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Merge branch 'mqnifestkelvin-feature_xml_3' into test_xml3
2 parents 78735ed + df17fd0 commit fcb356d

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‎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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from modelspec.utils import save_to_xml_file
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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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@@ -70,10 +71,12 @@ class Document(Base):
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doc.to_json_file("document.json")
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doc.to_yaml_file("document.yaml")
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doc.to_bson_file("document.bson")
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doc.to_xml_file("document.xml")
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print(" >> Full document details in YAML format:\n")
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print(doc.to_yaml())
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print(doc.to_xml())
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doc_md = doc.generate_documentation(format="markdown")
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@@ -106,3 +109,5 @@ class Document(Base):
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with open("document.specification.bson", "wb") as d:
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d.write(bson.encode(doc_dict))
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save_to_xml_file(doc_dict, "document.specification.xml")

‎examples/document.specification.xml

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<?xml version="1.0" ?>
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<modelspec>
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<Document>
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<definition>A model for documents.</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 unique id of the document</description>
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</id>
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<title>
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<type>str</type>
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<description>The document title</description>
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</title>
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<ISBN>
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<type>int</type>
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<description>International Standard Book Number</description>
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</ISBN>
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</allowed_parameters>
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<allowed_children>
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<sections>
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<type>Section</type>
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<description>The sections of the document</description>
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</sections>
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</allowed_children>
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</Document>
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<Section>
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<definition>A model of a section of the :class:`Document`. Will contain one :class:`Paragraph` or more, i.e the :class:`Paragraph`(s) in the section, probably related to the :code:`title` of the `Document &lt;#document&gt;`_.</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 section</description>
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</id>
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</allowed_parameters>
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<allowed_children>
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<paragraphs>
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<type>Paragraph</type>
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<description>The paragraphs</description>
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</paragraphs>
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</allowed_children>
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</Section>
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<Paragraph>
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<definition>A model of a paragraph.</definition>
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<allowed_parameters>
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<contents>
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<type>str</type>
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<description>Paragraph contents, which make up the :class:`Section`s.</description>
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</contents>
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</allowed_parameters>
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</Paragraph>
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</modelspec>

‎examples/document.xml

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<?xml version="1.0" ?>
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<modelspec>
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<MyBook>
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<title>My life in Python</title>
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<sections>
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<Abstract>
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<paragraphs>
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<contents>Blah blah blah</contents>
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</paragraphs>
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<paragraphs>
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<contents>Blah2</contents>
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</paragraphs>
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</Abstract>
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<Chapter_1>
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<paragraphs>
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<contents>More...</contents>
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</paragraphs>
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</Chapter_1>
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</sections>
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</MyBook>
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</modelspec>

‎examples/neuroml2/NeuroML2.specification.xml

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<?xml version="1.0" ?>
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<modelspec>
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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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<izhikevich2007Cells>
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<type>Izhikevich2007Cell</type>
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<description/>
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</izhikevich2007Cells>
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<pulseGenerators>
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<type>PulseGenerator</type>
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<description/>
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</pulseGenerators>
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<networks>
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<type>Network</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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<Izhikevich2007Cell>
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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 cell...</description>
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</id>
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<C>
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<type>str</type>
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<description/>
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</C>
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<v0>
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<type>str</type>
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<description/>
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</v0>
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<k>
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<type>str</type>
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<description/>
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</k>
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<vr>
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<type>str</type>
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<description/>
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</vr>
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<vt>
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<type>str</type>
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<description/>
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</vt>
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<vpeak>
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<type>str</type>
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<description/>
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</vpeak>
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<a>
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<type>str</type>
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<description/>
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</a>
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<b>
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<type>str</type>
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<description/>
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</b>
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<c>
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<type>str</type>
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<description/>
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</c>
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<d>
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<type>str</type>
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<description/>
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</d>
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</allowed_parameters>
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</Izhikevich2007Cell>
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<PulseGenerator>
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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 pulseGenerator</description>
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</id>
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<delay>
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<type>str</type>
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<description>the delay</description>
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</delay>
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<duration>
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<type>str</type>
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<description>the duration</description>
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</duration>
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<amplitude>
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<type>str</type>
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<description>the amplitude</description>
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</amplitude>
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</allowed_parameters>
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</PulseGenerator>
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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>Population</type>
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<description>the pops in the net</description>
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</populations>
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<explicitInputs>
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<type>ExplicitInput</type>
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<description/>
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</explicitInputs>
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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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<ExplicitInput>
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<definition>Some description...</definition>
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<allowed_parameters>
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<target>
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<type>str</type>
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<description>the target of the input</description>
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</target>
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<input>
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<type>str</type>
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<description>the input, e.g. pulseGenerator</description>
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</input>
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</allowed_parameters>
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</ExplicitInput>
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</modelspec>

‎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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<izhikevich2007Cells>
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<izh2007RS0>
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<C>100pF</C>
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<v0>-60mV</v0>
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<k>0.7nS_per_mV</k>
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<vr>-60mV</vr>
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<vt>-40mV</vt>
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<vpeak>35mV</vpeak>
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<a>0.03per_ms</a>
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<b>-2nS</b>
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<c>-50.0mV</c>
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<d>100pA</d>
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</izh2007RS0>
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</izhikevich2007Cells>
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<pulseGenerators>
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<pulseGen_0>
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<delay>100ms</delay>
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<duration>800ms</duration>
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<amplitude>0.07 nA</amplitude>
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</pulseGen_0>
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</pulseGenerators>
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<networks>
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<IzNet>
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<populations>
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<IzhPop0>
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<component>izh2007RS0</component>
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<size>1</size>
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</IzhPop0>
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</populations>
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<explicitInputs>
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<target>IzhPop0[0]</target>
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<input>pulseGen_0</input>
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</explicitInputs>
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</IzNet>
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</networks>
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</TestNeuroML>
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</modelspec>

‎examples/neuroml2/neuroml2_spec.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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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)
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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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print("Generating documentation...")
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yy = yaml.dump(doc_dict, indent=4, sort_keys=False)
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print(yy)
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d.write(yy)
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save_to_xml_file(doc_dict, "NeuroML2.specification.xml")

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