/docs/NeuroMLlite_specification.yaml b/docs/NeuroMLlite_specification.yaml
index 654994c..c05d843 100644
--- a/docs/NeuroMLlite_specification.yaml
+++ b/docs/NeuroMLlite_specification.yaml
@@ -1,4 +1,4 @@
-version: NeuroMLlite v0.5.3
+version: NeuroMLlite v0.5.7
 specification:
     Network:
         definition: A Network containing multiple Population's, connected by Projection's
@@ -178,7 +178,8 @@ specification:
                 type: str
                 description: Unique identifier for this Population
             size:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: The size of the population.
             component:
                 type: str
@@ -276,10 +277,12 @@ specification:
                     (for gap junctions) or continuousProjection (for analogue/graded
                     synapses)'
             delay:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Delay to use (default: 0)'
             weight:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Weight to use (default: 1)'
             random_connectivity:
                 type: RandomConnectivity
@@ -298,7 +301,8 @@ specification:
                 type: str
                 description: ''
             probability:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: Random probability of connection.
     ConvergentConnectivity:
         definition: A ConvergentConnectivity definition.
@@ -331,19 +335,24 @@ specification:
                 type: str
                 description: Population to target
             cell_ids:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: Specific ids of _Cell_s to apply this input to (cannot
                     be used with percentage
             percentage:
-                type: float
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: Percentage of Cells to apply input to
             number_per_cell:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Number of individual inputs per selected Cell (default:
                     1)'
             segment_ids:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Which segments to target (default: [0])'
             weight:
-                type: Union[EvaluableExpression, T, VT, ndarray, int, float, str]
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: 'Weight to use (default: 1)'
diff --git a/docs/README.md b/docs/README.md
index a56c868..1833050 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,4 +1,4 @@
-# Specification of NeuroMLlite v0.5.3
+# Specification of NeuroMLlite v0.5.7
 **Note: the NeuroMLlite specification is still in development! Subject to change...**
 
 ## Network
@@ -404,7 +404,7 @@ A Population definition.
 
   <tr>
     <td><b>size</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>The size of the population.</i></td>
  </tr>
 
@@ -622,14 +622,14 @@ A Projection definition.
 
   <tr>
     <td><b>delay</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Delay to use (default: 0)</i></td>
  </tr>
 
 
   <tr>
     <td><b>weight</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Weight to use (default: 1)</i></td>
  </tr>
 
@@ -671,7 +671,7 @@ A RandomConnectivity definition.
 
   <tr>
     <td><b>probability</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Random probability of connection.</i></td>
  </tr>
 
@@ -748,35 +748,35 @@ An Input definition.
 
   <tr>
     <td><b>cell_ids</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Specific ids of <a href="#cell">Cell</a>s to apply this input to (cannot be used with percentage</i></td>
  </tr>
 
 
   <tr>
     <td><b>percentage</b></td>
-    <td>float</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Percentage of Cells to apply input to</i></td>
  </tr>
 
 
   <tr>
     <td><b>number_per_cell</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Number of individual inputs per selected Cell (default: 1)</i></td>
  </tr>
 
 
   <tr>
     <td><b>segment_ids</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Which segments to target (default: [0])</i></td>
  </tr>
 
 
   <tr>
     <td><b>weight</b></td>
-    <td>Union[EvaluableExpression, T, VT, ndarray, int, float, str]</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Weight to use (default: 1)</i></td>
  </tr>
 
diff --git a/docs/conf.py b/docs/conf.py
index b6ff8df..0360d77 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -53,7 +53,7 @@
     # space here is important since __version__ is used in generation of
     # version_info also
     if "__version__ =" in aline:
-        version = aline.split("\"")[1]
+        version = aline.split('"')[1]
 # The full version, including alpha/beta/rc tags.
 release = version
 
diff --git a/docs/generate.py b/docs/generate.py
index 1cd6075..1c89d2b 100644
--- a/docs/generate.py
+++ b/docs/generate.py
@@ -2,7 +2,6 @@
 
 
 if __name__ == "__main__":
-
     net = neuromllite.Network(id="net")
     doc = net.generate_documentation(format="markdown")
     print(doc)
diff --git a/examples/Example10_Lorenz.json b/examples/Example10_Lorenz.json
index 49faf0d..5380a74 100644
--- a/examples/Example10_Lorenz.json
+++ b/examples/Example10_Lorenz.json
@@ -1,6 +1,6 @@
 {
     "Example10_Lorenz": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 10: Lorenz",
         "parameters": {
             "N": 1,
diff --git a/examples/Example10_Lorenz.mdf.yaml b/examples/Example10_Lorenz.mdf.yaml
index 618c1e4..15b70bc 100644
--- a/examples/Example10_Lorenz.mdf.yaml
+++ b/examples/Example10_Lorenz.mdf.yaml
@@ -1,25 +1,32 @@
 Example10_Lorenz:
-    format: ModECI MDF v0.3
+    format: ModECI MDF v0.4
     graphs:
         Example10_Lorenz:
             notes: 'Example 10: Lorenz'
             nodes:
-                lorenzPop_0:
+                lorenzPop:
                     parameters:
                         sigma:
-                            value: 10.0
+                            value:
+                            - 10.0
                         b:
-                            value: 2.67
+                            value:
+                            - 2.67
                         r:
-                            value: 28.0
+                            value:
+                            - 28.0
                         x0:
-                            value: 1.0
+                            value:
+                            - 1.0
                         y0:
-                            value: 1.0
+                            value:
+                            - 1.0
                         z0:
-                            value: 1.0
+                            value:
+                            - 1.0
                         sec:
-                            value: 1.0
+                            value:
+                            - 1.0
                         x:
                             default_initial_value: x0
                             time_derivative: ( sigma * (y - x) ) / sec
diff --git a/examples/Example11_Synapses.json b/examples/Example11_Synapses.json
index 0e158ac..e8a3ace 100644
--- a/examples/Example11_Synapses.json
+++ b/examples/Example11_Synapses.json
@@ -1,6 +1,6 @@
 {
     "Example11_Synapses": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 11: synaptic properties",
         "parameters": {
             "input_amp": 0.23,
@@ -87,7 +87,7 @@
             "stim": {
                 "input_source": "i_clamp",
                 "population": "pop0",
-                "percentage": 100.0
+                "percentage": 100
             }
         }
     }
diff --git a/examples/Example11_Synapses.net.nml b/examples/Example11_Synapses.net.nml
index ea27c89..34f2db2 100644
--- a/examples/Example11_Synapses.net.nml
+++ b/examples/Example11_Synapses.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example11_Synapses">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example11_Synapses
     Generation seed: 1234
     NeuroMLlite parameters: 
diff --git a/examples/Example12.py b/examples/Example12.py
index c7d183b..adfcba0 100644
--- a/examples/Example12.py
+++ b/examples/Example12.py
@@ -1,5 +1,12 @@
 from neuromllite import Network, Cell, InputSource, Population, Synapse
-from neuromllite import Projection, RandomConnectivity, Input, Simulation, RectangularRegion, RandomLayout
+from neuromllite import (
+    Projection,
+    RandomConnectivity,
+    Input,
+    Simulation,
+    RectangularRegion,
+    RandomLayout,
+)
 import sys
 
 ################################################################################
@@ -11,21 +18,23 @@
 net.seed = 1234
 net.temperature = 32.0
 
-net.parameters = {"N": 20,
-                  "fractionE": 0.7,
-                  "weightInput": 0.7,
-                  "prob_e_e": 0.1,
-                  "prob_e_i": 0.9,
-                  "prob_i_e": 0.8,
-                  "prob_i_i": 0.3,
-                  "global_delay": 2}
-
-r1 = RectangularRegion(
-    id="region1", x=0, y=0, z=0, width=1000, height=100, depth=1000
-)
+net.parameters = {
+    "N": 20,
+    "fractionE": 0.7,
+    "weightInput": 0.7,
+    "prob_e_e": 0.1,
+    "prob_e_i": 0.9,
+    "prob_i_e": 0.8,
+    "prob_i_i": 0.3,
+    "global_delay": 2,
+}
+
+r1 = RectangularRegion(id="region1", x=0, y=0, z=0, width=1000, height=100, depth=1000)
 net.regions.append(r1)
 
-pyr_cell = Cell(id="pyr_4_sym", neuroml2_source_file="test_files/acnet2/pyr_4_sym.cell.nml")
+pyr_cell = Cell(
+    id="pyr_4_sym", neuroml2_source_file="test_files/acnet2/pyr_4_sym.cell.nml"
+)
 net.cells.append(pyr_cell)
 bask_cell = Cell(id="bask", neuroml2_source_file="test_files/acnet2/bask.cell.nml")
 net.cells.append(bask_cell)
@@ -61,17 +70,24 @@
 net.populations.append(pE)
 net.populations.append(pI)
 
-syn_e_e = Synapse(id="AMPA_syn", neuroml2_source_file="test_files/acnet2/AMPA_syn.synapse.nml")
+syn_e_e = Synapse(
+    id="AMPA_syn", neuroml2_source_file="test_files/acnet2/AMPA_syn.synapse.nml"
+)
 net.synapses.append(syn_e_e)
-syn_e_i = Synapse(id="AMPA_syn_inh", neuroml2_source_file="test_files/acnet2/AMPA_syn_inh.synapse.nml")
+syn_e_i = Synapse(
+    id="AMPA_syn_inh", neuroml2_source_file="test_files/acnet2/AMPA_syn_inh.synapse.nml"
+)
 net.synapses.append(syn_e_i)
-syn_i_e = Synapse(id="GABA_syn", neuroml2_source_file="test_files/acnet2/GABA_syn.synapse.nml")
+syn_i_e = Synapse(
+    id="GABA_syn", neuroml2_source_file="test_files/acnet2/GABA_syn.synapse.nml"
+)
 net.synapses.append(syn_i_e)
-syn_i_i = Synapse(id="GABA_syn_inh", neuroml2_source_file="test_files/acnet2/GABA_syn_inh.synapse.nml")
+syn_i_i = Synapse(
+    id="GABA_syn_inh", neuroml2_source_file="test_files/acnet2/GABA_syn_inh.synapse.nml"
+)
 net.synapses.append(syn_i_i)
 
 
-
 net.projections.append(
     Projection(
         id="projEE",
@@ -94,7 +110,6 @@
 )
 
 
-
 net.projections.append(
     Projection(
         id="projIE",
@@ -136,7 +151,7 @@
 ###   Build Simulation object & save as JSON
 
 sim = Simulation(
-    id="Sim%s"%net.id,
+    id="Sim%s" % net.id,
     network=new_file,
     duration="1000",
     seed="1111",
@@ -145,7 +160,7 @@
     record_spikes={
         pE.id: "*",
         pI.id: "*",
-    }
+    },
 )
 
 sim.to_json_file()
diff --git a/examples/Example12_MultiComp.json b/examples/Example12_MultiComp.json
index 8ab0a7a..899d352 100644
--- a/examples/Example12_MultiComp.json
+++ b/examples/Example12_MultiComp.json
@@ -1,6 +1,6 @@
 {
     "Example12_MultiComp": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 12: Multicompartmental cells...",
         "parameters": {
             "N": 20,
@@ -113,7 +113,7 @@
             "stim": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop_pyr",
-                "percentage": 100.0,
+                "percentage": 100,
                 "weight": "weightInput"
             }
         },
diff --git a/examples/Example1_TestNetwork.json b/examples/Example1_TestNetwork.json
index b6d0c4c..76a405a 100644
--- a/examples/Example1_TestNetwork.json
+++ b/examples/Example1_TestNetwork.json
@@ -1,6 +1,6 @@
 {
     "TestNetwork": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "A simple network with 2 populations & projection between them. No info yet on what the cells are so network can't be simulated.",
         "populations": {
             "pop0": {
diff --git a/examples/Example2_TestNetwork.json b/examples/Example2_TestNetwork.json
index b203682..42e386d 100644
--- a/examples/Example2_TestNetwork.json
+++ b/examples/Example2_TestNetwork.json
@@ -1,6 +1,6 @@
 {
     "Example2_TestNetwork": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "A simple network with 2 populations & projection between them. Cells are specified to be NeuroML 2 HH cell models & pre population is given a spiking input.",
         "cells": {
             "hhcell": {
@@ -71,7 +71,7 @@
             "stim_pop0": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop0",
-                "percentage": 80.0
+                "percentage": 80
             }
         }
     }
diff --git a/examples/Example2_TestNetwork.net.nml b/examples/Example2_TestNetwork.net.nml
index 4fa2e83..e1de4e8 100644
--- a/examples/Example2_TestNetwork.net.nml
+++ b/examples/Example2_TestNetwork.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example2_TestNetwork">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example2_TestNetwork
     Generation seed: 1234</notes>
     <include href="test_files/inputs.nml"/>
diff --git a/examples/Example3.py b/examples/Example3.py
index 67cda1d..58bf606 100644
--- a/examples/Example3.py
+++ b/examples/Example3.py
@@ -11,7 +11,8 @@
 net.id = "Example3_Network"
 net.notes = "Example 3: simple network with 2 populations of NeuroML2 cells, a projection between them and spiking input."
 print(net)
-new_file = net.to_json_file()
+
+new_json_file = net.to_json_file()
 
 ################################################################################
 ###   Build Simulation object & save as JSON
@@ -19,7 +20,7 @@
 
 sim = Simulation(
     id="SimExample3",
-    network=new_file,
+    network=new_json_file,
     duration="1000",
     dt="0.025",
     record_traces={"all": "*"},
diff --git a/examples/Example3_Network.json b/examples/Example3_Network.json
index b333ee4..a323ac5 100644
--- a/examples/Example3_Network.json
+++ b/examples/Example3_Network.json
@@ -1,6 +1,6 @@
 {
     "Example3_Network": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 3: simple network with 2 populations of NeuroML2 cells, a projection between them and spiking input.",
         "cells": {
             "hhcell": {
@@ -71,7 +71,7 @@
             "stim_pop0": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop0",
-                "percentage": 80.0
+                "percentage": 80
             }
         }
     }
diff --git a/examples/Example3_Network.net.nml b/examples/Example3_Network.net.nml
index 4da93af..8993003 100644
--- a/examples/Example3_Network.net.nml
+++ b/examples/Example3_Network.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example3_Network">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example3_Network
     Generation seed: 1234</notes>
     <include href="test_files/inputs.nml"/>
diff --git a/examples/Example4.py b/examples/Example4.py
index 9ed8afb..d579f83 100644
--- a/examples/Example4.py
+++ b/examples/Example4.py
@@ -125,7 +125,7 @@
 
 sim.to_json_file()
 sim.network = net_yaml_file
-sim.to_yaml_file('%s.yaml'%sim.id)
+sim.to_yaml_file("%s.yaml" % sim.id)
 
 sim.network = net_json_file  # reverting, for call below...
 
diff --git a/examples/Example4_PyNN.json b/examples/Example4_PyNN.json
index 23ac327..69ae655 100644
--- a/examples/Example4_PyNN.json
+++ b/examples/Example4_PyNN.json
@@ -1,6 +1,6 @@
 {
     "Example4_PyNN": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 4: a network with PyNN cells & inputs",
         "parameters": {
             "input_amp": 0.99
@@ -120,7 +120,7 @@
             "stim": {
                 "input_source": "i_clamp",
                 "population": "pop0",
-                "percentage": 50.0
+                "percentage": 50
             }
         }
     }
diff --git a/examples/Example4_PyNN.net.nml b/examples/Example4_PyNN.net.nml
index 1acf9cd..20d156f 100644
--- a/examples/Example4_PyNN.net.nml
+++ b/examples/Example4_PyNN.net.nml
@@ -1,14 +1,14 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example4_PyNN">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example4_PyNN
     Generation seed: 1234
     NeuroMLlite parameters: 
         input_amp = 0.99</notes>
     <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.99nA"/>
-    <IF_cond_alpha id="testcell" cm="1." i_offset="0.1" tau_syn_E="0.3" tau_syn_I="0.5" v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="0." e_rev_I="-70."/>
-    <IF_cond_alpha id="testcell2" cm="1." i_offset="-0.1" tau_syn_E="2." tau_syn_I="10." v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="-10." e_rev_I="-80."/>
-    <alphaCondSynapse id="ampaSyn" tau_syn="2." e_rev="-10."/>
-    <alphaCondSynapse id="gabaSyn" tau_syn="10." e_rev="-80."/>
+    <IF_cond_alpha id="testcell" cm="1.0" i_offset="0.1" tau_syn_E="0.3" tau_syn_I="0.5" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
+    <IF_cond_alpha id="testcell2" cm="1.0" i_offset="-0.1" tau_syn_E="2.0" tau_syn_I="10.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="-10.0" e_rev_I="-80.0"/>
+    <alphaCondSynapse id="ampaSyn" tau_syn="2.0" e_rev="-10.0"/>
+    <alphaCondSynapse id="gabaSyn" tau_syn="10.0" e_rev="-80.0"/>
     <network id="Example4_PyNN">
         <notes>Example 4: a network with PyNN cells &amp; inputs</notes>
         <property tag="recommended_dt_ms" value="0.01"/>
diff --git a/examples/Example4_PyNN.yaml b/examples/Example4_PyNN.yaml
index 811518d..b9895fb 100644
--- a/examples/Example4_PyNN.yaml
+++ b/examples/Example4_PyNN.yaml
@@ -1,5 +1,5 @@
 Example4_PyNN:
-    version: NeuroMLlite v0.5.3
+    version: NeuroMLlite v0.5.7
     notes: 'Example 4: a network with PyNN cells & inputs'
     parameters:
         input_amp: 0.99
@@ -88,4 +88,4 @@ Example4_PyNN:
         stim:
             input_source: i_clamp
             population: pop0
-            percentage: 50.0
+            percentage: 50
diff --git a/examples/Example6.py b/examples/Example6.py
index a03dde3..8fbf52e 100644
--- a/examples/Example6.py
+++ b/examples/Example6.py
@@ -6,7 +6,6 @@
 
 
 def generate(ref="Example6_PyNN", add_inputs=True):
-
     ################################################################################
     ###   Build new network
 
@@ -69,7 +68,6 @@ def generate(ref="Example6_PyNN", add_inputs=True):
     layers = ["L23", "L4", "L5", "L6"]
 
     for l in layers:
-
         i = 3 - layers.index(l)
         r = RectangularRegion(
             id=l,
@@ -83,7 +81,6 @@ def generate(ref="Example6_PyNN", add_inputs=True):
         net.regions.append(r)
 
         for t in ["E", "I"]:
-
             try:
                 import opencortex.utils.color as occ
 
@@ -223,7 +220,6 @@ def generate(ref="Example6_PyNN", add_inputs=True):
 
