metabo-depthcharge

Library for depthcharge-based metabolomics models.

Installation

Not yet on PyPI — install from GitHub.

# pip
pip install git+https://github.com/bittremieuxlab/metabo-depthcharge.git

# conda (env only; package itself via pip)
conda create -n mdc python=3.11 && conda activate mdc
pip install git+https://github.com/bittremieuxlab/metabo-depthcharge.git

See the documentation for the full user guide.

Development setup

Requires uv.

uv sync --extra dev

Run tests

uv run pytest tests/ --ignore=tests/characterization

Lint and format

# Check only
uv run ruff check .
uv run ruff format --check .

# Fix in place
uv run ruff check --fix .
uv run ruff format .

Pre-commit hooks

uv run pre-commit install

After that, ruff and pytest run automatically on every commit.

Characterization tests

Characterization tests compare behaviour against the original upstream implementations. Run locally only, before modifying a module:

uv run pytest tests/characterization/ \
    --spectrawl-path /path/to/spectrawl \
    --metabo-src-path /path/to/metabo-depthcharge