Merge pull request #212 from NeuroML/fix/issue-211

fix(cells.xml): match proximal/distal properties to schema

NeuroML2CoreTypes/Cells.xml

@@ -667,19 +667,19 @@
 
 
     <ComponentType name="inhomogeneousParameter" description="An inhomogeneous parameter specified across the _segmentGroup_ (see _variableParameter_ for usage).">
-        <Child name="proximal" type="proximalProperties"/>
-        <Child name="distal" type="distalProperties"/>
+        <Child name="proximal" type="proximalDetails"/>
+        <Child name="distal" type="distalDetails"/>
         <Text name="variable"/>
         <Text name="metric"/>
     </ComponentType>
 
 
-    <ComponentType name="proximalProperties" description="What to do at the proximal point when creating an inhomogeneous parameter">
+    <ComponentType name="proximalDetails" description="What to do at the proximal point when creating an inhomogeneous parameter">
         <Text name="translationStart"/>
     </ComponentType>
 
 
-    <ComponentType name="distalProperties" description="What to do at the distal point when creating an inhomogeneous parameter">
+    <ComponentType name="distalDetails" description="What to do at the distal point when creating an inhomogeneous parameter">
         <Text name="normalizationEnd"/>
     </ComponentType>
 

README.md

@@ -26,5 +26,5 @@ Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin,
 
 For information on how to contribute to the NeuroML initiative, see [here](https://docs.neuroml.org/Devdocs/DevSOP.html).
 
-This code is distributed under the terms of the GNU Lesser General Public License.
+This code is distributed under the terms of the [GNU Lesser General Public License](https://github.com/NeuroML/NeuroML2/blob/master/LICENSE.lesser).
 

docs/Channels.html

@@ -15,7 +15,7 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </a>
-      <a class="brand" href="#">NeuroML v2.2 Component Types</a>
+      <a class="brand" href="#">NeuroML v2.3 Component Types</a>
       <div class="nav-collapse">
         <ul class="nav">
           <li><a href="Cells.html">Cells</a></li>
@@ -243,10 +243,10 @@
     </div><!--/.well -->
     </div><!--/span-->
     <div class="span7">
-   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/Channels.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.2</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
+   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/Channels.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.3</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
     <table class="table table-bordered"><tr><td ><h3>Channels</h3></td></tr>
     <tr><td><span  style="color:dimgrey"><i>Defines voltage (and concentration) gated ion channel models. Ion channels will generally extend <a href="Channels.html#baseIonChannel" title="Base for all ion channel ComponentTypes "><span  style="color:#85ACE1;font-style:italic">baseIonChannel</span></a>. The most commonly used voltage dependent gate will extend <a href="Channels.html#baseGate" title="Base ComponentType for a voltage and/or concentration dependent gate "><span  style="color:#85ACE1;font-style:italic">baseGate</span></a>. </i></span></td></tr>
-    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Channels.xml">Channels.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.2.xsd">NeuroML_v2.2.xsd</a></td></tr>
+    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Channels.xml">Channels.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.3.xsd">NeuroML_v2.3.xsd</a></td></tr>
     </table><br/>
 <a name="baseVoltageDepRate">&nbsp;</a>
 <table class="table table-bordered">

docs/Inputs.html

@@ -15,7 +15,7 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </a>
-      <a class="brand" href="#">NeuroML v2.2 Component Types</a>
+      <a class="brand" href="#">NeuroML v2.3 Component Types</a>
       <div class="nav-collapse">
         <ul class="nav">
           <li><a href="Cells.html">Cells</a></li>
@@ -95,10 +95,10 @@
     </div><!--/.well -->
     </div><!--/span-->
     <div class="span7">
-   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/Inputs.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.2</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
+   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/Inputs.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.3</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
     <table class="table table-bordered"><tr><td ><h3>Inputs</h3></td></tr>
     <tr><td><span  style="color:dimgrey"><i>A number of ComponentTypes for providing spiking (e.g. <a href="Inputs.html#spikeGeneratorPoisson" title="Generator of spikes whose ISI is distributed according to an exponential PDF with scale: 1 / averageRate ">spikeGeneratorPoisson</a>, <a href="Inputs.html#spikeArray" title="Set of spike ComponentTypes, each emitting one spike at a certain time. Can be used to feed a predetermined spike train into a cell ">spikeArray</a>) and current inputs (e.g. <a href="Inputs.html#pulseGenerator" title="Generates a constant current pulse of a certain amplitude for a specified duration after a delay. Scaled by weight, if set ">pulseGenerator</a>, <a href="Inputs.html#voltageClamp" title="Voltage clamp. Applies a variable current i to try to keep parent at targetVoltage. Not yet fully tested!!! Consider using voltageClampTriple!! ">voltageClamp</a>, <a href="Inputs.html#timedSynapticInput" title="Spike array connected to a single synapse, producing a current triggered by each spike in the array. ">timedSynapticInput</a>, <a href="Inputs.html#poissonFiringSynapse" title="Poisson spike generator firing at averageRate, which is connected to single synapse that is triggered every time a spike is generated, producing an input current. See also transientPoissonFiringSynapse. ">poissonFiringSynapse</a>) to other ComponentTypes </i></span></td></tr>
-    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Inputs.xml">Inputs.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.2.xsd">NeuroML_v2.2.xsd</a></td></tr>
+    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Inputs.xml">Inputs.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.3.xsd">NeuroML_v2.3.xsd</a></td></tr>
     </table><br/>
 <a name="basePointCurrent">&nbsp;</a>
 <table class="table table-bordered">

