james-rocker / afm_process

AFM_process

Pre-requisites

You will need a copy of python 3. Ideally 3.7.10 onwards as specified in the python-version config file, but it's not essential Link to download python.

Use a 64 bit version if possible. It'll be faster.

Make sure on installation of python to check Add Python to PATH. This will allow you to use commands in the commandline.

Setup

Navigate to this project folder in cmd or bash Create a venv environment with python3 -m venv ./venv
Activate the virtual environment with source venv/bin/activate
From there you have an independent project space to start install modules

To install the required modules, use pip install -r requirements.txt
If you have installed more modules with pip install. Update the requirements file with pip freeze > requirements.txt

Where to put my boxfiles

In the HepG2/curves folder within this project

To run

In your activated virtual environment shell, use python3 main.py

Replacing graphs

You don't need to worry about that, just place your box text files in the HepG2/curves folder then run. This will overwrite existing graphs in the output directory

Adding code

If you plan on adding code, please use the command black . to auto lint when it when you are done (saves arguments and makes things more readable)