Python Programming II

Purpose: To test your fundamental Python package development skills.

Pre-requisites: Required: Python Programming I

Instructions

The following instructions describe the requirements to complete this task and earn the Python Programming II badge 🏆. They also provide guidance to help you along the way.

A few things to keep in mind:

1. Please remember at all times to abide by the BRN Code of Conduct and Academic Honesty Policy. If you notice violations of these policies, please contact codeofconduct@bioresnet.org.
2. Please remember to reach out if you get stuck, find bugs, or even just have a question!

Good luck and have fun! 😊

~ BRN Bot 🤖

Requirements

Badge Requirements:

Testing environment:

Assessment Premise:

TLDR; Take the functions from Python Programming I and turn them into a package called "bioutils"

After you completed the tasks your supervisor gave you in Python Programming I, you get a call from HR. Apparently, your functions were so useful that you have been promoted from a Bioinformatics Assistant to Bioinformatics Associate 🚀. Your first task will be to turn your utils.py script into a package, bioutils, for the whole bioinformatics team to use 🎯. The package should contain all the functions you wrote in utils.py, but properly formatted as a package and well-documented. This will enable your colleagues to easily install your package and use the functions contained within!

Users will use your package like so:

import bioutils as bu

cancer = "ATCGCATACGA"
normal = "ATCCCAGATGA"

bu.protein_variant(cancer, normal)

Automated testing / checking

Prior to releasing the package, your new supervisor will make sure that everything works correctly and that it is well-formatted. She will deploy a bot to run automated checks on your package -- they should produce no errors or warnings.

Automated checks

The bot will initiate an Python v3.10.4 session and install bioutils package by running:

pip install .

Then it will test the package by running:

pytest

Next, it will check the style of the package using flake8 from the linux command line:

flake8 .

Note: You do not need to write any unit tests as these have already been created for you in the tests/ folder.

Guidance

Most guidance for this assessment is identical to Python Programming I.

Additional resources

To learn about building and documenting Python packages, visit the following link: Python Packages Tutorial

Additional resources:

1. Free code camp
2. The joy of packaging
3. Youtube tutorial

Getting help

If you find a bug or get confused, please don't hesitate to contact the BRN Skill Assessment maintainers on the #help-skill-assessments Slack channel, and they will assist you.