A Python library for working with NeuroML descriptions of neuronal models
Project description
Introduction
This package provides Python libNeuroML, for working with neuronal models specified in NeuroML 2.
For more about libNeuroML 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 libNeuroML!
Documentation is available at http://readthedocs.org/docs/libneuroml/en/latest/
For installation instructions, see http://readthedocs.org/docs/libneuroml/en/latest/install.html
For an overview of all NeuroML related libraries/documentation/publications see https://docs.neuroml.org
pyNeuroML
A related package, pyNeuroML builds on this and provides functionality, scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.
pyNeuroML builds on: libNeuroML & PyLEMS and wraps functionality from jNeuroML.
Development process for libNeuroML
Most of the work happens in the development branch. That branch is kept up to date with the development branches for NeuroML 2 and related libraries. See https://docs.neuroml.org/ for an overview of the various NeuroML libraries.
Changelog
See also https://github.com/NeuralEnsemble/libNeuroML/releases.
version 0.5.8
- drop py3.7, add py3,12
- fix loader to check for given path and fall back to relative path
- extend
get_segment_groups_from_substringto also include anunbranchedfilter - more type hint/doc fixes
version 0.5.7
- more documentation for writes/loaders
version 0.5.6
- documentation fixes to writer modules
version 0.5.5
- update schema, changes for NML 2.3 release
version 0.5.4
- use natsort to improve sorting of segments/groups when optimising
version 0.5.3
- add links to schema documentation
- move from legacy setup.py to pyproject.toml build system
version 0.5.2
- explicitly depend on numpy
version 0.5.1
- updates to GHA
version 0.5.0
- enable CI on py3.11
- fix to loaders
- format code with black
- add graph representation for morphology, and methods to calculate distances b/w segments
version 0.4.1
- add multiple cell builder utility functions
- performance improvements in generic helper functions
- documentation fixes/improvements
- add type annotations to all nml classes to aid users
- add level 1 validation method
- add generic component inspection methods
version 0.4.0
- update to use schema version 2.3
- drop python 2 support
version 0.3.1
- include schema documentation in generated
nml.pyAPI - introduce generic methods to add child/children elements to components
version 0.2.58
- multiple documentation fixes
version 0.2.57
- Enable Python 3.10 support
- Regenerate nml.py with generateDS using Python 3
- Add generic
addmethod to all NeuroML ComponentType classes that allows users to easily construct their NeuroML documents. - Improve unit tests
- DEPRECATION notice:
append_to_elementwill be deprecated in future releases, please use theaddmethod instead
version 0.2.56
- Documentation updates for RTD and other minor fixes.
version 0.2.55
- Patch release with minor changes under the hood.
- Use PyTest for testing.
- Enable CI on GitHub Actions
version 0.2.54
- Using Schema for NeuroML v2.1. Better compatibility with Python 3
version 0.2.50
- Updated to use the final stable Schema for NeuroML v2.0
version 0.2.47
- Updated to use the final stable Schema for NeuroML v2beta5
version 0.2.18
- Updated to use the final stable Schema for NeuroML v2beta4
- Tested with Python 3
version 0.2.4
- Updated to use the Schema for NeuroML v2beta4
version 0.2.2
- Updated to use the Schema for NeuroML v2beta3
- Ensures numpy & pytables are only required when using non-XML loaders/writers
version 0.2.0
- Updated to use the Schema for NeuroML v2beta2
version 0.1.9
- Minor release: Update to latest schema
version 0.1.8
- Several Bug fixes and small enhamcements
- Support for latest NeuroML schema (see change outline)
- JSON serialization
- MongoDB backend
- HDF5 serialization
- Improved installation process
- All usage examples are now run on the Travis-CI continuous integration server to confirm that that they do not error.
- Schema validation utility
- Improved documentation and documentation new look
:copyright: Copyright 2023 by the libNeuroML team, see AUTHORS. Modified BSD License, see LICENSE for details.
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