Python Programming in PyPI for Translational Medicine

Yoshiyasu Takefuji

doi:10.3390/ijtm1030019

Abstract

This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, researchers need to deal with big data. This paper describes how to build an executable Python Package Index (PyPI) code and package. PyPI is a repository of software for the Python programming language with 5,019,737 files and 544,359 users (programmers) as of 19 October 2021. First, programmers must understand how to scrape a dataset over the Internet; second, they must read the dataset file in csv format; third, build a program to compute the target values; fourth, convert the Python program to the PyPI package.; and fifth, upload the PyPI package. This paper depicts a covidlag executable package as an example for calculating the accurate case fatality rate (CFR) and the lag time from infection to death. You can install the covidlag by pip terminal command and test it. This paper also introduces deathdaily and scorecovid packages on PyPI Stats, which can inform how many users have downloaded the specified PyPI package. The usefulness and applicability of a developed tool can be verified by PyPI Stats with the number of downloaded users.

Highlights

With the rapid progress of open-source software [1,2,3], many researchers have used a Python language for translational medicine and other medical applications in general [4,5,6]
Python Package Index (PyPI) is a repository of software for the Python programming language with 5,019,737 files and 544,359 users as of 19 October 2021
Programmers must understand how to scrape a dataset over the Internet; second, they must read the dataset file in csv format; third, build a program to compute the target values; fourth, convert the Python program to the PyPI package.; and fifth, upload the PyPI package

Summary

Introduction

With the rapid progress of open-source software [1,2,3], many researchers have used a Python language for translational medicine and other medical applications in general [4,5,6]. The useful libraries and packages are available in public and can be installed by a simple pip terminal-line command. In order to install scikit-learn for example, run the following command. On Windows 10, install Cygwin and click the Cygwin to open the bash command terminal: https://www.cygwin.com/ (accessed on 23 November 2021). The number of sampled days and its range (start and end dates) have to be manually determined in order to calculate a value of the CFR The covidlag in this tutorial automatically calculates the CFR by exploiting maxima and minima points with strong correlation between infection and death. The more examples that are available in open-source libraries, the easier it is for users to create the desired code This tutorial was written from the experience of nine PyPI projects: https://pypi.org/.

Testing Python Environment

PyPI Package

How to Upload a PyPI Package

Discussion

Materials and Methods

Methods