pyneuroml

A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.

https://github.com/neuroml/pyneuroml

Science Score: 59.0%

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

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CITATION.cff file
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codemeta.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
4 of 20 committers (20.0%) from academic institutions
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Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary

Keywords from Contributors

lems neuroml python-template neuroscience differential-equations openworm closember degoogle

Last synced: 6 months ago · JSON representation

Repository

A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.

Basic Info

Host: GitHub
Owner: NeuroML
License: lgpl-3.0
Language: Python
Default Branch: master
Homepage: https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html
Size: 296 MB

Statistics

Stars: 46
Watchers: 12
Forks: 35
Open Issues: 43
Releases: 58

Created about 11 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing License

README.md

pyNeuroML

A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.

Builds on: libNeuroML & PyLEMS and wraps functionality from jNeuroML.

Installation

Dependencies

pyNeuroML relies on additional software to carry out its functions:

Java Runtime environment (JRE)
dot (from Graphviz)
lxml

On most Linux systems, these can be installed using the default package manager. On Ubuntu based distributions:

sudo apt-get install python-lxml graphviz openjdk-11-jdk

Pip

pyNeuroML can be installed with pip (preferably in a virtual environment):

pip install pyneuroml

A number of extra packages are also provided for convenience. You can install these to pull in other dependencies if required:

pip install pyneuroml[neuron]       # for NEURON simulation backend
pip install pyneuroml[brian]        # for Brian2 simulation backend
pip install pyneuroml[netpyne]      # for NetPyNE simulation backend
pip install pyneuroml[povray]       # for povray functions
pip install pyneuroml[hdf5]         # for HDF5 support
pip install pyneuroml[analysis]     # for analysis functions
pip install pyneuroml[tune]         # for tuning/fitting functions
pip install pyneuroml[vispy]        # for 3D interactive morphology plotting using vispy
pip install pyneuroml[plotly]       # for interactive plotting with plotly
pip install pyneuroml[nsg]          # pulls in pynsgr to use NSG
pip install pyneuroml[combine]      # includes libsbml, libsedml
pip install pyneuroml[tellurium]    # for Tellurium simulation backend
pip install pyneuroml[all]          # installs all of the above
pip install pyneuroml[dev]          # installs all of the above and other test related packages
pip install pyneuroml[doc]          # for building documentation

Please see the setup.cfg file for more details.

Fedora

The NeuroFedora community initiative provides pyNeuroML for use on the Fedora Linux Distribution. Fedora users can install pyNeuroML using the following commands:

sudo dnf copr enable @neurofedora/neurofedora-extra
sudo dnf install python3-pyneuroml

This will also pull in all the necessary dependencies (Java, lxml, graphviz). Please see the project documentation for more information.

Installation from the source

Clone the repository:

git clone https://github.com/NeuroML/pyNeuroML.git
cd pyNeuroML

It should be possible to install pyNeuroML using just:

pip install .

To develop pyNeuroML, you can use the dev extra and the development branch:

git clone https://github.com/NeuroML/pyNeuroML.git
cd pyNeuroML
git checkout development
pip install .[dev]

Current/planned features

1) Single Python package for NeuroML2/LEMS

One Python package which can be installed using pip & a user has everything they need to work with NeuroML2/LEMS files:

libNeuroML
PyLEMS
A bundled version of jNeuroML which can be used to run simulations

2) Run models using jNeuroML or PyLEMS

Ability to run NeuroML2/LEMS models using jLEMS/jNeuroML (with bundled jar) or PyLEMS (todo...)

Uses similar command line interface to jNeuroML, i.e. based on jnml

Try:

pynml -h

to list current options.

3) Access to export & import options of jNeuroML

All export & import options of jNeuroML available through easy command line interface (see here for progress) & through Python methods.

Example of export of NeuroML2/LEMS to NEURON and execution of generated code using single method is here.

