UBDS^3 2026 Basic-python-2026

Repo for basic Python track of UBDS^3

Basic Python course for UBDS^3 2026, focusing on intro to programming, data types, dataframes, and intro to data science

Day	Topic
1	Python - variables, lists - notebook
2	Functions, expressions, dictionary, loops - Chapter 2, Chapter 3, Chapter 4
3	Writing functions, reading errors, debugging, classes - notebook, alignment practical
4	Pandas & matplotlib - intro notebook, GFF notebook
5	EDA, statistics, regression - notebook

Install Git

Git is needed to download the course repository and switch between versions.

Windows

Download and install Git for Windows from:

https://git-scm.com/download/win

After installation, open PowerShell or Git Bash and check:

git --version

macOS

With Homebrew:

brew install git

Without Homebrew, install Apple's command line tools:

xcode-select --install

Then check:

git --version

Linux

Ubuntu or Debian:

sudo apt update
sudo apt install git

Fedora:

sudo dnf install git

Then check:

git --version

Install all practical dependencies with uv

This repository includes a shared pyproject.toml for all practicals.

1. Install uv

Windows PowerShell:

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

macOS with Homebrew:

brew install uv

macOS without Homebrew:

curl -LsSf https://astral.sh/uv/install.sh | sh

Linux:

curl -LsSf https://astral.sh/uv/install.sh | sh

After installing, close and reopen the terminal, then check that uv works:

uv --version

2. Install everything for the course

From the Basic-python-2026 folder, run:

uv sync

This creates a local virtual environment in .venv and installs Jupyter, BioPython, NumPy, pandas, matplotlib, SciPy, statsmodels, scikit-learn, seaborn, and pytest.

If you need to recreate or update the lock file, run:

uv lock

3. Open the notebooks

Use Jupyter from the uv environment:

uv run jupyter notebook

You can also run tests for the day 3 alignment practical:

uv run pytest day3/real_aligment/tests

Useful uv commands

uv init creates a new Python project by adding a pyproject.toml file. You do not need to run it for this repository because the project file is already here.

uv init

uv add installs a new package and records it in pyproject.toml. Use this if a new practical needs an extra package.

uv add package-name

For example:

uv add requests

uv sync installs everything listed in pyproject.toml and uv.lock into the local .venv environment.

uv sync

uv lock resolves package versions and updates uv.lock. Use it after changing dependencies, then share the updated uv.lock with the repository.

uv lock

To run commands inside the uv environment, prefix them with uv run:

uv run python --version
uv run jupyter notebook