docs/Networks.html

@@ -15,7 +15,7 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </a>
-      <a class="brand" href="#">NeuroML v2.2 Component Types</a>
+      <a class="brand" href="#">NeuroML v2.3 Component Types</a>
       <div class="nav-collapse">
         <ul class="nav">
           <li><a href="Cells.html">Cells</a></li>
@@ -137,10 +137,10 @@
     </div><!--/.well -->
     </div><!--/span-->
     <div class="span7">
-   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/Networks.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.2</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
+   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/Networks.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.3</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
     <table class="table table-bordered"><tr><td ><h3>Networks</h3></td></tr>
     <tr><td><span  style="color:dimgrey"><i>Network descriptions for NeuroML 2. Describes <a href="Networks.html#network" title="Network containing: populations (potentially of type populationList, and so specifying a list of cell locations); projections (with lists of connections) and/or explicitConnections; and inputLists (with lists of inputs) and/or explicitInputs. Note: often in NeuroML this will be of type networkWithTemperature if there are temperature dependent elements (e.g. ion channels). ">network</a> elements containing <a href="Networks.html#population" title="A population of components, with just one parameter for the size, i.e. number of components to create. Note: quite often this is used with type=populationList which means the size is determined by the number of instances (with locations) in the list. The size attribute is still set, and there will be a validation error if this does not match the number in the list. ">population</a>s (potentially of type <a href="Networks.html#populationList" title="An explicit list of instances (with locations) of components in the population.  ">populationList</a>, and so specifying a list of cell <a href="Networks.html#location" title="Specifies the (x,y,z) location of a single instance of a component in a population ">location</a>s), <a href="Networks.html#projection" title="Projection from one population, presynapticPopulation to another, postsynapticPopulation, through synapse. Contains lists of connection or connectionWD elements. ">projection</a>s (i.e. lists of <a href="Networks.html#connection" title="Event connection directly between named components, which gets processed via a new instance of a synapse component which is created on the target component. Normally contained inside a projection element. ">connection</a>s) and <a href="Networks.html#input" title="Specifies a single input to a target, optionally giving the segmentId (default 0) and fractionAlong the segment (default 0.5). ">input</a>s. </i></span></td></tr>
-    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Networks.xml">Networks.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.2.xsd">NeuroML_v2.2.xsd</a></td></tr>
+    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Networks.xml">Networks.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.3.xsd">NeuroML_v2.3.xsd</a></td></tr>
     </table><br/>
 <a name="network">&nbsp;</a>
 <table class="table table-bordered">

docs/NeuroMLCoreCompTypes.html

@@ -15,7 +15,7 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </a>
-      <a class="brand" href="#">NeuroML v2.2 Component Types</a>
+      <a class="brand" href="#">NeuroML v2.3 Component Types</a>
       <div class="nav-collapse">
         <ul class="nav">
           <li><a href="Cells.html">Cells</a></li>
@@ -91,10 +91,10 @@
     </div><!--/.well -->
     </div><!--/span-->
     <div class="span7">
-   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/NeuroMLCoreCompTypes.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.2</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
+   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/NeuroMLCoreCompTypes.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.3</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
     <table class="table table-bordered"><tr><td ><h3>NeuroMLCoreCompTypes</h3></td></tr>
     <tr><td><span  style="color:dimgrey"><i>NeuroML2 ComponentType definitions from NeuroMLCoreCompTypes.xml </i></span></td></tr>
-    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml">NeuroMLCoreCompTypes.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.2.xsd">NeuroML_v2.2.xsd</a></td></tr>
+    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml">NeuroMLCoreCompTypes.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.3.xsd">NeuroML_v2.3.xsd</a></td></tr>
     </table><br/>
 <a name="notes">&nbsp;</a>
 <table class="table table-bordered">

docs/NeuroMLCoreDimensions.html

@@ -15,7 +15,7 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </a>
-      <a class="brand" href="#">NeuroML v2.2 Component Types</a>
+      <a class="brand" href="#">NeuroML v2.3 Component Types</a>
       <div class="nav-collapse">
         <ul class="nav">
           <li><a href="Cells.html">Cells</a></li>
@@ -134,10 +134,10 @@
     </div><!--/.well -->
     </div><!--/span-->
     <div class="span7">
-   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/NeuroMLCoreDimensions.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.2</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
+   <div class="alert alert-error"><br/><p><b>  NOTE: the latest version of this documentation can be found on <a href="https://docs.neuroml.org/Userdocs/Schemas/NeuroMLCoreDimensions.html">docs.neuroml.org</a>!</b></p><br/>For more information on NeuroML 2 and LEMS see <a href="http://www.neuroml.org/neuromlv2">here</a>. <br/>Note: these descriptions have been updated to the latest    <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2">NeuroML v2.3</a> definitions, using    <a href="https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS">the latest version of LEMS</a>!</div>
     <table class="table table-bordered"><tr><td ><h3>NeuroMLCoreDimensions</h3></td></tr>
     <tr><td><span  style="color:dimgrey"><i>NeuroML2 ComponentType definitions from NeuroMLCoreDimensions.xml </i></span></td></tr>
-    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/NeuroMLCoreDimensions.xml">NeuroMLCoreDimensions.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.2.xsd">NeuroML_v2.2.xsd</a></td></tr>
+    <tr><td>Original LEMS ComponentType definitions: <a href="https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/NeuroMLCoreDimensions.xml">NeuroMLCoreDimensions.xml</a><br/>    Schema against which NeuroML based on these should be valid: <a href="https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.3.xsd">NeuroML_v2.3.xsd</a></td></tr>
     </table><br/>
 <a name="area">&nbsp;</a>
 <table class="table table-bordered">