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pgleesonpgleeson
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Merge branch 'development' into experimental
2 parents f25194c + cd27217 commit 268e72a

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‎.github/workflows/ci.yml

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on:
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push:
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branches: [ main, development, experimental ]
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branches: [ main, development, experimental, test* ]
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pull_request:
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branches: [ main, development, experimental ]
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branches: [ main, development, experimental, test* ]
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jobs:
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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steps:
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- uses: actions/checkout@v2

‎.github/workflows/python-publish.yml

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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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name: Upload Python Package
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on:
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release:
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types: [published]
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v3
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with:
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python-version: '3.x'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build package
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run: python -m build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.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/document.md

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@@ -13,7 +13,7 @@ A model for documents.
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<tr>
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<td><b>title</b></td>
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<td>str</td>
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<td><i>Document title</i></td>
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<td><i>The document title</i></td>
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</tr>
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‎examples/document.py

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@@ -40,7 +40,7 @@ class Document(Base):
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Args:
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id: The unique id of the document
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title: Document title
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title: The document title
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ISBN: International Standard Book Number
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sections: The sections of the document
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"""
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print(doc)
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print(doc.sections[0].paragraphs[0].contents)
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print(doc.sections[0].paragraphs[0].__getattribute__("contents"))
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print(doc.sections[0].paragraphs[1].__getattribute__("contents"))
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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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print(" >> Full document details in YAML format:\n")
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print(doc.to_yaml())
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doc_md = doc.generate_documentation(format="markdown")
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with open("document.md", "w") as d:
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d.write(doc_md)
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doc_rst = doc.generate_documentation(format="rst")
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with open("document.rst", "w") as d:
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d.write(doc_rst)
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print("\nGenerating specification in dict form")
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print("\n >> Generating specification in dict form...")
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doc_dict = doc.generate_documentation(format="dict")
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import json
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with open("document.specification.json", "w") as d:
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d.write(json.dumps(doc_dict, indent=4))
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print("Generating specification in YAML")
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print(" >> Generating specification in YAML...\n")
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with open("document.specification.yaml", "w") as d:
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d.write(yaml.dump(doc_dict, indent=4, sort_keys=False))
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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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with open("document.specification.bson", "wb") as d:
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d.write(bson.encode(doc_dict))

‎examples/document.rst

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Allowed field Data Type Description
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=============== =========== ==================================
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**id** str The unique id of the document
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**title** str Document title
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**title** str The document title
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**ISBN** int International Standard Book Number
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=============== =========== ==================================
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‎examples/document.specification.json

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},
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"title": {
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"type": "str",
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"description": "Document title"
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"description": "The document title"
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},
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"ISBN": {
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"type": "int",

‎examples/document.specification.yaml

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description: The unique id of the document
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title:
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type: str
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description: Document title
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description: The document title
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ISBN:
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type: int
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description: International Standard Book Number

‎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>

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