viprs 0.1.0

v0.1.0

on Python PyPI

A large scale restructuring of the code base to improve efficiency and usability.

Changed

• Moved plotting script to its own separate module.
• Updated some method names / commandline flags to be consistent throughout.
• Updated the VIPRS class to allow for more flexibility in the optimization process.
• Removed the VIPRSAlpha model for now. This will be re-implemented in the future,
  using better interfaces / data structures.
• Moved all hyperparameter search classes/models to their own directory.
• Restructured the viprs_fit commandline script to make the code cleaner,
  do better sanity checking, and introduce process parallelism over chromosomes.

Added

• Basic integration testing with pytest and GitHub workflows.
• Documentation for the entire package using mkdocs.
• Integration testing / automating building with GitHub workflows.
• New self-contained implementation of E-Step in Cython and C++.
  • Uses OpenMP for parallelism across chunks of variants.
  • Allows for de-quantization on the fly of the LD matrix.
  • Uses BLAS linear algebra operations where possible.
  • Allows model fitting with only
• Benchmarking scripts (benchmark_e_step.py) to compare computational performance of different implementations.
• Added functionality to allow the user to track time / memory utilization in viprs_fit.
• Added OptimizeResult class to keep track of the info/parameters of EM optimization.
• New evaluation metrics
  • pseudo_metrics has been moved to its own module to allow for more flexibility in evaluation.
  • New evaluation metrics for binary traits: nagelkerke_r2, mcfadden_r2,
    cox_snell_r2 liability_r2, liability_probit_r2, liability_logit_r2.
  • New function to compute standard errors / test statistics for all R-Squared metrics.