 
 if __name__ == "__main__":
-
     if "-noinputs" in sys.argv:
         sim, net = generate("Example6_PyNN_noinputs", False)
     else:
diff --git a/examples/Example6_PyNN.json b/examples/Example6_PyNN.json
index 782817b..90719f4 100644
--- a/examples/Example6_PyNN.json
+++ b/examples/Example6_PyNN.json
@@ -1,6 +1,6 @@
 {
     "Example6_PyNN": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Another network for PyNN - work in progress...",
         "parameters": {
             "N_scaling": 0.005,
diff --git a/examples/Example6_PyNN.net.nml b/examples/Example6_PyNN.net.nml
index a3783c6..4fe9d45 100644
--- a/examples/Example6_PyNN.net.nml
+++ b/examples/Example6_PyNN.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example6_PyNN">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example6_PyNN
     Generation seed: 1234
     NeuroMLlite parameters: 
@@ -8,7 +8,7 @@
         input_weight = 0.1
         layer_height = 400
         width = 100</notes>
-    <IF_curr_exp id="CorticalCell" cm="0.25" i_offset="0." tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65." tau_m="10." tau_refrac="2." v_reset="-65." v_rest="-65." v_thresh="-50."/>
+    <IF_curr_exp id="CorticalCell" cm="0.25" i_offset="0.0" tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65.0" tau_m="10.0" tau_refrac="2.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0"/>
     <expCurrSynapse id="ampa" tau_syn="0.5"/>
     <expCurrSynapse id="gaba" tau_syn="0.5"/>
     <SpikeSourcePoisson id="InputCell" start="0.0ms" duration="10000000000.0ms" rate="150.0Hz"/>
@@ -2779,7009 +2779,7009 @@
             <connectionWD id="13" preCellId="../L6_I_input/13/InputCell" postCellId="../L6_I/13/CorticalCell" weight="0.1" delay="2ms"/>
         </projection>
         <projection id="proj_L23_E_L23_E" presynapticPopulation="L23_E" postsynapticPopulation="L23_E" synapse="ampa">
-            <connectionWD id="0" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/1/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="1" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/4/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="2" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/27/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="3" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/32/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="4" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/36/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="5" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/39/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="6" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/3/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="7" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/6/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="8" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/12/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="9" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/51/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="10" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/56/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="11" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/59/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="12" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/65/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="13" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/70/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="14" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/74/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="15" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/76/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="16" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/86/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="17" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/6/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="18" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/30/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="19" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/46/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="20" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/47/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="21" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/61/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="22" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/64/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="23" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/74/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="24" preCellId="../L23_E/2/CorticalCell" postCellId="../L23_E/93/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="25" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/10/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="26" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/26/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="27" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/27/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="28" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/29/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="29" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/30/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="30" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/34/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="31" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/37/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="32" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/42/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="33" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/52/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="34" preCellId="../L23_E/3/CorticalCell" postCellId="../L23_E/69/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="35" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/7/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="36" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/8/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="37" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/21/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="38" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/31/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="39" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/36/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="40" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/51/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="41" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/52/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="42" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/63/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="43" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/90/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="44" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/100/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="45" preCellId="../L23_E/4/CorticalCell" postCellId="../L23_E/101/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="46" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/13/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="47" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/48/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="48" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/62/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="49" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/72/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="50" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/79/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="51" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/81/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="52" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/82/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="53" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/84/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="54" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/87/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="55" preCellId="../L23_E/5/CorticalCell" postCellId="../L23_E/102/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="56" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/15/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="57" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/16/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="58" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/22/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="59" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/28/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="60" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/31/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="61" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/40/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="62" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/56/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="63" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/58/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="64" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/72/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="65" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/82/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="66" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/86/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="67" preCellId="../L23_E/6/CorticalCell" postCellId="../L23_E/92/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="68" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/7/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="69" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/19/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="70" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/22/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="71" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/27/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="72" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/45/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="73" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/84/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="74" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/85/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="75" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/94/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="76" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/95/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="77" preCellId="../L23_E/7/CorticalCell" postCellId="../L23_E/101/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="78" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/15/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="79" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/21/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="80" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/24/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="81" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/27/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="82" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/36/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="83" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/48/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="84" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/50/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="85" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/61/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="86" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/75/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="87" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/76/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="88" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/96/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="89" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/98/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="90" preCellId="../L23_E/8/CorticalCell" postCellId="../L23_E/99/CorticalCell" weight="1." delay="1ms"/>
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+            <connectionWD id="9" preCellId="../L6_I/4/CorticalCell" postCellId="../L6_I/9/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="10" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="11" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/10/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="12" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/11/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="13" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/12/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="14" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_I/2/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="15" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="16" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/4/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="17" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/8/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="18" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_I/8/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="19" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_I/13/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="20" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_I/4/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="21" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_I/7/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="22" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_I/13/CorticalCell" weight="-1.0" delay="1ms"/>
         </projection>
     </network>
 </neuroml>
diff --git a/examples/Example6_PyNN_noinputs.json b/examples/Example6_PyNN_noinputs.json
index b07d755..a141bf4 100644
--- a/examples/Example6_PyNN_noinputs.json
+++ b/examples/Example6_PyNN_noinputs.json
@@ -1,6 +1,6 @@
 {
     "Example6_PyNN_noinputs": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Another network for PyNN - work in progress...",
         "parameters": {
             "N_scaling": 0.005,
diff --git a/examples/Example6_PyNN_noinputs.net.nml b/examples/Example6_PyNN_noinputs.net.nml
index 5809fe1..acc00d0 100644
--- a/examples/Example6_PyNN_noinputs.net.nml
+++ b/examples/Example6_PyNN_noinputs.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example6_PyNN_noinputs">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example6_PyNN_noinputs
     Generation seed: 1234
     NeuroMLlite parameters: 
@@ -8,7 +8,7 @@
         input_weight = 0.1
         layer_height = 400
         width = 100</notes>
-    <IF_curr_exp id="CorticalCell" cm="0.25" i_offset="0." tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65." tau_m="10." tau_refrac="2." v_reset="-65." v_rest="-65." v_thresh="-50."/>
+    <IF_curr_exp id="CorticalCell" cm="0.25" i_offset="0.0" tau_syn_E="0.5" tau_syn_I="0.5" v_init="-65.0" tau_m="10.0" tau_refrac="2.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0"/>
     <expCurrSynapse id="ampa" tau_syn="0.5"/>
     <expCurrSynapse id="gaba" tau_syn="0.5"/>
     <network id="Example6_PyNN_noinputs">
@@ -1202,7096 +1202,7096 @@
             </instance>
         </population>
         <projection id="proj_L23_E_L23_E" presynapticPopulation="L23_E" postsynapticPopulation="L23_E" synapse="ampa">
-            <connectionWD id="0" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/3/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="1" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/7/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="2" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/23/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="3" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/33/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="4" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/63/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="5" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/85/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="6" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/93/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="7" preCellId="../L23_E/0/CorticalCell" postCellId="../L23_E/98/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="8" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/8/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="9" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/11/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="10" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/13/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="11" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/16/CorticalCell" weight="1." delay="1ms"/>
-            <connectionWD id="12" preCellId="../L23_E/1/CorticalCell" postCellId="../L23_E/22/CorticalCell" weight="1." delay="1ms"/>
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+            <connectionWD id="146" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_E/68/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="147" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_E/69/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="148" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/4/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="149" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/7/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="150" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/10/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="151" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/11/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="152" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/16/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="153" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/21/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="154" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/26/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="155" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/27/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="156" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/46/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="157" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/48/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="158" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/51/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="159" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/54/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="160" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/59/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="161" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/60/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="162" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/62/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="163" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/65/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="164" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/69/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="165" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_E/70/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="166" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/0/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="167" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/2/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="168" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/9/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="169" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/28/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="170" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/32/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="171" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/45/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="172" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/48/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="173" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/59/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="174" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/62/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="175" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/65/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="176" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_E/68/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="177" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/5/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="178" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/7/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="179" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/15/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="180" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/19/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="181" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/25/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="182" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/28/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="183" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/32/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="184" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/36/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="185" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/45/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="186" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/50/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="187" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/51/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="188" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/63/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="189" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/64/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="190" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_E/65/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="191" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="192" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/11/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="193" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/15/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="194" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/16/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="195" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/17/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="196" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/19/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="197" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/23/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="198" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/24/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="199" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/25/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="200" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/26/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="201" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/27/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="202" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/32/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="203" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/45/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="204" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/48/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="205" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/57/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="206" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/61/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="207" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/65/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="208" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/66/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="209" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_E/69/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="210" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/5/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="211" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/7/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="212" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/14/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="213" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/22/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="214" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/29/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="215" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/32/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="216" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/36/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="217" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/37/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="218" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/41/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="219" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/49/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="220" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/50/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="221" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/52/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="222" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/54/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="223" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/55/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="224" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/59/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="225" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/61/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="226" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/64/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="227" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/68/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="228" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_E/69/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="229" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/3/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="230" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/4/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="231" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/5/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="232" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/27/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="233" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/29/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="234" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/37/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="235" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/42/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="236" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/45/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="237" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/49/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="238" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/53/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="239" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/54/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="240" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/61/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="241" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/62/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="242" preCellId="../L6_I/13/CorticalCell" postCellId="../L6_E/64/CorticalCell" weight="-1.0" delay="1ms"/>
         </projection>
         <projection id="proj_L6_I_L6_I" presynapticPopulation="L6_I" postsynapticPopulation="L6_I" synapse="gaba">
-            <connectionWD id="0" preCellId="../L6_I/0/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="1" preCellId="../L6_I/0/CorticalCell" postCellId="../L6_I/6/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="2" preCellId="../L6_I/1/CorticalCell" postCellId="../L6_I/0/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="3" preCellId="../L6_I/1/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="4" preCellId="../L6_I/1/CorticalCell" postCellId="../L6_I/11/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="5" preCellId="../L6_I/3/CorticalCell" postCellId="../L6_I/5/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="6" preCellId="../L6_I/3/CorticalCell" postCellId="../L6_I/8/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="7" preCellId="../L6_I/4/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="8" preCellId="../L6_I/5/CorticalCell" postCellId="../L6_I/2/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="9" preCellId="../L6_I/5/CorticalCell" postCellId="../L6_I/11/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="10" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/6/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="11" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/12/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="12" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="13" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_I/2/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="14" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_I/6/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="15" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/5/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="16" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/7/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="17" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/9/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="18" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/12/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="19" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_I/0/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="20" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_I/7/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="21" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_I/11/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="22" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="23" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_I/9/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="24" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_I/5/CorticalCell" weight="-1." delay="1ms"/>
-            <connectionWD id="25" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_I/8/CorticalCell" weight="-1." delay="1ms"/>
+            <connectionWD id="0" preCellId="../L6_I/0/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="1" preCellId="../L6_I/0/CorticalCell" postCellId="../L6_I/6/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="2" preCellId="../L6_I/1/CorticalCell" postCellId="../L6_I/0/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="3" preCellId="../L6_I/1/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="4" preCellId="../L6_I/1/CorticalCell" postCellId="../L6_I/11/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="5" preCellId="../L6_I/3/CorticalCell" postCellId="../L6_I/5/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="6" preCellId="../L6_I/3/CorticalCell" postCellId="../L6_I/8/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="7" preCellId="../L6_I/4/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="8" preCellId="../L6_I/5/CorticalCell" postCellId="../L6_I/2/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="9" preCellId="../L6_I/5/CorticalCell" postCellId="../L6_I/11/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="10" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/6/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="11" preCellId="../L6_I/6/CorticalCell" postCellId="../L6_I/12/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="12" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="13" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_I/2/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="14" preCellId="../L6_I/7/CorticalCell" postCellId="../L6_I/6/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="15" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/5/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="16" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/7/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="17" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/9/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="18" preCellId="../L6_I/8/CorticalCell" postCellId="../L6_I/12/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="19" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_I/0/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="20" preCellId="../L6_I/9/CorticalCell" postCellId="../L6_I/7/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="21" preCellId="../L6_I/10/CorticalCell" postCellId="../L6_I/11/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="22" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_I/1/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="23" preCellId="../L6_I/11/CorticalCell" postCellId="../L6_I/9/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="24" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_I/5/CorticalCell" weight="-1.0" delay="1ms"/>
+            <connectionWD id="25" preCellId="../L6_I/12/CorticalCell" postCellId="../L6_I/8/CorticalCell" weight="-1.0" delay="1ms"/>
         </projection>
     </network>
 </neuroml>
diff --git a/examples/Example7.py b/examples/Example7.py
index 8914e69..0a080ad 100644
--- a/examples/Example7.py
+++ b/examples/Example7.py
@@ -14,7 +14,6 @@
 
 
 def generate():
-
     dt = 0.025
     simtime = 1000
 
@@ -228,9 +227,7 @@ def generate():
 
 
 if __name__ == "__main__":
-
     if "-sweep" in sys.argv:
-
         from neuromllite.sweep.ParameterSweep import *
 
         sim, net = generate()
@@ -298,7 +295,6 @@ def generate():
         plt.show()
 
     if "-sweep2" in sys.argv:
-
         sim, net = generate()
         sim.record_traces = {}
 
@@ -372,7 +368,6 @@ def generate():
         plt.show()
 
     else:
-
         sim, net = generate()
 
         ################################################################################
diff --git a/examples/Example7_Brunel2000.json b/examples/Example7_Brunel2000.json
index b307816..1876d95 100644
--- a/examples/Example7_Brunel2000.json
+++ b/examples/Example7_Brunel2000.json
@@ -1,6 +1,6 @@
 {
     "Example7_Brunel2000": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 7: based on network of Brunel 2000",
         "parameters": {
             "g": 4,
diff --git a/examples/Example7_Brunel2000.net.nml b/examples/Example7_Brunel2000.net.nml
index a2e3f6a..767a913 100644
--- a/examples/Example7_Brunel2000.net.nml
+++ b/examples/Example7_Brunel2000.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="Example7_Brunel2000">
-    <notes>Generated by NeuroMLlite v0.5.3
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Example7_Brunel2000
     Generation seed: 1234
     NeuroMLlite parameters: 
@@ -14,7 +14,7 @@
         tauRef = 2.0
         tauSyn = 0.1
         theta = 20.0</notes>
-    <IF_curr_alpha id="ifcell" cm="0.001" i_offset="0." tau_syn_E="0.1" tau_syn_I="0.1" v_init="0." tau_m="20." tau_refrac="2." v_reset="0." v_rest="0." v_thresh="20."/>
+    <IF_curr_alpha id="ifcell" cm="0.001" i_offset="0.0" tau_syn_E="0.1" tau_syn_I="0.1" v_init="0.0" tau_m="20.0" tau_refrac="2.0" v_reset="0.0" v_rest="0.0" v_thresh="20.0"/>
     <alphaCurrSynapse id="ampa" tau_syn="0.1"/>
     <alphaCurrSynapse id="gaba" tau_syn="0.1"/>
     <SpikeSourcePoisson id="poisson_input" start="0.0ms" duration="1000000000.0ms" rate="10000.0Hz"/>
diff --git a/examples/Example8.py b/examples/Example8.py
index 2731db3..504f846 100644
--- a/examples/Example8.py
+++ b/examples/Example8.py
@@ -9,7 +9,7 @@
 net.notes = "Example 8: general testing..."
 
 net.seed = 7890
-net.temperature = 32.0
+net.temperature = 32
 
 net.parameters = {"N": 10, "fractionE": 0.8, "weightInput": 1}
 
diff --git a/examples/Example8_Extension.json b/examples/Example8_Extension.json
index 38eea78..ca00411 100644
--- a/examples/Example8_Extension.json
+++ b/examples/Example8_Extension.json
@@ -1,6 +1,6 @@
 {
     "Example8_Extension": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 8: general testing...",
         "parameters": {
             "N": 10,
@@ -57,7 +57,7 @@
             "stim": {
                 "input_source": "poissonFiringSyn",
                 "population": "Epop",
-                "percentage": 50.0,
+                "percentage": 50,
                 "weight": "weightInput"
             }
         },
diff --git a/examples/Example9_HindmarshRose.json b/examples/Example9_HindmarshRose.json
index f63356f..7792ec6 100644
--- a/examples/Example9_HindmarshRose.json
+++ b/examples/Example9_HindmarshRose.json
@@ -1,6 +1,6 @@
 {
     "Example9_HindmarshRose": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 9: HindmarshRose",
         "parameters": {
             "N": 1,
diff --git a/examples/LEMS_SimExample3.xml b/examples/LEMS_SimExample3.xml
index 8f64f8c..c683160 100644
--- a/examples/LEMS_SimExample3.xml
+++ b/examples/LEMS_SimExample3.xml
@@ -2,7 +2,7 @@
     
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.6 (libNeuroML v0.4.2)
+        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
 
      -->
     
diff --git a/examples/LEMS_SimExample4.xml b/examples/LEMS_SimExample4.xml
index 3de6589..449619e 100644
--- a/examples/LEMS_SimExample4.xml
+++ b/examples/LEMS_SimExample4.xml
@@ -2,7 +2,7 @@
     
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.6 (libNeuroML v0.4.2)
+        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
 
      -->
     
diff --git a/examples/SimExample10.json b/examples/SimExample10.json
index c7c4731..3326ea9 100644
--- a/examples/SimExample10.json
+++ b/examples/SimExample10.json
@@ -1,6 +1,6 @@
 {
     "SimExample10": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example10_Lorenz.json",
         "duration": 10000.0,
         "dt": 1.0,
diff --git a/examples/SimExample11.json b/examples/SimExample11.json
index 93717d6..e816096 100644
--- a/examples/SimExample11.json
+++ b/examples/SimExample11.json
@@ -1,6 +1,6 @@
 {
     "SimExample11": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example11_Synapses.json",
         "duration": 1000.0,
         "dt": 0.01,
diff --git a/examples/SimExample12_MultiComp.json b/examples/SimExample12_MultiComp.json
index a627bcb..7833778 100644
--- a/examples/SimExample12_MultiComp.json
+++ b/examples/SimExample12_MultiComp.json
@@ -1,6 +1,6 @@
 {
     "SimExample12_MultiComp": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example12_MultiComp.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample3.json b/examples/SimExample3.json
index cf8b948..30e11d9 100644
--- a/examples/SimExample3.json
+++ b/examples/SimExample3.json
@@ -1,6 +1,6 @@
 {
     "SimExample3": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example3_Network.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample4.json b/examples/SimExample4.json
index 0692a20..309083d 100644
--- a/examples/SimExample4.json
+++ b/examples/SimExample4.json
@@ -1,6 +1,6 @@
 {
     "SimExample4": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example4_PyNN.json",
         "duration": 1000.0,
         "dt": 0.01,
diff --git a/examples/SimExample4.yaml b/examples/SimExample4.yaml
index d142ce5..875fcf9 100644
--- a/examples/SimExample4.yaml
+++ b/examples/SimExample4.yaml
@@ -1,5 +1,5 @@
 SimExample4:
-    version: NeuroMLlite v0.5.3
+    version: NeuroMLlite v0.5.7
     network: Example4_PyNN.yaml
     duration: 1000.0
     dt: 0.01
diff --git a/examples/SimExample6_PyNN.json b/examples/SimExample6_PyNN.json
index 764dd2f..a0686d6 100644
--- a/examples/SimExample6_PyNN.json
+++ b/examples/SimExample6_PyNN.json
@@ -1,6 +1,6 @@
 {
     "SimExample6_PyNN": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example6_PyNN.json",
         "duration": 100.0,
         "dt": 0.025,
diff --git a/examples/SimExample7.json b/examples/SimExample7.json
index a4ed679..b827ae4 100644
--- a/examples/SimExample7.json
+++ b/examples/SimExample7.json
@@ -1,6 +1,6 @@
 {
     "SimExample7": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example7_Brunel2000.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample8.json b/examples/SimExample8.json
index d317ad4..e7924ab 100644
--- a/examples/SimExample8.json
+++ b/examples/SimExample8.json
@@ -1,6 +1,6 @@
 {
     "SimExample8": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example8_Extension.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample9.json b/examples/SimExample9.json
index 8d355b9..31eefa7 100644
--- a/examples/SimExample9.json
+++ b/examples/SimExample9.json
@@ -1,6 +1,6 @@
 {
     "SimExample9": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Example9_HindmarshRose.json",
         "duration": 1000000.0,
         "dt": 25.0,
diff --git a/examples/arbor/ArborExample.json b/examples/arbor/ArborExample.json
index f8dc49d..3b7acec 100644
--- a/examples/arbor/ArborExample.json
+++ b/examples/arbor/ArborExample.json
@@ -1,6 +1,6 @@
 {
     "ArborExample": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example for testing Arbor",
         "parameters": {
             "v_init": -50,
diff --git a/examples/arbor/ArborExample.py b/examples/arbor/ArborExample.py
index 5167798..03df74d 100644
--- a/examples/arbor/ArborExample.py
+++ b/examples/arbor/ArborExample.py
@@ -103,7 +103,7 @@
 
 net.projections[0].random_connectivity = RandomConnectivity(probability=0.5)
 
-'''
+"""
 net.synapses.append(Synapse(id='gabaSyn',
                             pynn_receptor_type='inhibitory',
                             pynn_synapse_type='cond_alpha',
@@ -116,10 +116,10 @@
                                   synapse='gabaSyn',
                                   delay=2,
                                   weight=0.01))
-net.projections[1].random_connectivity=RandomConnectivity(probability=1)'''
+net.projections[1].random_connectivity=RandomConnectivity(probability=1)"""
 
 net.inputs.append(
-    Input(id="stim", input_source=input_source.id, population=p0.id, cell_ids=[1,2])
+    Input(id="stim", input_source=input_source.id, population=p0.id, cell_ids=[1, 2])
 )
 
 print(net.to_json())
@@ -141,7 +141,7 @@
 
 sim.to_json_file()
 sim.network = new_file_yaml
-sim.to_yaml_file('%s.yaml'%sim.id)
+sim.to_yaml_file("%s.yaml" % sim.id)
 
 
 ################################################################################
diff --git a/examples/arbor/ArborExample.yaml b/examples/arbor/ArborExample.yaml
index 9920bbb..f3d8586 100644
--- a/examples/arbor/ArborExample.yaml
+++ b/examples/arbor/ArborExample.yaml
@@ -1,5 +1,5 @@
 ArborExample:
-    version: NeuroMLlite v0.5.3
+    version: NeuroMLlite v0.5.7
     notes: Example for testing Arbor
     parameters:
         v_init: -50
diff --git a/examples/arbor/SimArborExample.json b/examples/arbor/SimArborExample.json
index 3abbb01..ca27e3b 100644
--- a/examples/arbor/SimArborExample.json
+++ b/examples/arbor/SimArborExample.json
@@ -1,6 +1,6 @@
 {
     "SimArborExample": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "ArborExample.json",
         "duration": 100.0,
         "dt": 0.01,
diff --git a/examples/arbor/SimArborExample.yaml b/examples/arbor/SimArborExample.yaml
index 5fdeeb4..6951a5b 100644
--- a/examples/arbor/SimArborExample.yaml
+++ b/examples/arbor/SimArborExample.yaml
@@ -1,5 +1,5 @@
 SimArborExample:
-    version: NeuroMLlite v0.5.3
+    version: NeuroMLlite v0.5.7
     network: ArborExample.yaml
     duration: 100.0
     dt: 0.01
diff --git a/examples/clean.sh b/examples/clean.sh
index 0d3afdd..17ca103 100755
--- a/examples/clean.sh
+++ b/examples/clean.sh
@@ -1,4 +1,4 @@
 mkdir ~/temp/dump
-mv -v report*txt *.pdf *.dat *.spikes *.gdf *.pkl *.hoc *.mod  *~ *.log *nrn.py NET_*nml *brian.py *brian2.py *nest.py *pynn.py *definition.py  *netpyne.py  *moose.py  *.nestml *.png *.ini *.svg *.pov *.gv *cell.json *synapse.json *main.json tmp* *csv ~/temp/dump
-rm -rf x86_64 i386 umac *.pyc *.c *.so *~ .*~
+mv -v report*txt *.pdf *.dat *.spikes *.gdf *.pkl *.hoc *.mod  *~ *.log *nrn.py NET_*nml *brian.py *brian2.py *nest.py *pynn.py *definition.py  *netpyne.py  *moose.py  *.nestml *.png *.ini *.svg *.pov *.gv *cell.json *synapse.json *main.json tmp* *csv *mdf.json *mdf.yaml *.mdf *eden.py ~/temp/dump
+rm -rf x86_64 i386 umac arm64  *.pyc *.c *.so  __pycache__ *~ .*~
 rm -rf ./test_files/test_inputs/x86_64 ./test_files/x86_64 ./spikeratetest/x86_64
diff --git a/examples/sonatatest/analyze_output.py b/examples/sonatatest/analyze_output.py
index 9e26ccf..f48a33c 100644
--- a/examples/sonatatest/analyze_output.py
+++ b/examples/sonatatest/analyze_output.py
@@ -5,7 +5,6 @@
 from analyze_output_utils import plot_data
 
 if __name__ == "__main__":
-
     plot_data(
         "output/membrane_potential.h5", "mV", "Membrane Potential", show_already=True
     )
diff --git a/examples/sonatatest/analyze_output_utils.py b/examples/sonatatest/analyze_output_utils.py
index b9c8fad..fe0b264 100644
--- a/examples/sonatatest/analyze_output_utils.py
+++ b/examples/sonatatest/analyze_output_utils.py
@@ -16,7 +16,6 @@ def plot_data(reports_file, y_axis, title, show_already=True, max_num_traces=Non
             pop_prefixes = {pop: "/report/%s/" % pop}
 
     for pop in pop_prefixes:
-
         gids = np.array(cellvar_h5["%smapping/gids" % pop_prefixes[pop]])
 
         soma_locs = np.array(
diff --git a/examples/sonatatest/run_bmtk.py b/examples/sonatatest/run_bmtk.py
index 0964873..193efbc 100644
--- a/examples/sonatatest/run_bmtk.py
+++ b/examples/sonatatest/run_bmtk.py
@@ -4,7 +4,6 @@
 
 
 def run(config_file, simulator):
-
     if simulator == "NEURON":
         from bmtk.simulator import bionet
 
