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Merge remote-tracking branch 'upstream/development' into feature_xml_3
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‎.gitignore

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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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.idea/
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/examples/document.specification.bson
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/examples/neuroml2/hello_world.v.dat

‎examples/neuroml2/LEMS_hello_world.xml

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<Lems>
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<!--
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This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.2)
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-->
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<!-- Specify which component to run -->
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<Target component="hello_world"/>
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<!-- Include core NeuroML2 ComponentType definitions -->
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<Include file="Cells.xml"/>
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<Include file="Networks.xml"/>
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<Include file="Simulation.xml"/>
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<Include file="hello_world_neuroml.net.nml"/>
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<Simulation id="hello_world" length="1000ms" step="0.1ms" target="IzNet" seed="123"> <!-- Note seed: ensures same random numbers used every run -->
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<OutputFile id="output0" fileName="hello_world.v.dat">
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<OutputColumn id="IzhPop0[0]" quantity="IzhPop0[0]/v"/>
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</OutputFile>
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</Simulation>
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</Lems>

‎examples/neuroml2/NeuroML2.md

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## NeuroML
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Some description...
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### Allowed parameters
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<table>
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<tr>
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<td><b>id</b></td>
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<td>str</td>
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<td><i>The id of the NeuroML 2 document</i></td>
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</tr>
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<tr>
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<td><b>version</b></td>
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<td>str</td>
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<td><i>NeuroML version used</i></td>
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</tr>
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</table>
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### Allowed children
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<table>
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<tr>
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<td><b>networks</b></td>
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<td><a href="#network">Network</a></td>
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<td><i>The networks present</i></td>
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</tr>
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</table>
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## Network
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Some description...
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### Allowed parameters
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<table>
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<tr>
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<td><b>id</b></td>
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<td>str</td>
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<td><i>The id of the network</i></td>
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</tr>
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</table>
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### Allowed children
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<table>
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<tr>
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<td><b>populations</b></td>
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<td><a href="#population">Population</a></td>
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<td><i>the pops in the net</i></td>
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</tr>
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</table>
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## Population
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Some description...
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### Allowed parameters
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<table>
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<tr>
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<td><b>id</b></td>
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<td>str</td>
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<td><i>The id of the population</i></td>
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</tr>
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<tr>
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<td><b>component</b></td>
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<td>str</td>
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<td><i>the component to use in the population</i></td>
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</tr>
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<tr>
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<td><b>size</b></td>
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<td>int</td>
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<td><i>the size of the population</i></td>
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</tr>
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</table>

‎examples/neuroml2/NeuroML2.rst

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=======
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NeuroML
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=======
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Some description...
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**Allowed parameters**
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=============== =========== ================================
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Allowed field Data Type Description
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=============== =========== ================================
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**id** str The id of the NeuroML 2 document
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**version** str NeuroML version used
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=============== =========== ================================
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**Allowed children**
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=============== ====================== ====================
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Allowed child Data Type Description
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=============== ====================== ====================
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**networks** `Network <#network>`__ The networks present
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=============== ====================== ====================
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=======
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Network
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=======
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Some description...
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**Allowed parameters**
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=============== =========== =====================
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Allowed field Data Type Description
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=============== =========== =====================
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**id** str The id of the network
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=============== =========== =====================
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**Allowed children**
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=============== ============================ ===================
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Allowed child Data Type Description
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=============== ============================ ===================
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**populations** `Population <#population>`__ the pops in the net
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=============== ============================ ===================
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==========
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Population
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==========
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Some description...
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**Allowed parameters**
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=============== =========== ======================================
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Allowed field Data Type Description
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=============== =========== ======================================
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**id** str The id of the population
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**component** str the component to use in the population
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**size** int the size of the population
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=============== =========== ======================================

‎examples/neuroml2/NeuroML2.specification.json

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{
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"NeuroML": {
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"definition": "Some description...",
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"allowed_parameters": {
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"id": {
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"type": "str",
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"description": "The id of the NeuroML 2 document"
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},
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"version": {
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"type": "str",
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"description": "NeuroML version used"
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}
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},
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"allowed_children": {
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"networks": {
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"type": "Network",
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"description": "The networks present"
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}
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}
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},
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"Network": {
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"definition": "Some description...",
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"allowed_parameters": {
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"id": {
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"type": "str",
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"description": "The id of the network"
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}
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},
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"allowed_children": {
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"populations": {
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"type": "Population",
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"description": "the pops in the net"
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}
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}
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},
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"Population": {
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"definition": "Some description...",
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"allowed_parameters": {
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"id": {
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"type": "str",
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"description": "The id of the population"
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},
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"component": {
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"type": "str",
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"description": "the component to use in the population"
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},
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"size": {
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"type": "int",
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"description": "the size of the population"
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}
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}
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}
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}

‎examples/neuroml2/NeuroML2.specification.yaml

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NeuroML:
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definition: Some description...
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allowed_parameters:
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id:
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type: str
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description: The id of the NeuroML 2 document
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version:
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type: str
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description: NeuroML version used
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allowed_children:
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networks:
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type: Network
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description: The networks present
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Network:
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definition: Some description...
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allowed_parameters:
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id:
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type: str
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description: The id of the network
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allowed_children:
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populations:
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type: Population
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description: the pops in the net
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Population:
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definition: Some description...
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allowed_parameters:
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id:
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type: str
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description: The id of the population
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component:
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type: str
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description: the component to use in the population
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size:
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type: int
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description: the size of the population

‎examples/neuroml2/TestNeuroML.bson

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‎examples/neuroml2/TestNeuroML.json

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{
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"TestNeuroML": {
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"version": "NeuroML_v2.3",
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"networks": {
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"net0": {
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"populations": {
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"pop0": {
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"component": "izh2007RS0",
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"size": 1
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}
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}
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}
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}
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}
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}

‎examples/neuroml2/TestNeuroML.yaml

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TestNeuroML:
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version: NeuroML_v2.3
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networks:
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net0:
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populations:
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pop0:
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component: izh2007RS0
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size: 1

‎examples/neuroml2/hello_world_neuroml.net.nml

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<neuroml
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xmlns="http://www.neuroml.org/schema/neuroml2"
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xmlns:xs="http://www.w3.org/2001/XMLSchema"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd"
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id="IzhNeuron">
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<izhikevich2007Cell id="izh2007RS0" C="100pF" v0="-60mV" k="0.7nS_per_mV" vr="-60mV" vt="-40mV" vpeak="35mV" a="0.03per_ms" b="-2nS" c="-50.0mV" d="100pA"/>
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<pulseGenerator id="pulseGen_0" delay="100ms" duration="800ms" amplitude="0.07 nA"/>
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<network id="IzNet">
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<population id="IzhPop0" component="izh2007RS0" size="1"/>
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<explicitInput target="IzhPop0[0]" input="pulseGen_0"/>
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</network>
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</neuroml>

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