mipscripts

mipscripts is a python package containing various tools for use with MIPTools pipelines.

Installation

You may install using pip:

pip install mipscripts

Usage

mipscripts is setup as one uniform program containing multiple subcommands, each designed for a different purpose. To use, simply type the name of the package, followed by the subcommand:

python3 -m mipscripts subcommand [options]

Developer Notes

When developing mipscripts, we recommend the use of a virtual environment:

python3 -m venv env
source env/bin/activate

The packages used during development are saved in the requirements.txt file. To install, use pip:

pip install -r requirements.txt

If you update packages or add any new ones into the virtual environment, please make sure to freeze the package versions before committing:

pip freeze > requirements.txt

After adding any new code, we encourage writing unit tests to test functionality. mipscripts is tested via the pytest framework. To test the code, run:

python3 -m pytest