@@ -25,5 +24,4 @@ def run(config_file, simulator):
 
 
 if __name__ == "__main__":
-
     run("config.json", "NEST")
diff --git a/examples/spikeratetest/SimSpikers.json b/examples/spikeratetest/SimSpikers.json
index 5229831..65b72b0 100644
--- a/examples/spikeratetest/SimSpikers.json
+++ b/examples/spikeratetest/SimSpikers.json
@@ -1,6 +1,6 @@
 {
     "SimSpikers": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Spikers.json",
         "duration": 10000.0,
         "dt": 0.025,
diff --git a/examples/spikeratetest/Spikers.json b/examples/spikeratetest/Spikers.json
index 8e24bd0..9ce401e 100644
--- a/examples/spikeratetest/Spikers.json
+++ b/examples/spikeratetest/Spikers.json
@@ -1,6 +1,6 @@
 {
     "Spikers": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example with spiking entities..",
         "parameters": {
             "N": 10,
@@ -85,18 +85,18 @@
             "stim0": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop0",
-                "percentage": 50.0,
+                "percentage": 50,
                 "weight": "weightInput"
             },
             "stim1": {
                 "input_source": "iclamp1",
                 "population": "pop1",
-                "percentage": 100.0
+                "percentage": 100
             },
             "stim2": {
                 "input_source": "iclamp1",
                 "population": "pop2",
-                "percentage": 50.0
+                "percentage": 50
             }
         }
     }
diff --git a/examples/test_files/.test.ex7.nmllite.pynnnest.omt b/examples/test_files/.test.ex7.nmllite.pynnnest.omt
index 21eccf3..91f7084 100644
--- a/examples/test_files/.test.ex7.nmllite.pynnnest.omt
+++ b/examples/test_files/.test.ex7.nmllite.pynnnest.omt
@@ -12,7 +12,7 @@ experiments:
           path: ../SimExample7.expoisson.spikes
           format: ID_TIME
           ids: '*'
-        tolerance:  0.00020894387195494345
+        tolerance:  0.0019478218091029704
         
   spike_rate_inh_in:
     observables:
@@ -21,7 +21,7 @@ experiments:
           path: ../SimExample7.inpoisson.spikes
           format: ID_TIME
           ids: '*'
-        tolerance: 0.0025532645162897097
+        tolerance: 0.004952617763644412
         
   spike_rate_e:
     observables:
@@ -30,7 +30,7 @@ experiments:
           path: ../SimExample7.Epop.spikes
           format: ID_TIME
           ids: '*'
-        tolerance: 0.00
+        tolerance: 0.02167593418697938
 
   spike_rate_i:
     observables:
@@ -39,4 +39,4 @@ experiments:
           path: ../SimExample7.Ipop.spikes
           format: ID_TIME
           ids: '*'
-        tolerance: 0.00
+        tolerance: 0.017234417194577856
diff --git a/examples/test_files/.test.validate.omt b/examples/test_files/.test.validate.omt
index 3f0f9e9..14ba677 100644
--- a/examples/test_files/.test.validate.omt
+++ b/examples/test_files/.test.validate.omt
@@ -1,5 +1,5 @@
 # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
 
 # This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml
-target: "*.nml"
+target: "../Example2_TestNetwork.net.nml ../Example3_Network.net.nml ../Example4_PyNN.net.nml ../Example6_PyNN.net.nml ../Example7_Brunel2000.net.nml ../Example12_MultiComp.net.nml *.nml"
 engine: jNeuroML_validate
diff --git a/neuromllite/ArborHandler.py b/neuromllite/ArborHandler.py
index 2e0bd61..22792cb 100644
--- a/neuromllite/ArborHandler.py
+++ b/neuromllite/ArborHandler.py
@@ -16,7 +16,6 @@
 
 
 class ArborHandler(DefaultNetworkHandler):
-
     pops_vs_components = {}
     proj_weights = {}
     proj_delays = {}
@@ -42,7 +41,6 @@ def handle_document_start(self, id, notes):
         print_v("Document: %s" % id)
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         if temperature:
             print_v("  Temperature: " + temperature)
@@ -52,7 +50,6 @@ def handle_network(self, network_id, notes, temperature=None):
     def handle_population(
         self, population_id, component, size=-1, component_obj=None, properties={}
     ):
-
         sizeInfo = " as yet unspecified size"
         if size >= 0:
             sizeInfo = ", size: " + str(size) + " cells"
@@ -107,7 +104,6 @@ def handle_projection(
         synapse_obj=None,
         pre_synapse_obj=None,
     ):
-
         synInfo = ""
         if synapse_obj:
             synInfo += " (syn: %s)" % synapse_obj.__class__.__name__
@@ -164,7 +160,6 @@ def handle_connection(
         delay=0,
         weight=1,
     ):
-
         self.print_connection_information(
             projName, id, prePop, postPop, synapseType, preCellId, postCellId, weight
         )
@@ -191,7 +186,6 @@ def handle_connection(
     def finalise_projection(
         self, projName, prePop, postPop, synapse=None, type="projection"
     ):
-
         print_v(
             "Projection finalising: "
             + projName
@@ -208,7 +202,6 @@ def finalise_projection(
     def handle_input_list(
         self, inputListId, population_id, component, size, input_comp_obj=None
     ):
-
         self.print_input_information(inputListId, population_id, component, size)
         if input_comp_obj:
             print("Input comp: %s" % input_comp_obj)
@@ -228,7 +221,6 @@ def handle_input_list(
     def handle_single_input(
         self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
     ):
-
         population_id, component, input_comp_obj = self.input_info[inputListId]
 
         print_v(
@@ -261,8 +253,6 @@ def finalise_document(self):
         )
 
 
-
-
 # Create a NeuroML recipe
 class NeuroML_Arbor_Recipe(arbor.recipe):
     def __init__(
@@ -289,11 +279,8 @@ def __init__(
         self.input_info = input_info
         self.input_lists = input_lists
 
-
     def create_arbor_cell(self, cell, gid, pop_id, index):
-
         if cell.arbor_cell == "cable_cell":
-
             default_tree = arbor.segment_tree()
             radius = (
                 evaluate(cell.parameters["radius"], self.nl_network.parameters)
@@ -323,21 +310,26 @@ def create_arbor_cell(self, cell, gid, pop_id, index):
 
             decor.paint('"soma"', arbor.density(cell.parameters["mechanism"]))
 
-            decor.place('"center"', arbor.spike_detector(0), "detector")
+            decor.place('"center"', arbor.threshold_detector(0), "detector")
 
             for ip in self.input_info:
                 if self.input_info[ip][0] == pop_id:
-                    print_v("Stim: %s (%s) being placed on %s" % (ip,self.input_info[ip],pop_id))
+                    print_v(
+                        "Stim: %s (%s) being placed on %s"
+                        % (ip, self.input_info[ip], pop_id)
+                    )
                     for il in self.input_lists[ip]:
                         cellId, segId, fract, weight = il
                         if cellId == index:
-                            if self.input_info[ip][1] == 'i_clamp': # TODO: remove hardcoding of this...
+                            if (
+                                self.input_info[ip][1] == "i_clamp"
+                            ):  # TODO: remove hardcoding of this...
                                 ic = arbor.iclamp(
                                     self.nl_network.parameters["input_del"],
                                     self.nl_network.parameters["input_dur"],
                                     self.nl_network.parameters["input_amp"],
                                 )
-                                print_v("Stim: %s on %s" % (ic,gid))
+                                print_v("Stim: %s on %s" % (ic, gid))
                                 decor.place('"center"', ic, "iclamp")
 
             # (2) Mark location for synapse at the midpoint of branch 1 (the first dendrite).
@@ -345,7 +337,7 @@ def create_arbor_cell(self, cell, gid, pop_id, index):
             # (4) Attach a single synapse.
             decor.place('"synapse_site"', arbor.synapse("expsyn"), "syn")
 
-            default_cell = arbor.cable_cell(default_tree, labels, decor)
+            default_cell = arbor.cable_cell(default_tree, labels=labels, decor=decor)
 
             print_v("Created a new cell for gid %i: %s" % (gid, cell))
             print_v("%s" % (default_cell))
@@ -384,7 +376,6 @@ def cell_description(self, gid):
         )
         return a_cell
 
-
     # The kind method returns the type of cell with gid.
     # Note: this must agree with the type returned by cell_description.
     def cell_kind(self, gid):
@@ -452,10 +443,10 @@ def num_sources(self, gid):
     # (9) Attach a generator to the first cell in the ring.
     def event_generators(self, gid):
         egs = []
-        '''
+        """
         if gid == 0:
             sched = arbor.explicit_schedule([1])
-            egs = [arbor.event_generator("syn", 0.1, sched)]'''
+            egs = [arbor.event_generator("syn", 0.1, sched)]"""
 
         print_v("Getting event_generators for %s: %s" % (gid, egs))
         return egs
diff --git a/neuromllite/BBPConnectomeReader.py b/neuromllite/BBPConnectomeReader.py
index ffa97b4..8e2478c 100644
--- a/neuromllite/BBPConnectomeReader.py
+++ b/neuromllite/BBPConnectomeReader.py
@@ -8,11 +8,9 @@
 
 
 class BBPConnectomeReader(NetworkReaderX):
-
     component_objects = {}  # Store cell ids vs objects, e.g. NeuroML2 based object
 
     def __init__(self, **parameters):
-
         print_v("Creating BBPConnectomeReader with %s..." % parameters)
         self.parameters = parameters
         self.current_population = None
@@ -20,7 +18,6 @@ def __init__(self, **parameters):
         self.post_pop = None
 
     def parse(self, handler):
-
         filename = os.path.abspath(self.parameters["filename"])
         id = filename.split("/")[-1].split(".")[0]
 
@@ -87,7 +84,6 @@ def parse_dataset(self, d):
 
         # Population
         if self.current_population and d.name == "locations":
-
             perc_cells = (
                 self.parameters["percentage_cells_per_pop"]
                 if "percentage_cells_per_pop" in self.parameters
@@ -180,7 +176,6 @@ def parse_dataset(self, d):
                     "   There are %i cells in: %s" % (size, self.current_population)
                 )
                 for i in range(0, d.shape[0]):
-
                     if i < size:
                         row = d[i, :]
                         x = row[0]
@@ -198,7 +193,6 @@ def parse_dataset(self, d):
 
         # Projection
         elif self.pre_pop != None and self.post_pop != None:
-
             proj_id = "Proj__%s__%s" % (self.pre_pop, self.post_pop)
             synapse = "gaba"
             if (
@@ -263,7 +257,6 @@ def parse_dataset(self, d):
 
 
 if __name__ == "__main__":
-
     filename = "test_files/cons_locs_pathways_mc0_Column.h5"
 
     percentage_cells_per_pop = 1
diff --git a/neuromllite/BindsNETHandler.py b/neuromllite/BindsNETHandler.py
index 8f10a0e..6e9aee5 100644
--- a/neuromllite/BindsNETHandler.py
+++ b/neuromllite/BindsNETHandler.py
@@ -16,7 +16,6 @@
 
 
 class BindsNETHandler(DefaultNetworkHandler):
-
     pops_vs_components = {}
     pops_vs_bn_layers = {}
 
@@ -46,7 +45,6 @@ def handle_document_start(self, id, notes):
         print_v("Document: %s" % id)
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         if temperature:
             print_v("  Temperature: " + temperature)
@@ -56,7 +54,6 @@ def handle_network(self, network_id, notes, temperature=None):
     def handle_population(
         self, population_id, component, size=-1, component_obj=None, properties={}
     ):
-
         sizeInfo = " as yet unspecified size"
         if size >= 0:
             sizeInfo = ", size: " + str(size) + " cells"
@@ -103,7 +100,6 @@ def handle_projection(
         synapse_obj=None,
         pre_synapse_obj=None,
     ):
-
         synInfo = ""
         if synapse_obj:
             synInfo += " (syn: %s)" % synapse_obj.__class__.__name__
@@ -160,7 +156,6 @@ def handle_connection(
         delay=0,
         weight=1,
     ):
-
         self.print_connection_information(
             projName, id, prePop, postPop, synapseType, preCellId, postCellId, weight
         )
@@ -187,7 +182,6 @@ def handle_connection(
     def finalise_projection(
         self, projName, prePop, postPop, synapse=None, type="projection"
     ):
-
         print_v(
             "Projection finalising: "
             + projName
@@ -204,7 +198,6 @@ def finalise_projection(
     def handle_input_list(
         self, inputListId, population_id, component, size, input_comp_obj=None
     ):
-
         self.print_input_information(inputListId, population_id, component, size)
         if input_comp_obj:
             print("Input comp: %s" % input_comp_obj)
@@ -223,7 +216,6 @@ def handle_input_list(
     def handle_single_input(
         self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
     ):
-
         population_id, component = self.input_info[inputListId]
 
         print_v(
diff --git a/neuromllite/ConnectivityHandler.py b/neuromllite/ConnectivityHandler.py
index 81ba023..a33bc76 100644
--- a/neuromllite/ConnectivityHandler.py
+++ b/neuromllite/ConnectivityHandler.py
@@ -10,7 +10,6 @@
 
 
 class ConnectivityHandler(DefaultNetworkHandler):
-
     CUTOFF_INH_SYN_MV = -50  # erev below -50mV => inhibitory, above => excitatory
 
     include_ext_inputs = False
@@ -44,11 +43,9 @@ class ConnectivityHandler(DefaultNetworkHandler):
     input_comp_obj_ils = {}
 
     def handle_document_start(self, id, notes):
-
         print_v("Document: %s" % id)
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         self.network_id = network_id
 
@@ -88,7 +85,6 @@ def get_size_post_pop(self, projName):
         return self.pop_sizes[self.proj_post_pops[projName]]
 
     def get_reversal_potential_mV(self, synapse_obj):
-
         if hasattr(synapse_obj, "erev"):
             return convert_to_units(synapse_obj.erev, "mV")
 
@@ -99,7 +95,6 @@ def get_reversal_potential_mV(self, synapse_obj):
             return None
 
     def _get_gbase_nS(self, projName, return_orig_string_also=False):
-
         gbase_nS = None
         gbase = "???"
         # print('Getting gbase for %s'%projName)
@@ -123,7 +118,6 @@ def _get_gbase_nS(self, projName, return_orig_string_also=False):
         return gbase_nS
 
     def _scale_individual_weight(self, weight, projName):
-
         orig_weight = weight
 
         if self.scale_by_post_pop_cond:
@@ -138,7 +132,6 @@ def _scale_individual_weight(self, weight, projName):
         return weight
 
     def _scale_population_weight(self, weight, projName):
-
         orig_weight = weight
         if self.scale_by_post_pop_size:
             weight /= self.get_size_post_pop(projName)
@@ -155,7 +148,6 @@ def _scale_population_weight(self, weight, projName):
         return weight
 
     def handle_location(self, id, population_id, component, x, y, z):
-
         pass
 
     def handle_connection(
@@ -174,7 +166,6 @@ def handle_connection(
         delay=0,
         weight=1.0,
     ):
-
         # print_v(" - Connection for %s, cell %i -> %i, w: %s"%(projName, preCellId, postCellId, weight))
         self.proj_conns[projName] += 1
         self.proj_tot_weight[projName] += weight
@@ -194,7 +185,6 @@ def handle_connection(
     def finalise_projection(
         self, projName, prePop, postPop, synapse=None, type="projection"
     ):
-
         # weight = self.proj_tot_weight[projName]
         # self.max_weight = max(self.max_weight, weight)
         # self.min_weight = min(self.min_weight, weight)
diff --git a/neuromllite/DefaultNetworkHandler.py b/neuromllite/DefaultNetworkHandler.py
index 2e64ca8..6e27813 100644
--- a/neuromllite/DefaultNetworkHandler.py
+++ b/neuromllite/DefaultNetworkHandler.py
@@ -21,7 +21,6 @@
 
 
 class DefaultNetworkHandler:
-
     #
     #  Internal info method, can be reused in overriding classes for debugging
     #
@@ -82,7 +81,6 @@ def print_input_information(self, inputName, population_id, component, size=-1):
     #  Should be overridden
     #
     def handle_document_start(self, id, notes):
-
         print_v("Document: %s started..." % id)
         if notes:
             print_v("  Notes: " + notes)
@@ -91,14 +89,12 @@ def handle_document_start(self, id, notes):
     #  Should be overridden
     #
     def finalise_document(self):
-
         print_v("Document ended...")
 
     #
     #  Should be overridden to create network
     #
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         if temperature:
             print_v("  Temperature: " + temperature)
@@ -139,7 +135,6 @@ def handle_location(self, id, population_id, component, x, y, z):
         self.print_location_information(id, population_id, component, x, y, z)
 
     def finalise_population(self, population_id):
-
         pass
 
     #
@@ -157,7 +152,6 @@ def handle_projection(
         synapse_obj=None,
         pre_synapse_obj=None,
     ):
-
         synInfo = ""
         if synapse_obj:
             synInfo += " (syn: %s)" % synapse_obj.__class__.__name__
@@ -198,7 +192,6 @@ def handle_connection(
         delay=0,
         weight=1,
     ):
-
         self.print_connection_information(
             projName, id, prePop, postPop, synapseType, preCellId, postCellId, weight
         )
@@ -223,7 +216,6 @@ def handle_connection(
     def finalise_projection(
         self, projName, prePop, postPop, synapse=None, type="projection"
     ):
-
         print_v(
             "Projection: "
             + projName
@@ -240,7 +232,6 @@ def finalise_projection(
     def handle_input_list(
         self, inputListId, population_id, component, size, input_comp_obj=None
     ):
-
         self.print_input_information(inputListId, population_id, component, size)
 
         if size < 0:
@@ -255,7 +246,6 @@ def handle_input_list(
     def handle_single_input(
         self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
     ):
-
         print_v(
             "  Input: %s[%s], cellId: %i, seg: %i, fract: %f, weight: %f"
             % (inputListId, id, cellId, segId, fract, weight)
diff --git a/neuromllite/GraphVizHandler.py b/neuromllite/GraphVizHandler.py
index 0b9f9ad..118fc06 100644
--- a/neuromllite/GraphVizHandler.py
+++ b/neuromllite/GraphVizHandler.py
@@ -27,7 +27,6 @@
 
 
 class GraphVizHandler(ConnectivityHandler):
-
     DEFAULT_POP_SHAPE = "ellipse"
     EXC_POP_SHAPE = "ellipse"
     INH_POP_SHAPE = "ellipse"
@@ -54,7 +53,6 @@ def __init__(
         output_format="png",
         view_on_render=True,
     ):
-
         self.nl_network = nl_network
         self.level = level
         self.engine = engine
@@ -106,7 +104,6 @@ def print_settings(self):
         print_v("**************************************")
 
     def get_weight_fraction_and_line(self, w, max_w, min_w):
-
         if max_w == min_w:
             return 1.0, 1.0
         # fractional weight, 0->1
@@ -122,7 +119,6 @@ def get_weight_fraction_and_line(self, w, max_w, min_w):
         return fweight, lweight
 
     def finalise_document(self):
-
         max_abs_weight = {}
         min_abs_weight = {}
 
@@ -137,7 +133,6 @@ def finalise_document(self):
             min_abs_weight[t] = 1e100
 
         if self.is_cell_level() and self.level <= -1:
-
             for projName in self.proj_weights:
                 # ws = self.proj_individual_weights[projName]
                 ws = self.proj_individual_scaled_weights[projName]
@@ -151,7 +146,6 @@ def finalise_document(self):
                     )
 
             for projName in self.proj_weights:
-
                 pre_pop = self.proj_pre_pops[projName]
                 post_pop = self.proj_post_pops[projName]
                 proj_type = self.proj_types[projName]
@@ -209,7 +203,6 @@ def finalise_document(self):
                             ][pre_i][post_i]
 
                             if w != 0:
-
                                 weight_used = w
 
                                 cond_scale = None
@@ -279,17 +272,14 @@ def finalise_document(self):
                                     self.graph.edge(pre_pop_i, post_pop_i)
 
         else:
-
             for projName in self.proj_tot_weight:
                 t = self.proj_types[projName]
 
                 if self.proj_tot_weight[projName] != 0:
-
                     weight_used = float(self.proj_tot_weight[projName])
                     weight_used = self._scale_population_weight(weight_used, projName)
 
                     if abs(weight_used) >= self.min_weight_to_show:
-
                         max_abs_weight[t] = max(max_abs_weight[t], abs(weight_used))
                         min_abs_weight[t] = min(min_abs_weight[t], abs(weight_used))
                         print_v(
@@ -316,17 +306,14 @@ def finalise_document(self):
                         )
 
             for projName in self.proj_tot_weight:
-
                 proj_type = self.proj_types[projName]
 
                 if self.proj_tot_weight[projName] != 0:
-
                     # weight_used = self.proj_weights[projName]
                     weight_used = float(self.proj_tot_weight[projName])
                     weight_used = self._scale_population_weight(weight_used, projName)
 
                     if abs(weight_used) >= self.min_weight_to_show:
-
                         if max_abs_weight[proj_type] == min_abs_weight[proj_type]:
                             fweight = 1
                             lweight = 1
@@ -415,9 +402,7 @@ def finalise_document(self):
                                     )
 
                                 if self.level >= 5:
-
                                     if self.proj_conns[projName] > 0:
-
                                         pre_avg = (
                                             float(self.proj_conns[projName])
                                             / self.pop_sizes[
@@ -490,7 +475,6 @@ def finalise_document(self):
             )
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         self.network_id = network_id
 
@@ -570,7 +554,6 @@ def handle_population(
         if self.level >= 3:
             label += "<br/><i>%s cell%s</i>" % (size, "" if size == 1 else "s")
         if self.level >= 4:
-
             from neuroml import SpikeSourcePoisson
 
             if component_obj and isinstance(component_obj, SpikeSourcePoisson):
@@ -592,7 +575,6 @@ def handle_population(
         label += ">"
 
         if properties and "region" in properties:
-
             with self.graph.subgraph(name="cluster_%s" % properties["region"]) as c:
                 c.attr(color="#444444", fontcolor="#444444")
                 c.attr(label=properties["region"])
@@ -631,7 +613,6 @@ def handle_projection(
         synapse_obj=None,
         pre_synapse_obj=None,
     ):
-
         shape = self.EXC_CONN_ARROW_SHAPE
         line = "solid"
 
@@ -706,7 +687,6 @@ def handle_projection(
     def finalise_projection(
         self, projName, prePop, postPop, synapse=None, type="projection"
     ):
-
         # weight = self.proj_tot_weight[projName]
         # self.max_weight = max(self.max_weight, weight)
         # self.min_weight = min(self.min_weight, weight)
@@ -715,19 +695,16 @@ def finalise_projection(
         # print_v("Projection finalising: "+projName+" from "+prePop+" to "+postPop+" completed")
 
     def finalise_input_source(self, inputListId):
-
         if self.include_ext_inputs:
             # self.print_input_information('FINAL: '+inputListId, self.pops_ils[inputListId], '...', self.sizes_ils[inputListId])
 
             if self.level >= 2:
-
                 label = "<%s" % inputListId
                 if self.level >= 3:
                     size = self.sizes_ils[inputListId]
                     label += "<br/><i>%s input%s</i>" % (size, "" if size == 1 else "s")
 
                 if self.level >= 4:
-
                     from neuroml import PulseGenerator
                     from neuroml import TransientPoissonFiringSynapse
                     from neuroml import PoissonFiringSynapse
@@ -755,7 +732,6 @@ def finalise_input_source(self, inputListId):
                     if input_comp_obj and isinstance(
                         input_comp_obj, PoissonFiringSynapse
                     ):
-
                         average_rate = convert_to_units(
                             input_comp_obj.average_rate, "Hz"
                         )
@@ -770,7 +746,6 @@ def finalise_input_source(self, inputListId):
                     if input_comp_obj and isinstance(
                         input_comp_obj, TransientPoissonFiringSynapse
                     ):
-
                         start = convert_to_units(input_comp_obj.delay, "ms")
                         if start == int(start):
                             start = int(start)
diff --git a/neuromllite/MDFHandler.py b/neuromllite/MDFHandler.py
index e2b882c..b6bb48e 100644
--- a/neuromllite/MDFHandler.py
+++ b/neuromllite/MDFHandler.py
@@ -6,6 +6,8 @@
 
 from neuromllite.DefaultNetworkHandler import DefaultNetworkHandler
 from neuromllite.utils import print_v
+from neuromllite.NetworkGenerator import _extract_pynn_components_to_neuroml
+
 from modelspec.utils import save_to_json_file
 from modelspec.utils import save_to_yaml_file
 from modelspec.utils import locate_file
@@ -14,6 +16,12 @@
 
 import lems.api as lems  # from pylems
 
+import numpy
+
+DEFAULT_CURRENT_INPUT_PORT = "synapses_i"
+SPIKE_INPUT_PORT_ID = "spike_input"
+WEIGHTED_SPIKE_INPUTS = "weighted_inputs"
+
 
 class MDFHandler(DefaultNetworkHandler):
     def __init__(self, nl_network):
@@ -23,15 +31,16 @@ def __init__(self, nl_network):
         self.input_list_vs_comps = {}
         self.input_list_vs_pops = {}
 
-    def handle_document_start(self, id, notes):
+        self.pop_ids_vs_size = {}
 
-        print_v("Parsing for PsyNeuLink export: %s" % id)
+    def handle_document_start(self, id, notes):
+        print_v("Parsing for MDF export: %s" % id)
         self.id = id
 
         self.mdf_info = {}
 
         # from modeci_mdf import MODECI_MDF_VERSION
-        MODECI_MDF_VERSION = "0.3"
+        MODECI_MDF_VERSION = "0.4"
 
         self.mdf_info[self.id] = {}
         self.mdf_info[self.id]["format"] = "ModECI MDF v%s" % MODECI_MDF_VERSION
@@ -40,7 +49,6 @@ def handle_document_start(self, id, notes):
         self.pnl_additions = False
 
     def finalise_document(self):
-
         print_v("Writing file for...: %s" % self.id)
 
         save_to_json_file(self.mdf_info, "%s.mdf.json" % self.id, indent=4)
@@ -48,7 +56,6 @@ def finalise_document(self):
         """save_to_json_file(self.mdf_info_hl, '%s.bids-mdf.highlevel.json'%self.id, indent=4)"""
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         self.network_id = network_id
 
@@ -64,12 +71,17 @@ def handle_network(self, network_id, notes, temperature=None):
 
         self.mdf_info[self.id]["graphs"][network_id] = self.mdf_graph
 
-    def _convert_value(self, val):
+    def _get_input_port_name(self, name):
+        if name == "in":
+            return SPIKE_INPUT_PORT_ID
+        else:
+            return name
 
+    def _convert_value(self, val):
         funcs = ["exp"]
         for f in funcs:
             if "%s(" % f in val:
-                val = val.replace("%s(" % f, "math.%s(" % f)
+                val = val.replace("%s(" % f, "numpy.%s(" % f)
 
         val = evaluate(val)  # catch if it's an int etc.
         return val
@@ -77,7 +89,6 @@ def _convert_value(self, val):
     def handle_population(
         self, population_id, component, size=-1, component_obj=None, properties={}
     ):
-
         sizeInfo = " as yet unspecified size"
         if size >= 0:
             sizeInfo = ", size: " + str(size) + " cells"
@@ -86,182 +97,456 @@ def handle_population(
         else:
             compInfo = ""
 
-        print_v(
+        self.pop_ids_vs_size[population_id] = size
+
+        info = (
             "Population: "
             + population_id
             + ", component: "
             + component
             + compInfo
             + sizeInfo
-            + ", properties: %s"% properties
+            + ", properties: %s" % properties
         )
+        print_v("  = %s" % info)
 
-        if size >= 0:
-            for i in range(size):
-                node_id = "%s_%i" % (population_id, i)
-
-                cell_comp = self.nl_network.get_child(component, "cells")
-
-                if cell_comp is not None:
-                    node = self._comp_to_mdf_node(cell_comp, component, node_id, properties)
-
-                self.mdf_graph["nodes"][node_id] = node
-
-
-    def _comp_to_mdf_node(self, nmllite_comp, lems_comp_id, node, properties=None):
-
-       base_dir = "./"  # for now...
-
-       node = {}
-       if properties:
-           node["metadata"] = properties
-
-       node["parameters"] = {}
-       node["input_ports"] = {}
-       node["output_ports"] = {}
-
-       if nmllite_comp.lems_source_file:
-           print_v("  It's defined in custom lems..." )
-           fname = locate_file(nmllite_comp.lems_source_file, base_dir)
-           model = MDFHandler._load_lems_file_with_neuroml2_types(fname)
-           lems_comp = model.components.get(lems_comp_id)
-
-       elif hasattr(nmllite_comp,'neuroml2_cell'):
-           print_v("  It's a cell..." )
-           model = MDFHandler._get_lems_model_with_neuroml2_types()
-           lems_comp = lems.Component(
-               id_=nmllite_comp.id, type_=nmllite_comp.neuroml2_cell
-           )
-           for p in nmllite_comp.parameters:
-               lems_comp.set_parameter(
-                   p,
-                   evaluate(
-                       nmllite_comp.parameters[p], self.nl_network.parameters
-                   ),
-               )
-
-       elif hasattr(nmllite_comp,'neuroml2_input'):
-           print_v("  It's an input..." )
-           model = MDFHandler._get_lems_model_with_neuroml2_types()
-           lems_comp = lems.Component(
-               id_=nmllite_comp.id, type_=nmllite_comp.neuroml2_input
-           )
-           for p in nmllite_comp.parameters:
-               lems_comp.set_parameter(
-                   p,
-                   evaluate(
-                       nmllite_comp.parameters[p], self.nl_network.parameters
-                   ),
-               )
-
-       print_v("All LEMS comps in model: %s" % model.components.keys())
-       print_v("This comp: %s" % lems_comp)
-       comp_type_name = lems_comp.type
-       lems_comp_type = model.component_types.get(comp_type_name)
-       print_v("lems_comp_type: %s" % lems_comp_type)
-       notes = "Cell: [%s] is defined in %s and in Lems is: %s" % (
-           nmllite_comp,
-           nmllite_comp.lems_source_file,
-           lems_comp,
-       )
-
-       node["notes"] = notes
-
-       for p in lems_comp.parameters:
-           node["parameters"][p] = {
-               "value": get_value_in_si(evaluate(lems_comp.parameters[p]))
-           }
-
-       for c in lems_comp_type.constants:
-           node["parameters"][c.name] = {"value": get_value_in_si(c.value)}
-
-       for sv in lems_comp_type.dynamics.state_variables:
-           node["parameters"][sv.name] = {}
-           if sv.exposure:
-               node["output_ports"][sv.exposure] = {"value": sv.name}
-
-       for dv in lems_comp_type.dynamics.derived_variables:
-
-           print_v(
-               "Converting: %s (exp: %s) = [%s] or [%s]"
-               % (dv.name, dv.exposure, dv.value, dv.select)
-           )
-           if dv.name == "INPUT":
-               node["input_ports"][dv.name] = {}
-           else:
-               if dv.value is not None:
-                   node["parameters"][dv.name] = {
-                       "value": self._convert_value(dv.value)
-                   }
-                   if dv.exposure:
-                       node["output_ports"][dv.exposure] = {
-                           "value": dv.name
-                       }
-               if dv.select is not None:
-                   in_port = dv.select.replace("[*]/", "_")
-                   node["input_ports"][in_port] = {}
-                   node["parameters"][dv.name] = {"value": in_port}
-
-       conditions = 0
-       for eh in lems_comp_type.dynamics.event_handlers:
-
-           print_v("Converting: %s (type: %s)" % (eh, type(eh)))
-           if type(eh) == lems.OnStart:
-               for a in eh.actions:
-                   if type(a) == lems.StateAssignment:
-                       node["parameters"][a.variable][
-                           "default_initial_value"
-                       ] = a.value
-           if type(eh) == lems.OnCondition:
-               test = (
-                   eh.test.replace(".gt.", ">")
-                   .replace(".geq.", ">=")
-                   .replace(".lt.", "<")
-                   .replace(".leq.", "<=")
-                   .replace(".eq.", "==")
-                   .replace(".and.", "and")
-               )
-               for a in eh.actions:
-                   if type(a) == lems.StateAssignment:
-                       if (
-                           not "conditions"
-                           in node["parameters"][a.variable]
-                       ):
-                           node["parameters"][a.variable][
-                               "conditions"
-                           ] = {}
-
-                       node["parameters"][a.variable]["conditions"][
-                           "condition_%i" % conditions
-                       ] = {"test": test, "value": a.value}
-               conditions += 1
-
-       for td in lems_comp_type.dynamics.time_derivatives:
-           node["parameters"][td.variable][
-               "time_derivative"
-           ] = self._convert_value(td.value)
-
-       return node
+        node_id = "%s" % (population_id)
+
+        cell_comp = self.nl_network.get_child(component, "cells")
+
+        if cell_comp is not None:
+            node = self._comp_to_mdf_node(
+                nmllite_comp=cell_comp,
+                lems_comp_id=component,
+                size=size,
+                properties=properties,
+            )
+
+        self.mdf_graph["nodes"][node_id] = node
+
+    def _comp_to_mdf_node(self, nmllite_comp, lems_comp_id, size=1, properties=None):
+        base_dir = "./"  # for now...
+
+        node = {}
+
+        if properties:
+            node["metadata"] = properties
+
+        node["parameters"] = {}
+        node["input_ports"] = {}
+        node["output_ports"] = {}
+
+        if nmllite_comp.lems_source_file:
+            print_v("  It's a component defined in custom lems...")
+            fname = locate_file(nmllite_comp.lems_source_file, base_dir)
+            model = MDFHandler._load_lems_file_with_neuroml2_types(fname)
+            lems_comp = model.components.get(lems_comp_id)
+
+        elif (
+            hasattr(nmllite_comp, "neuroml2_cell")
+            and nmllite_comp.neuroml2_cell is not None
+        ):
+            print_v(
+                "  It is a NeuroML2 cell (%s, %s)..."
+                % (nmllite_comp.id, nmllite_comp.neuroml2_cell)
+            )
+            model = MDFHandler._get_lems_model_with_neuroml2_types()
+            lems_comp = lems.Component(
+                id_=nmllite_comp.id, type_=nmllite_comp.neuroml2_cell
+            )
+            if nmllite_comp.parameters is not None:
+                for p in nmllite_comp.parameters:
+                    lems_comp.set_parameter(
+                        p,
+                        evaluate(
+                            nmllite_comp.parameters[p], self.nl_network.parameters
+                        ),
+                    )
+        elif nmllite_comp.neuroml2_source_file is not None:
+            print_v(
+                "  It is a NeuroML2 cell (%s, %s)..."
+                % (nmllite_comp.id, nmllite_comp.neuroml2_source_file)
+            )
+            model = MDFHandler._get_lems_model_with_neuroml2_types()
+            lems_comp = lems.Component(
+                id_=nmllite_comp.id, type_=nmllite_comp.neuroml2_cell
+            )
+            if nmllite_comp.parameters is not None:
+                for p in nmllite_comp.parameters:
+                    lems_comp.set_parameter(
+                        p,
+                        evaluate(
+                            nmllite_comp.parameters[p], self.nl_network.parameters
+                        ),
+                    )
+
+        elif hasattr(nmllite_comp, "pynn_cell"):
+            print_v("  It's a PyNN cell...")
+
+            nml2_doc_temp = _extract_pynn_components_to_neuroml(self.nl_network)
+
+            model = MDFHandler._get_lems_model_with_neuroml2_types(nml2_doc_temp)
+
+            lems_comp = model.components[nmllite_comp.id]
+
+            for p in nmllite_comp.parameters:
+                lems_comp.set_parameter(
+                    p,
+                    evaluate(nmllite_comp.parameters[p], self.nl_network.parameters),
+                )
+
+        elif hasattr(nmllite_comp, "pynn_synapse_type"):
+            print_v("  It's a PyNN synapse...")
 
+            nml2_doc_temp = _extract_pynn_components_to_neuroml(self.nl_network)
+
+            model = MDFHandler._get_lems_model_with_neuroml2_types(nml2_doc_temp)
+
+            lems_comp = model.components[nmllite_comp.id]
+
+            for p in nmllite_comp.parameters:
+                lems_comp.set_parameter(
+                    p,
+                    evaluate(nmllite_comp.parameters[p], self.nl_network.parameters),
+                )
+
+        elif (
+            hasattr(nmllite_comp, "neuroml2_input")
+            and nmllite_comp.neuroml2_input is not None
+        ):
+            print_v("  It's a NeuroML input...")
+            model = MDFHandler._get_lems_model_with_neuroml2_types()
+            lems_comp = lems.Component(
+                id_=nmllite_comp.id, type_=nmllite_comp.neuroml2_input
+            )
+            for p in nmllite_comp.parameters:
+                lems_comp.set_parameter(
+                    p,
+                    evaluate(nmllite_comp.parameters[p], self.nl_network.parameters),
+                )
+
+        elif hasattr(nmllite_comp, "pynn_input"):
+            print_v(
+                "  It's a PyNN input: %s - %s..."
+                % (nmllite_comp.id, nmllite_comp.pynn_input)
+            )
+
+            nml2_doc_temp = _extract_pynn_components_to_neuroml(self.nl_network)
+
+            model = MDFHandler._get_lems_model_with_neuroml2_types(nml2_doc_temp)
+
+            lems_comp = model.components[nmllite_comp.id]
+            """
+            for p in nmllite_comp.parameters:
+                lems_comp.set_parameter(
+                    p,
+                    evaluate(
+                        nmllite_comp.parameters[p], self.nl_network.parameters
+                    ),
+                )"""
+
+        else:
+            raise Exception(
+                "Can't determine the source of the component definition in: %s"
+                % nmllite_comp
+            )
+
+        print_v(
+            "All LEMS Components in known LEMS model: %s"
+            % sorted(list(model.components.keys()))
+        )
+        print_v(
+            "All LEMS ComponentTypes in known LEMS model: %s"
+            % sorted(list(model.component_types.keys()))
+        )
+        print_v("This LEMS comp: %s" % lems_comp)
+        comp_type_name = lems_comp.type
+        lems_comp_type = model.component_types.get(comp_type_name)
+        print_v("lems_comp_type: %s" % lems_comp_type)
+        notes = "Cell: [%s] is defined in %s and in Lems is: %s" % (
+            nmllite_comp,
+            nmllite_comp.lems_source_file,
+            lems_comp,
+        )
+
+        node["notes"] = notes
+
+        for p in lems_comp.parameters:
+            node["parameters"][p] = {
+                "value": [get_value_in_si(evaluate(lems_comp.parameters[p]))] * size
+            }
+
+        properties = self._get_all_elements_in_lems(lems_comp_type, model, "properties")
+        for prop in properties:
+            node["parameters"][prop.name] = {
+                "value": [get_value_in_si(evaluate(prop.default_value))] * size
+            }
+
+        # if lems_comp_types.is_or_extends()
+
+        consts = self._get_all_elements_in_lems(lems_comp_type, model, "constant")
+        for c in consts:
+            node["parameters"][c.name] = {"value": [get_value_in_si(c.value)] * size}
+
+        event_ports = self._get_all_elements_in_lems(
+            lems_comp_type, model, "event_port"
+        )
+        for ep in event_ports:
+            if ep.direction == "out":
+                node["parameters"][ep.name] = {"value": [0] * size}
+                node["output_ports"][ep.name] = {"value": ep.name}
+            elif ep.direction == "in":
+                ep_name = self._get_input_port_name(ep.name)
+                node["input_ports"][ep_name] = {"shape": [size], "reduce": "add"}
+
+        if hasattr(lems_comp_type, "dynamics"):
+            for sv in lems_comp_type.dynamics.state_variables:
+                node["parameters"][sv.name] = {}
+
+            for reg in lems_comp_type.dynamics.regimes:
+                node["parameters"]["ACTIVE_REGIME"] = {"value": [1] * size}
+                node["parameters"]["INACTIVE_REGIME"] = {"value": [0] * size}
+
+                reg_param = "REGIME_%s" % reg.name
+                # node["parameters"][reg_param] = {"value": 'ACTIVE_REGIME' if reg.initial else 'INACTIVE_REGIME'}
+
+                if not reg_param in node["parameters"]:
+                    node["parameters"][reg_param] = {}
+                node["parameters"][reg_param]["value"] = reg_param
+                node["parameters"][reg_param]["default_initial_value"] = (
+                    "ACTIVE_REGIME" if reg.initial else "INACTIVE_REGIME"
+                )
+
+                node["output_ports"][reg_param] = {"value": reg_param}
+
+                for td in reg.time_derivatives:
+                    node["parameters"][td.variable][
+                        "time_derivative"
+                    ] = self._convert_value("%s * (%s)" % (reg_param, td.value))
+
+                for eh in reg.event_handlers:
+                    print_v(
+                        "Converting the event handler: %s (type: %s)" % (eh, type(eh))
+                    )
+
+                    if type(eh) == lems.OnCondition:
+                        # TODO: remove when global t available
+                        node["parameters"]["t"] = {
+                            "default_initial_value": 0,
+                            "time_derivative": "1",
+                        }
+
+                        test = "(%s == ACTIVE_REGIME) * (%s)" % (
+                            reg_param,
+                            self._replace_in_condition_test(eh.test),
+                        )
+                        # test = "%s == ACTIVE_REGIME" % (reg_param)
+                        if not "conditions" in node["parameters"][reg_param]:
+                            node["parameters"][reg_param]["conditions"] = {}
+
+                        node["parameters"][reg_param]["conditions"][
+                            "regime_exit_condition"
+                        ] = {"test": test, "value": "INACTIVE_REGIME"}
+
+                        for a in eh.actions:
+                            if type(a) == lems.Transition:
+                                reg_to_id = a.regime
+                                print_v(
+                                    "  Transition: %s -> %s" % (reg_param, reg_to_id)
+                                )
+                                reg_to_param = "REGIME_%s" % reg_to_id
+                                if not reg_to_param in node["parameters"]:
+                                    node["parameters"][reg_to_param] = {}
+                                reg_to = lems_comp_type.dynamics.regimes[reg_to_id]
+                                if not "conditions" in node["parameters"][reg_to_param]:
+                                    node["parameters"][reg_to_param]["conditions"] = {}
+
+                                node["parameters"][reg_to_param]["conditions"][
+                                    "regime_entry_condition"
+                                ] = {"test": test, "value": "ACTIVE_REGIME"}
+
+                                for eh in reg_to.event_handlers:
+                                    print_v(
+                                        "Converting an event handler: %s (type: %s)"
+                                        % (eh, type(eh))
+                                    )
+
+                                    if type(eh) == lems.OnEntry:
+                                        for a in eh.actions:
+                                            if type(a) == lems.StateAssignment:
+                                                if (
+                                                    not "conditions"
+                                                    in node["parameters"][a.variable]
+                                                ):
+                                                    node["parameters"][a.variable][
+                                                        "conditions"
+                                                    ] = {}
+
+                                                node["parameters"][a.variable][
+                                                    "conditions"
+                                                ]["entering_regime_%s" % reg_to_id] = {
+                                                    "test": test,
+                                                    "value": a.value,
+                                                }
+
+                            if type(a) == lems.EventOut:
+                                del node["parameters"][a.port]["value"]
+                                node["parameters"][a.port] = {
+                                    "default_initial_value": [0] * size
+                                }
+
+                                if not "conditions" in node["parameters"][a.port]:
+                                    node["parameters"][a.port]["conditions"] = {}
+
+                                node["parameters"][a.port]["conditions"][
+                                    "condition_%s_on" % a.port
+                                ] = {"test": test, "value": 1}
+                                node["parameters"][a.port]["conditions"][
+                                    "condition_%s_off" % a.port
+                                ] = {"test": "%s > 0" % a.port, "value": 0}
+
+            for sv in lems_comp_type.dynamics.state_variables:
+                # node["parameters"][sv.name]["value"] = [0]*size
+
+                node["output_ports"][sv.name] = {"value": sv.name}
+                print_v("Adding %s as an output port"%sv.name)
+                if sv.exposure:
+                    node["output_ports"][sv.exposure] = {"value": sv.name}
+
+            for dv in lems_comp_type.dynamics.derived_variables:
+                print_v(
+                    "Converting derived variable: %s (exp: %s) = [%s] or [%s]"
+                    % (dv.name, dv.exposure, dv.value, dv.select)
+                )
+                if dv.name == "INPUT":
+                    node["input_ports"][dv.name] = {}
+                else:
+                    if dv.value is not None:
+                        dv_name = dv.name
+                        node["parameters"][dv_name] = {
+                            "value": self._convert_value(dv.value)
+                        }
+                        if dv.exposure:
+                            node["output_ports"][dv.exposure] = {"value": dv_name}
+                    if dv.select is not None:
+                        in_port = dv.select.replace("[*]/", "_").replace("/", "_")
+                        node["input_ports"][in_port] = {}
+                        """ "shape": [size],
+                            "reduce": "add","""
+
+                        node["parameters"][dv.name] = {"value": in_port}
+
+            conditions = 0
+            for eh in lems_comp_type.dynamics.event_handlers:
+                print_v("Converting an event handler: %s (type: %s)" % (eh, type(eh)))
+
+                if type(eh) == lems.OnEvent:
+                    ep_name = self._get_input_port_name(eh.port)
+                    for a in eh.actions:
+                        if type(a) == lems.StateAssignment:
+                            if not "conditions" in node["parameters"][a.variable]:
+                                node["parameters"][a.variable]["conditions"] = {}
+
+                            to_check = ep_name
+                            if to_check == SPIKE_INPUT_PORT_ID:
+                                to_check = WEIGHTED_SPIKE_INPUTS
+                            node["parameters"][a.variable]["conditions"][
+                                "condition_%s_on_eh" % ep_name
+                            ] = {"test": "%s > 0" % to_check, "value": a.value}
+
+                if type(eh) == lems.OnStart:
+                    for a in eh.actions:
+                        if type(a) == lems.StateAssignment:
+                            node["parameters"][a.variable][
+                                "default_initial_value"
+                            ] = a.value
+                        if "value" in node["parameters"][a.variable]:
+                            node["parameters"][a.variable].pop("value")
+
+                if type(eh) == lems.OnCondition:
+                    test = self._replace_in_condition_test(eh.test)
+
+                    for a in eh.actions:
+                        if type(a) == lems.StateAssignment:
+                            if not "conditions" in node["parameters"][a.variable]:
+                                node["parameters"][a.variable]["conditions"] = {}
+
+                            node["parameters"][a.variable]["conditions"][
+                                "condition_%i" % conditions
+                            ] = {"test": test, "value": a.value}
+
+                        if type(a) == lems.EventOut:
+                            del node["parameters"][a.port]["value"]
+                            node["parameters"][a.port] = {
+                                "default_initial_value": [0] * size
+                            }
+
+                            if not "conditions" in node["parameters"][a.port]:
+                                node["parameters"][a.port]["conditions"] = {}
+
+                            node["parameters"][a.port]["conditions"][
+                                "condition_%i_on" % conditions
+                            ] = {"test": test, "value": 1}
+                            node["parameters"][a.port]["conditions"][
+                                "condition_%i_off" % conditions
+                            ] = {"test": "%s > 0" % a.port, "value": 0}
+
+                    conditions += 1
+
+            for td in lems_comp_type.dynamics.time_derivatives:
+                node["parameters"][td.variable][
+                    "time_derivative"
+                ] = self._convert_value(td.value)
+
+                if not "default_initial_value" in node["parameters"][td.variable]:
+                    node["parameters"][td.variable]["default_initial_value"] = [
+                        0
+                    ] * size
+
+        return node
+
+    def _replace_in_condition_test(self, test):
+        return (
+            test.replace(".gt.", ">")
+            .replace(".geq.", ">=")
+            .replace(".lt.", "<")
+            .replace(".leq.", "<=")
+            .replace(".eq.", "==")
+            .replace(".and.", "and")
+        )
 
