Code

Optimize downsample-tips, add CLI#197

Code

Merged

mmore500 merged 28 commits intomastermmore500/hstrat:masterfrom downsample-tipsmmore500/hstrat:downsample-tipsCopy head branch name to clipboardJan 5, 2025

+392-66

Commits

Commits on Jan 4, 2025

• Optimize prune_extinct_lineages for contiguous ids

  mmore500

  committed
  bf78c15

• Fixup joinem cli help message details, and test

  mmore500

  committed
  9b2b7c8

• Fix tidy

  mmore500

  committed
  3f3b238

• fixup! Fixup joinem cli help message details, and test

  mmore500

  committed
  d436dac

• Fix typo

  mmore500

  committed
  a7d8caf

• Fix fstring

  mmore500

  committed
  a027804

• Fix lazyframe handling in polars coercion

  mmore500

  committed
  90785f2

• Draft downsample tips CLI

  mmore500

  committed
  a4cfd1c

• Update docstring

  mmore500

  committed
  eca6bcb

• fixup! Fix lazyframe handling in polars coercion

  mmore500

  committed
  39dd681

• fixup! fixup! Fixup joinem cli help message details, and test

  mmore500

  committed
  1a037f9

• Update CLI command listing

  mmore500

  committed
  78ae9db

• Fix downstream overriden_arguments API use

  mmore500

  committed
  a8a76c3

• Fix typo

  mmore500

  committed
  976c8cf

• Re-enable commented out test

  mmore500

  committed
  d6bb8c6

• Enable jit for prune extinct lineages

  mmore500

  committed
  0d55881

• Optimize leaf identification

  mmore500

  committed
  64d19a0

• Fix type hint

  mmore500

  committed
  0862347

• Optimize alifestd_find_leaf_ids

  mmore500

  committed
  60ba403

• Fix tidy

  mmore500

  committed
  8e8cc51

• Further optimize find leaf ids

  mmore500

  committed
  1e7296d

• Fix typo, clarify flow

  mmore500

  committed
  bd0497f

• Fix bad default arg

  mmore500

  committed
  681b71b

Commits on Jan 5, 2025

• Add another optimized impl for prune extinct lineages asexual

  mmore500

  committed
  f9a7a05

• Bugfix: ensure tips sampled without replacement

  mmore500

  committed
  b8021e1

• Fix array/list compat in tests

  mmore500

  committed
  dc25072

• Fix copy/paste race condition

  mmore500

  committed
  b542226

• fixup! Fix array/list compat in tests

  mmore500

  committed
  bf8c592