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Merge pull request #85 from LEMS/development
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Changes for NeuroML v2.3.1 release
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pgleeson authored Aug 20, 2024
2 parents 373a259 + 538c7a6 commit b63c53f
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Showing 37 changed files with 570 additions and 608 deletions.
8 changes: 4 additions & 4 deletions .github/workflows/ci.yml
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Expand Up @@ -13,14 +13,14 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.7", "3.9", "3.10", "3.11"]
python-version: ["3.9", "3.10", "3.11", "3.12"]
runs-on: [ubuntu-latest, windows-latest, macos-latest]

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

Expand All @@ -30,7 +30,7 @@ jobs:
python -m pip install pytest pytest-cov
- name: Checkout NeuroML2
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: NeuroML/NeuroML2
ref: development
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4 changes: 2 additions & 2 deletions .github/workflows/examples.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- uses: nelonoel/[email protected]

# https://stackoverflow.com/questions/58033366/how-to-get-current-branch-within-github-actions
Expand All @@ -21,7 +21,7 @@ jobs:
id: extract_branch

- name: Checkout jlems
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: LEMS/jLEMS
ref: ${{ steps.extract_branch.outputs.branch }}
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4 changes: 2 additions & 2 deletions .github/workflows/python-publish.yml
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Expand Up @@ -18,9 +18,9 @@ jobs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: '3.x'
- name: Install dependencies
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7 changes: 5 additions & 2 deletions .readthedocs.yaml
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Expand Up @@ -9,7 +9,10 @@ build:
sphinx:
configuration: doc/conf.py


python:
install:
- requirements: doc/requirements.txt
- method: pip
path: .
extra_requirements:
- doc

2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -5,7 +5,7 @@
[![Documentation Status](https://readthedocs.org/projects/pylems/badge/?version=latest)](https://pylems.readthedocs.io/en/latest/?badge=latest)
[![PyPI](https://img.shields.io/pypi/v/pylems)](https://pypi.org/project/pylems/)

A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 models (see [here](https://docs.neuroml.org/Userdocs/Software/pyLEMS.html)).
A [LEMS](http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 models (see [here](https://docs.neuroml.org/Userdocs/Software/pyLEMS.html)).

For more about PyLEMS see:

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1 change: 0 additions & 1 deletion doc/requirements.txt

This file was deleted.

9 changes: 1 addition & 8 deletions examples/SimpleNetwork.xml
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Expand Up @@ -4,7 +4,6 @@
<Children name="connectivities" type="EventConnectivity"/>
</ComponentType>


<ComponentType name="Population">
<ComponentReference name="component" type="Component"/>
<Parameter name="size" dimension="none"/>
Expand All @@ -13,8 +12,6 @@
</Structure>
</ComponentType>



<ComponentType name="EventConnectivity">
<Link name="source" type="Population"/>
<Link name="target" type="Population"/>
Expand All @@ -23,17 +20,13 @@

<ComponentType name="ConnectionPattern"/>



<ComponentType name="AllAll" extends="ConnectionPattern">
<Structure>
<ForEach instances="../source" as="a">
<ForEach instances="../target" as="b">
<EventConnection from="a" to="b"/>
</ForEach>
</ForEach>
</ForEach>
</Structure>

</ComponentType>

</Lems>
25 changes: 2 additions & 23 deletions examples/SingleSimulation.xml
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@@ -1,22 +1,17 @@
<Lems>


<ComponentType name="Display">
<Text name="title"/>
<Text name="title"/>
<Parameter name="xmin" dimension="none"/>
<Parameter name="xmax" dimension="none"/>
<Parameter name="ymin" dimension="none"/>
<Parameter name="ymax" dimension="none"/>

<Parameter name="timeScale" dimension="time"/>
<Children name="lines" type="Line"/>

<Simulation>
<DataDisplay title="title" dataRegion="xmin,xmax,ymin,ymax"/>
</Simulation>
</ComponentType>


<ComponentType name="Line">
<Parameter name="scale" dimension="*"/>
<Parameter name="timeScale" dimension="*"/>
Expand All @@ -27,49 +22,33 @@
</Simulation>
</ComponentType>


<ComponentType name="OutputFile">
<Text name="path"/>
<Text name="fileName"/>

<Children name="outputColumn" type="OutputColumn"/>

<Simulation>
<DataWriter path="path" fileName="fileName"/>
</Simulation>

</ComponentType>


<ComponentType name="OutputColumn">
<Path name="quantity"/>
<Simulation>
<Record quantity="quantity"/>
</Simulation>
</ComponentType>



<ComponentType name="Simulation">
<Parameter name="length" dimension="time"/>
<Parameter name="step" dimension="time"/>

<ComponentReference name="target" type="Component"/>


<Children name="displays" type="Display"/>

<Children name="outputs" type="OutputFile"/>

<Dynamics>
<StateVariable name="t" dimension="time"/>
</Dynamics>

<Simulation>
<Run component="target" variable="t" increment="step" total="length"/>
</Simulation>
</ComponentType>



</Lems>
</Lems>
3 changes: 1 addition & 2 deletions examples/elecdims.xml
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Expand Up @@ -4,5 +4,4 @@
<Dimension name="conductance" m="-1" l="-2" t="3" i="2"/>
<Dimension name="capacitance" m="-1" l="-2" t="4" i="2"/>
<Dimension name="current" i="1"/>

</Lems>
</Lems>
10 changes: 4 additions & 6 deletions examples/ex2dims.xml
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@@ -1,5 +1,4 @@
<Lems>

<Lems>
<Dimension name="voltage" m="1" l="2" t="-3" i="-1"/>
<Dimension name="time" t="1"/>
<Dimension name="per_time" t="-1"/>
Expand All @@ -8,8 +7,8 @@
<Dimension name="current" i="1"/>
<Dimension name="temperature" k="1"/>

<Unit symbol="mV" dimension="voltage" power="-3"/>
<Unit symbol="ms" dimension="time" power="-3"/>
<Unit symbol="mV" dimension="voltage" power="-3"/>
<Unit symbol="ms" dimension="time" power="-3"/>
<Unit symbol="pS" dimension="conductance" power="-12"/>
<Unit symbol="nS" dimension="conductance" power="-9"/>
<Unit symbol="uF" dimension="capacitance" power="-6"/>
Expand All @@ -19,5 +18,4 @@
<Unit symbol="pA" dimension="current" power="-12"/>
<Unit symbol="nA" dimension="current" power="-9"/>
<Unit symbol="degC" dimension="temperature" offset="273.15"/>

</Lems>
</Lems>
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