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@stevenweaver stevenweaver released this 06 Oct 15:28
· 2 commits to master since this release
2.5.103
1ac8cf4

HyPhy Version Update: 2.5.103

This release supersedes 2.5.102, which was tagged before its version-string bump and therefore produced binaries that self-report as 2.5.101 (#2030, caught during the Homebrew update). 2.5.103 is functionally identical to 2.5.102 with a correct version string; users and packagers should skip 2.5.102 and move directly to 2.5.103.

The substantive changes, carried over from 2.5.102:

  • GARD AICc singularity guard (#2025, #2027): math.GetIC now returns infinity when parameters ≥ samples, and GARD's pre-flight check correctly counts unrooted-tree branches (2S−3) and rate-variation parameters, halting ineligible alignments at startup with an informative message.
  • Optimizer: TOLERATE_NUMERICAL_ERRORS honored in ConjugateGradientDescent (#2026): sub-machine-precision "worsened likelihood" events now warn and restore the previous state instead of fatally aborting long runs.
  • GARD breakpoint coordinates (#2010): consistent coordinate units in NEXUS CHARSET export and JSON breakpoint output.
  • BUSTED-PH label-order asymmetry (#2020, #2023): the shared-distributions null is now seeded symmetrically (tree-length-weighted initialization, size-directed slaving), making the comparative test invariant to foreground/background label order.
  • contrast-meme typo fix (#2007) and alignment-handling cleanups.
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