     # TODO: move to pylems!
     @classmethod
-    def _get_all_children_in_lems(cls, component_type, model, child_type):
-        c = []
+    def _get_all_elements_in_lems(cls, component_type, model, child_type):
+        ee = []
         if child_type == "exposure":
-            for e in component_type.exposures:
-                c.append(e)
+            if hasattr(component_type, "exposures"):
+                for e in component_type.exposures:
+                    ee.append(e)
+        elif child_type == "constant":
+            if hasattr(component_type, "constants"):
+                for c in component_type.constants:
+                    ee.append(c)
+        elif child_type == "event_port":
+            if hasattr(component_type, "event_ports"):
+                for e in component_type.event_ports:
+                    ee.append(e)
+        elif child_type == "properties":
+            if hasattr(component_type, "properties"):
+                for p in component_type.properties:
+                    ee.append(p)
+        else:
+            raise Exception("Cannot get child of type: %s in LEMS model" % child_type)
 
-        if component_type.extends:
+        if hasattr(component_type, "extends") and component_type.extends:
             ect = model.component_types[component_type.extends]
-            c.extend(cls._get_all_children_in_lems(ect, model, child_type))
+            ee.extend(cls._get_all_elements_in_lems(ect, model, child_type))
 
-        return c
+        return ee
 
     # TODO: move to pyneuroml!
     @classmethod
-    def _get_lems_model_with_neuroml2_types(cls):
-
+    def _get_lems_model_with_neuroml2_types(cls, nml_doc=None):
         from pyneuroml.pynml import get_path_to_jnml_jar
         from pyneuroml.pynml import read_lems_file
         from lems.parser.LEMS import LEMSFileParser
@@ -290,12 +575,27 @@ def _get_lems_model_with_neuroml2_types(cls):
         new_lems = jar.read("NeuroML2CoreTypes/Inputs.xml")
         parser.parse(new_lems)
 
+        if nml_doc is not None:
+            import io
+
+            sf = io.StringIO()
+
+            from neuroml.writers import NeuroMLWriter
+
+            print(
+                "Adding nml elements from this doc to new lems model: %s"
+                % nml_doc.summary()
+            )
+
+            NeuroMLWriter.write(nml_doc, sf, close=False)
+            sf.seek(0)
+            parser.parse(sf.read())
+
         return lems_model
 
     # TODO: move to pyneuroml!
     @classmethod
     def _load_lems_file_with_neuroml2_types(cls, lems_filename):
-
         from pyneuroml.pynml import read_lems_file
 
         lems_model = cls._get_lems_model_with_neuroml2_types()
@@ -318,9 +618,122 @@ def handle_location(self, id, population_id, component, x, y, z):
         pass
 
     def finalise_population(self, population_id):
-
         pass
 
+    def handle_projection(
+        self,
+        projName,
+        prePop,
+        postPop,
+        synapse,
+        hasWeights=False,
+        hasDelays=False,
+        type="projection",
+        synapse_obj=None,
+        pre_synapse_obj=None,
+    ):
+        synInfo = ""
+        if synapse_obj:
+            synInfo += " (syn: %s)" % synapse_obj.__class__.__name__
+
+        if pre_synapse_obj:
+            synInfo += " (pre comp: %s)" % pre_synapse_obj.__class__.__name__
+
+        print_v(
+            "  = Projection: "
+            + projName
+            + " ("
+            + type
+            + ") from "
+            + prePop
+            + " to "
+            + postPop
+            + " with syn: "
+            + synapse
+            + synInfo
+        )
+
+        syn_node_id = "%s_%s" % (projName, synapse)
+        syn_node = {}
+
+        syn_comp = self.nl_network.get_child(synapse, "synapses")
+
+        print("Converting syn %s; %s" % (synapse_obj, syn_comp))
+
+        pre_pop_size = self.pop_ids_vs_size[prePop]
+        post_pop_size = self.pop_ids_vs_size[postPop]
+
+        syn_node = self._comp_to_mdf_node(
+            nmllite_comp=syn_comp,
+            lems_comp_id=synapse,
+            size=post_pop_size,
+            properties={},
+        )
+        if SPIKE_INPUT_PORT_ID in syn_node["input_ports"]:
+            syn_node["input_ports"][SPIKE_INPUT_PORT_ID]["shape"] = [pre_pop_size]
+            syn_node["parameters"][WEIGHTED_SPIKE_INPUTS] = {
+                "value": numpy.zeros([pre_pop_size, post_pop_size]).tolist()
+            }
+            syn_node["parameters"]["weight"] = {}
+            syn_node["parameters"]["weight"]["function"] = "MatMul"
+            syn_node["parameters"]["weight"]["args"] = {
+                "A": SPIKE_INPUT_PORT_ID,
+                "B": WEIGHTED_SPIKE_INPUTS,
+            }
+
+        self.mdf_graph["nodes"][syn_node_id] = syn_node
+
+        #### Edge pre_node -> syn
+
+        pre_node_id = prePop
+        pre_node = self.mdf_graph["nodes"][pre_node_id]
+
+        pre_syn_edge_id = "%s_TO_%s" % (pre_node_id, syn_node_id)
+        pre_syn_edge = {}
+        pre_syn_edge["name"] = pre_syn_edge_id
+
+        pre_ports = list(pre_node["output_ports"].keys())
+        pre_syn_edge["sender_port"] = (
+            "OUTPUT" if "OUTPUT" in pre_ports else pre_ports[0]
+        )
+
+        post_ports = list(syn_node["input_ports"].keys())
+        pre_syn_edge["receiver_port"] = (
+            "INPUT" if "INPUT" in post_ports else post_ports[0]
+        )
+        pre_syn_edge["sender"] = pre_node_id
+        pre_syn_edge["receiver"] = syn_node_id
+
+        self.mdf_graph["edges"][pre_syn_edge_id] = pre_syn_edge
+
+        #### Edge syn -> post_node
+
+        post_node_id = postPop
+        post_node = self.mdf_graph["nodes"][post_node_id]
+
+        syn_post_edge_id = "%s_TO_%s" % (syn_node_id, post_node_id)
+        syn_post_edge = {}
+        syn_post_edge["name"] = syn_post_edge_id
+
+        syn_ports = list(syn_node["output_ports"].keys())
+
+        syn_post_edge["sender_port"] = (
+            "OUTPUT"
+            if "OUTPUT" in syn_ports
+            else ("i" if "i" in syn_ports else syn_ports[0])
+        )
+
+        post_ports = list(post_node["input_ports"].keys())
+        syn_post_edge["receiver_port"] = (
+            "INPUT"
+            if "INPUT" in post_ports
+            else ("synapses_i" if "synapses_i" in post_ports else post_ports[0])
+        )
+        syn_post_edge["sender"] = syn_node_id
+        syn_post_edge["receiver"] = post_node_id
+
+        self.mdf_graph["edges"][syn_post_edge_id] = syn_post_edge
+
     #
     #  Should be overridden to handle network connection
     #
@@ -340,43 +753,41 @@ def handle_connection(
         delay=0,
         weight=1,
     ):
-
         # self.print_connection_information(projName, id, prePop, postPop, synapseType, preCellId, postCellId, weight)
         print_v(
-            ">>>>>> Src cell: %d, seg: %f, fract: %f -> Tgt cell %d, seg: %f, fract: %f; weight %s, delay: %s ms"
+            ">>>>>> Src pop: %s, cell: %d, seg: %f, fract: %f -> Tgt pop %s, cell %d, seg: %f, fract: %f; syn: %s, weight %s, delay: %s ms"
             % (
+                prePop,
                 preCellId,
                 preSegId,
                 preFract,
+                postPop,
                 postCellId,
                 postSegId,
                 postFract,
+                synapseType,
                 weight,
                 delay,
             )
         )
 
-        pre_node_id = "%s_%i" % (prePop, preCellId)
-        post_node_id = "%s_%i" % (postPop, postCellId)
-        edge_id = "Edge %s to %s" % (pre_node_id, post_node_id)
-        edge = {}
-        edge["name"] = edge_id
-        # edge['type'] = {}
-        # edge['type']['NeuroML'] = synapseType
-        # edge['parameters'] = {}
-        # edge['functions'] = {}
-        edge["sender_port"] = "OUTPUT"
-        edge["receiver_port"] = "INPUT"
-        edge["sender"] = pre_node_id
-        edge["receiver"] = post_node_id
-        edge["weight"] = weight
+        if preSegId != 0 or postSegId != 0:
+            raise Exception(
+                "MDF export does not support connections on anything other than segment id = 0"
+            )
 
-        """edge['type'] =  {
-                        "PNL": "MappingProjection",
-                        "generic": None
-                    }"""
+        syn_node_id = "%s_%s" % (projName, synapseType)
+        node = self.mdf_graph["nodes"][syn_node_id]
+        if WEIGHTED_SPIKE_INPUTS in node["parameters"]:
+            # Weight used inside input
+            node["parameters"][WEIGHTED_SPIKE_INPUTS]["value"][preCellId][
+                postCellId
+            ] = weight
+            print(node["parameters"][WEIGHTED_SPIKE_INPUTS]["value"])
 
-        self.mdf_graph["edges"][edge_id] = edge
+    def _get_input_list_node_id(self, inputListId):
+        return "InputList_%s" % (inputListId)
+        # return "%s" % (inputListId)
 
     #
     #  Should be overridden to create input source array
@@ -384,48 +795,62 @@ def handle_connection(
     def handle_input_list(
         self, inputListId, population_id, component, size, input_comp_obj=None
     ):
-
         self.input_list_vs_comps[inputListId] = component
         self.input_list_vs_pops[inputListId] = population_id
 
-    #
-    #  Should be overridden to to connect each input to the target cell
-    #
-    def handle_single_input(
-        self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
-    ):
-        component = self.input_list_vs_comps[inputListId]
         print_v(
-            "Input: %s[%s], cellId: %i, seg: %i, fract: %f, weight: %f, component: %s"
-            % (inputListId, id, cellId, segId, fract, weight, component)
+            "InputList: %s, population_id: %s, component: %s, size: %i, input_comp_obj: %s"
+            % (inputListId, population_id, component, size, input_comp_obj)
         )
 
-        node_id = "Input_%s_%i" % (inputListId, id)
+        node_id = self._get_input_list_node_id(inputListId)
 
         comp = self.nl_network.get_child(component, "input_sources")
 
-        node = self._comp_to_mdf_node(comp, component, node_id)
+        node = self._comp_to_mdf_node(nmllite_comp=comp, lems_comp_id=component, size=1)
 
         # TODO: remove when global t available
-        node['parameters']['t']={'default_initial_value': 0, 'time_derivative': '1'}
+        node["parameters"]["t"] = {"default_initial_value": 0, "time_derivative": "1"}
+
+        pop_size = self.pop_ids_vs_size[population_id]
+        node["parameters"]["weight"] = {"value": [0.0] * pop_size}
 
         self.mdf_graph["nodes"][node_id] = node
 
         pre_node_id = node_id
-        post_node_id = "%s_%i" % (self.input_list_vs_pops[inputListId], cellId)
+        post_node_id = "%s" % population_id
         edge_id = "Edge %s to %s" % (pre_node_id, post_node_id)
         edge = {}
         edge["name"] = edge_id
         edge["sender_port"] = "i"
-        edge["receiver_port"] = "synapses_i"
+        edge["receiver_port"] = DEFAULT_CURRENT_INPUT_PORT
         edge["sender"] = pre_node_id
         edge["receiver"] = post_node_id
 
-        # Weight used inside input
-        node['parameters']['weight']={'value': weight}
-
         self.mdf_graph["edges"][edge_id] = edge
 
+    #
+    #  Should be overridden to to connect each input to the target cell
+    #
+    def handle_single_input(
+        self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
+    ):
+        if segId != 0:
+            raise Exception(
+                "MDF export does not support inputs on anything other than segment id = 0"
+            )
+
+        component = self.input_list_vs_comps[inputListId]
+        print_v(
+            "Input: %s[%s], cellId: %i, seg: %i, fract: %f, weight: %f, component: %s"
+            % (inputListId, id, cellId, segId, fract, weight, component)
+        )
+
+        node = self.mdf_graph["nodes"][self._get_input_list_node_id(inputListId)]
+
+        # Weight used inside input
+        node["parameters"]["weight"]["value"][cellId] = weight
+
     #
     #  Should be overridden to to connect each input to the target cell
     #
@@ -434,7 +859,6 @@ def finalise_input_source(self, inputName):
 
 
 if __name__ == "__main__":
-
     lems_model = MDFHandler._load_lems_file_with_neuroml2_types(
         "../../git/MDF/examples/NeuroML/LEMS_SimIzhikevichTest.xml"
     )
diff --git a/neuromllite/MatrixHandler.py b/neuromllite/MatrixHandler.py
index 868f002..de1c859 100644
--- a/neuromllite/MatrixHandler.py
+++ b/neuromllite/MatrixHandler.py
@@ -14,13 +14,11 @@
 
 
 class MatrixHandler(ConnectivityHandler):
-
     colormaps_used = []
 
     weight_arrays_to_show = {}
 
     def __init__(self, level=10, nl_network=None):
-
         self.nl_network = nl_network
         self.level = level
 
@@ -62,7 +60,6 @@ def _get_conn_label(self, template, pclass):
         return label
 
     def finalise_document(self):
-
         entries = []
         # print_v('Finals: %s -> %s'%(self.proj_pre_pops, self.proj_post_pops))
         all_pops = []
@@ -144,7 +141,6 @@ def finalise_document(self):
             ] = "conductance * sign (nS)"
 
         for projName in self.proj_weights:
-
             pre_pop = self.proj_pre_pops[projName]
             post_pop = self.proj_post_pops[projName]
             proj_type = self.proj_types[projName]
@@ -174,7 +170,6 @@ def finalise_document(self):
             )
 
             if self.is_cell_level():
-
                 for pre_i in range(self.pop_sizes[pre_pop]):
                     for post_i in range(self.pop_sizes[post_pop]):
                         pre_pop_i = entries.index(
@@ -217,7 +212,6 @@ def finalise_document(self):
                 if abs(self.proj_tot_weight[projName]) != abs(
                     self.proj_weights[projName]
                 ):
-
                     self.weight_arrays_to_show[
                         self._get_conn_label(matrix_single_conns, pclass)
                     ][pre_pop_i][post_pop_i] += (
@@ -250,7 +244,6 @@ def finalise_document(self):
                 % (proj_type, weight_array.min(), weight_array.max())
             )
             if not (weight_array.max() == 0 and weight_array.min() == 0):
-
                 fig, ax = plt.subplots()
                 title = "%s" % (proj_type)
                 title2 = "%s" % (proj_type)
@@ -445,7 +438,6 @@ def handle_projection(
         synapse_obj=None,
         pre_synapse_obj=None,
     ):
-
         weight = 1.0
         self.proj_pre_pops[projName] = prePop
         self.proj_post_pops[projName] = postPop
@@ -513,7 +505,6 @@ def handle_projection(
     def finalise_projection(
         self, projName, prePop, postPop, synapse=None, type="projection"
     ):
-
         pass
         # print_v("Projection finalising: "+projName+" -> "+prePop+" to "+postPop+" completed (%s; w: %s, conns: %s, tot w: %s)" % \
         #           (self.proj_types[projName], self.proj_weights[projName], self.proj_conns[projName], self.proj_tot_weight[projName]))
@@ -524,5 +515,4 @@ def finalise_projection(
     input_comp_obj_ils = {}
 
     def finalise_input_source(self, inputListId):
-
         pass
diff --git a/neuromllite/NetworkGenerator.py b/neuromllite/NetworkGenerator.py
index 04be0dd..f057388 100644
--- a/neuromllite/NetworkGenerator.py
+++ b/neuromllite/NetworkGenerator.py
@@ -18,15 +18,17 @@
 DEFAULT_SIMULATION_SEED = 5678
 
 
-
 def __TEMP_CHECK_IF_SET(value):
     """
     Should just be a check for None! Update in modelspec...
     """
-    if value is None: return False
-    if value == '': return False
+    if value is None:
+        return False
+    if value == "":
+        return False
     return True
 
+
 def _get_rng_for_network(nl_model):
     """
     Get a random number generator and the seed used to generate it
@@ -66,7 +68,6 @@ def generate_network(
     rng, seed = _get_rng_for_network(nl_model)
 
     if nl_model.network_reader:
-
         exec(
             "from neuromllite.%s import %s"
             % (nl_model.network_reader.type, nl_model.network_reader.type)
@@ -90,13 +91,16 @@ def generate_network(
                 if not p == "__builtins__":
                     notes += "\n        %s = %s" % (p, nl_model.parameters[p])
         handler.handle_document_start(nl_model.id, notes)
-        temperature = "%sdegC" % nl_model.temperature if nl_model.temperature is not None else None
+        temperature = (
+            "%sdegC" % nl_model.temperature
+            if nl_model.temperature is not None
+            else None
+        )
         handler.handle_network(nl_model.id, nl_model.notes, temperature=temperature)
 
     nml2_doc_temp = _extract_pynn_components_to_neuroml(nl_model)
 
     for c in nl_model.cells:
-
         if c.neuroml2_source_file:
             from pyneuroml import pynml
 
@@ -117,11 +121,10 @@ def generate_network(
             )
             synapse_objects[s.id] = nml2_doc.get_by_id(s.id)
 
-        if hasattr(s, 'pynn_synapse') and s.pynn_synapse is not None:
+        if hasattr(s, "pynn_synapse") and s.pynn_synapse is not None:
             synapse_objects[s.id] = nml2_doc_temp.get_by_id(s.id)
 
     for p in nl_model.populations:
-
         size = evaluate(p.size, nl_model.parameters)
         properties = p.properties if p.properties else {}
 
@@ -136,7 +139,6 @@ def generate_network(
             and not p.relative_layout
             and not always_include_props
         ):
-
             # If there are no positions (abstract network), and <property>
             # is added to <population>, jLems doesn't like it... (it has difficulty
             # interpreting pop0[0]/v, etc.)
@@ -197,7 +199,6 @@ def generate_network(
 
     if include_connections:
         for p in nl_model.projections:
-
             type = p.type if p.type else "projection"
 
             synapse_obj = (
@@ -242,7 +243,6 @@ def generate_network(
                                 nl_model.parameters,
                                 rng,
                             ):
-
                                 delay = (
                                     evaluate(p.delay, nl_model.parameters, rng)
                                     if p.delay
@@ -272,9 +272,7 @@ def generate_network(
                                 conn_count += 1
 
                 if p.convergent_connectivity:
-
                     for post_i in range(len(pop_locations[p.postsynaptic])):
-
                         for count in range(int(p.convergent_connectivity.num_per_post)):
                             found = False
                             while not found:
@@ -322,7 +320,6 @@ def generate_network(
                             len(pop_locations[p.postsynaptic]),
                         )
                     ):
-
                         # print_v("Adding connection %i with weight: %s, delay: %s"%(conn_count, weight, delay))
                         handler.handle_connection(
                             p.id,
@@ -347,7 +344,6 @@ def generate_network(
 
     if include_inputs:
         for input in nl_model.inputs:
-
             handler.handle_input_list(
                 input.id,
                 input.population,
@@ -365,7 +361,11 @@ def generate_network(
                         % input
                     )
                 for i in input.cell_ids:
-                    weight = input.weight if input.weight else 1
+                    weight = (
+                        evaluate(input.weight, nl_model.parameters, rng)
+                        if input.weight
+                        else 1
+                    )
 
                     if input.number_per_cell and input.segment_ids:
                         raise Exception(
@@ -389,7 +389,11 @@ def generate_network(
                             input_count,
                             i,
                             segId=seg_id,
-                            weight=evaluate(weight, nl_model.parameters),
+                            weight=(
+                                evaluate(input.weight, nl_model.parameters, rng)
+                                if input.weight
+                                else 1
+                            ),
                         )
                         input_count += 1
 
@@ -401,9 +405,12 @@ def generate_network(
                     )
                 for i in range(len(pop_locations[input.population])):
                     flip = rng.random()
-                    weight = input.weight if input.weight else 1
-                    if flip * 100.0 < input.percentage:
-
+                    weight = (
+                        evaluate(input.weight, nl_model.parameters, rng)
+                        if input.weight
+                        else 1
+                    )
+                    if flip * 100.0 < evaluate(input.percentage, nl_model.parameters, rng):
                         if input.number_per_cell and input.segment_ids:
                             raise Exception(
                                 "On input: %s, only one of number_per_cell or segment_ids is allowed"
@@ -426,7 +433,11 @@ def generate_network(
                                 input_count,
                                 i,
                                 segId=seg_id,
-                                weight=evaluate(weight, nl_model.parameters),
+                                weight=(
+                                    evaluate(input.weight, nl_model.parameters, rng)
+                                    if input.weight
+                                    else 1
+                                ),
                             )
                             input_count += 1
 
@@ -502,12 +513,10 @@ def check_to_generate_or_run(argv, sim):
         generate_and_run(sim, simulator="mdf")
 
     elif "-nml" in argv or "-neuroml" in argv:
-
         network = load_network(sim.network)
         generate_neuroml2_from_network(network, simulation=sim, validate=True)
 
     elif "-nmlh5" in argv or "-neuromlh5" in argv:
-
         network = load_network(sim.network)
         generate_neuroml2_from_network(
             network, simulation=sim, validate=True, format="hdf5"
@@ -515,7 +524,6 @@ def check_to_generate_or_run(argv, sim):
 
     else:
         for a in argv:
-
             if "-jnmlnetpyne" in a:
                 num_processors = 1
                 if len(a) > len("-jnmlnetpyne"):
@@ -527,7 +535,9 @@ def check_to_generate_or_run(argv, sim):
                 show_graph = True
                 if "-nogui" in argv:
                     show_graph = False
-                generate_and_run(sim, simulator=a[1:], nogui= not show_graph)  # Will not "run" obviously...
+                generate_and_run(
+                    sim, simulator=a[1:], nogui=not show_graph
+                )  # Will not "run" obviously...
             elif "matrix" in a:  # e.g. -matrix2
                 generate_and_run(sim, simulator=a[1:])  # Will not "run" obviously...
 
