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PyLEMS\n\n[![Build](https://github.com/LEMS/pylems/actions/workflows/ci.yml/badge.svg)](https://github.com/LEMS/pylems/actions/workflows/ci.yml)\n[![Check LEMS examples](https://github.com/LEMS/pylems/actions/workflows/examples.yml/badge.svg)](https://github.com/LEMS/pylems/actions/workflows/examples.yml)\n[![Documentation Status](https://readthedocs.org/projects/pylems/badge/?version=latest)](https://pylems.readthedocs.io/en/latest/?badge=latest)\n[![PyPI](https://img.shields.io/pypi/v/pylems)](https://pypi.org/project/pylems/)\n\nA [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)).\n\nFor more about PyLEMS see:\n\nMichael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig Gleeson,\n**libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience**\n[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00038/abstract), doi: 10.3389/fninf.2014.00038\n\n_**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_  \n\nFor more details on LEMS see:\n\nRobert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver,\n**LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**,\n[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract), doi: 10.3389/fninf.2014.00079\n\n### Installation\n\nA stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/PyLEMS) using [pip](https://pip.pypa.io/en/latest/installing.html):\n\n```\npip install pylems\n```\n\nAlternatively, you can obtain the latest version with\n\n```\ngit clone https://github.com/LEMS/pylems.git\ncd pylems\ngit checkout development   # optional\npip install .\n```\n\n### Usage as a LEMS model simulator\n\n```\npylems [options] LEMS_file\n```\n\n**Options**\n\n- -I/-include path - Adds a directory to the model file include search path\n\n### Examples\n\n**NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)**\n\n- Example 0 --  Working\n- Example 1 --  Working\n- Example 2 --  Working\n- Example 3 --  Working\n- Example 4 --  Not working (Unsupported in PyLEMS: KSChannel)\n- Example 5 --  Working\n- Example 6 --  Working\n- Example 7 --  Working\n- Example 8 --  Working\n- Example 9 --  Working\n- Example 10 -- Working\n- Example 11 -- Working\n- Example 12 -- Not working (Unsupported in PyLEMS: Property)\n- Example 13 -- Working\n- Example 14 -- Not working (Unsupported in PyLEMS: Property)\n- Example 15 -- Working\n- Example 16 -- Working (apart from spikeArray)\n- Example 17 -- Working\n- Example 18 -- Working\n\n**LEMS examples (in directory examples)**\n\n- example1.xml --  Working\n- example2.xml --  Working\n- example3.xml --  Working\n- example4.xml --  Not working (Unsupported in PyLEMS: KSChannel)\n- example5.xml --  Not working (Unsupported in PyLEMS: KSChannel)\n- example6.xml --  Working\n\nTODO: Rest of examples require an update to the `\u003cSimulation\u003e` element, i.e. use `\u003cSimulation...\u003e` not `\u003cSimulationSet...\u003e`, to work in PyLEMS\n\n**LEMS elements that do not work**\n\n- KSChannel\n- Property\n- XPath based parameters - PathParameter\n- Assertions\n\n**Tasks TODO**\n\n- Implement flattening\n- Decouple events from runnables\n- Improve dimension-checking on expressions.\n\nThis code is distributed under the terms of the GNU Lesser General Public License.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flems%2Fpylems","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flems%2Fpylems","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flems%2Fpylems/lists"}