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v0.6.0 — repository, documentation, and reproducibility

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@bennettek99-spec bennettek99-spec released this 17 Jul 20:38
v0.6.0
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Archaic DNA Processing Pipeline v0.6.0

This release makes the public repository match the maturity and scientific boundaries of the pipeline.

Highlights

  • focused README plus structured setup, methods, study/report, and data-policy documentation
  • canonical MIT license with the retained PRJEB10597 BAM exception documented by accession, MD5, SHA-256, and evidence limits
  • corrected distinction between calculated Neanderthal percentages, relative Denisovan affinity, and literature-derived combined-ancestry context
  • portable public provenance with machine-specific paths removed
  • community files, issue and pull-request templates, Dependabot, and private vulnerability reporting
  • CI across Python 3.10-3.12, a 50% coverage floor, package builds, documentation/version/BAM provenance checks, and a Windows smoke job

Validation

  • 56 tests passed locally with 58.57% coverage
  • all five GitHub checks passed, including Windows smoke
  • pyflakes, repository documentation checks, package builds, and diff checks passed

The five published Sima de los Huesos BAM files remain in the repository by design and were not removed or rewritten.

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