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 when installing Python packages using pip to prevent these from conflicting with other system libraries.
This will support the default XML serialization. To install all of requirements to include the other serialisations, use
# On Ubuntu based systems
sudo apt-get install libhdf5-dev
pip install libNeuroML[full]
The apt line is required at time of writing because PyTables’ wheels for python 3.7 depend on the system libhdf5.
On Fedora based systems¶
On Fedora Linux systems, the NeuroFedora community provides libNeuroML in the standard Fedora repos and can be installed using the following commands:
sudo dnf install python3-libNeuroML
Install from source¶
You can clone the GitHub repository 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. To build and install libNeuroML, you can use the standard install method for Python packages (preferably in a virtual environment):
python setup.py install
To use the latest development version of libNeuroML, switch to the development branch:
git checkout development
sudo python setup.py install
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 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
To ignore some tests, like the MongoDB test which requires a MongoDB setup, run:
pytest -v -k "not mongodb" --strict -W all