Installation¶
It is recommended that you use pip to install into
NeuroM
into a virtualenv:
Virtualenv setup¶
$ virtualenv --system-site-packages nrm # creates a virtualenv called "nrm" in nrm directory
$ source nrm/bin/activate # activates virtualenv
(nrm)$ # now we are in the nrm virtualenv
Here, the --system-site-packages
option has been used. This is because dependencies such as
matplotlib
aren’t trivial to build in a virtualenv
. This setting allows python packages
installed in the system to be used inside the virtualenv
.
The prompt indicates that the virtualenv
has been activated. To de-activate it,
(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.
NeuroM installation¶
Once the virtualenv
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@neurom-v0.0.8
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
.