Inflam

Inflam is a command line tool that generates basic statistical plots for clinical trial inflammation data.

Key features:

• Supports inflammation clinical trial data in CSV (comma-separated value) format
• Generates a PNG image plot for basic statistical measures, with mean, minimum, maximum, and standard deviation currently supported
• Supports batch generation of plots on multiple input inflammation datasets
• Based on Python, Numpy and Matplotlib, it's highly portable across platforms

Prerequisites

Inflam has been developed and tested on the following:

• Python 3.11
• Numpy 1.24.1
• Matplotlib 3.6.2

For running the unit tests:

• Pytest 7.2.0

Installation

First obtain the contents of this repository:

git clone https://github.com/steve-crouch/readme-example
cd readme-example

Then set up a Python virtual environment and install Inflam's prerequisites into that environment:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Getting Started

To run Inflam over a single inflammation dataset file, and output the generated plot to a particular directory:

./inflam.py data/input/inflammation-01.csv --outputdir data/output

You can also specify an arbitrary number of inflammation datasets

./inflam.py data/input/inflammation-01.csv data/input/inflammation-02.csv --outputdir data/output

Running the Tests

To run the unit tests written using the pytest framework, ensure you have the prerequisites installed (see above), then do:

python -m pytest tests/test_models.py

Authors

• Steve Crouch
• A.N.Other
• S.Omebody Else

Contributing

TODO: add example CONTRIBUTING.md and link to it

License

This software is licensed under the MIT Licence.