ViMMS Installation Guide

🌟 Stable Release

ViMMS is designed for Python 3 and above. Install the latest stable release with the following command:

pip install vimms

Check out the latest versions on the Release page or PyPi.

🕰 Older Releases

For those interested in ViMMS version 1.0 as used in our original paper, you can get it here. Be aware that it’s quite outdated now. For other previous releases, head over to the Releases page on GitHub. This include releases to support other papers.

🔧 Development Version

To get the latest features and fixes (still under development), clone the repository:

$ git clone https://github.com/glasgowcompbio/vimms.git

You can then set up the environment using Anaconda Python or Poetry. We recommend using Conda.

There is also support for using Pipenv through the included Pipfile in the repo, but going forward that will not be maintained anymore.

Setting up with Anaconda:

$ cd vimms
$ conda env create --file environment.yml
$ conda activate vimms
$ jupyter lab (to test notebooks)

Setting up with Poetry:

$ cd vimms
$ pip install poetry (if you don't have it)
$ poetry install
$ poetry shell
$ jupyter lab (to test notebooks)

Setting up with Pipenv:

$ cd vimms
$ pip install pipenv (if you don't have it)
$ pipenv install
$ pipenv shell

🧪 Testing ViMMS

Unit tests are located in the tests folder. Use the scripts run_tests.sh or run_tests.bat to execute them.

Run individual test classes with:

$ python -m pytest <module>::<class>

For example:

$ python -m pytest tests/integration/test_controllers.py::TestSMARTROIController

Include -s switch for test output:

$ python -m pytest -s tests/integration/test_controllers.py::TestSMARTROIController