@@ -548,7 +558,6 @@ def _extract_pynn_components_to_neuroml(nl_model, nml_doc=None):
 
     for c in nl_model.cells:
         if c.pynn_cell:
-
             if nml_doc.get_by_id(c.id) == None:
                 import pyNN.neuroml
 
@@ -556,7 +565,6 @@ def _extract_pynn_components_to_neuroml(nl_model, nml_doc=None):
                 for p in cell_params:
                     cell_params[p] = evaluate(cell_params[p], nl_model.parameters)
                 for proj in nl_model.projections:
-
                     synapse = nl_model.get_child(proj.synapse, "synapses")
                     post_pop = nl_model.get_child(proj.postsynaptic, "populations")
                     if post_pop.component == c.id:
@@ -572,7 +580,8 @@ def _extract_pynn_components_to_neuroml(nl_model, nml_doc=None):
                             )
 
                 temp_cell = eval("pyNN.neuroml.%s(**cell_params)" % c.pynn_cell)
-                if c.pynn_cell != "SpikeSourcePoisson":
+
+                if c.pynn_cell != "SpikeSourcePoisson" and c.pynn_cell != "HH_cond_exp":
                     temp_cell.default_initial_values["v"] = temp_cell.parameter_space[
                         "v_rest"
                     ].base_value
@@ -583,7 +592,6 @@ def _extract_pynn_components_to_neuroml(nl_model, nml_doc=None):
 
     for s in nl_model.synapses:
         if nml_doc.get_by_id(s.id) == None:
-
             if s.pynn_synapse_type and s.pynn_receptor_type:
                 import neuroml
 
@@ -606,7 +614,6 @@ def _extract_pynn_components_to_neuroml(nl_model, nml_doc=None):
                     nml_doc.alpha_curr_synapses.append(syn)
 
     for i in nl_model.input_sources:
-
         if i.pynn_input:
             import pyNN.neuroml
 
@@ -673,7 +680,6 @@ def generate_neuroml2_from_network(
             )
 
     for i in nl_model.input_sources:
-
         if i.lems_source_file:
             fname = locate_file(i.lems_source_file, base_dir)
 
@@ -686,7 +692,7 @@ def generate_neuroml2_from_network(
             for comp in model.components:
                 if i.id == comp.id:
                     print_v("Found a component: %s in %s" % (comp, fname))
-                    if hasattr(i, 'parameters') and len(i.parameters) > 0:
+                    if hasattr(i, "parameters") and len(i.parameters) > 0:
                         for p in i.parameters:
                             comp.set_parameter(
                                 p, evaluate(i.parameters[p], nl_model.parameters)
@@ -713,14 +719,13 @@ def generate_neuroml2_from_network(
 
         if nml_doc.get_by_id(i.id) == None:
             if i.neuroml2_source_file:
-
                 incl = neuroml.IncludeType(
                     locate_file(i.neuroml2_source_file, base_dir)
                 )
                 if not incl in nml_doc.includes:
                     nml_doc.includes.append(incl)
 
-            if hasattr(i, 'neuroml2_input') and i.neuroml2_input is not None:
+            if hasattr(i, "neuroml2_input") and i.neuroml2_input is not None:
                 input_params = i.parameters if i.parameters else {}
 
                 # TODO make more generic...
@@ -745,7 +750,6 @@ def generate_neuroml2_from_network(
 
     for c in nl_model.cells:
         if c.neuroml2_source_file:
-
             incl = neuroml.IncludeType(locate_file(c.neuroml2_source_file, base_dir))
             found_cell = False
             for cell in nml_doc.cells:
@@ -802,7 +806,6 @@ def generate_neuroml2_from_network(
                 nml_doc.includes.append(incl)
 
         if c.neuroml2_cell:
-
             cell_params = c.parameters if c.parameters else {}
             # TODO make more generic...
             if c.neuroml2_cell.lower() == "spikegenerator":
@@ -910,7 +913,6 @@ def generate_neuroml2_from_network(
         extra_lems_components.export_to_file(extra_lems_file)
 
     if validate and format == "xml":
-
         from pyneuroml import pynml
 
         success = pynml.validate_neuroml2(nml_file_name, verbose_validate=False)
@@ -998,7 +1000,6 @@ def _generate_neuron_files_from_neuroml(network, verbose=False, dir_for_mod_file
                 % (dir_for_mod_files, os.getcwd(), locations_mods_loaded_from)
             )
             try:
-
                 from neuron import load_mechanisms
 
                 if os.getcwd() == dir_for_mod_files:
@@ -1041,7 +1042,6 @@ def generate_and_run(
 
     try:
         if simulator == "NEURON":  # NOT YET WORKING...
-
             _generate_neuron_files_from_neuroml(network, dir_for_mod_files=target_dir)
 
             from neuromllite.NeuronHandler import NeuronHandler
@@ -1060,7 +1060,6 @@ def generate_and_run(
                 )
 
         elif simulator.lower() == "mdf":
-
             from neuromllite.MDFHandler import MDFHandler
 
             mdf_handler = MDFHandler(nl_network=network)
@@ -1068,7 +1067,6 @@ def generate_and_run(
             generate_network(network, mdf_handler)
 
         elif simulator.lower() == "psyneulink":
-
             from neuromllite.PsyNeuLinkHandler import PsyNeuLinkHandler
 
             pnl_handler = PsyNeuLinkHandler(nl_network=network)
@@ -1158,7 +1156,6 @@ def generate_value_array(node, index, context='{0}', param='value'):
             print_v("Done with PsyNeuLink...")
 
         elif simulator.lower() == "sonata":
-
             target_simulator = "NEST"
 
             from neuromllite.SonataHandler import SonataHandler
@@ -1173,7 +1170,6 @@ def generate_value_array(node, index, context='{0}', param='value'):
 
             for c in network.cells:
                 if c.pynn_cell:
-
                     cell_params = {}
                     if c.parameters:
                         for p in c.parameters:
@@ -1254,7 +1250,7 @@ def generate_value_array(node, index, context='{0}', param='value'):
 
             sim_file_info["inputs"] = {}
             for input in sonata_handler.input_info:
-                print('Handling: %s: %s'%(input, sonata_handler.input_info[input]))
+                print("Handling: %s: %s" % (input, sonata_handler.input_info[input]))
                 sim_file_info["inputs"][input] = {}
                 input_comp = sonata_handler.input_info[input][1]
                 c = temp_nml_doc.get_by_id(input_comp)
@@ -1320,12 +1316,10 @@ def run(config_file, simulator):
             print_v("Done with Sonata...")
 
         elif simulator.lower().startswith("graph"):  # Will not "run" obviously...
-
             from neuromllite.GraphVizHandler import GraphVizHandler, engines
 
             try:
                 if simulator[-1].isalpha():
-
                     engine = engines[simulator[-1]]
                     level = int(simulator[5:-1])
                 else:
@@ -1339,7 +1333,9 @@ def run(config_file, simulator):
                 )
                 return
 
-            handler = GraphVizHandler(level, engine=engine, nl_network=network, view_on_render = not nogui)
+            handler = GraphVizHandler(
+                level, engine=engine, nl_network=network, view_on_render=not nogui
+            )
 
             generate_network(
                 network, handler, always_include_props=True, base_dir=base_dir
@@ -1348,7 +1344,6 @@ def run(config_file, simulator):
             print_v("Done with GraphViz...")
 
         elif simulator.lower().startswith("matrix"):  # Will not "run" obviously...
-
             from neuromllite.MatrixHandler import MatrixHandler
 
             try:
@@ -1369,7 +1364,6 @@ def run(config_file, simulator):
             print_v("Done with MatrixHandler...")
 
         elif simulator == "BindsNET":
-
             from neuromllite.BindsNETHandler import BindsNETHandler
             import bindsnet
 
@@ -1434,7 +1428,6 @@ def run(config_file, simulator):
                 return traces, events
 
         elif simulator == "Arbor":
-
             from neuromllite.ArborHandler import ArborHandler
             import arbor
 
@@ -1484,7 +1477,7 @@ def run(config_file, simulator):
             # (12) Create a default execution context, domain decomposition and simulation
             context = arbor.context()
             decomp = arbor.partition_load_balance(arbor_recipe, context)
-            sim = arbor.simulation(arbor_recipe, decomp, context)
+            sim = arbor.simulation(arbor_recipe, domains=decomp, context=context)
 
             # (13) Set spike generators to record
             sim.record(arbor.spike_recording.all)
@@ -1507,7 +1500,6 @@ def run(config_file, simulator):
             for pop_id in trace_pop_indices_seg_ids:
                 indices = trace_pop_indices_seg_ids[pop_id].keys()
                 for index in indices:
-
                     filename = "%s.%s.%s.v.dat" % (simulation.id, pop_id, index)
                     # all_columns = []
                     gid = arbor_recipe.get_gid(pop_id, index)
@@ -1565,7 +1557,6 @@ def run(config_file, simulator):
                 return traces, events
 
         elif simulator.startswith("PyNN"):
-
             # _generate_neuron_files_from_neuroml(network)
             simulator_name = simulator.split("_")[1].lower()
 
@@ -1575,7 +1566,6 @@ def run(config_file, simulator):
 
             syn_cell_params = {}
             for proj in network.projections:
-
                 synapse = network.get_child(proj.synapse, "synapses")
                 post_pop = network.get_child(proj.postsynaptic, "populations")
 
@@ -1633,7 +1623,6 @@ def run(config_file, simulator):
             pynn_handler.set_receptor_types(receptor_types)
 
             for input_source in network.input_sources:
-
                 # TODO: change this when noisyCurrentSource is integrated into the core of NeuroML
                 if input_source.pynn_input or input_source.lems_source_file:
                     pynn_handler.add_input_source(input_source, network)
@@ -1686,6 +1675,14 @@ def run(config_file, simulator):
             events = {}
 
             if not "NeuroML" in simulator:
+                # Temp! See https://github.com/NeuralEnsemble/PyNN/pull/762
+                def get_source_id(spiketrain):
+                    if "source_id" in spiketrain.annotations:
+                        return spiketrain.annotations["source_id"]
+                    elif (
+                        "channel_id" in spiketrain.annotations
+                    ):  # See https://github.com/NeuralEnsemble/PyNN/pull/762
+                        return spiketrain.annotations["channel_id"]
 
                 for pop_id in trace_pop_indices_seg_ids:
                     pynn_pop = pynn_handler.populations[pop_id]
@@ -1748,8 +1745,8 @@ def run(config_file, simulator):
                     ff = open(filename, "w")
 
                     for spiketrain in spiketrains:
-                        source_id = spiketrain.annotations["source_id"]
-                        source_index = spiketrain.annotations["source_index"]
+                        source_id = get_source_id(spiketrain)
+                        source_index = pynn_pop.id_to_index(source_id)
                         if source_index in indices:
                             # print_v("Writing spike data for cell %s[%s] (gid: %i): %i spikes "%(pynn_pop.label,source_index, source_id, len(spiketrain)), self.verbose)
                             ref = "%s/%i/???" % (pynn_pop.label, source_index)
@@ -1766,7 +1763,6 @@ def run(config_file, simulator):
                 return traces, events
 
         elif simulator == "NetPyNE":
-
             if target_dir == None:
                 target_dir = "./"
 
@@ -1861,7 +1857,6 @@ def run(config_file, simulator):
                 preComp = netpyne_handler.pop_ids_vs_components[prePop]
 
                 for conn in netpyne_handler.connections[projName]:
-
                     (
                         pre_id,
                         pre_seg,
@@ -1883,7 +1878,6 @@ def run(config_file, simulator):
                     }
 
                     if ptype == "electricalProjection":
-
                         if weight != 1:
                             raise Exception(
                                 "Cannot yet support inputs where weight !=1!"
@@ -2000,7 +1994,6 @@ def run(config_file, simulator):
             or simulator == "jNeuroML_Brian2"
             or simulator == "EDEN"
         ):
-
             from pyneuroml.lems import generate_lems_file_for_neuroml
             from pyneuroml import pynml
 
@@ -2046,7 +2039,6 @@ def run(config_file, simulator):
             pops = network.populations
             pops.sort(key=id)
             for p in pops:
-
                 if p.id in spike_pop_indices:
                     pops_spike_save.append(p.id)
 
diff --git a/neuromllite/NeuronHandler.py b/neuromllite/NeuronHandler.py
index 854806d..3a426f4 100644
--- a/neuromllite/NeuronHandler.py
+++ b/neuromllite/NeuronHandler.py
@@ -15,7 +15,6 @@
 
 
 class NeuronHandler(DefaultNetworkHandler):
-
     h = hoc.HocObject()
 
     globalPreSynId = 10000000
@@ -26,7 +25,6 @@ class NeuronHandler(DefaultNetworkHandler):
     #   Helper function for printing hoc before executing it
     #
     def executeHoc(self, command):
-
         cmdPrefix = "hoc >>>>>>>>>>: "
 
         if len(command) > 0:
@@ -37,7 +35,6 @@ def executeHoc(self, command):
     #  Overridden from NetworkHandler
     #
     def handlePopulation(self, population_id, component, size=-1, component_obj=None):
-
         if size >= 0:
             sizeInfo = ", size " + str(size) + " cells"
 
@@ -56,7 +53,6 @@ def handlePopulation(self, population_id, component, size=-1, component_obj=None
             )
 
         else:
-
             print_v(
                 "Population: "
                 + population_id
@@ -136,7 +132,6 @@ def handleProjection(
         synapse_obj=None,
         pre_synapse_obj=None,
     ):
-
         print_v("Projection: " + projName + " from " + prePop + " to " + postPop)
 
     #
@@ -158,7 +153,6 @@ def handleConnection(
         delay=0,
         weight=1,
     ):
-
         # self.printConnectionInformation(projName, id, prePop, postPop, synapseType, preCellId, postCellId, localWeight)
 
         print_v(
diff --git a/neuromllite/PsyNeuLinkHandler.py b/neuromllite/PsyNeuLinkHandler.py
index ad2e593..c0220f2 100644
--- a/neuromllite/PsyNeuLinkHandler.py
+++ b/neuromllite/PsyNeuLinkHandler.py
@@ -14,7 +14,6 @@
 
 
 class PsyNeuLinkHandler(DefaultNetworkHandler):
-
     bids_mdf_info = {}
     bids_mdf_info["graphs"] = []
 
@@ -26,19 +25,16 @@ def __init__(self, nl_network):
         self.nl_network = nl_network
 
     def handle_document_start(self, id, notes):
-
         print_v("Parsing for PsyNeuLink export: %s" % id)
         self.id = id
 
     def finalise_document(self):
-
         print_v("Writing file for...: %s" % self.id)
 
         save_to_json_file(self.bids_mdf_info, "%s.bids-mdf.json" % self.id, indent=4)
         """save_to_json_file(self.bids_mdf_info_hl, '%s.bids-mdf.highlevel.json'%self.id, indent=4)"""
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         self.network_id = network_id
 
@@ -71,7 +67,6 @@ def handle_network(self, network_id, notes, temperature=None):
     def handle_population(
         self, population_id, component, size=-1, component_obj=None, properties={}
     ):
-
         sizeInfo = " as yet unspecified size"
         if size >= 0:
             sizeInfo = ", size: " + str(size) + " cells"
@@ -172,7 +167,6 @@ def handle_location(self, id, population_id, component, x, y, z):
         pass
 
     def finalise_population(self, population_id):
-
         pass
 
     #
@@ -194,7 +188,6 @@ def handle_connection(
         delay=0,
         weight=1,
     ):
-
         # self.print_connection_information(projName, id, prePop, postPop, synapseType, preCellId, postCellId, weight)
         print_v(
             ">>>>>> Src cell: %d, seg: %f, fract: %f -> Tgt cell %d, seg: %f, fract: %f; weight %s, delay: %s ms"
@@ -235,7 +228,6 @@ def handle_connection(
     def handle_input_list(
         self, inputListId, population_id, component, size, input_comp_obj=None
     ):
-
         pass
 
     #
@@ -244,7 +236,6 @@ def handle_input_list(
     def handle_single_input(
         self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
     ):
-
         print_v(
             "Input: %s[%s], cellId: %i, seg: %i, fract: %f, weight: %f"
             % (inputListId, id, cellId, segId, fract, weight)
diff --git a/neuromllite/PsyNeuLinkReader.py b/neuromllite/PsyNeuLinkReader.py
index fdc63ef..cc6eb80 100644
--- a/neuromllite/PsyNeuLinkReader.py
+++ b/neuromllite/PsyNeuLinkReader.py
@@ -7,14 +7,12 @@
 
 
 class PsyNeuLinkReader(NetworkReader):
-
     component_objects = {}  # Store cell ids vs objects, e.g. NeuroML2 based object
 
     PRE_SYN = "silentSyn"
     POST_SYN = "rsDL"
 
     def __init__(self, **parameters):
-
         print_v("Creating PsyNeuLinkReader with %s..." % parameters)
         self.parameters = parameters
         self.current_population = None
@@ -27,7 +25,6 @@ def _generate_id(self, name):
         )
 
     def parse(self, handler):
-
         FORMAT = "BIDS-MDF"
         filename = os.path.abspath(self.parameters["filename"])
         id = filename.split("/")[-1].split(".")[0]
@@ -266,7 +263,6 @@ def parse_dataset(self, d):
 
 
 if __name__ == "__main__":
-
     test_files = [
         "../../neuroConstruct/osb/showcase/PsyNeuLinkShowcase/PsyNeuLink/model_with_simple_graph.json"
     ]
diff --git a/neuromllite/PyNNHandler.py b/neuromllite/PyNNHandler.py
index a87236b..d799153 100644
--- a/neuromllite/PyNNHandler.py
+++ b/neuromllite/PyNNHandler.py
@@ -14,7 +14,6 @@
 
 
 class PyNNHandler(DefaultNetworkHandler):
-
     populations = {}
     projections = {}
     input_sources = {}
@@ -80,11 +79,9 @@ def add_input_source(self, input_source, network):
         # print(['%s (%s): %s'%(i, type(self.input_sources[i]),self.input_sources[i].simple_parameters()) for i in self.input_sources])
 
     def handle_document_start(self, id, notes):
-
         print_v("Document: %s" % id)
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         if temperature:
             print_v("  Temperature: " + temperature)
@@ -94,7 +91,6 @@ def handle_network(self, network_id, notes, temperature=None):
     def handle_population(
         self, population_id, component, size=-1, component_obj=None, properties={}
     ):
-
         sizeInfo = " as yet unspecified size"
         if size >= 0:
             sizeInfo = ", size: " + str(size) + " cells"
@@ -141,7 +137,6 @@ def handle_projection(
         synapse_obj=None,
         pre_synapse_obj=None,
     ):
-
         synInfo = ""
         if synapse_obj:
             synInfo += " (syn: %s)" % synapse_obj.__class__.__name__
@@ -184,7 +179,6 @@ def handle_connection(
         delay=0,
         weight=1,
     ):
-
         # self.print_connection_information(projName, id, prePop, postPop, synapseType, preCellId, postCellId, weight)
         # print_v("Src cell: %d, seg: %f, fract: %f -> Tgt cell %d, seg: %f, fract: %f; weight %s, delay: %s ms" % (preCellId,preSegId,preFract,postCellId,postSegId,postFract, weight, delay))
 
@@ -199,7 +193,6 @@ def handle_connection(
     def finalise_projection(
         self, projName, prePop, postPop, synapse=None, type="projection"
     ):
-
         print_v(
             "Projection finalising: "
             + projName
@@ -233,7 +226,6 @@ def finalise_projection(
     def handle_input_list(
         self, inputListId, population_id, component, size, input_comp_obj=None
     ):
-
         self.print_input_information(inputListId, population_id, component, size)
 
         if size < 0:
@@ -250,7 +242,6 @@ def handle_input_list(
     def handle_single_input(
         self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
     ):
-
         # print_v("Input: %s[%s], cellId: %i, seg: %i, fract: %f, weight: %f" % (inputListId,id,cellId,segId,fract,weight))
 
         population_id, component = self.input_info[inputListId]
diff --git a/neuromllite/SonataHandler.py b/neuromllite/SonataHandler.py
index e11f7d1..8f3b413 100644
--- a/neuromllite/SonataHandler.py
+++ b/neuromllite/SonataHandler.py
@@ -14,7 +14,6 @@
 
 
 class SonataHandler(DefaultNetworkHandler):
-
     positions = {}
     pop_indices = {}
 
@@ -28,7 +27,6 @@ def __init__(self):
         print_v("Initiating Sonata handler")
 
     def handle_document_start(self, id, notes):
-
         print_v("Parsing for Sonata export: %s" % id)
 
         self.config_file_info = {}
@@ -64,7 +62,6 @@ def handle_document_start(self, id, notes):
         self.circuit_file_info["networks"]["nodes"].append({})
 
     def finalise_document(self):
-
         print_v("Writing file...: %s" % id)
         self.sonata_nodes.close()
 
@@ -97,7 +94,6 @@ def finalise_document(self):
         save_to_json_file(self.circuit_file_info, "circuit_config.json", indent=2)
 
     def handle_network(self, network_id, notes, temperature=None):
-
         print_v("Network: %s" % network_id)
         self.network_id = network_id
 
