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Fix formatting for README.md and bump to v0.6.4 fornew release
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pgleeson committed Jun 22, 2023
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27 changes: 13 additions & 14 deletions README.md
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[![Check LEMS examples](https://github.com/LEMS/pylems/actions/workflows/examples.yml/badge.svg)](https://github.com/LEMS/pylems/actions/workflows/examples.yml)
[![Documentation Status](https://readthedocs.org/projects/pylems/badge/?version=latest)](https://pylems.readthedocs.io/en/latest/?badge=latest)


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:
Expand All @@ -21,33 +20,35 @@ Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin,
**LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**,
[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract), doi: 10.3389/fninf.2014.00079


### Installation

A stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/PyLEMS) using [pip](https://pip.pypa.io/en/latest/installing.html):

pip install pylems
```
pip install pylems
```

Alternatively, you can obtain the latest version with

git clone https://github.com/LEMS/pylems.git
cd pylems
git checkout development # optional
pip install .

```
git clone https://github.com/LEMS/pylems.git
cd pylems
git checkout development # optional
pip install .
```

### Usage as a LEMS model simulator

pylems [options] LEMS_file
```
pylems [options] LEMS_file
```

**Options**

- -I/-include path - Adds a directory to the model file include search path


### Examples


**NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)**

- Example 0 -- Working
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- Example 17 -- Working
- Example 18 -- Working


**LEMS examples (in directory examples)**

- example1.xml -- Working
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- example4.xml -- Not working (Unsupported in PyLEMS: KSChannel)
- example5.xml -- Not working (Unsupported in PyLEMS: KSChannel)
- example6.xml -- Working
-- TODO: Rest of examples require an update to the `<Simulation>` element,
i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS

TODO: Rest of examples require an update to the `<Simulation>` element, i.e. use `<Simulation...>` not `<SimulationSet...>`, to work in PyLEMS

**LEMS elements that do not work**

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2 changes: 1 addition & 1 deletion setup.cfg
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[metadata]
name = PyLEMS
version = 0.6.3
version = 0.6.4
author = PyLEMS authors and contributors
author_email = [email protected], [email protected]
maintainer_email = [email protected]
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