NeuroML · pgleeson · May 10, 2025 · Apr 11, 2025 · Apr 11, 2025 · May 1, 2025
diff --git a/LICENSE.lesser b/LICENSE.lesser
@@ -163,4 +163,3 @@ whether future versions of the GNU Lesser General Public License shall
 apply, that proxy's public statement of acceptance of any version is
 permanent authorization for you to choose that version for the
 Library.
-
diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@ A single package in Python unifying scripts and modules for reading, writing, si
 
 Builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML).
 
-Installation
+Installation 
 ------------
 
 ### Dependencies

diff --git a/docs/source/_static/pynml_jnml.svg b/docs/source/_static/pynml_jnml.svg
diff --git a/docs/source/pyneuroml.analysis.rst b/docs/source/pyneuroml.analysis.rst
@@ -29,4 +29,3 @@ pyneuroml.analysis.ChannelHelper module
    :members:
    :undoc-members:
    :show-inheritance:
-
diff --git a/docs/source/pyneuroml.channelml.rst b/docs/source/pyneuroml.channelml.rst
@@ -5,4 +5,3 @@ pyneuroml.channelml package
    :members:
    :undoc-members:
    :show-inheritance:
-
diff --git a/docs/source/pyneuroml.neuron.rst b/docs/source/pyneuroml.neuron.rst
@@ -13,4 +13,3 @@ pyneuroml.neuron.analysis module
    :members:
    :undoc-members:
    :show-inheritance:
-
diff --git a/docs/source/pyneuroml.povray.rst b/docs/source/pyneuroml.povray.rst
@@ -29,4 +29,3 @@ pyneuroml.povray.OverlaySimulation module
    :members:
    :undoc-members:
    :show-inheritance:
-
diff --git a/docs/source/refs.bib b/docs/source/refs.bib
@@ -20,4 +20,3 @@ @Article{Vella2014
   timestamp    = {2019-02-20},
   year         = {2014},
 }
-
diff --git a/examples/IM.channel.nml b/examples/IM.channel.nml
@@ -6,33 +6,33 @@
     <ionChannel id="IM" conductance="10pS" type="ionChannelHH" species="k">
 
         <notes>Slow M-type K+ current for spike frequency adaptation
-            
+
 Comment from original mod file:
 M-current, responsible for the adaptation of firing rate and the afterhyperpolarization (AHP) of cortical pyramidal cells
 First-order model described by hodgkin-Hyxley like equations.
 K+ current, activated by depolarization, noninactivating.
 
-Model taken from Yamada, W.M., Koch, C. and Adams, P.R.  Multiple channels and calcium dynamics.  In: Methods in Neuronal Modeling, 
+Model taken from Yamada, W.M., Koch, C. and Adams, P.R.  Multiple channels and calcium dynamics.  In: Methods in Neuronal Modeling,
 edited by C. Koch and I. Segev, MIT press, 1989, p 97-134.
-    
-See also: McCormick, D.A., Wang, Z. and Huguenard, J. Neurotransmitter control of neocortical neuronal activity and excitability. 
+
+See also: McCormick, D.A., Wang, Z. and Huguenard, J. Neurotransmitter control of neocortical neuronal activity and excitability.
 Cerebral Cortex 3: 387-398, 1993.
 
 Written by Alain Destexhe, Laval University, 1995
         </notes>
-                
+
         <annotation>
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                 <rdf:Description rdf:about="IM">
-                    
+
                     <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
                         <rdf:Bag>
                             <rdf:li>Minimal Hodgkin-Huxley type models for different classes of cortical and thalamic neurons</rdf:li>
                             <rdf:li rdf:resource="19011929"/>
                         </rdf:Bag>
                     </bqmodel:isDescribedBy>
 
-                
+
                     <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                         <rdf:Bag>
                             <rdf:li>K channels</rdf:li>
@@ -48,7 +48,7 @@ Written by Alain Destexhe, Laval University, 1995
             <timeCourse type="IM_p_tau_tau"/>
             <steadyState type="IM_p_inf_inf"/>
         </gate>
-                            
+
     </ionChannel>
 
     <ComponentType name="IM_p_tau_tau" extends="baseVoltageDepTime">

diff --git a/examples/KConductance.channel.nml b/examples/KConductance.channel.nml
@@ -1,19 +1,19 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" 
-         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_v2beta4.xsd" 
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
+         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_v2beta4.xsd"
          id="KConductance">
 
     <notes>Channel file containing a single channel description</notes>
 
     <ionChannel id="KConductance" conductance="10pS" type="ionChannelHH" species="k">
 
         <notes>HH K Channel</notes>
-                
+
         <annotation>
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                 <rdf:Description rdf:about="KConductance">
-                    
+
                     <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
                         <rdf:Bag>
                             <rdf:li>A. L. Hodgkin and A. F. Huxley, A quantitative description of membrane current and its application
@@ -22,7 +22,7 @@
                         </rdf:Bag>
                     </bqmodel:isDescribedBy>
 
