Installation

Installation

Requirements

• Python 3.12, 3.13, or 3.14
• pip or uv for package management
• An internet connection (first fetch downloads from ProteomeCentral)

Install from source (recommended for development)

git clone https://github.com/LangeLab/pxseek.git
cd pxseek
uv sync

This creates a virtual environment and installs all runtime dependencies. Run the CLI from the repo root:

uv run pxseek --help

The repo includes a pinned uv.lock and a .python-version file, so you get the same dependency versions every time.

Install with pip from source

If you do not use uv:

git clone https://github.com/LangeLab/pxseek.git
cd pxseek
pip install .

Install from PyPI

After a maintainer publishes a release:

pip install pxseek

Or pin a specific version:

pip install pxseek==0.5.1

Optional extras

• pxseek[dev] installs pytest and ruff for running tests and linting.
• pxseek[rich] enables richer terminal output (used automatically when available).

With uv:

uv sync --extra dev
uv sync --extra rich

With pip:

pip install "pxseek[dev,rich]"

Included example files

The repo ships with a keyword file at examples/pediatric_cancer_keywords.txt. You can pass this file directly to pxseek filter -k (see Search Recipes).

Verify the installation

pxseek --version
pxseek fetch --help
pxseek filter --help
pxseek lookup --help

Each --help flag should print the command's options and exit cleanly.