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v0.1.4

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@shz9 shz9 released this 04 Jul 22:19

Added

  • Added cloud-streamable UK Biobank LD matrix paths hosted on Hugging Face, allowing users to pass
    hf://datasets/shz9/ukb-ld/<POP>/chr_*.zip directly to viprs_fit without pre-downloading archives.
  • Added uv and Apptainer installation examples to the documentation.
  • Added a DockerHub publishing workflow and modernized the CLI Docker image for release as
    shadizabad/viprs.
  • Added uv.lock for reproducible development environments.
  • Added tests to ensure runtime package version metadata stays synchronized.

Changed

  • Restricted supported Python versions to Python 3.10 through 3.13, inclusive.
  • Centralized package version metadata in viprs/_version.py and reused it across runtime and packaging metadata.
  • Updated pyproject.toml metadata and dependencies to match the package's runtime, optional, test, and docs
    requirements.
  • Split wheel build/testing and PyPI publishing into separate GitHub Actions workflows.
  • Updated GitHub Actions runners and wheel builds to use current Linux, Windows, Intel macOS, and Apple Silicon
    macOS targets.
  • Modernized the CLI Dockerfile to use python:3.11-slim-bookworm, OCI labels, configurable install targets,
    and installation smoke tests.
  • Updated LD matrix documentation to put provenance and QC information before download/streaming instructions.

Fixed

  • Fixed the binary f1 metric so it fits a logistic model on top of PRS values and thresholds predicted
    probabilities, instead of passing continuous PRS values directly to sklearn.metrics.f1_score.
  • Made BLAS discovery in setup.py tolerate missing system pkg-config and fall back to the existing
    no-BLAS build path.