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Installation

To install Saber, you will need python3.6. If not already installed, python3 can be installed via

Note

Run python --version at the command line to make sure installation was successful. You may need to type python3 (not just python) depending on your install method.

(OPTIONAL) Activate your virtual environment (see below for help)

$ conda activate saber
# Notice your command prompt has changed to indicate that the environment is active
(saber) $

Latest PyPI stable release

PyPI-Status PyPI-Downloads Libraries-Dependents

(saber) $ pip install saber

Error

The install from PyPI is currently broken, please install using the instructions below.

Latest development release on GitHub

GitHub-Status GitHub-Stars GitHub-Forks GitHub-Commits GitHub-Updated

Pull and install straight from GitHub

(saber) $ pip install git+https://github.com/BaderLab/saber.git

or install by cloning the repository

(saber) $ git clone https://github.com/BaderLab/saber.git
(saber) $ cd saber

and then using either pip

(saber) $ pip install -e .
or setuptools

(saber) $ python setup.py install

Note

See Running tests for a way to verify your installation.

(OPTIONAL) Creating and activating virtual environments

When using pip it is generally recommended to install packages in a virtual environment to avoid modifying system state. To create a virtual environment named saber

Using virtualenv or venv

Using virtualenv

$ virtualenv --python=python3 /path/to/new/venv/saber

Using venv

$ python3 -m venv /path/to/new/venv/saber

Next, you need to activate the environment.

$ source /path/to/new/venv/saber/bin/activate
# Notice your command prompt has changed to indicate that the environment is active
(saber) $

Using Conda

If you use Conda / Miniconda, you can create an environment named saber by running

$ conda create -n saber python=3.6

To activate the environment

$ conda activate saber
# Notice your command prompt has changed to indicate that the environment is active
(saber) $

Note

You do not need to name the environment saber.

Running tests

Sabers test suite can be found in saber/tests. If Saber is already installed, you can run pytest on the installation directory

# Install pytest
(saber) $ pip install pytest
# Find out where Saber is installed
(saber) $ INSTALL_DIR=$(python -c "import os; import saber; print(os.path.dirname(saber.__file__))")
# Run tests on that installation directory
(saber) $ python -m pytest $INSTALL_DIR

Alternatively, to clone Saber, install it, and run the test suite all in one go

(saber) $ git clone https://github.com/BaderLab/saber.git
(saber) $ cd saber
(saber) $ python setup.py test