PyPop 1.2.0

Install via PyPI

pip install -U pypop-genomics

1.2.0 - 2025-02-04

Features

• Add support for new HLA nomenclature including remote MSF sequence retrieval by @alexlancaster (#252)
• Build Linux (aarch64) using new ARM64 runners by @alexlancaster (#250)
• [EXPERIMENTAL] Build Windows ARM64-compatible wheels by @alexlancaster (#235)

Bug Fixes

• Update all HLA nomenclature to correct version 3 allele names in unit tests and documentation by @alexlancaster (#251)
• Restore makeNewPops and fix ParseAlleleCount, major doc upgrade by @alexlancaster (#247)
• Restore functionality for [Sequence] filters: Python 3 upgrades by @alexlancaster (#244)
• fix generation of schema.org citation format by @alexlancaster (#233)

Internal

• Generate .zenodo.json metadata from CITATION.cff by @alexlancaster (#253)
• Update numpy requirement from <=2.2.1 to <=2.2.2 by @dependabot[bot] (#245)
• Port metadata from setup.py to pyproject.toml by @alexlancaster (#242)
• Overhaul C extension code: pre-commit and fix compiler warnings by @alexlancaster (#239)
• Major cleanup of codebase: add and enforce pre-commit checks by @alexlancaster (#238)
• Bump stefanzweifel/git-auto-commit-action from 4 to 5 in the actions group by @dependabot[bot] (#237)
• Code cleanups: address warnings and add pre-commit checks by @alexlancaster (#236)
• Move codeql tests to ubuntu-latest by @alexlancaster (#234)
• Update numpy requirement from <=2.2.0 to <=2.2.1 by @dependabot[bot] (#232)
• Update numpy requirement from <=2.1.3 to <=2.2.0 by @dependabot[bot] (#231)
• Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 in the actions group by @dependabot[bot] (#230)
• Bump actions/setup-python from 4 to 5 in the actions group by @dependabot[bot] (#229)

Documentation

• Update all HLA nomenclature to correct version 3 allele names in unit tests and documentation by @alexlancaster (#251)
• Update documentation for makeNewPops filter by @alexlancaster (#247)
• Documentation updates for [Sequence] filters: by @alexlancaster (#244)
• Add information on pre-commit checks by @alexlancaster (#240)

A full history of changes is available in NEWS.md.

Full Changelog: v1.1.2...v1.2.0