Installing¶

The Genome package can be installed in any computer running Python 3 or above. Genome does require Theano Python computational libraries to be installed first. It is recommended that users install a stable branch of Theano either through pip, conda or directly from the Github project page.

Users should also be familiar with using Git, though that is not a requirement. The latest code should always be pulled from the Github project repository.

Tip

Users can install Theano directly to their computer by the git clone and pip3 install command:

git clone https://github.com/Theano/Theano.git
pip3 install --user Theano

Requirements¶

Python 3.5 or later
Numpy 1.15 or later (base N-dimensional array package)
Scipy 1.2.0 or later (library for scientific computing)
Theano 1.0.0 or later

Installing using pip (recommended)¶

To install the latest version of Genome, download the repository from the command line:

git clone https://github.com/mwong009/Genome.git

then run pip (assuming no admin privileges):

pip3 install --user Genome

--user option installs the library the local dist-packages.

To update to the latest version, go into the project directory and execute git pull origin master.

You can also install from the Github repo directly (without cloning). Use the --user flag if necessary:

pip3 install -U --user https://github.com/mwong009/Genome/archive/master.tar.gz

To uninstall the package:

pip3 uninstall genome -y

Virtual environments¶

Use a virtual environment to manage the dependencies for your project, both in development and in testing.

Virtual environments are independent groups of Python libraries, one for each project. Packages installed for one project will not affect other projects or the operating system’s packages.

Create an environment

Create a project folder and a venv folder:

mkdir myproject
cd myproject
python3 -m venv venv

Activate the environment

Activate the corresponding enviornment from the project folder:

. venv/bin/activate

Installing Genome in venv

Within the activated virtual environment, install Genone. You can install it directly from the the master branch:

pip3 install -U https://github.com/mwong009/Genome/archive/master.tar.gz

Test your installation¶

To test if the package has been installed, run the following command from a Python environment, e.g. Jupyter:

>>> import genome
>>> genome.version()

If everything is installed correctly, there will not be any error messages. If you encounter error during the installation process, report the output of the tests under the issue tracker.

Basic Usage¶

TODO