Installation
============

Using Pip
----------

On most systems with a Python installation, libNeuroML can be installed using the default Python package manager, Pip:

::

    pip install libNeuroML

It is recommended to use a `virtual environment <https://docs.python.org/3/tutorial/venv.html>`_ when installing Python packages using `pip` to prevent these from conflicting with other system libraries.

This will support the default XML serialization.
Note that you may be required to install libhdf5 using your package manager because PyTables' wheels for python 3.7+ depend on the system libhdf5 to build.

::

    # On Ubuntu based systems
    sudo apt-get install libhdf5-dev
    pip install libNeuroML


On Fedora based systems
------------------------

On `Fedora <https://getfedora.org>`_ Linux systems, the `NeuroFedora <https://neuro.fedoraproject.org>`_ community provides libNeuroML in the `standard Fedora repos <https://src.fedoraproject.org/rpms/python-libNeuroML>`_ and can be installed using the following commands:

::

    sudo dnf install python3-libNeuroML


Install from source
--------------------

You can clone the `GitHub repository <https://github.com/NeuralEnsemble/libNeuroML/>`_ and also build libNeuroML from the sources.
For this, you will need `git`_:

::

    git clone git://github.com/NeuralEnsemble/libNeuroML.git
    cd libNeuroML


More details about the git repository and making your own branch/fork are `here <how_to_contribute.html>`_.
To build and install libNeuroML, you can use the standard install method for Python packages (preferably in a virtual environment):

::

    pip install .

To use the **latest development version of libNeuroML**, switch to the development branch:

::

    git checkout development
    pip install .


To install developer dependencies and other extras, use the extras declared in the `setup.cfg` file. E.g.:

::

    pip install .[dev]
    pip install .[test]
    pip install .[doc]


Run an example
--------------

Some sample scripts are included in `neuroml/examples`, e.g. :

::

    cd neuroml/examples
    python build_network.py

The standard examples can also be found :doc:`examples`.

Unit tests
----------

To run unit tests cd to the directory `neuroml/test` and use the Python unittest module discover method:

::

    cd neuroml/test/
    python -m unittest discover

If all tests passed correctly, your output should look something like this:

::

    .......
    ----------------------------------------------------------------------
    Ran 55 tests in 40.1s
    
    OK

You can also use PyTest to run tests.

::

    pip install pytest
    pytest -v --strict -W all


.. _Git: https://git-scm.com