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Merge pull request #52 from ModECI/test_xml3
Valid NeuroML generation
2 parents 322953f + 6339fd0 commit c6497f0

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‎.github/workflows/ci.yml

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cd test
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python test.py
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## Test NeuroML example
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cd ../neuroml2
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python neuroml2_spec.py
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pip install pyneuroml
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# Requires: pip install pyneuroml
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pynml -validate hello_world_neuroml.net.nml
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pynml -validate TestNeuroML.xml
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- name: Run pytest
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run: |
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pytest tests

‎docs/sphinx/source/api/examples/document.py

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from modelspec import field, instance_of, optional
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from modelspec.base_types import Base
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from typing import List
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import sys
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# Example showing how to create a model of a document and use it to create/serialize instances
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doc.to_json_file("document.json")
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doc.to_yaml_file("document.yaml")
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print(" >> Full document details in YAML format:\n")
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print(doc.to_yaml())
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doc.to_bson_file("document.bson")
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print(" >> Full document details in YAML format:\n")
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if sys.version_info >= (3, 8):
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doc.to_xml_file("document.xml")
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print(" >> Full document details in XML format:\n")
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print(doc.to_xml())
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print(doc.to_yaml())
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doc_md = doc.generate_documentation(format="markdown")
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‎docs/sphinx/source/api/examples/document.xml

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<?xml version="1.0" ?>
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<Document id="MyBook" title="My life in Python" ISBN="None">
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<Section id="Abstract">
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<Paragraph contents="Blah blah blah"/>
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<Paragraph contents="Blah2"/>
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</Section>
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<Section id="Chapter 1">
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<Paragraph contents="More..."/>
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</Section>
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</Document>

‎examples/document.py

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from modelspec import field, instance_of, optional
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from modelspec.base_types import Base
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from typing import List
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import sys
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# Example showing how to create a model of a document and use it to create/serialize instances
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doc.to_json_file("document.json")
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doc.to_yaml_file("document.yaml")
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print(" >> Full document details in YAML format:\n")
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print(doc.to_yaml())
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doc.to_bson_file("document.bson")
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print(" >> Full document details in YAML format:\n")
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if sys.version_info >= (3, 8):
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doc.to_xml_file("document.xml")
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print(" >> Full document details in XML format:\n")
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print(doc.to_xml())
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print(doc.to_yaml())
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doc_md = doc.generate_documentation(format="markdown")
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‎examples/document.xml

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<?xml version="1.0" ?>
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<Document id="MyBook" title="My life in Python" ISBN="None">
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<Section id="Abstract">
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<Paragraph contents="Blah blah blah"/>
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<Paragraph contents="Blah2"/>
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</Section>
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<Section id="Chapter 1">
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<Paragraph contents="More..."/>
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</Section>
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</Document>

‎examples/neuroml2/NeuroML2.md

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## NeuroML
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## neuroml
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Some description...
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### Allowed parameters
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<tr>
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<td><b>version</b></td>
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<td><b>xmlns</b></td>
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<td>str</td>
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<td><i>NeuroML version used</i></td>
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<td><i>Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2</i></td>
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</tr>
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<table>
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<tr>
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<td><b>izhikevich2007Cells</b></td>
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<td><a href="#izhikevich2007cell">Izhikevich2007Cell</a></td>
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<td><a href="#izhikevich2007cell">izhikevich2007Cell</a></td>
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<td><i></i></td>
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</tr>
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<tr>
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<td><b>pulseGenerators</b></td>
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<td><a href="#pulsegenerator">PulseGenerator</a></td>
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<td><a href="#pulsegenerator">pulseGenerator</a></td>
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<td><i></i></td>
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</tr>
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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><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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## Izhikevich2007Cell
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## izhikevich2007Cell
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Some description...
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### Allowed parameters
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</table>
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## PulseGenerator
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## pulseGenerator
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Some description...
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### Allowed parameters
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</table>
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## Network
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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>populations</b></td>
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<td><a href="#population">Population</a></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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<tr>
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<td><b>explicitInputs</b></td>
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<td><a href="#explicitinput">ExplicitInput</a></td>
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<td><a href="#explicitinput">explicitInput</a></td>
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<td><i></i></td>
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</tr>
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</table>
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## Population
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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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## ExplicitInput
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## explicitInput
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Some description...
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### Allowed parameters

‎examples/neuroml2/NeuroML2.rst

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=======
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NeuroML
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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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=============== =========== ====================================================================
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Allowed field Data Type Description
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=============== =========== ================================
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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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**xmlns** str Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2
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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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**izhikevich2007Cells** `Izhikevich2007Cell <#izhikevich2007cell>`__
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**pulseGenerators** `PulseGenerator <#pulsegenerator>`__
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**networks** `Network <#network>`__ The networks present
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**izhikevich2007Cells** `izhikevich2007Cell <#izhikevich2007cell>`__
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**pulseGenerators** `pulseGenerator <#pulsegenerator>`__
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**networks** `network <#network>`__ The networks present
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======================= ============================================ ====================
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==================
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Izhikevich2007Cell
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izhikevich2007Cell
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==================
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Some description...
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=============== =========== =====================
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==============
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PulseGenerator
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pulseGenerator
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==============
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Some description...
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=============== =========== ============================
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=======
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Network
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network
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=======
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Some description...
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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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**explicitInputs** `ExplicitInput <#explicitinput>`__
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**populations** `population <#population>`__ the pops in the net
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**explicitInputs** `explicitInput <#explicitinput>`__
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================== ================================== ===================
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==========
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Population
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population
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==========
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Some description...
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=============== =========== ======================================
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=============
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ExplicitInput
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explicitInput
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=============
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Some description...
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‎examples/neuroml2/NeuroML2.specification.json

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{
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"NeuroML": {
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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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"xmlns": {
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"type": "str",
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"description": "NeuroML version used"
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"description": "Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2"
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}
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},
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"allowed_children": {
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"izhikevich2007Cells": {
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"type": "Izhikevich2007Cell",
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"type": "izhikevich2007Cell",
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"description": ""
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},
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"pulseGenerators": {
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"type": "PulseGenerator",
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"type": "pulseGenerator",
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"description": ""
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},
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"networks": {
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"type": "Network",
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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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"Izhikevich2007Cell": {
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"izhikevich2007Cell": {
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"definition": "Some description...",
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"allowed_parameters": {
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"id": {
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}
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}
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},
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"PulseGenerator": {
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"pulseGenerator": {
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"definition": "Some description...",
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"allowed_parameters": {
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"id": {
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}
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}
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},
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"Network": {
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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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},
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"allowed_children": {
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"populations": {
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"type": "Population",
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"type": "population",
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"description": "the pops in the net"
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},
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"explicitInputs": {
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"type": "ExplicitInput",
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"type": "explicitInput",
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"description": ""
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}
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}
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},
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"Population": {
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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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}
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}
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},
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"ExplicitInput": {
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"explicitInput": {
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"definition": "Some description...",
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"allowed_parameters": {
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"target": {

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