libNeuroML 0.6.7
A Python library for working with NeuroML descriptions of neuronal models
License: BSD-2-Clause

## Introduction

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This package provides Python libNeuroML, for working with neuronal models specified in [NeuroML 2](http://neuroml.org/neuromlv2).

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](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 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](https://github.com/NeuroML/pyNeuroML)** builds on this and provides functionality, scripts and modules for reading, writing, **simulating** and analysing NeuroML2/LEMS models.

pyNeuroML builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML).

## Development process for libNeuroML

Most of the work happens in the [development branch](https://github.com/NeuralEnsemble/libNeuroML/tree/development).
That branch is kept up to date with the development branches for [NeuroML 2](https://github.com/NeuroML/NeuroML2/tree/development) 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_substring` to also include an `unbranched` filter
- 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.py` API
- 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 `add` method to all NeuroML ComponentType classes that allows users to easily construct their NeuroML documents.
- Improve unit tests
- DEPRECATION notice: `append_to_element` will be deprecated in future releases, please use the `add` method 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](AUTHORS). Modified BSD License, see [LICENSE](LICENSE) for details.