Installation

Requirements

• Python 3.12 or newer
• (Recommended) A virtual environment such as venv, pipenv, or uv

Runtime dependencies are installed automatically. They include anndata / mudata for the data container, polars for reading search-engine output, scipy / scikit-learn / statsmodels / inmoose for the statistics, directlfq for protein rollup, sdrf-pipelines for SDRF parsing, pyopenms for precursor isolation purity, and plotly for plotting.

Install with pip

It is strongly recommended to create virtual environment.

From Source Distribution

pippipenv

curl <_RELEASE_BINARY_URL_>
pip install msmu-<version>.tar.gz
python -c "import msmu; print('msmu:', msmu.__version__)"

curl <_RELEASE_BINARY_URL_>
pipenv install msmu-<version>.tar.gz
pipenv run python -c "import msmu; print('msmu:', msmu.__version__)"

From PyPI

pippipenv

pip install msmu
python -c "import msmu; print('msmu:', msmu.__version__)"

pipenv install msmu
pipenv run python -c "import msmu; print('msmu:', msmu.__version__)"

From Source Repository

If you want the latest version from the repository:

pippipenv

git clone https://github.com/bertis-informatics/msmu.git
cd msmu
pip install -e .
python -c "import msmu; print('msmu:', msmu.__version__)"

git clone https://github.com/bertis-informatics/msmu.git
cd msmu
pipenv install -e .
pipenv run python -c "import msmu; print('msmu:', msmu.__version__)"