Changelog

Changelog#

Unreleased#

Added#

  • casanovoutils mgf pipeline: chain shuffle, downsample, and purge-redundant in a single command with each stage independently optional.

  • casanovoutils mgf purge-redundant: remove near-duplicate peaks within each spectrum based on a configurable m/z epsilon threshold.

  • casanovoutils denovo: subcommands for loading MGF and mzTab files into Polars DataFrames and joining them into a ground-truth table.

  • casanovoutils dump-residues dump: export the default residue mass table.

  • Module-level COMMANDS constants in each submodule, assembled into a single nested CLI via casanovoutils.main.

  • configure_logging in package __init__ is a no-op if already called, preventing duplicate handler registration when functions are composed.

Changed#

  • All CLI entry points consolidated into a single casanovoutils command with nested subcommands (mgf, denovo, dump-residues). The previous separate entry points (graph-prec-cov, downsample-ms, mgf-utils, casanovo-utils) are removed.

  • write_spectra now converts PathLike paths to str before passing to pyteomics.mgf.write, fixing a PosixPath compatibility bug.

  • shuffle no longer writes the output file twice.