Installation¶
It is recommended that you use pip version 8.1.0
or higher to install into
NeuroM
into a virtualenv. For details on
how to set it up, see Virtualenv setup
Once the virtualenv is set up 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:
(nrm)$ pip install neurom
Install a specific version:
(nrm)$ pip install neurom==1.2.3
Install from git¶
Install a particular release:
(nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.git@v0.1.0
Install the latest version:
(nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.git
Install from source¶
Clone the repository and install it:
(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
.
Virtualenv setup¶
$ 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 pre-installed dependencies, you may use
the --system-site-packages
option, which allows globally installed python packages
to be used inside the virtualenv
:
$ 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:
$(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.
$(nrm) pip --version # New version should be >= 8.0.0
This will allow use of pre-compiled python packages most platforms.
To de-activate the virtualenvr run the deactivate
command:
(nrm)$ 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.