Modernize to pip-installable package (v2.0)

[jonasscheid]

Summary

Transforms OptiType into a modern, pip-installable Python package.

Key changes:

• Package structure: src-layout with pyproject.toml (hatchling)
• CLI: Click-based with subcommands (optitype run, check-deps, init-config)
• Data format: HDF5 → Parquet (92MB → 370KB)
• Python: 3.10+ only (removed Python 2.7 compatibility)
• CI/CD: GitHub Actions with PyPI trusted publishing
• API: Programmatic interface (run_hla_typing())

Installation:

pip install optitype

Usage:

optitype run -i reads_1.fq -i reads_2.fq --dna -o results/

Results verified against baseline - HLA typing output unchanged.

Exome (1.3.5 top, 2.0.0 botton)

RNA (1.3.5 top,, 2.0.0 botton)

🤖 Generated with Claude Code

[jonasscheid]

@andras86 @b-schubert @lkuchenb @christopher-mohr

Would be great to have a modern optitype package. I would like to ask you to give feedback and help pushing a new optitype version to pypi. On top of this, new small features can be simply added, e.g. reference update etc.