@@ -123,7 +119,6 @@ def handle_network(self, network_id, notes, temperature=None):
     def handle_population(
         self, population_id, component, size=-1, component_obj=None, properties={}
     ):
-
         sizeInfo = " as yet unspecified size"
         if size >= 0:
             sizeInfo = ", size: " + str(size) + " cells"
@@ -159,7 +154,6 @@ def handle_population(
         )
 
     def handle_location(self, id, population_id, component, x, y, z):
-
         if not population_id in self.positions:
             self.positions[population_id] = np.array([[x, y, z]])
             self.pop_indices[population_id] = np.array([id])
@@ -172,7 +166,6 @@ def handle_location(self, id, population_id, component, x, y, z):
             )
 
     def finalise_population(self, population_id):
-
         self.sonata_nodes.create_dataset(
             "nodes/%s/0/positions" % population_id, data=self.positions[population_id]
         )
@@ -202,7 +195,6 @@ def finalise_population(self, population_id):
     def handle_input_list(
         self, inputListId, population_id, component, size, input_comp_obj=None
     ):
-
         self.print_input_information(inputListId, population_id, component, size)
 
         if size < 0:
@@ -219,7 +211,6 @@ def handle_input_list(
     def handle_single_input(
         self, inputListId, id, cellId, segId=0, fract=0.5, weight=1
     ):
-
         print_v(
             "Input: %s[%s], cellId: %i, seg: %i, fract: %f, weight: %f"
             % (inputListId, id, cellId, segId, fract, weight)
diff --git a/neuromllite/SonataReader.py b/neuromllite/SonataReader.py
index 8371c07..a94615e 100644
--- a/neuromllite/SonataReader.py
+++ b/neuromllite/SonataReader.py
@@ -19,7 +19,6 @@
 
 
 def _get_default_nest_syn(nml_doc):
-
     if nml_doc.get_by_id(DEFAULT_NEST_SPIKE_SYN):
         return nml_doc.get_by_id(DEFAULT_NEST_SPIKE_SYN)
 
@@ -90,7 +89,6 @@ class SonataReader(NetworkReader):
     nml_includes = ["PyNN.xml"]
 
     def __init__(self, **parameters):
-
         print_v("Creating SonataReader with %s..." % parameters)
         self.parameters = parameters
 
@@ -361,11 +359,9 @@ def parse(self, handler):
 
                 properties["color"] = color
                 if True or not "locations" in self.cell_info[sonata_pop]["0"]:
-
                     properties = {}  #############  temp for LEMS...
 
                 if model_type != "virtual":
-
                     self.handler.handle_population(
                         nml_pop_id,
                         pop_comp,
@@ -379,7 +375,6 @@ def parse(self, handler):
             self.cell_info[sonata_pop]["pop_map"] = {}
 
             for i in self.cell_info[sonata_pop]["types"]:
-
                 pop = types_vs_pops[self.cell_info[sonata_pop]["types"][i]]
 
                 if not pop in self.cell_info[sonata_pop]["pop_count"]:
@@ -412,7 +407,6 @@ def parse(self, handler):
         #  Load simulation info into self.simulation_config
 
         if self.simulation_config:
-
             if self.simulation_config:
                 for m in self.simulation_config["manifest"]:
                     path = self.subs(self.simulation_config["manifest"][m])
@@ -505,7 +499,6 @@ def parse(self, handler):
             node_set = info["node_set"]
 
             if info["input_type"] == "current_clamp":
-
                 comp = "PG_%s" % input
                 self.input_comp_info[input][info["input_type"]][comp] = {
                     "amp": info["amp"],
@@ -514,7 +507,6 @@ def parse(self, handler):
                 }
 
                 for nml_pop_id in self.node_set_mappings[node_set]:
-
                     input_list_id = "il_%s_%s" % (input, nml_pop_id)
                     indices = self.node_set_mappings[node_set][nml_pop_id]
 
@@ -579,7 +571,6 @@ def parse(self, handler):
 
         projections_created = []
         for conn in self.conn_info:
-
             pre_node = self.conn_info[conn]["pre_node"]
             post_node = self.conn_info[conn]["post_node"]
 
@@ -663,7 +654,6 @@ def parse(self, handler):
 
                 if not pop_type_pre == "virtual":
                     if not proj_id in projections_created:
-
                         self.handler.handle_projection(
                             proj_id, pre_pop, post_pop, synapse
                         )
@@ -743,7 +733,6 @@ def parse_group(self, g):
                     self.conn_info[self.current_edge] = {}
 
                 if g._v_name == self.current_edge:
-
                     self.current_pre_node = g._v_name.split("_to_")[0]
                     self.current_post_node = g._v_name.split("_to_")[1]
                     # print('  Found edge %s -> %s'%(self.current_pre_node, self.current_post_node))
@@ -785,7 +774,6 @@ def parse_dataset(self, d):
         elif (
             self.current_sonata_pop
         ):  # e.g. parent group is cortex with child datasets node_id etc.
-
             if d.name == "node_group_id":
                 for i in range(0, d.shape[0]):
                     if not d[i] == 0:
@@ -857,7 +845,6 @@ def add_neuroml_components(self, nml_doc):
                 info["model_type"] == "point_process"
                 and model_template == "nest:iaf_psc_alpha"
             ):
-
                 is_nest = True
                 from neuroml import IF_curr_alpha
 
@@ -881,7 +868,6 @@ def add_neuroml_components(self, nml_doc):
                 info["model_type"] == "point_process"
                 and model_template == "NEURON_IntFire1"
             ):
-
                 contents = """<Lems>
     <intFire1Cell id="%s" thresh="1mV" reset="0mV" tau="%sms" refract="%sms"/>
 </Lems>""" % (
@@ -901,7 +887,6 @@ def add_neuroml_components(self, nml_doc):
                 )
 
             else:
-
                 from neuroml import IafRefCell
 
                 IafRefCell0 = IafRefCell(
@@ -947,7 +932,6 @@ def add_neuroml_components(self, nml_doc):
                 "level_of_detail" in dyn_params
                 and dyn_params["level_of_detail"] == "instanteneous"
             ):
-
                 contents = """<Lems>
     <impulseSynapse id="%s"/>
 </Lems>""" % (
@@ -1164,7 +1148,6 @@ def process_args():
 
 
 def _get_nml_pop_id(quantity):
-
     if "[" in quantity:
         nml_pop = quantity.split("[")[0]
         nml_index = int(quantity.split("[")[1].split("]")[0])
@@ -1177,7 +1160,6 @@ def _get_nml_pop_id(quantity):
 
 
 def run(args):
-
     print_v(
         "Reading Sonata file: %s and generating network: %s"
         % (args.sonata_config_file, args.network_reference)
@@ -1197,12 +1179,10 @@ def run(args):
     print_v("Generated LEMS file to run network: %s" % (lems_file_name))
 
     if args.jnml or args.neuron:
-
         traces = None
         events = None
 
         if args.jnml:
-
             from pyneuroml import pynml
 
             traces, events = pynml.run_lems_with_jneuroml(
@@ -1213,7 +1193,6 @@ def run(args):
                 reload_events=True,
             )
         if args.neuron:
-
             from pyneuroml import pynml
 
             traces, events = pynml.run_lems_with_jneuroml_neuron(
@@ -1245,7 +1224,6 @@ def run(args):
             nml_q_vs_node_id = {}
 
             for nml_q in traces.keys():
-
                 if nml_q != "t":
                     nml_pop, nml_index = _get_nml_pop_id(nml_q)
                     (sonata_node, sonata_node_id) = sr.nml_ids_vs_gids[nml_pop][
@@ -1256,7 +1234,6 @@ def run(args):
             ordered = sorted(nml_q_vs_node_id, key=nml_q_vs_node_id.get)
 
             for nml_q in ordered:
-
                 if nml_q != "t":
                     v = traces[nml_q]
                     nml_pop, nml_index = _get_nml_pop_id(nml_q)
@@ -1273,7 +1250,6 @@ def run(args):
                     node_info[sonata_node]["gids"].append(sonata_node_id)
 
             for sonata_node in node_info:
-
                 node_grp = h5file.create_group(report_grp, sonata_node)
                 mapping_grp = h5file.create_group(node_grp, "mapping")
 
@@ -1334,7 +1310,6 @@ def run(args):
 
 
 def main(args=None):
-
     if "-test" in sys.argv:
         id = "9_cells"
         id = "300_cells"
@@ -1368,7 +1343,6 @@ def main(args=None):
         NeuroMLHdf5Writer.write(nml_doc,nml_file_name)
         print('Written to: %s'%nml_file_name) """
     else:
-
         if args is None:
             args = process_args()
         run(args=args)
diff --git a/neuromllite/__init__.py b/neuromllite/__init__.py
index 33e64e0..ca81abc 100644
--- a/neuromllite/__init__.py
+++ b/neuromllite/__init__.py
@@ -1,6 +1,6 @@
 import collections
 
-__version__ = "0.5.3"
+__version__ = "0.5.7"
 
 # import pyNN
 # import nest
@@ -41,6 +41,7 @@ def get_locations(self):
 @modelspec.define
 class NMLBase(Base):
     """Base class for NeuroML objects."""
+
     notes: str = field(kw_only=True, default=None, validator=optional(instance_of(str)))
 
 
@@ -59,9 +60,14 @@ class Cell(NMLBase):
         arbor_cell: Name of standard Arbor cell type
         bindsnet_node: Name of standard BindsNET node
     """
+
     id: str = field(validator=instance_of(str))
-    parameters: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-    neuroml2_source_file: str = field(default=None, validator=optional(instance_of(str)))
+    parameters: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
+    neuroml2_source_file: str = field(
+        default=None, validator=optional(instance_of(str))
+    )
     lems_source_file: str = field(default=None, validator=optional(instance_of(str)))
     neuroml2_cell: str = field(default=None, validator=optional(instance_of(str)))
     pynn_cell: str = field(default=None, validator=optional(instance_of(str)))
@@ -82,12 +88,22 @@ class Synapse(NMLBase):
         pynn_synapse_type: The pynn synapse type. Valid values are: "curr_exp", "curr_alpha", "cond_exp", "cond_alpha".
         pynn_receptor_type: The pynn receptor type. Valid values are: "excitatory", "inhibitory".
     """
+
     id: str = field(validator=instance_of(str))
-    parameters: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-    neuroml2_source_file: str = field(default=None, validator=optional(instance_of(str)))
+    parameters: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
+    neuroml2_source_file: str = field(
+        default=None, validator=optional(instance_of(str))
+    )
     lems_source_file: str = field(default=None, validator=optional(instance_of(str)))
-    pynn_synapse_type: str = field(default=None, validator=optional(in_(["curr_exp", "curr_alpha", "cond_exp", "cond_alpha"])))
-    pynn_receptor_type: str = field(default=None, validator=optional(in_(["excitatory", "inhibitory"])))
+    pynn_synapse_type: str = field(
+        default=None,
+        validator=optional(in_(["curr_exp", "curr_alpha", "cond_exp", "cond_alpha"])),
+    )
+    pynn_receptor_type: str = field(
+        default=None, validator=optional(in_(["excitatory", "inhibitory"]))
+    )
 
 
 @modelspec.define
@@ -103,9 +119,14 @@ class InputSource(NMLBase):
         lems_source_file: File name of LEMS file defining the input source
         pynn_input: Name of PyNN input
     """
+
     id: str = field(validator=instance_of(str))
-    parameters: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-    neuroml2_source_file: str = field(default=None, validator=optional(instance_of(str)))
+    parameters: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
+    neuroml2_source_file: str = field(
+        default=None, validator=optional(instance_of(str))
+    )
     neuroml2_input: str = field(default=None, validator=optional(instance_of(str)))
     lems_source_file: str = field(default=None, validator=optional(instance_of(str)))
     pynn_input: str = field(default=None, validator=optional(instance_of(str)))
@@ -125,6 +146,7 @@ class RectangularRegion(NMLBase):
         height: height of the rectangular region
         depth: depth of the rectangular region
     """
+
     id: str = field(validator=instance_of(str))
     x: float = field(validator=instance_of(float), converter=convert2float)
     y: float = field(validator=instance_of(float), converter=convert2float)
@@ -142,6 +164,7 @@ class RandomLayout(NMLBase):
     Args:
         region: Region in which to place population
     """
+
     region: str = field(validator=instance_of(str))
 
 
@@ -156,6 +179,7 @@ class RelativeLayout(NMLBase):
         y: y position relative to y coordinate of Region
         z: z position relative to z coordinate of Region
     """
+
     region: str = field(validator=instance_of(str))
     x: float = field(validator=instance_of(float), converter=convert2float)
     y: float = field(validator=instance_of(float), converter=convert2float)
@@ -172,6 +196,7 @@ class Location(NMLBase):
         y: y coordinate of location
         z: z coordinate of location
     """
+
     x: float = field(validator=instance_of(float), converter=convert2float)
     y: float = field(validator=instance_of(float), converter=convert2float)
     z: float = field(validator=instance_of(float), converter=convert2float)
@@ -185,6 +210,7 @@ class SingleLocation(NMLBase):
     Args:
         location: Location of the single Cell.
     """
+
     location: Location = field(validator=instance_of(Location))
 
 
@@ -202,13 +228,22 @@ class Population(NMLBase):
         relative_layout: Position relative to RectangularRegion.
         single_location: Explicit location of the one Cell in the population
     """
+
     id: str = field(validator=instance_of(str))
     size: ValueExprType = field(validator=instance_of(value_expr_types))
     component: str = field(validator=instance_of(str))
-    properties: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-    random_layout: RandomLayout = field(default=None, validator=optional(instance_of(RandomLayout)))
-    relative_layout: RelativeLayout = field(default=None, validator=optional(instance_of(RelativeLayout)))
-    single_location: SingleLocation = field(default=None, validator=optional(instance_of(SingleLocation)))
+    properties: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
+    random_layout: RandomLayout = field(
+        default=None, validator=optional(instance_of(RandomLayout))
+    )
+    relative_layout: RelativeLayout = field(
+        default=None, validator=optional(instance_of(RelativeLayout))
+    )
+    single_location: SingleLocation = field(
+        default=None, validator=optional(instance_of(SingleLocation))
+    )
 
     def has_positions(self):
         """
@@ -235,6 +270,7 @@ class RandomConnectivity(NMLBase):
     Args:
         probability: Random probability of connection.
     """
+
     probability: ValueExprType = field(validator=instance_of(value_expr_types))
 
 
@@ -243,6 +279,7 @@ class OneToOneConnector(NMLBase):
     """
     A OneToOneConnector definition.
     """
+
     pass
 
 
@@ -255,6 +292,7 @@ class ConvergentConnectivity(NMLBase):
     Args:
         num_per_post: Number per post-synaptic neuron.
     """
+
     num_per_post: float = field(validator=instance_of(float), converter=convert2float)
 
 
@@ -278,17 +316,28 @@ class Projection(NMLBase):
         one_to_one_connector: Connect cell index i in pre pop to cell index i in post pop for all i
 
     """
+
     id: str = field(validator=instance_of(str))
     presynaptic: str = field(validator=optional(instance_of(str)))
     postsynaptic: str = field(validator=optional(instance_of(str)))
     synapse: str = field(validator=optional(instance_of(str)))
     pre_synapse: str = field(default=None, validator=optional(instance_of(str)))
     type: str = field(default="projection", validator=optional(instance_of(str)))
-    delay: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-    weight: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-    random_connectivity: RandomConnectivity = field(default=None, validator=optional(instance_of(RandomConnectivity)))
-    convergent_connectivity: ConvergentConnectivity = field(default=None, validator=optional(instance_of(ConvergentConnectivity)))
-    one_to_one_connector: OneToOneConnector = field(default=None, validator=optional(instance_of(OneToOneConnector)))
+    delay: ValueExprType = field(
+        default=None, validator=optional(instance_of(value_expr_types))
+    )
+    weight: ValueExprType = field(
+        default=None, validator=optional(instance_of(value_expr_types))
+    )
+    random_connectivity: RandomConnectivity = field(
+        default=None, validator=optional(instance_of(RandomConnectivity))
+    )
+    convergent_connectivity: ConvergentConnectivity = field(
+        default=None, validator=optional(instance_of(ConvergentConnectivity))
+    )
+    one_to_one_connector: OneToOneConnector = field(
+        default=None, validator=optional(instance_of(OneToOneConnector))
+    )
 
 
 @modelspec.define
@@ -310,11 +359,21 @@ class Input(NMLBase):
     id: str = field(validator=instance_of(str))
     input_source: str = field(default=None, validator=optional(instance_of(str)))
     population: str = field(default=None, validator=optional(instance_of(str)))
-    cell_ids: ValueExprType = field(default="", validator=optional(instance_of(value_expr_types)))
-    percentage: float = field(default=None, validator=optional(instance_of(float)), converter=convert2float)
-    number_per_cell: ValueExprType = field(default="", validator=optional(instance_of(value_expr_types)))
-    segment_ids: ValueExprType = field(default="", validator=optional(instance_of(value_expr_types)))
-    weight: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
+    cell_ids: ValueExprType = field(
+        default="", validator=optional(instance_of(value_expr_types))
+    )
+    percentage: ValueExprType = field(
+        default=None, validator=optional(instance_of(value_expr_types))
+    )
+    number_per_cell: ValueExprType = field(
+        default="", validator=optional(instance_of(value_expr_types))
+    )
+    segment_ids: ValueExprType = field(
+        default="", validator=optional(instance_of(value_expr_types))
+    )
+    weight: ValueExprType = field(
+        default=None, validator=optional(instance_of(value_expr_types))
+    )
 
 
 @modelspec.define
@@ -326,8 +385,11 @@ class NetworkReader(NMLBase):
         type: The type of NetworkReader
         parameters: Dictionary of parameters for the NetworkReader
     """
+
     type: str = field(default=None, validator=optional(instance_of(str)))
-    parameters: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
+    parameters: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
 
 
 @modelspec.define
@@ -349,16 +411,35 @@ class Simulation(NMLBase):
         plots2D: Work in progress...
         plots3D: Work in progress...
     """
+
     id: str = field(validator=instance_of(str))
-    version: str = field(default=f"NeuroMLlite v{__version__}", validator=optional(instance_of(str)), metadata={"omit_if_default": False})
+    version: str = field(
+        default=f"NeuroMLlite v{__version__}",
+        validator=optional(instance_of(str)),
+        metadata={"omit_if_default": False},
+    )
     network: str = field(default=None, validator=optional(instance_of(str)))
-    duration: float = field(default=None, validator=optional(instance_of(float)), converter=convert2float)
-    dt: float = field(default=None, validator=optional(instance_of(float)), converter=convert2float)
-    seed: int = field(default=None, validator=optional(instance_of(int)), converter=convert2int)
-    record_traces: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-    record_spikes: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-    record_rates: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-    record_variables: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
+    duration: float = field(
+        default=None, validator=optional(instance_of(float)), converter=convert2float
+    )
+    dt: float = field(
+        default=None, validator=optional(instance_of(float)), converter=convert2float
+    )
+    seed: int = field(
+        default=None, validator=optional(instance_of(int)), converter=convert2int
+    )
+    record_traces: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
+    record_spikes: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
+    record_rates: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
+    record_variables: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
     plots2D: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
     plots3D: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
 
@@ -386,7 +467,9 @@ class Network(NMLBase):
     """
 
     id: str = field(validator=instance_of(str))
-    parameters: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
+    parameters: Dict[str, Any] = field(
+        default=None, validator=optional(instance_of(dict))
+    )
     cells: List[Cell] = field(factory=list, validator=instance_of(list))
     synapses: List[Synapse] = field(factory=list, validator=instance_of(list))
     input_sources: List[InputSource] = field(factory=list, validator=instance_of(list))
@@ -394,14 +477,19 @@ class Network(NMLBase):
     populations: List[Population] = field(factory=list, validator=instance_of(list))
     projections: List[Projection] = field(factory=list, validator=instance_of(list))
     inputs: List[Input] = field(factory=list, validator=instance_of(list))
-    version: str = field(default=f"NeuroMLlite v{__version__}", validator=instance_of(str), metadata={"omit_if_default": False})
+    version: str = field(
+        default=f"NeuroMLlite v{__version__}",
+        validator=instance_of(str),
+        metadata={"omit_if_default": False},
+    )
     seed: int = field(default=None, validator=optional(instance_of(int)))
-    temperature: float = field(default=None, validator=optional(instance_of(float)), converter=convert2float)
+    temperature: float = field(
+        default=None, validator=optional(instance_of(float)), converter=convert2float
+    )
     network_reader: NetworkReader = field(default=None)
 
 
 if __name__ == "__main__":
-
     net = Network(id="net")
     doc = net.generate_documentation(format="markdown")
     print(doc)
diff --git a/neuromllite/gui/NMLliteUI.py b/neuromllite/gui/NMLliteUI.py
index 70f9bb1..d54bbbb 100644
--- a/neuromllite/gui/NMLliteUI.py
+++ b/neuromllite/gui/NMLliteUI.py
@@ -2,8 +2,8 @@
 from os.path import realpath
 import sys
 
-from PyQt5.QtGui import *
-from PyQt5.QtWidgets import *
+from PyQt6.QtGui import *
+from PyQt6.QtWidgets import *
 
 from matplotlib.backends.backend_qt5agg import FigureCanvas
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
@@ -16,34 +16,31 @@
 from neuromllite.utils import evaluate
 from neuromllite.utils import print_v, print_
 from neuromllite.utils import is_spiking_input_population
-from pyneuroml.pynml import get_next_hex_color
+from pyneuroml.utils.plot import get_next_hex_color
 
 from functools import partial
 
 
 class ParameterSpinBox(QDoubleSpinBox):
-
-    value_type=float
+    value_type = float
 
     def __init__(self, value, value_type=float):
-
         super(QDoubleSpinBox, self).__init__()
         self.value_type = value_type
         self.setDecimals(18)
         self.setMaximum(1e16)
         self.setMinimum(-1e16)
-        if self.value_type==int:
+        if self.value_type == int:
             self.setSingleStep(1)
         else:
             self.setSingleStep(value / 20.0)
         self.setValue(value_type(value))
 
-
-        #print('ParameterSpinBox: %s/%s (%s/%s), %s'%(value, self.value(), value_type, type(self.value()),self.singleStep()))
+        # print('ParameterSpinBox: %s/%s (%s/%s), %s'%(value, self.value(), value_type, type(self.value()),self.singleStep()))
 
     # TODO: handle a spinner on values like -60mV etc.
     def textFromValue(self, value):
-        return "%i" % value if self.value_type==int else "%s" % value
+        return "%i" % value if self.value_type == int else "%s" % value
 
