mzmlpy 0.3.1

A lightweight Python library for parsing mzML mass spectrometry files.

A lightweight Python library for parsing mzML mass spectrometry files. Implements a type-safe, lazy-loading API with direct support for modern mzML structures (>= 1.1.0).

Installation

pip install mzmlpy

Optional extras:

pip install mzmlpy[numpress]   # MS-Numpress decoding
pip install mzmlpy[zstd]       # Zstandard compression

Quick Start

from mzmlpy import Mzml

with Mzml("path/to/file.mzML") as reader:
    print(f"File: {reader.file_name}  |  Spectra: {len(reader.spectra)}")

    for spectrum in reader.spectra:
        mz = spectrum.mz
        intensity = spectrum.intensity
        print(f"  {spectrum.id} MS{spectrum.ms_level} — {len(mz)} peaks")

Both .mzML and .mzML.gz files are supported. Metadata is parsed eagerly; binary data is decoded on demand.

For full usage examples see the Getting Started guide and API Reference.

Development

just lint     # ruff check
just format   # ruff isort + format
just ty       # ty type checker
just test     # pytest

# or all at once:
just check