4) Helper Python scripts

Lots of helper scripts for commonly used functions, e.g. generating a firing frequency vs injected current plot, generating a LEMS file for use with a NeuroML2 file,

5) Analysis of ion channels

Generation of plots of activation rates for ion channels from NeuroML2 channel file (example):

pynml-channelanalysis NaConductance.channel.nml

Generation of plots of activation rates for ion channels from NEURON mod file (example):

pynml-modchananalysis NaConductance -modFile NaConductance.mod

See here for more.

6) Home for existing functionality distributed in various places

Incorporate ChannelML2NeuroML2beta.xsl for updating ChannelML (coming soon...)

7) NEURON to NeuroML2

Scripts for converting NEURON to NeuroML2

Export morphologies (plus channels, soon). See here.
mod files - make best guess at initial NeuroML2 form (todo)

8) Export of images/movies from cell/networks

Files can be generated for POV-Ray which can be used to generate high resolution images and even sequences of images for creating movies. try:

pynml-povray -h

9) Tuning cell models in NeuroML 2

Builds on Neurotune and pyelectro. See here for example.

9) Planned functionality

Built in viewer of cells in 3D? Mayavi? More closely tied to PyNN?

Contributors

_{Padraig Gleeson} 🐛 💻 🖋 🔣 📖 🎨 📋 🤔 🚇 🚧 🧑‍🏫 📦 📆 💬 🔬 👀 🔧 ✅ 📢 📓	_{Ankur Sinha} 🐛 💻 🖋 🔣 📖 🎨 📋 🤔 🧑‍🏫 📦 💬 🔬	_{Boris Marin} 🐛 💻 🖋 🔣 📖 🎨 📋 🤔 🚇 🚧 📦 💬 🔬 👀 🔧 📓	_{Richard C Gerkin} 🐛 💻 🤔 🚧 📦 🔬 👀 🔧 📓	_{David Lung} 🐛 💻 🚧 🔧 📓	_{Mark Watts} 🐛 💻	_{Chaitanya Chintaluri} 🐛 💻
_34383c 🐛 💻	_{Johannes Rieke} 🐛 💻	_{András Ecker} 🐛 💻	_{Rokas Stanislovas} 🐛 💻	_{Robert Vickerstaff} 💻 ⚠️	_{Giannis Daras} 🐛 🤔 👀 💻	_{Dhruvanshu-Joshi} 🐛 🤔
_{AdityaBITMESRA} 🐛 🤔 💻 👀	_{Y. Budhachandra} 💻 ⚠️	_Stella 💻 🤔
Add your contributions

Owner

Name: NeuroML
Login: NeuroML
Kind: organization
Email: info@neuroml.org

Website: https://docs.neuroml.org
Repositories: 24
Profile: https://github.com/NeuroML

Repositories for the NeuroML language specification and supporting software libraries

GitHub Events

Total

Create event: 17
Release event: 6
Issues event: 18
Watch event: 12
Delete event: 11
Issue comment event: 55
Push event: 59
Pull request event: 31
Fork event: 4

Last Year

Create event: 17
Release event: 6
Issues event: 18
Watch event: 12
Delete event: 11
Issue comment event: 55
Push event: 59
Pull request event: 31
Fork event: 4

Committers

Last synced: 10 months ago

All Time

Total Commits: 1,912
Total Committers: 20
Avg Commits per committer: 95.6
Development Distribution Score (DDS): 0.453

Past Year

Commits: 226
Committers: 6
Avg Commits per committer: 37.667
Development Distribution Score (DDS): 0.558