-                
+
                     <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                         <rdf:Bag>
                             <rdf:li>K channels</rdf:li>
@@ -38,7 +38,7 @@
             <forwardRate type="HHExpLinearRate" rate="0.1per_ms" scale="10mV" midpoint="-55mV"/>
             <reverseRate type="HHExpRate" rate="0.125per_ms" scale="-80mV" midpoint="-65mV"/>
         </gate>
-                            
+
     </ionChannel>
 
 </neuroml>
diff --git a/examples/Kd.channel.nml b/examples/Kd.channel.nml
@@ -6,7 +6,7 @@
     <ionChannel id="Kd" conductance="10pS" type="ionChannelHH" species="k">
 
         <notes>Delayed rectifier K+ current based on Traub and Miles 1991.
-            
+
 Comment from original mod file: Hippocampal HH channels
 Fast Na+ and K+ currents responsible for action potentials
 Iterative equations
@@ -16,19 +16,19 @@ Equations modified by Traub, for Hippocampal Pyramidal cells, in: Traub and Mile
 - range variable vtraub adjust threshold
 - Written by Alain Destexhe, Salk Institute, Aug 1992
 - Modified Oct 96 for compatibility with Windows: trap low values of arguments</notes>
-                
+
         <annotation>
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                 <rdf:Description rdf:about="Kd">
-                    
+
                     <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
                         <rdf:Bag>
                             <rdf:li>Minimal Hodgkin-Huxley type models for different classes of cortical and thalamic neurons</rdf:li>
                             <rdf:li rdf:resource="19011929"/>
                         </rdf:Bag>
                     </bqmodel:isDescribedBy>
 
-                
+
                     <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                         <rdf:Bag>
                             <rdf:li>K channels</rdf:li>
@@ -44,7 +44,7 @@ Equations modified by Traub, for Hippocampal Pyramidal cells, in: Traub and Mile
             <forwardRate type="Kd_n_alpha_rate"/>
             <reverseRate type="Kd_n_beta_rate"/>
         </gate>
-                            
+
     </ionChannel>
 
     <ComponentType name="Kd_n_alpha_rate" extends="baseVoltageDepRate">

diff --git a/examples/LEMS_NML2_Ex5_DetCell.xml b/examples/LEMS_NML2_Ex5_DetCell.xml
@@ -3,8 +3,8 @@
     <!-- Example with Simple cell specifying segment details-->
 
     <!-- This is a file which can be read and executed by the LEMS Interpreter.
-         It imports the LEMS definitions of the core NeuroML 2 Components, 
-         imports in "pure" NeuroML 2 and contains some LEMS elements for running 
+         It imports the LEMS definitions of the core NeuroML 2 Components,
+         imports in "pure" NeuroML 2 and contains some LEMS elements for running
          a simulation -->
 
 
@@ -23,7 +23,7 @@
 
 
     <Simulation id="sim1" length="300ms" step="0.01ms" target="net1">
-    
+
         <Display id="d1" title="Ex5: HH cell with simple morphology: voltage" timeScale="1ms" xmin="0" xmax="300" ymin="-90" ymax="50">
                 <Line id="v" quantity="hhpop[0]/v" scale="1mV" color="#ffffff" timeScale="1ms"/>
                 <Line id="spiking" quantity="hhpop[0]/spiking" scale="0.1V"  color="#004040" timeScale="1ms"/>
@@ -42,20 +42,20 @@
                 <Line id="gna" quantity="hhpop[0]/bioPhys1/membraneProperties/NaConductances/gDensity" scale="1"  color="#000000" timeScale="1ms"/>
                 <Line id="gk" quantity="hhpop[0]/bioPhys1/membraneProperties/KConductances/gDensity" scale="1"  color="#ff0000" timeScale="1ms"/>
         </Display>
-    
-    
+
+
         <OutputFile id="of0" fileName="results/ex5_v.dat">
-            <OutputColumn id="v" quantity="hhpop[0]/v"/> 
-        </OutputFile>  
-        
+            <OutputColumn id="v" quantity="hhpop[0]/v"/>
+        </OutputFile>
+
         <OutputFile id="of1" fileName="results/ex5_vars.dat">
-            <OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/NaConductances/NaConductance/m/q"/> 
-            <OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/NaConductances/NaConductance/h/q"/> 
-            <OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/KConductances/KConductance/n/q"/> 
-        </OutputFile>  
-    
-        
+            <OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/NaConductances/NaConductance/m/q"/>
+            <OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/NaConductances/NaConductance/h/q"/>
+            <OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/KConductances/KConductance/n/q"/>
+        </OutputFile>
+
+
     </Simulation>
 
 
-</Lems>
+</Lems>
diff --git a/examples/LEMS_NML2_Ex9_FN.xml b/examples/LEMS_NML2_Ex9_FN.xml
@@ -2,15 +2,15 @@
 
