applied-biostats-helper 0.1.0

Helper package for Applied Biostats course - simplifies Colab environment setup and grading

Applied Biostats Helper

A Python package that simplifies environment setup for the Applied Biostats course, particularly for Google Colab notebooks. This package replaces complex setup blocks with a single function call.

Features

• One-line environment setup for Colab and local Jupyter notebooks
• Automatic dependency management (installs otter-grader if needed)
• Seamless test file downloading from GitHub repositories
• Environment detection (automatically detects Colab vs local)
• Clean error handling and user feedback

Installation

From GitHub (Recommended for testing)

pip install git+https://github.com/DamLabResources/applied-biostats-helper.git.

From PyPI (when published)

pip install applied-biostats-helper

Local Development

git clone https://github.com/DamLabResources/applied-biostats-helper.git
cd applied-biostats-helper
pip install -e .

Quick Start

Before (Complex setup block)

# Setting up the Colab environment. DO NOT EDIT!
import os
import warnings
warnings.filterwarnings("ignore")

try:
    import otter
except ImportError:
    ! pip install -q otter-grader==4.0.0
    import otter

if not os.path.exists('walkthrough-tests'):
    zip_files = [f for f in os.listdir() if f.endswith('.zip')]
    assert len(zip_files)>0, 'Could not find any zip files!'
    assert len(zip_files)==1, 'Found multiple zip files!'
    ! unzip {zip_files[0]}

grader = otter.Notebook(colab=True, tests_dir='walkthrough-tests')

After (Simple one-liner)

from applied_biostats import setup_environment

grader = setup_environment('Module02_walkthrough')

Usage

Main Function: setup_environment()

The primary function that handles all setup tasks:

from applied_biostats import setup_environment

# Basic usage
grader = setup_environment('Module02_walkthrough')

# With custom branch
grader = setup_environment('Module02_walkthrough',
                          branch='dev')

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests if applicable
5. Submit a pull request

Support

For issues and questions:

• Open an issue on GitHub
• Contact the course instructors

Changelog

v0.1.0

• Initial release
• Basic environment setup functionality
• GitHub integration for test file downloads
• Colab and local Jupyter support