Metadata-Version: 2.0
Name: nineml
Version: 1.0
Summary: A tool for reading, writing and generally working with 9ML objects and files.
Home-page: http://nineml-python.readthedocs.io
Author: Andrew P. Davison, Thomas G. Close, Mike Hull, Eilif Muller
Author-email: tom.g.close@gmail.com
License: BSD 3 License
Description-Content-Type: UNKNOWN
Keywords: computational neuroscience modeling interoperability XML YAMLHDF5 JSON
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4
Requires-Dist: lxml (>=3.7.3)
Requires-Dist: future (>=0.16.0)
Requires-Dist: h5py (>=2.7.0)
Requires-Dist: PyYAML (>=3.1)
Requires-Dist: sympy (>=1.1)

NineML Python Library
=====================

.. image:: https://travis-ci.org/INCF/nineml-python.svg?branch=master
   :target: https://travis-ci.org/ICNF/nineml-python
   :alt: Unit Test Status
.. image:: https://coveralls.io/repos/github/INCF/nineml-python/badge.svg?branch=master
   :target: https://coveralls.io/github/INCF/nineml-python?branch=master
   :alt: Unit Test Coverage
.. image:: https://img.shields.io/pypi/pyversions/nineml.svg
    :target: https://pypi.python.org/pypi/nineml/
    :alt: Supported Python versions
.. image:: https://img.shields.io/pypi/v/nineml.svg
    :target: https://pypi.python.org/pypi/nineml/
    :alt: Latest Version    
.. image:: https://readthedocs.org/projects/nineml-python/badge/?version=latest
   :target: http://nineml-python.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

NineML (9ML) is a language for describing the dynamics and connectivity of
neuronal network simulations (http://nineml.net), which is defined by the
`NineML specification`_.

The NineML Python Library is a software package written in Python, which maps
the NineML object model onto Python classes for convenient creation,
manipulation and validation of NineML models, as well as handling their
serialisation to and from XML_, JSON_, YAML_, and HDF5_.


Links
-----

* Documentation: http://nineml-python.readthedocs.org
* Mailing list: `NeuralEnsemble Google Group`_
* Issue tracker: https://github.com/INCF/nineml-python/issues


Relation to the NineML Specification
------------------------------------

The layout of the Python modules and classes in the NineML Python Library
relates closely to the structure of the `NineML specification`_ (v1.0). However,
there are notable exceptions where the NineML Python Library uses names and
relationships that are planned to be changed in v2.0 of the specification
(the NineML Python Library will be backwards compatible), such as the
renaming of ``ComponentClass`` elements to separate ``Dynamics``,
``ConnectionRule`` and ``RandomDistribution`` elements
(see https://github.com/INCF/nineml/issues/94).
A full list of changes planned for NineML v2.0 can be found at
https://github.com/INCF/nineml/milestone/3. When serializing 9ML models
the version 1.0 syntax is used unless the ``version=2`` keyword argument is
provided.

In addition to classes that directly correspond to the 9ML object model, a
range of shorthand notations ("syntactic sugar") exist to make writing 9ML
models by hand more convenient (see the ``nineml.sugar`` module). These
notations are frequently demonstrated in the *examples* directory of the
repository.


The NineML Catalog
------------------

The `NineML Catalog`_ contains a collection of validated NineML models, which
can be loaded and maninpulated with the NineML Python Library. If you create a
model that you believe will be of wider use to the computational neuroscience
community please consider contributing to the catalog via a pull request.


Installation
------------

HDF5 (dev)
~~~~~~~~~~

To add support to read or write HDF5_ serialisations you must first install
a HDF5_ dev library (i.e. with the C headers). 

On macOS HDF5_ can be installed using Homebrew_::

    $ brew install hdf5

On Ubuntu/Debian HDF5_ can be installed by one of the following packages:

* libhdf5-serial-dev (serial)
* libhdf5-openmpi-dev (parallel with Open MPI)
* libhdf5-mpich-dev (parallel with MPICH)

If you don't install HDF5_ the other serialisation formats can still be used
but you will need to install the package manually (i.e. not use *pip*).

Pip
~~~

The NineML Python Library can be installed using *pip*::

    $ pip install nineml

:copyright: Copyright 20011-2017 by the NineML Python Library team, see AUTHORS.
:license: BSD 3, see LICENSE for details.


.. _HDF5: http://support.hdfgroup.org/HDF5/
.. _YAML: http://yaml.org
.. _JSON: http://www.json.org
.. _XML: http://www.w3.org/XML/
.. _h5py: http://h5py.org/
.. _pyyaml: http://pyyaml.org/
.. _sympy: http://sympy.org
.. _lxml: http://pypi.python.org/pypi/lxml
.. _virtualenv: https://virtualenv.readthedocs.io/en/latest/
.. _Homebrew: https://brew.sh/
.. _NineML specification: http://nineml-spec.readthedocs.io
.. _`NeuralEnsemble Google Group`: http://groups.google.com/group/neuralensemble
.. _`NineML Catalog`: http://github.com/INCF/nineml-catalog



