Installation

Installation instructions may be found on the GitHub project README, but we include them here also.

From source

Source code for PyGOM can be downloaded from the GitHub repository: ukhsa-collaboration/pygom

git clone https://github.com/ukhsa-collaboration/pygom.git

Please be aware that there may be redundant files within the package as it is under active development.

Note

The latest fully reviewed version of PyGOM will be on the master branch and we recommend that users install the version from there.

Activate the relevant branch for installation via Git Bash:

git activate relevant-branch-name

Package dependencies can be found in the file requirements.txt. An easy way to install these is to create a new conda environment via:

conda env create -f conda-env.yml

which you should ensure is active for the installation process using:

conda activate pygom

Alternatively, you may add dependencies to your own environment.

pip install -r requirements.txt

The final prerequisite, if you are working on a Windows machine, is that you will also need to install:

• Graphviz

• Microsoft Visual C++ 14.0 or greater, which you can get with Microsoft C++ Build Tools

You you should be able to install the PyGOM package via command line:

python setup.py install

If you anticipate making your own frequent changes to the PyGOM source files, it might be more convenient to install in develop mode instead:

python setup.py develop

From PyPI

Alternatively, the latest release can be installed from PyPI:

pip install pygom

Testing the package

Test files should then be run from the command line to check that installation has completed successfully

python setup.py test

This can take some minutes to complete.