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accompanying files from merge with upstream development branch
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‎examples/neuroml2/NeuroML2.md

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@@ -23,7 +23,7 @@ Some description...
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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><a href="#list">List</a></td>
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<td><i>The networks present</i></td>
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</tr>
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@@ -48,7 +48,7 @@ Some description...
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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="#list">List</a></td>
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<td><i>the pops in the net</i></td>
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</tr>
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‎examples/neuroml2/NeuroML2.rst

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@@ -14,11 +14,11 @@ Allowed field Data Type Description
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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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Allowed child Data Type Description
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=============== ================ ====================
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**networks** `List <#list>`__ The networks present
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=============== ================ ====================
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=======
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Network
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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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Allowed child Data Type Description
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=============== ================ ===================
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**populations** `List <#list>`__ the pops in the net
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=============== ================ ===================
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==========
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Population

‎examples/neuroml2/NeuroML2.specification.json

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@@ -13,7 +13,7 @@
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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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"type": "List",
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"description": "The networks present"
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}
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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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"type": "List",
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"description": "the pops in the net"
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}
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}

‎examples/neuroml2/NeuroML2.specification.xml

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<?xml version="1.0" ?>
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<root>
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<NeuroML>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the NeuroML 2 document</description>
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</id>
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<version>
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<type>str</type>
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<description>NeuroML version used</description>
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</version>
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</allowed_parameters>
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<allowed_children>
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<networks>
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<type>List</type>
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<description>The networks present</description>
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</networks>
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</allowed_children>
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</NeuroML>
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<Network>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the network</description>
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</id>
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</allowed_parameters>
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<allowed_children>
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<populations>
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<type>List</type>
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<description>the pops in the net</description>
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</populations>
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</allowed_children>
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</Network>
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<Population>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the population</description>
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</id>
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<component>
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<type>str</type>
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<description>the component to use in the population</description>
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</component>
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<size>
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<type>int</type>
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<description>the size of the population</description>
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</size>
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</allowed_parameters>
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</Population>
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</root>

‎examples/neuroml2/NeuroML2.specification.yaml

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@@ -9,7 +9,7 @@ NeuroML:
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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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type: List
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description: The networks present
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Network:
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definition: Some description...
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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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type: List
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description: the pops in the net
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Population:
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definition: Some description...

‎examples/neuroml2/TestNeuroML.xml

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<?xml version="1.0" ?>
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<modelspec>
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<TestNeuroML>
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<version>NeuroML_v2.3</version>
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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</component>
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<size>1</size>
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</pop0>
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</populations>
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</net0>
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</networks>
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</TestNeuroML>
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</modelspec>

‎examples/neuroml2/neuroml2_spec.py

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@@ -2,6 +2,7 @@
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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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from modelspec.utils import save_to_xml_file
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# Example showing ...
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nml_doc.to_json_file("%s.json" % nml_doc.id)
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nml_doc.to_yaml_file("%s.yaml" % nml_doc.id)
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nml_doc.to_bson_file("%s.bson" % nml_doc.id)
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# nml_doc.to_xml_file("%s.xml"%nml_doc.id)
72+
nml_doc.to_xml_file("%s.xml" % nml_doc.id)
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print(" >> Full document details in YAML format:\n")
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print(nml_doc.to_yaml())
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print(nml_doc.to_xml())
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doc_md = nml_doc.generate_documentation(format="markdown")
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@@ -99,3 +101,5 @@ class NeuroML(Base):
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yy = yaml.dump(doc_dict, indent=4, sort_keys=False)
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print(yy)
101103
d.write(yy)
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save_to_xml_file(doc_dict, "NeuroML2.specification.xml")

‎src/modelspec/base_types.py

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@@ -121,7 +121,7 @@ def to_xml(self) -> str:
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"""
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from modelspec.utils import build_xml_element
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124-
root = ET.Element("root")
124+
root = ET.Element("modelspec")
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build_xml_element(root, self.to_dict())
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127127
xml_string = ET.tostring(
@@ -265,14 +265,14 @@ def to_xml_file(
265265
self,
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filename: Optional[str] = None,
267267
include_metadata: bool = True,
268-
root="modelspec",
268+
root_name="modelspec",
269269
) -> str:
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from modelspec.utils import build_xml_element
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272272
if filename is None:
273273
filename = f"{self.id}.xml"
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275-
root = ET.Element(root)
275+
root = ET.Element(root_name)
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build_xml_element(root, self.to_dict())
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