PyProphet 3.0.0

Release Highlights (Major Version Update)

This release introduces significant structural changes to improve modularity:

• Introduced I/O Module: I/O logic is now modularized by file type (e.g., SQLite .osw, Parquet), to support new parquet format support.

• Configurable Data Classes: Core algorithms (scoring, IPF, levels contexts) now use configuration dataclasses for cleaner parameter management and easier extension.

• Click CLI Restructure: Command chaining has been removed to enable grouped subcommands (e.g., peptide, protein, peptidoform) for better CLI organization.

• Deprecation Notice: Original flat subcommands remain for backwards compatibility but will be removed in a future release.

• Added readthedocs for API and CLI documentation

• Added linear SVM classifier model for scoring module.

All existing functionality should continue to work as is. Please report any issues if any.

What's Changed

• Patch/pq memory opt by @singjc in #141
• Refactor/codebase by @singjc in #142

Full Changelog: 2.3.4...3.0.0