.. Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
   All rights reserved.

   This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>

   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are met:

       1. Redistributions of source code must retain the above copyright
          notice, this list of conditions and the following disclaimer.
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          notice, this list of conditions and the following disclaimer in the
          documentation and/or other materials provided with the distribution.
       3. Neither the name of the copyright holder nor the names of
          its contributors may be used to endorse or promote products
          derived from this software without specific prior written permission.

   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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.. _installation-label:

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

It is recommended that you use `pip <https://pip.pypa.io/en/stable/>`_ version 8.1.0
or higher to install into
``NeuroM`` into a `virtualenv <https://virtualenv.pypa.io/en/stable/>`_. For details on
how to set it up, see :ref:`venv-label`

Once the :ref:`virtualenv is set up<venv-label>` is set up,
there are three ways to install ``NeuroM``

#. From the official Python Package Index server (PyPI)
#. From the git repository
#. From source (for NeuroM developers)

Install from the official PyPI server
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Install the latest release:

.. code-block:: bash

    (nrm)$ pip install neurom

Install a specific version:

.. code-block:: bash

    (nrm)$ pip install neurom==1.2.3

Install from git
^^^^^^^^^^^^^^^^

Install a particular release:

.. code-block:: bash

    (nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.git@v0.1.0

Install the latest version:

.. code-block:: bash

    (nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.git


Install from source
^^^^^^^^^^^^^^^^^^^

Clone the repository and install it:

.. code-block:: bash

    (nrm)$ git clone https://github.com/BlueBrain/NeuroM.git
    (nrm)$ pip install -e ./NeuroM

This installs ``NeuroM`` into your ``virtualenv`` in "editable" mode. That means
that changes made to the source code after the installation procedure are seen by the
installed package. To install in read-only mode, omit the ``-e``.


.. _venv-label:

Virtualenv setup
^^^^^^^^^^^^^^^^

.. code-block:: bash

    $ virtualenv nrm           # creates a virtualenv called "nrm" in nrm directory
    $ source nrm/bin/activate  # activates virtualenv
    (nrm)$                     # now we are in the nrm virtualenv

This will create a virtualenv that is isolated from system-wide python packages. If you
prefer to use :ref:`pre-installed dependencies<pre-dep-label>`, you may use
the ``--system-site-packages`` option, which allows globally installed python packages
to be used inside the ``virtualenv``:

.. code-block:: bash

    $ virtualenv --system-site-packages nrm   # creates a virtualenv called "nrm" in nrm directory

The prompt indicates that the ``virtualenv`` has been activated.

For efficient installation of dependencies with C extensions, it is recommended to
use ``pip`` version 8 or higher. You can check your ``virtuanenv``'s version
with ``pip --version``, and upgrade if it is too low:

.. code-block:: bash

    $(nrm) pip --version               # Check pip version. Should output version >= 8.0.0
    $(nrm) pip install --upgrade pip   # Install newest pip inside virtualenv if version too old.
    $(nrm) pip --version               # New version should be >= 8.0.0

This will allow use of pre-compiled python packages most platforms.

To de-activate the virtualenvr run the ``deactivate`` command:

.. code-block:: bash

    (nrm)$ deactivate

Note that you do not have to work in the ``nrm`` directory. This is where python
packages will get installed, but you can work anywhere on your file system, as long as
you have activated the ``virtualenv``.

.. note::

    In following code samples, the prompts ``(nrm)$`` and ``$`` are used to indicate
    that the user virtualenv is *activated* or *deactivated* respectively.

.. note::

    In following code samples, the prompt ``>>>`` indicates a python interpreter session
    started *with the virtualenv activated*. That gives access to the ``neurom``
    installation.