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Installation

Requirements

  • Python 3.10 or higher
  • uv (recommended) or pip

uv is a fast Python package installer and resolver. It's significantly faster than pip and provides better dependency resolution.

Install uv

# macOS and Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

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

Install BioEPIC Skills

# Clone the repository
git clone https://github.com/bioepic-data/bioepic_skills.git
cd bioepic_skills

# Install with all dependencies
uv sync

# Or install without dev dependencies
uv sync --no-dev

Using pip

For traditional pip installation:

# From source
git clone https://github.com/bioepic-data/bioepic_skills.git
cd bioepic_skills
pip install -e ".[dev]"

# Or once published to PyPI
pip install bioepic_skills

Verify Installation

Verify the installation by checking the version:

import bioepic_skills
print(bioepic_skills.__version__)

Virtual Environments

uv automatically manages virtual environments for you. When you run uv sync, it creates a .venv directory in your project.

To activate the virtual environment manually:

# Unix/macOS
source .venv/bin/activate

# Windows
.venv\Scripts\activate

However, with uv, you typically don't need to activate the environment - just use uv run to execute commands:

uv run python script.py
uv run pytest
uv run mkdocs serve

Dependencies

Core Dependencies

The following packages are installed automatically:

  • pandas (≥2.2.3) - Data manipulation and analysis
  • requests (≥2.32.3) - HTTP library for API calls
  • matplotlib (≥3.10.0) - Plotting library

Development Dependencies

For development work, additional packages are installed:

  • pytest (≥7.0.0) - Testing framework
  • pytest-cov (≥4.0.0) - Coverage plugin for pytest
  • python-dotenv (≥1.0.0) - Environment variable management
  • mkdocs (≥1.5.0) - Documentation generator
  • mkdocs-material (≥9.0.0) - Material theme for MkDocs
  • mkdocstrings[python] (≥0.24.0) - Python documentation plugin
  • ruff (≥0.1.0) - Fast Python linter

These are automatically installed when you run uv sync.

Working with uv

Common Commands

# Install/sync dependencies
uv sync

# Add a new dependency
uv add package-name

# Add a dev dependency
uv add --dev package-name

# Remove a dependency
uv remove package-name

# Run a command in the virtual environment
uv run python script.py
uv run pytest

# Update dependencies
uv lock --upgrade

Next Steps

After installation, proceed to the Quick Start Guide to learn how to use the library.