Installation

Pype9 itself is a pure Python application and can be installed from the Python Package Index (PyPI) with Pip:

$ pip install pype9

If you would like to use the plot command you will also need to install matplotlib, which can be done separately or by specifying the ‘plot’ extra:

$ pip install pype9[plot]

With just the Python packages installed you will be able to use the convert and plot pipelines but in order to run simulations with Pype9 you will need to install at least one of the supported simulator backends (see below).

Simulator Backends

Pype9 currently works with the following simulator backends

There are various configurations in which to install them, with the best choice dependent on your operating system/development configuration and your own personal preference.

Manual Installation from Source (Linux/MacOS)

Detailed instructions on how to install NEST can be found on the official NEST docs.

Good instructions on how to install Neuron from source can be found in Andrew Davisons notes.

Homebrew/Linuxbrew (MacOS/Linux)

Homebrew is a package manager that was developed for MacOS, but which has proven so successful that it has been ported to Linux (Linuxbrew) to complement in-built package managers (Linuxbrew installs packages to a users home directory).

The Pype9 command line interface (CLI), Neuron and NEST can all be installed using Homebrew in one line with:

$ brew install tclose/pype9/pype9

The following options can be provided to the formula

  • with-python3 - Install Pype9, Neuron and NEST using Python 3
  • with-mpi - Install Pype9, Neuron and NEST with MPI support

Warning

As of 2.14.0 NEST will need to be reinstalled using brew reinstall NEST --HEAD in order to include commit that installs the required C++ header files to the install prefix (instead of leaving them in the build directory, which is deleted after the build). In future versions of NEST this step will not be necessary.

Note that this Homebrew formula installs the Pype9 package and all its Python dependencies in a virtual environment inside the Homebrew Cellar. Therefore, if you would like to access Pype9’s Python API you should only install the Neuron and NEST dependencies via Homebrew and Pype9 and its Python dependencies via Pip:

$ brew install --only-dependencies tclose/pype9/pype9
$ pip install pype9

or for Python 3:

$ brew install --only-dependencies tclose/pype9/pype9 --with-python3
$ pip3 install pype9

Please see the notes on how Homebrew handles Python, to ensure that you use the same installation for Neuron, NEST and Pype9, taking special note of the sections on bottling if not passing options to the build (i.e. --with-python3 or --with-mpi).

If you don’t have a strong preference for which Python you use I would recommend using a Homebrew Python installation (either 2 or 3, but probably 3 is best since support for Python 2 ends in 2020) as the system Python on MacOS has been slightly altered and can break some packages.

Note

To set Hombrew’s Python 2 to be the default Python used from your terminal add /opt/brew/opt/python/libexec/bin to your PATH variable.

Install scripts (Linux/MacOS)

To install Neuron and NEST from source you can use the scripts that Pype9 uses to set up its automated testing environment, which can be found in the install directory of the Pype9 repo. For example, to install NEST 2.14.0 with Python 3 bindings to the prefix /opt/nest/2.14.0:

$ wget https://raw.githubusercontent.com/tclose/pype9/develop/install/nest.sh
$ ./nest.sh 2.14.0 3 /opt/nest/2.14.0

or Neuron 7.5:

$ wget https://raw.githubusercontent.com/tclose/pype9/develop/install/neuron.sh
$ ./neuron.sh 7.5 3 /opt/neuron/7.5

These install scripts also work well within a virtualenv, where they will install NEST and Neuron to the virtualenv prefix by default. This allows you to maintain different versions of Neuron, NEST on your system, which is useful when upgrading.

When installing to a virtualenv, the Python version and install prefix don’t need to be supplied to the install scripts:

$ wget https://raw.githubusercontent.com/tclose/pype9/develop/install/nest.sh
$ wget https://raw.githubusercontent.com/tclose/pype9/develop/install/neuron.sh
$ pip install virtualenvwrapper
$ mkvirtualenv -p python3 pype9
$ ./nest.sh 2.14.0
$ ./neuron.sh 7.5

On Ubuntu, the installation requires the following packages

  • build-essential
  • autoconf
  • automake
  • libtool
  • libreadline6-dev
  • libncurses5-dev
  • libgsl0-dev
  • python-dev
  • python3-dev
  • openmpi-bin
  • libopenmpi-dev
  • inkscape
  • libhdf5-serial-dev
  • libyaml-dev

Similar packages can be found in other package managers on other distributions/systems (e.g. Homebrew).

Docker (Windows/Linux/MacOS)

A complete installation of Neuron, NEST and Pype9 (with MPI and against Python 3) can be found on the Docker image, https://hub.docker.com/r/tclose/pype9.

  1. Install Docker (see https://docs.docker.com/engine/installation/)

  2. Pull the Pype9 Docker image:

    $ docker pull tclose/pype9

  3. Create a Docker container from the downloaded image:

    $ docker run -v `pwd`/<your-local-output-dir>:/home/docker/output \
    -t -i tclose/pype9 /bin/bash

This will create a folder called <your-local-output-dir> in the directory you are running the docker container, which you can access from your host computer (i.e. outside of the container) and view the output figures from.

  1. From inside the running container, you will be able to run pype9, e.g.:

    (pype9)docker@b3eca79b5209:~$ pype9 simulate \
    ~/catalog/neuron/HodgkinHuxley.xml#PyNNHodgkinHuxleyProperties \
    nest 500.0 0.001 \
    --init_value v 65 mV \
    --init_value m 0.0 unitless \
    --init_value h 1.0 unitless \
    --init_value n 0.0 unitless \
    --record v ~/output/hh-v.neo.pkl

(pype9)docker@b3eca79b5209:~$ pype9 plot ~/output/hh-v.neo.pkl \
    --save ~/output/hh-v.png

Supply the –help option to see a full list of options for each example.

5. Edit the xml descriptions in the ~/catalog directory to alter the simulated models as desired.