Top Committers

Name	Email	Commits
Ankur Sinha (Ankur Sinha Gmail)	s**r@g**m	1,046
Padraig Gleeson	p**n@g**m	547
Aditya Pandey	a**6@g**m	114
Richard C Gerkin	r**n@a**u	58
lej0hn	j**s@g**m	42
Robert Vickerstaff	r**f@u**k	35
allcontributors[bot]	4****]	20
YBCS	b**7@g**m	16
Boris Marin	b**n@g**m	7
RokasSt	r**3@u**k	6
lungd	l**m@g**m	5
Stella	3****s	3
shayanshafquat	s**n@g**m	3
Chaitanya Chintaluri	c**i@g**m	2
Mark Watts	w**5@g**m	2
34383c	3****c	2
András Ecker	a**r@e**h	1
Padraig Gleeson	p**g@P**l	1
Padraig Gleeson	p**g@P**l	1
Johannes Rieke	j**e@g**m	1

Committer Domains (Top 20 + Academic)

ucl.ac.uk: 2 epfl.ch: 1 asu.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 92
Total pull requests: 244
Average time to close issues: 8 months
Average time to close pull requests: 21 days
Total issue authors: 13
Total pull request authors: 12
Average comments per issue: 2.05
Average comments per pull request: 1.62
Merged pull requests: 207
Bot issues: 0
Bot pull requests: 10

Past Year

Issues: 10
Pull requests: 36
Average time to close issues: about 2 months
Average time to close pull requests: 28 days
Issue authors: 4
Pull request authors: 3
Average comments per issue: 1.9
Average comments per pull request: 1.03
Merged pull requests: 28
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sanjayankur31 (67)
jonrkarr (9)
pgleeson (8)
christian-oreilly (2)
JustasB (1)
harshagurnani (1)
Sietse20 (1)
subhacom (1)
clausagerskov (1)
lej0hn (1)
LucianSheen (1)
adampdp (1)

Pull Request Authors

sanjayankur31 (177)
pgleeson (76)
lej0hn (19)
AdityaBITMESRA (17)
allcontributors[bot] (15)
robertvi (11)
YBCS (5)
shayan823 (2)
borismarin (2)
stellaprins (2)
Dhruvanshu-Joshi (2)
samkitshah1262 (2)

Top Labels

Issue Labels

T: enhancement (63) good first issue (21) Help wanted (17) T: bug (15) T: question (4) S: needs info (4) P: low (3) S: release pending (2) S: ready for review (2) C: docs (1)

Pull Request Labels

T: enhancement (104) S: ready for review (65) S: waiting on reporter (9) T: bug (7) C: docs (4) P: low (3) S: release pending (3) S: needs info (2)

Packages

Total packages: 1
Total downloads:
- pypi 10,664 last-month

Total dependent packages: 5
Total dependent repositories: 18
Total versions: 83
Total maintainers: 1

pypi.org: pyneuroml

Python utilities for NeuroML

Homepage: https://github.com/NeuroML/pyNeuroML
Documentation: https://pyneuroml.readthedocs.io/
License: LGPL-3.0-only
Latest release: 1.3.21
published 8 months ago

Versions: 83
Dependent Packages: 5
Dependent Repositories: 18
Downloads: 10,664 Last month

Rankings

Dependent packages count: 1.6%

Dependent repos count: 3.4%

Downloads: 5.3%

Average: 5.9%

Forks count: 7.8%

Stargazers count: 11.3%

Maintainers (1)

pgleeson

Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi

airspeed *
argparse *
graphviz *
inspyred master
libneuroml *
lxml *
matplotlib *
neuromllite *
neurotune *
opencv-python *
pyelectro *
pyelectro master
pylems *
scipy *
sphinxcontrib-bibtex *

requirements-dev.txt pypi

NEURON * development
airspeed >=0.5.5 development
argparse * development
graphviz * development
inspyred master development
libNeuroML master development
matplotlib * development
modelspec >=0.1.3 development
neurotune master development
ppft * development
pyelectro master development
pylems master development
pytest * development

setup.py pypi

airspeed >=0.5.5
argparse *
graphviz *
lxml *
matplotlib *
neuromllite >=0.4.1
pylems >=0.5.7
typing *

.github/workflows/ci.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite