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pylems

LEMS interpreter implemented in Python

https://github.com/lems/pylems

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: frontiersin.org
  • ✓
    Committers with academic emails
    2 of 10 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary

Keywords

lems neuroml

Keywords from Contributors

neuroscience biological-simulations computational-neuroscience neuron brian brian2 code-generation differential-equations simulation-framework spiking-neural-networks
Last synced: 6 months ago · JSON representation

Repository

LEMS interpreter implemented in Python

Basic Info
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 19
  • Open Issues: 13
  • Releases: 7
Topics
lems neuroml
Created almost 14 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

PyLEMS

Build Check LEMS examples Documentation Status PyPI

A LEMS simulator written in Python which can be used to run NeuroML2 models (see here).

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, 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, doi: 10.3389/fninf.2014.00079

Installation

A stable version of PyLEMS is available on PyPI using pip:

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 .

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.

This code is distributed under the terms of the GNU Lesser General Public License.

Owner

  • Name: LEMS
  • Login: LEMS
  • Kind: organization

The Low Entropy Model Specification language

GitHub Events

Total
  • Create event: 3
  • Issues event: 1
  • Release event: 1
  • Watch event: 2
  • Delete event: 1
  • Issue comment event: 3
  • Push event: 12
  • Pull request event: 8
  • Fork event: 2
Last Year
  • Create event: 3
  • Issues event: 1
  • Release event: 1
  • Watch event: 2
  • Delete event: 1
  • Issue comment event: 3
  • Push event: 12
  • Pull request event: 8
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 547
  • Total Committers: 10
  • Avg Commits per committer: 54.7
  • Development Distribution Score (DDS): 0.501
Past Year
  • Commits: 25
  • Committers: 3
  • Avg Commits per committer: 8.333
  • Development Distribution Score (DDS): 0.36
Top Committers
Name Email Commits
Gautham Ganapathy g****m@l****g 273
Padraig Gleeson p****n@g****m 168
Ankur Sinha (Ankur Sinha Gmail) s****r@g****m 68
Gautham Ganapathy g****m@t****m 11
Boris Marin b****n@g****m 9
dokato r****2@g****m 9
Richard C Gerkin r****n@a****u 5
Padraig Gleeson p****g@P****l 2
Richard C Gerkin r****1@g****g 1
Werner Van Geit w****t@e****h 1
Committer Domains (Top 20 + Academic)
epfl.ch: 1 gerkin.org: 1 asu.edu: 1 textensor.com: 1 lisphacker.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 32
  • Total pull requests: 61
  • Average time to close issues: 6 months
  • Average time to close pull requests: 14 days
  • Total issue authors: 10
  • Total pull request authors: 7
  • Average comments per issue: 0.91
  • Average comments per pull request: 0.48
  • Merged pull requests: 58
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 7
  • Average time to close issues: 1 minute
  • Average time to close pull requests: about 2 months
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.29
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pgleeson (14)
  • dokato (5)
  • sanjayankur31 (4)
  • rgerkin (3)
  • jakirkham (1)
  • borismarin (1)
  • kmantel (1)
  • lisphacker (1)
  • leon-k-martin (1)
  • bmerrihort (1)
Pull Request Authors
  • pgleeson (32)
  • sanjayankur31 (28)
  • dokato (5)
  • leon-k-martin (2)
  • rgerkin (2)
  • DeLaVlag (1)
  • wvangeit (1)
Top Labels
Issue Labels
T: enhancement (5) T: bug (4) S: needs comment (1) T: question (1)
Pull Request Labels
T: bug (7) T: enhancement (6) help wanted (1) S: needs comment (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 5,881 last-month
  • Total dependent packages: 4
    (may contain duplicates)
  • Total dependent repositories: 12
    (may contain duplicates)
  • Total versions: 35
  • Total maintainers: 1
pypi.org: pylems

A Python library for working with the Low Entropy Model Specification language (LEMS)

  • Versions: 28
  • Dependent Packages: 3
  • Dependent Repositories: 12
  • Downloads: 5,881 Last month
Rankings
Dependent packages count: 1.6%
Downloads: 3.1%
Dependent repos count: 4.3%
Average: 7.1%
Forks count: 9.4%
Stargazers count: 17.1%
Maintainers (1)
pgleeson
Last synced: 7 months ago
conda-forge.org: pylems
  • Versions: 7
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 37.8%
Forks count: 38.1%
Stargazers count: 50.2%
Last synced: 7 months ago

Dependencies

doc/requirements.txt pypi
  • sphinxcontrib-bibtex *
setup.py pypi
  • lxml *
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/examples.yml actions
  • actions/checkout v2 composite
  • nelonoel/branch-name v1.0.1 composite
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite