Package: libNeuroML
IntroductionThis package provides Python libNeuroML, for working with neuronal models specified inNeuroML 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 neuroscienceFrontiers in Neuroinformatics 2014, doi: 10.3389/fninf.2014.00038PLEASE CITE THE PAPER ABOVE IF YOU USE libNeuroML!Documentation is available athttp://readthedocs.org/docs/libneuroml/en/latest/For installation instructions, seehttp://readthedocs.org/docs/libneuroml/en/latest/install.htmlFor an overview of all NeuroML related libraries/documentation/publications seehttps://docs.neuroml.orgpyNeuroMLA related package,pyNeuroMLbuilds on this and provides functionality, scripts and modules for reading, writing,simulatingand analysing NeuroML2/LEMS models.pyNeuroML builds on:libNeuroML&PyLEMSand wraps functionality fromjNeuroML.Development process for libNeuroMLMost of the work happens in thedevelopment branch.
That branch is kept up to date with the development branches forNeuroML 2and related libraries.
Seehttps://docs.neuroml.org/for an overview of the various NeuroML libraries.Changelogversion 0.5.6documentation fixes to writer modulesversion 0.5.5update schema, changes for NML 2.3 releaseversion 0.5.4use natsort to improve sorting of segments/groups when optimisingversion 0.5.3add links to schema documentationmove from legacy setup.py to pyproject.toml build systemversion 0.5.2explicitly depend on numpyversion 0.5.1updates to GHAversion 0.5.0enable CI on py3.11fix to loadersformat code with blackadd graph representation for morphology, and methods to calculate distances b/w segmentsversion 0.4.1add multiple cell builder utility functionsperformance improvements in generic helper functionsdocumentation fixes/improvementsadd type annotations to all nml classes to aid usersadd level 1 validation methodadd generic component inspection methodsversion 0.4.0update to use schema version 2.3drop python 2 supportversion 0.3.1include schema documentation in generatednml.pyAPIintroduce generic methods to add child/children elements to componentsversion 0.2.58multiple documentation fixesversion 0.2.57Enable Python 3.10 supportRegenerate nml.py with generateDS using Python 3Add genericaddmethod to all NeuroML ComponentType classes that allows users to easily construct their NeuroML documents.Improve unit testsDEPRECATION notice:append_to_elementwill be deprecated in future releases, please use theaddmethod insteadversion 0.2.56Documentation updates for RTD and other minor fixes.version 0.2.55Patch release with minor changes under the hood.Use PyTest for testing.Enable CI on GitHub Actionsversion 0.2.54Using Schema for NeuroML v2.1. Better compatibility with Python 3version 0.2.50Updated to use the final stable Schema for NeuroML v2.0version 0.2.47Updated to use the final stable Schema for NeuroML v2beta5version 0.2.18Updated to use the final stable Schema for NeuroML v2beta4Tested with Python 3version 0.2.4Updated to use the Schema for NeuroML v2beta4version 0.2.2Updated to use the Schema for NeuroML v2beta3Ensures numpy & pytables are only required when using non-XML loaders/writersversion 0.2.0Updated to use the Schema for NeuroML v2beta2version 0.1.9Minor release: Update to latest schemaversion 0.1.8Several Bug fixes and small enhamcementsSupport for latest NeuroML schema (see change outline)JSON serializationMongoDB backendHDF5 serializationImproved installation processAll usage examples are now run on the Travis-CI continuous integration server to confirm that that they do not error.Schema validation utilityImproved documentation and documentation new look:copyright: Copyright 2023 by the libNeuroML team, seeAUTHORS. Modified BSD License, seeLICENSEfor details.