ViMMS is designed for Python 3 and above. Install the latest stable release with the following command:
pip install vimmsCheck 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 Be aware that it's quite outdated now.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
Set up the development environment using Poetry:
$ cd vimms
$ pip install poetry (if you don't have it)
$ poetry install
$ poetry shell
$ jupyter lab (to test notebooks)
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