Metadata-Version: 2.1
Name: PyLEMS
Version: 0.6.0
Summary: A Python library for working with the Low Entropy Model Specification language (LEMS)
Home-page: https://github.com/LEMS/pylems
Author: PyLEMS authors and contributors
Author-email: gautham@lisphacker.org, p.gleeson@gmail.com
License: LGPL
Description: ## PyLEMS
        
        [![Build](https://github.com/LEMS/pylems/actions/workflows/ci.yml/badge.svg)](https://github.com/LEMS/pylems/actions/workflows/ci.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 (http://neuroml.org/neuroml2.php) models.
        
        For more about PyLEMS see:
        
        Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig Gleeson,
        **libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience**
        [Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00038/abstract), doi: 10.3389/fninf.2014.00038
        
        _**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_
        
        For more details on LEMS see:
        
        Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver,
        **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
        
        To install as root:
        
            sudo 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
            sudo python setup.py install
        
        ### Usage as a LEMS model simulator
        
            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
        - Example 1 --  Working
        - Example 2 --  Working
        - Example 3 --  Working
        - Example 4 --  Not working (Unsupported in PyLEMS: KSChannel)
        - Example 5 --  Working
        - Example 6 --  Working
        - Example 7 --  Working
        - Example 8 --  Working
        - Example 9 --  Working
        - Example 10 -- Working
        - Example 11 -- Working
        - Example 12 -- Not working (Unsupported in PyLEMS: Property)
        - Example 13 -- Working
        - Example 14 -- Not working (Unsupported in PyLEMS: Property)
        - Example 15 -- Working
        - Example 16 -- Working (apart from spikeArray)
        - Example 17 -- Working
        - Example 18 -- Working
        
        
        **LEMS examples (in directory examples)**
        
        - example1.xml --  Working
        - example2.xml --  Working
        - example3.xml --  Working
        - 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
        
        
        **LEMS elements that do not work**
        
        - KSChannel
        - Property
        - XPath based parameters - PathParameter
        - Assertions
        
        **Tasks TODO**
        
        - Implement flattening
        - Decouple events from runnables
        - Improve dimension-checking on expressions.
        
        
        ### Travis integration
        
        pylems is integrated with the the [Travis Continuous Integration service](http://travis-ci.com/).
        
        [![Build Status](https://travis-ci.com/LEMS/pylems.png?branch=master)](https://travis-ci.com/LEMS/pylems)
        
        This code is distributed under the terms of the GNU Lesser General Public License.
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
