Merge branch 'development' of github.com:LEMS/pylems into development

* 'development' of github.com:LEMS/pylems:
  Fix for flake - remove global
  Update README.md
  Remove whitespaces xml files
  Ran ruff on python
  Whitespaces removed
  Remove global when not required

Author: pgleeson

.readthedocs.yaml

@@ -15,4 +15,3 @@ python:
       path: .
       extra_requirements:
         - doc
-

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.
-

Makefile

@@ -73,4 +73,3 @@ bench:
 
 	@echo "PyPy"
 	@${TIME} pypy pylems -nogui ${BENCHFILE} > /dev/null
-

README.md

@@ -13,7 +13,7 @@ Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapa
 **libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience**
 [Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00038/abstract), doi: 10.3389/fninf.2014.00038
 
-_**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_  
+_**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_
 
 For more details on LEMS see:
 

ci/run-apitest.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Copyright 2023 LEMS contributors
-# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com> 
+# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
 # File : run-apitest.sh
 #
 # Run api tests on GitHub actions
@@ -18,4 +18,4 @@ if [ "$CI" = "true" ]; then
         sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py;
     fi
 fi
-python lems/dlems/exportdlems.py
+python lems/dlems/exportdlems.py

doc/conf.py

@@ -11,8 +11,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

doc/index.rst

@@ -11,4 +11,3 @@ User documentation
    :maxdepth: 3
 
    modules
-

examples/MultiRunSimulation.xml

@@ -4,15 +4,15 @@
 <ComponentType name="DisplayList">
     <Parameter name="timeScale" dimension="time"/>
     <Children name="lines" type="Line"/>
-    
-    <Text name="title"/>  
+
+    <Text name="title"/>
     <Text name="display"/>
 </ComponentType>
 
 
 
 <ComponentType name="Display">
-    <Text name="title"/>   
+    <Text name="title"/>
 	<Parameter name="xmin" dimension="none"/>
 	<Parameter name="xmax" dimension="none"/>
 	<Parameter name="ymin" dimension="none"/>
@@ -45,7 +45,7 @@
     <Dynamics>
         <StateVariable name="t" dimension="time"/>
     </Dynamics>
-    
+
     <Simulation>
         <Run component="target" variable="t" increment="step" total="length"/>
     </Simulation>
@@ -56,8 +56,8 @@
 <ComponentType name="SimulationSet">
     <Children name="simulations" type="Simulation"/>
     <Children name="displays" type="Display"/>
-    
-    
+
+
 </ComponentType>
 
-</Lems>
+</Lems>

examples/SimpleTest.xml

@@ -1,70 +1,70 @@
 <Lems>
 
     <Target component="sim1"/>
-    
+
     <!-- Include standard NeuroML2 ComponentType definitions -->
     <Include file="Simulation.xml"/>
-    
-    
+
+
     <ComponentType name="simpleCell">
-        
+
         <Parameter name="v0" dimension="voltage"/>
         <Parameter name="v1" dimension="voltage"/>
         <Parameter name="tau" dimension="time"/>
-        
+
         <Exposure name="v" dimension="voltage" description="Membrane potential"/>
-        
+
         <Child name="membrane" type="membrane"/>
-        
+
         <Dynamics>
             <DerivedVariable name="v" dimension="voltage" exposure="v" value="v0 + (t*(v1-v0)/tau)"/>
 
         </Dynamics>
 
     </ComponentType>
-    
+
     <ComponentType name="membrane">
-        
+
         <Parameter name="g" dimension="conductance"/>
         <Parameter name="E" dimension="voltage"/>
         <Exposure name="I" dimension="current"/>
         <Exposure name="I2" dimension="none"/>
         <Requirement name="v" dimension="voltage"/>
-        
+
         <Dynamics>
             <DerivedVariable name="I" dimension="current" exposure="I" value="g * (E-v)"/>
             <DerivedVariable name="I2" dimension="none" exposure="I2" value="v/E"/>
         </Dynamics>
 
     </ComponentType>
-    
-    
-    
+
+
+
     <simpleCell id="cell0" v0="-100 mV" v1="100 mV" tau="200 ms">
         <membrane g="10 pS" E="50 mV"/>
     </simpleCell>
-    
-    
+
+
     <Simulation id="sim1" length="5ms" step="1ms" target="cell0">
-    
+
         <Display id="d1" title="Voltage" timeScale="1ms" xmin="-20" xmax="220" ymin="-110" ymax="110">
             <Line id="v" quantity="v" scale="1mV"  color="#ffffff" timeScale="1ms"/>
         </Display>
-        
+
         <Display id="d2" title="Current" timeScale="1ms" xmin="-20" xmax="220" ymin="-1" ymax="2">
             <Line id="I" quantity="membrane/I" scale="1pS"  color="#ffffff" timeScale="1ms"/>
             <Line id="I2" quantity="membrane/I2" scale="1"  color="#f22fff" timeScale="1ms"/>
         </Display>
-    
+
 
         <OutputFile id="of0" fileName="simp.dat">
             <OutputColumn id="v" quantity="v"/>
             <OutputColumn id="m" quantity="membrane/I"/>
             <OutputColumn id="m" quantity="membrane/I2"/>
-        </OutputFile> 
+        </OutputFile>
 
     </Simulation>
 
 
 
-</Lems>
+</Lems>

examples/bounce-conditional.xml

@@ -1,12 +1,12 @@
 <Lems>
 
-    <Target component="sim"/> 
-  
+    <Target component="sim"/>
+
     <Dimension name="length" l="1" />
     <Dimension name="time" t="1" />
     <Dimension name="speed" l="1" t="-1"/>
     <Dimension name="acceleration" l="1" t="-2"/>
-	
+
     <Unit symbol="s" dimension="time"/>
     <Unit symbol="m" dimension="length"/>
     <Unit symbol="m_per_s" dimension="speed"/>
@@ -20,18 +20,18 @@
         <Parameter name="t1" dimension="time"/>
         <Parameter name="t2" dimension="time"/>
         <Exposure name="height" dimension="time"/>
-        
+
         <Constant name="AccG" dimension="acceleration" value="9.8m_per_s2"/>
-    
+
         <Dynamics>
             <StateVariable name="height" exposure="height" dimension="length"/>
             <StateVariable name="vel" dimension="speed"/>
-			
+
             <OnStart>
                 <StateAssignment variable="height" value="y0"/>
                 <StateAssignment variable="vel" value="0"/>
             </OnStart>
-	
+
             <ConditionalDerivedVariable name="effacc" dimension="acceleration">
                 <Case condition="t .lt. t1" value="-1 * AccG"/>
                 <Case condition="t .lt. t2" value="-0.1 * AccG"/>
@@ -48,25 +48,25 @@
             </OnCondition>
         </Dynamics>
     </ComponentType>
-        
- 
 
- 
+
+
+
     <ball id="ball" fbounce="0.9" y0="5m" t1="5s" t2="10s"/>
-	
-	
+
+
     <Include file="SingleSimulation.xml" />
- 
+
 
 
     <Simulation id="sim" length="20s" step="0.01s" target="ball">
         <Display id="disp1" title="Net1" xmin="0" xmax="30" ymin="-1" ymax="6" timeScale="1s">
             <Line id="g0"  timeScale="1s" quantity="height" scale="1m" color="#0000f0"/>
-        
-        </Display> 
- 	
-  
- 
+
+        </Display>
+
+
+
     </Simulation>
 
-</Lems>
+</Lems>