     # TODO: handle a spinner on values like -60mV etc.
     def final_value(self):
@@ -51,7 +48,6 @@ def final_value(self):
 
 
 class NMLliteUI(QWidget):
-
     default_vals = {}
 
     simulators = [
@@ -90,7 +86,6 @@ def updated_param(self, p):
             self.update_simulation_json()
 
     def update_network_json(self):
-
         self.nmlliteNetText.clear()
         try:
             j = self.network.to_json()
@@ -99,7 +94,6 @@ def update_network_json(self):
             self.nmlliteNetText.insertPlainText("Error parsing model: %s" % e)
 
     def update_simulation_json(self):
-
         self.nmlliteSimText.clear()
         try:
             j = self.simulation.to_json()
@@ -129,7 +123,6 @@ def add_tab(
         toolbar=False,
         options=False,
     ):
-
         if name in self.all_tabs:
             raise Exception("The name for a tab: %s is already taken!" % name)
 
@@ -170,13 +163,13 @@ def add_tab(
             label = QLabel(
                 "An image will be generated here. Push the appropriate button on the left"
             )
-            label.setBackgroundRole(QPalette.Base)
-            label.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Ignored)
+            # label.setBackgroundRole(QPalette.Base)
+            # label.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Ignored)
             label.setScaledContents(True)
             self.all_image_qlabels[name] = label
 
             scrollArea = QScrollArea()
-            scrollArea.setBackgroundRole(QPalette.Light)
+            # scrollArea.setBackgroundRole(QPalette.Light)
             scrollArea.setWidget(label)
             scrollArea.setVisible(True)
 
@@ -244,7 +237,6 @@ def get_value_entry(self, name, value, entry_map, value_type=float):
             entry.textChanged.connect(self.updated_param)
 
         else:
-
             try:
                 entry = ParameterSpinBox(value, value_type)
                 entry_map[name] = entry
@@ -269,10 +261,10 @@ def get_value_entry(self, name, value, entry_map, value_type=float):
 
     def dialog_popup(self, message):
         dialog = QMessageBox()
-        dialog.setIcon(QMessageBox.Warning)
+        dialog.setIcon(QMessageBox.Icon.Warning)
         dialog.setWindowTitle("Message")
         dialog.setText(message)
-        dialog.exec_()
+        dialog.exec()
 
     def __init__(self, nml_sim_file, parent=None):
         """Constructor for the GUI"""
@@ -301,7 +293,9 @@ def __init__(self, nml_sim_file, parent=None):
             self.sim_base_dir = "."
 
         if self.simulation.network is None:
-            print_v(f"ERROR: The provided simulation file, {nml_sim_file}, does not refer to a network.")
+            print_v(
+                f"ERROR: The provided simulation file, {nml_sim_file}, does not refer to a network."
+            )
             print_v("Please provide a NeuroMLlite simulation file.")
             sys.exit(-1)
 
@@ -338,7 +332,6 @@ def __init__(self, nml_sim_file, parent=None):
         self.plotTabs.addTab(self.heatmapTab, "Heatmap")
 
         if self.simulation.plots2D is not None:
-
             self.plot2DTab = QTabWidget()
             self.plotTabs.addTab(self.plot2DTab, "2D plots")
 
@@ -352,7 +345,6 @@ def __init__(self, nml_sim_file, parent=None):
                 )
 
         if self.simulation.plots3D is not None:
-
             self.plot3DTab = QTabWidget()
             self.plotTabs.addTab(self.plot3DTab, "3D plots")
 
@@ -542,7 +534,9 @@ def __init__(self, nml_sim_file, parent=None):
             pval = self.network.seed
             label = QLabel("Net generation seed")
             paramLayout.addWidget(label, rows, 0)
-            entry = self.get_value_entry("seed", pval, self.param_entries, value_type=int)
+            entry = self.get_value_entry(
+                "seed", pval, self.param_entries, value_type=int
+            )
             paramLayout.addWidget(entry, rows, 1)
 
         if self.network.temperature is not None:
@@ -602,8 +596,10 @@ def __init__(self, nml_sim_file, parent=None):
             if sval is not None:
                 label = QLabel("%s" % s)
                 paramLayout.addWidget(label, rows, 0)
-                value_type=int if s=='seed' else float
-                entry = self.get_value_entry(s, sval, self.sim_entries,value_type=value_type)
+                value_type = int if s == "seed" else float
+                entry = self.get_value_entry(
+                    s, sval, self.sim_entries, value_type=value_type
+                )
                 paramLayout.addWidget(entry, rows, 1)
 
         rows += 1
@@ -753,7 +749,7 @@ def show3Dimage(self):
         self.add_image(nml_view_file, self.IMAGE_3D_TAB)
 
     def showGraph(self):
-        """Generate graph buttom has been pressed"""
+        """Generate graph button has been pressed"""
 
         print_v("Graph button was clicked.")
 
@@ -806,8 +802,8 @@ def update_net_sim(self):
         """Set the parameters in the network/simulation from the GUI values"""
 
         for p in self.param_entries:
-            #print("Updating: %s to %s (%s)" % (p, self.param_entries[p], type(self.param_entries[p])))
-            if type(self.param_entries[p])==QLineEdit:
+            # print("Updating: %s to %s (%s)" % (p, self.param_entries[p], type(self.param_entries[p])))
+            if type(self.param_entries[p]) == QLineEdit:
                 v = self.param_entries[p].text()
             else:
                 v = self.param_entries[p].final_value()
@@ -855,6 +851,7 @@ def runSimulation(self):
             self.replotSimResults()
         except Exception as e:
             import traceback
+
             print(traceback.format_exc())
             self.dialog_popup("Error: %s" % e)
 
@@ -874,7 +871,6 @@ def _get_pop_size(self, pop_id):
         return evaluate(pop.size, self.network.parameters)
 
     def _get_pop_id_cell_id(self, quantity):
-
         if "[" in quantity:
             # e.g. Epop[5]/v
             pop_id = quantity.split("[")[0]
@@ -887,7 +883,6 @@ def _get_pop_id_cell_id(self, quantity):
         return pop_id, cell_id
 
     def traceSelect(self):
-
         print_v(
             "traceSelect button was clicked. Traces shown: %s; colours: %s"
             % (self.current_traces_shown, self.current_traces_colours)
@@ -896,7 +891,7 @@ def traceSelect(self):
         dialog = QDialog(self)
         dialog.setWindowTitle("Select which traces to plot")
 
-        QBtn = QDialogButtonBox.Ok  # | QDialogButtonBox.Cancel
+        QBtn = QDialogButtonBox.StandardButton.Ok  # | QDialogButtonBox.Cancel
 
         buttonBox = QDialogButtonBox(QBtn)
         buttonBox.accepted.connect(dialog.accept)
@@ -926,11 +921,10 @@ def traceSelect(self):
                 count += 1
 
         layout.addWidget(buttonBox, count, 1)
-        dialog.exec_()
+        dialog.exec()
         self.replotSimResults()
 
     def traceSelectClicked(self, key):
-
         cb = self.all_cbs[key]
         # print('Clicked: %s, %s, key: %s'%(cb.text(),cb.isChecked(), key))
         self.current_traces_shown[key] = cb.isChecked()
@@ -965,7 +959,6 @@ def _eval_at_all(self, expr, parameters, traces):
         return ret_val
 
     def replotSimResults(self):
-
         simulator = str(self.simulatorComboBox.currentText())
         self.traceSelectButton.setEnabled(True)
 
@@ -995,7 +988,6 @@ def replotSimResults(self):
         heat_array = []
 
         for key in sorted(self.current_traces.keys()):
-
             if not key in self.current_traces_shown:
                 self.current_traces_shown[key] = True
 
@@ -1065,7 +1057,6 @@ def replotSimResults(self):
         ## Plot 2D
 
         if self.simulation.plots2D is not None:
-
             for plot2D in self.simulation.plots2D:
                 info = self.simulation.plots2D[plot2D]
                 fig = self.all_figures[plot2D]
@@ -1130,7 +1121,6 @@ def replotSimResults(self):
         ## Plot 3D
 
         if self.simulation.plots3D is not None:
-
             for plot3D in self.simulation.plots3D:
                 info = self.simulation.plots3D[plot3D]
                 fig = self.all_figures[plot3D]
@@ -1204,7 +1194,6 @@ def replotSimResults(self):
         max_id = 0
 
         for pop_id in sorted(ids_for_pop.keys()):
-
             if pop_id in pop_colors:
                 c = pop_colors[pop_id]
             else:
@@ -1329,11 +1318,10 @@ def main():
     nmlui = NMLliteUI(nml_sim_file)
     nmlui.show()
 
-    sys.exit(app.exec_())
+    sys.exit(app.exec())
 
 
 def usage():
-
     from neuromllite import __version__ as version
 
     MAIN_CLA = "nmllite-ui"
diff --git a/neuromllite/sweep/GenerateTests.py b/neuromllite/sweep/GenerateTests.py
index 69e2e6f..4dbc9e8 100644
--- a/neuromllite/sweep/GenerateTests.py
+++ b/neuromllite/sweep/GenerateTests.py
@@ -5,7 +5,6 @@
 
 
 if __name__ == "__main__":
-
     hhcell = Cell(
         id="hhcell", neuroml2_source_file="../../examples/test_files/hhcell.cell.nml"
     )
diff --git a/neuromllite/sweep/ParameterSweep.py b/neuromllite/sweep/ParameterSweep.py
index 64fbf2a..9130c89 100644
--- a/neuromllite/sweep/ParameterSweep.py
+++ b/neuromllite/sweep/ParameterSweep.py
@@ -45,7 +45,6 @@ def __init__(
         show_plot_already=False,
         peak_threshold=0,
     ):
-
         self.sim = load_simulation_json(runner.nmllite_sim)
 
         self.colormap = "jet"
@@ -119,7 +118,6 @@ def _rem_key(self, d, key):
         return r
 
     def _sweep(self, v, f, reference=""):
-
         keys = list(v)
 
         if len(keys) > 1:
@@ -159,7 +157,6 @@ def _get_sim_duration_ms(self, parameters):
             return self.sim.duration
 
     def _run_all(self):
-
         import pp
 
         ppservers = ()
@@ -173,7 +170,6 @@ def _run_all(self):
 
         submitted = 0
         for ref in self.report["Simulations"]:
-
             report_here = self.report["Simulations"][ref]
 
             params = report_here["parameters"]
@@ -333,7 +329,6 @@ def _run_all(self):
         print_v("-------------------------------------------")
 
     def run(self):
-
         print_v("Running...")
         self._sweep(self.vary, self.fixed)
         self._run_all()
@@ -345,7 +340,6 @@ def run(self):
             plt.savefig(self.save_plot_all_to, bbox_inches="tight")
 
         if self.heatmap_all:
-
             self.hm_fig, self.hm_ax = plt.subplots()
             z = np.array(self.hm_z)
 
@@ -409,7 +403,6 @@ def run(self):
         return self.report
 
     def print_report(self):
-
         print_v("--- REPORT:")
         import json
 
@@ -424,7 +417,6 @@ def plotLines(
         logx=False,
         logy=False,
     ):
-
         all_pvals = OrderedDict()
         all_lines = OrderedDict()
 
@@ -490,7 +482,6 @@ def plotLines(
         maxy = -1 * sys.float_info.max
 
         for t in all_traces:
-
             for ref in all_lines[t]:
                 print_v("Add data %s, %s" % (t, ref))
 
@@ -546,7 +537,6 @@ def plotLines(
 
 
 def run_instance(runner, i, total, job_dir, params):
-
     print(
         "============================================================= \n\n"
         + "     Instance (%s of %s): %s\n" % (i, total, params)
@@ -564,7 +554,6 @@ def run_instance(runner, i, total, job_dir, params):
 
 class NeuroMLliteRunner:
     def __init__(self, nmllite_sim, simulator="jNeuroML"):
-
         real_sim = os.path.realpath(nmllite_sim)
         print_v("Created NeuroMLliteRunner to run %s in %s" % (real_sim, simulator))
 
@@ -577,7 +566,6 @@ def __init__(self, nmllite_sim, simulator="jNeuroML"):
     """
 
     def run_once(self, job_dir, **kwargs):
-
         from neuromllite.utils import print_v
         from neuromllite.utils import load_simulation_json, load_network_json
         from neuromllite.NetworkGenerator import generate_and_run
@@ -621,7 +609,6 @@ def run_once(self, job_dir, **kwargs):
 
 
 if __name__ == "__main__":
-
     if "-2d" in sys.argv:
         fixed = {"dt": 0.025}
         vary = {
@@ -759,7 +746,6 @@ def run_once(self, job_dir, **kwargs):
         plt.show()
 
     elif "-run" in sys.argv:
-
         simulator = "jNeuroML_NetPyNE"
         simulator = "jNeuroML"
         # simulator = 'PyNN_NEST'
diff --git a/neuromllite/test/sonata/test_sonata_reader.py b/neuromllite/test/sonata/test_sonata_reader.py
index 8a24b3d..97a906e 100644
--- a/neuromllite/test/sonata/test_sonata_reader.py
+++ b/neuromllite/test/sonata/test_sonata_reader.py
@@ -2,7 +2,6 @@
 
 
 def main():
-
     ids = ["5_cells_iclamp", "9_cells", "300_intfire", "300_cells"]
     ids += ["sim_tests/intfire/one_cell_iclamp_nest/input"]
     ids += ["sim_tests/intfire/ten_cells_iclamp_nest/input"]
diff --git a/neuromllite/test/test_base.py b/neuromllite/test/test_base.py
index 9fa4fbd..55c5f22 100644
--- a/neuromllite/test/test_base.py
+++ b/neuromllite/test/test_base.py
@@ -14,7 +14,6 @@
 
 
 def get_example_network():
-
     net = Network(id="net0", parameters={})
     net.notes = "...."
 
@@ -43,7 +42,6 @@ def get_example_network():
 
 
 def get_example_simulation():
-
     id = "Sim0"
     sim = Simulation(
         id=id,
@@ -57,7 +55,6 @@ def get_example_simulation():
 
 class TestCustomSaveLoad(unittest.TestCase):
     def test_save_load_json(self):
-
         @modelspec.define
         class NewCell(Base):
             """
@@ -67,8 +64,11 @@ class NewCell(Base):
                 id: the cell id
                 neuroml2_source_file: The path to the source file
             """
+
             id: str = field(validator=instance_of(str))
-            neuroml2_source_file: str = field(default=None, validator=optional(instance_of(str)))
+            neuroml2_source_file: str = field(
+                default=None, validator=optional(instance_of(str))
+            )
 
         @modelspec.define
         class NewSynapse(Base):
@@ -80,8 +80,11 @@ class NewSynapse(Base):
                 neuroml2_source_file: The path to the source file
                 tested: A boolean attribute
             """
+
             id: str = field(validator=instance_of(str))
-            neuroml2_source_file: str = field(default=None, validator=optional(instance_of(str)))
+            neuroml2_source_file: str = field(
+                default=None, validator=optional(instance_of(str))
+            )
             tested: bool = field(default=None, validator=optional(instance_of(bool)))
 
         @modelspec.define
@@ -93,7 +96,10 @@ class NewRandomConnectivity(Base):
                 probability: Random probability of connection
 
             """
-            probability: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
+
+            probability: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
 
         @modelspec.define
         class NewNetwork(Base):
@@ -110,22 +116,40 @@ class NewNetwork(Base):
                 parameters: Dictionary of global parameters for the network
                 random_connectivity: Use random connectivity
             """
+
             id: str = field(validator=instance_of(str))
             cells: List[NewCell] = field(factory=list)
             synapses: List[NewSynapse] = field(factory=list)
             version: str = field(default="NeuroMLlite 0.0", validator=instance_of(str))
             seed: int = field(default=None, validator=optional(instance_of(int)))
             stable: bool = field(default=None, validator=optional(instance_of(bool)))
-            parameters: Dict[str, Any] = field(default=None, validator=optional(instance_of(dict)))
-            random_connectivity: NewRandomConnectivity = field(default=None, validator=optional(instance_of(NewRandomConnectivity)))
-            ee0: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-            ee1: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-            ee2: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-            ee3: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-            ee4: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-            ee5: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-            ee6: ValueExprType = field(default=None, validator=optional(instance_of(value_expr_types)))
-
+            parameters: Dict[str, Any] = field(
+                default=None, validator=optional(instance_of(dict))
+            )
+            random_connectivity: NewRandomConnectivity = field(
+                default=None, validator=optional(instance_of(NewRandomConnectivity))
+            )
+            ee0: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
+            ee1: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
+            ee2: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
+            ee3: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
+            ee4: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
+            ee5: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
+            ee6: ValueExprType = field(
+                default=None, validator=optional(instance_of(value_expr_types))
+            )
 
         net = NewNetwork(id="netid", parameters={"size": 3, "name": None})
 
@@ -220,9 +244,7 @@ class NewNetwork(Base):
 
 class TestBaseSaveLoad(unittest.TestCase):
     def test_save_load_json(self):
-
         for o in [get_example_simulation(), get_example_network()]:
-
             str0 = str(o)
             json0 = o.to_json()
 
@@ -250,9 +272,7 @@ def test_save_load_json(self):
                 self.assertEqual(json0, json1)
 
     def test_save_load_pickle(self):
-
         for o in [get_example_simulation(), get_example_network()]:
-
             str0 = str(o)
             json0 = o.to_json()
 
@@ -272,7 +292,6 @@ def test_save_load_pickle(self):
 
 
 if __name__ == "__main__":
-
     # Some tests
     tc = TestCustomSaveLoad()
     tc.test_save_load_json()
diff --git a/neuromllite/test/test_generate.py b/neuromllite/test/test_generate.py
index d32a5f0..18d6440 100644
--- a/neuromllite/test/test_generate.py
+++ b/neuromllite/test/test_generate.py
@@ -13,7 +13,6 @@
 
 class TestGenerate(unittest.TestCase):
     def get_example_simulation(self):
-
         id = "Sim3"
         sim = Simulation(
             id=id,
@@ -25,7 +24,6 @@ def get_example_simulation(self):
         return sim
 
     def test_generate_nml(self):
-
         sim = self.get_example_simulation()
         network = load_network_json(sim.network)
 
diff --git a/neuromllite/test/test_utils.py b/neuromllite/test/test_utils.py
index aa2b4c7..9bc0fe0 100644
--- a/neuromllite/test/test_utils.py
+++ b/neuromllite/test/test_utils.py
@@ -16,7 +16,6 @@
 
 class TestUtils(unittest.TestCase):
     def test_pops_vs_cell_indices(self):
-
         from neuromllite.utils import get_pops_vs_cell_indices_seg_ids
 
         network = get_example_network()
@@ -26,7 +25,6 @@ def test_pops_vs_cell_indices(self):
         sim.record_rates = {}
 
         for recordSpec in [sim.record_traces, sim.record_spikes, sim.record_rates]:
-
             print("Testing...")
             recordSpec["all"] = "*"
             pvi = get_pops_vs_cell_indices_seg_ids(recordSpec, network)
diff --git a/neuromllite/utils.py b/neuromllite/utils.py
index c64dee9..86c67e6 100644
--- a/neuromllite/utils.py
+++ b/neuromllite/utils.py
@@ -80,6 +80,14 @@ def load_network_yaml(filename):
 
     return net
 
+def load_simulation(filename):
+    """
+    Load a NeuroMLlite simulation JSON/YAML file
+    """
+    if filename.endswith(".yaml") or filename.endswith(".yml"):
+        return load_simulation_yaml(filename)
+    else:
+        return load_simulation_json(filename)
 
 def load_simulation_json(filename: str) -> Optional[dict]:
     """
@@ -109,7 +117,6 @@ def load_simulation_json(filename: str) -> Optional[dict]:
 
 
 def get_pops_vs_cell_indices_seg_ids(recordSpec, network):
-
     pvc = {}
     if recordSpec is not None:
         for p in recordSpec:
@@ -132,7 +139,6 @@ def get_pops_vs_cell_indices_seg_ids(recordSpec, network):
 
 
 def _generate_cell_indices_seg_ids(pop_id, indices_segids, network):
-
     a = {}
     pop = network.get_child(pop_id, "populations")
 
@@ -159,7 +165,6 @@ def _generate_cell_indices_seg_ids(pop_id, indices_segids, network):
 
 
 def is_spiking_input_population(population, network):
-
     cell = network.get_child(population.component, "cells")
 
     return is_spiking_input_cell(cell)
@@ -195,7 +200,6 @@ def create_new_model(
     network_filename=None,
     simulation_filename=None,
 ):
-
     ################################################################################
     ###   Build a new network
 
@@ -208,7 +212,7 @@ def create_new_model(
     ################################################################################
     ###   Add some regions
 
-    if default_region:
+    if default_region is not None:
         if type(default_region) == str:
             r1 = RectangularRegion(
                 id=default_region, x=0, y=0, z=0, width=1000, height=100, depth=1000
@@ -241,9 +245,7 @@ def create_new_model(
             properties={"color": color_for_default_population},
         )
 
-        if default_region:
-            pop.region = default_region
-
+        if default_region is not None:
             pop.random_layout = RandomLayout(region=default_region.id)
 
         net.populations.append(pop)
@@ -263,7 +265,6 @@ def create_new_model(
     ###   Add some inputs
 
     if input_for_default_population:
-
         net.input_sources.append(input_for_default_population)
 
         net.inputs.append(
diff --git a/regenerateAndTest.sh b/regenerateAndTest.sh
index 0eaaef8..219d575 100755
--- a/regenerateAndTest.sh
+++ b/regenerateAndTest.sh
@@ -35,8 +35,8 @@ python Example4.py
 python Example4.py -netpyne
 if [[ "$CI" != "true" ]]; then
     python Example4.py -pynnnest
+    python Example4.py -pynnnrn
 fi
-python Example4.py -pynnnrn
 #python Example4.py -pynnbrian  # Not supported in python 3...
 python Example4.py -jnmlnetpyne
 python Example4.py -jnmlnrn
@@ -64,8 +64,8 @@ python Example7.py -jnmlnrn
 python Example7.py -jnml
 if [[ "$CI" != "true" ]]; then
     python Example7.py -pynnnest
+    python Example7.py -pynnnrn
 fi
-python Example7.py -pynnnrn
 
 echo
 echo "**** Running Example 8 ****"
diff --git a/setup.py b/setup.py
index 22bb74c..ba65143 100644
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,7 @@
     long_description=open("README.md").read(),
     long_description_content_type="text/markdown",
     install_requires=[
-        "libNeuroML>=0.4.0",
+        "libNeuroML>=0.5.1",
         "pyyaml",
         "numpy",
         "tables",
@@ -32,11 +32,11 @@
         "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Topic :: Scientific/Engineering",
     ],
 )