     <!-- Example with FitzHugh-Nagumo model -->
 
-    <!-- 
-    
-    
-    
-    
+    <!--
+
+
+
+
     Needs to be updated, see https://github.com/NeuroML/NeuroML2/issues/42
-    
-    
-    
+
+
+
     -->
 
 
@@ -41,13 +41,13 @@
             <Line id="V" quantity="fnPop1[0]/V" scale="1" color="#ee40FF" timeScale="1s" />
             <Line id="W" quantity="fnPop1[0]/W" scale="1" color="#BBA0AA" timeScale="1s" />
         </Display>
-    
+
         <OutputFile id="of1" fileName="results/ex9.dat">
-            <OutputColumn id="V" quantity="fnPop1[0]/V"/> 
-            <OutputColumn id="W" quantity="fnPop1[0]/W"/> 
-        </OutputFile> 
+            <OutputColumn id="V" quantity="fnPop1[0]/V"/>
+            <OutputColumn id="W" quantity="fnPop1[0]/W"/>
+        </OutputFile>
 
     </Simulation>
 
 
-</Lems>
+</Lems>
diff --git a/examples/LeakConductance.channel.nml b/examples/LeakConductance.channel.nml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" 
-         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_v2beta4.xsd" 
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
+         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_v2beta4.xsd"
          id="LeakConductance">
 
     <notes>Channel file containing a single Channel description</notes>

diff --git a/examples/LeakConductance.mod b/examples/LeakConductance.mod
@@ -13,7 +13,7 @@ NEURON {
     SUFFIX LeakConductance
     NONSPECIFIC_CURRENT i
     RANGE e
-    
+
     RANGE gion
     RANGE i__LeakConductance : a copy of the variable for current which makes it easier to access from outside the mod file
     RANGE gmax                              : Will be changed when ion channel mechanism placed on cell!
@@ -22,11 +22,11 @@ NEURON {
     RANGE fopen                             : exposure
     RANGE conductanceScale                  : derived variable
     RANGE fopen0                            : derived variable
-    
+
 }
 
 UNITS {
-    
+
     (nA) = (nanoamp)
     (uA) = (microamp)
     (mA) = (milliamp)
@@ -42,71 +42,70 @@ UNITS {
     (umol) = (micromole)
     (pC) = (picocoulomb)
     (S) = (siemens)
-    
+
 }
 
 PARAMETER {
-    
+
     gmax = 0  (S/cm2)                       : Will be changed when ion channel mechanism placed on cell!
-    
+
     conductance = 1.0E-5 (uS)              : was: 1.0E-11 (conductance)
 }
 
 ASSIGNED {
-    
+
     gion   (S/cm2)                          : Transient conductance density of the channel? Standard Assigned variables with ionChannel
     v (mV)
     celsius (degC)
     temperature (K)
     e (mV)
     i (mA/cm2)
     i__LeakConductance (mA/cm2)
-    
+
     conductanceScale                        : derived variable
     fopen0                                  : derived variable
     fopen                                   : derived variable
     g (uS)                                  : derived variable
-    
+
 }
 
 STATE {
-    
+
 }
 
 INITIAL {
     temperature = celsius + 273.15
-    
+
     rates()
     rates() ? To ensure correct initialisation.
-    
+
 }
 
 BREAKPOINT {
-    
+
     rates()
     ? DerivedVariable is based on path: conductanceScaling[*]/factor, on: Component(id=LeakConductance type=ionChannelHH), from conductanceScaling; null
     ? Path not present in component, using factor: 1
-    
-    conductanceScale = 1 
-    
+
+    conductanceScale = 1
+
     ? DerivedVariable is based on path: gates[*]/fcond, on: Component(id=LeakConductance type=ionChannelHH), from gates; null
     ? Path not present in component, using factor: 1
-    
-    fopen0 = 1 
-    
+
+    fopen0 = 1
+
     fopen = conductanceScale  *  fopen0 ? evaluable
     g = conductance  *  fopen ? evaluable
-    gion = gmax * fopen 
-    
+    gion = gmax * fopen
+
     i = gion * (v - e)
     i__LeakConductance = -1 * i  : set this variable to the current also - note -1 as channel current convention for LEMS used!
-    
+
 }
 
 PROCEDURE rates() {
-
-
-
-
-}
 
+
+
+
+}
Original file line number	Diff line number	Diff line change
Expand Up		@@ -163,4 +163,3 @@ whether future versions of the GNU Lesser General Public License shall
		apply, that proxy's public statement of acceptance of any version is
		permanent authorization for you to choose that version for the
		Library.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -29,4 +29,3 @@ pyneuroml.analysis.ChannelHelper module
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,4 +5,3 @@ pyneuroml.channelml package
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -13,4 +13,3 @@ pyneuroml.neuron.analysis module
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -29,4 +29,3 @@ pyneuroml.povray.OverlaySimulation module
		:members:
		:undoc-members:
		:show-inheritance:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -20,4 +20,3 @@ @Article{Vella2014
		timestamp = {2019-02-20},
		year = {2014},
		}