Code

PE, RPE and related optimisations#926

Code

Merged

shawnlaffan merged 27 commits intomastershawnlaffan/biodiverse:masterfrom rpe_2024shawnlaffan/biodiverse:rpe_2024Copy head branch name to clipboardMar 11, 2024

+452-235

Commits

Commits on Feb 27, 2024

• delete_params: avoid some looping

  shawnlaffan

  committed
  5c30781

• Indices: optimise RPE2

  Show description for 36facdf
  shawnlaffan

  committed
  36facdf

• simplify code a little

  Show description for fcb8315
  shawnlaffan

  committed
  fcb8315

• Indices: optimise calc_rpe2

  Show description for fa72208
  shawnlaffan

  committed
  fa72208

• Indices: calc_phylo_rpe2: re-order some early exit conditions

  shawnlaffan

  committed
  6904a8f

• Move comment, clarify it

  shawnlaffan

  committed
  ad97510

• Indices: move PE_RANGELIST out of _calc_pe

  Show description for 36eda2f
  shawnlaffan

  committed
  36eda2f

• fix some index metadata

  shawnlaffan

  committed
  d025dc9

• calc_phylo_rpe2: handle undef PE null score

  Show description for 44f0b56
  shawnlaffan

  committed
  44f0b56

• Indices metadata: calc_phylo_rpe2: remove dependency on calc_pe_lists

  Show description for 88734e1
  shawnlaffan

  committed
  88734e1

Commits on Feb 28, 2024

• Indices get_path_lengths_to_root_node: populate the path length hash with first path

  Show description for 1bd027d
  shawnlaffan

  committed
  1bd027d

• reduce calls to TreeNode->get_length

  Show description for cac1d78
  shawnlaffan

  committed
  cac1d78

• Indices _calc_abc_dispatcher: reorder some logic, use an empty array state var

  Show description for 1666094
  shawnlaffan

  committed
  1666094

Commits on Mar 4, 2024

• Indices: generalise early return condition in _calc_phylo_abc_lists

  Show description for d30dfea
  shawnlaffan

  committed
  d30dfea

• Indices: set _calc_phylo_abc_lists precalc to _calc_abc_any

  Show description for 9091eee
  shawnlaffan

  committed
  9091eee

Commits on Mar 6, 2024

• Indices: simplify use_wts logic in _calc_phylo_mpd_mntd

  Show description for 65ad9ad
  shawnlaffan

  committed
  65ad9ad

• Indices _calc_pe: refactor weights calcs

  Show description for 73d62d6
  shawnlaffan

  committed
  73d62d6

Commits on Mar 7, 2024

• Indices _calc_pe: micro-optimise

  Show description for 6bb3e92
  shawnlaffan

  committed
  6bb3e92

• Indices calc_phylo_rpe2: follow _calc_pe caching approach

  Show description for da2e198
  shawnlaffan

  committed
  da2e198

• Indices calc_phylo_rpe_central: process internally

  Show description for 58a4ed5
  shawnlaffan

  committed
  58a4ed5

• Indices calc_phylo_rpe_central: less nesting

  shawnlaffan

  committed
  b0197f8

• Indices: calc_phylo_rpe2: cleanup if branch and less nesting

  Show description for 5239765
  shawnlaffan

  committed
  5239765

Commits on Mar 8, 2024

• _calc_abc_any: micro-optimise

  Show description for 80b033e
  shawnlaffan

  committed
  80b033e

• Indices: list results from _calc_pe are now in _calc_pe_lists

  Show description for 711289f
  shawnlaffan

  committed
  711289f

• remove some redundant commented code

  shawnlaffan

  committed
  9231550

• Tests: change precision approach in Cluster2

  shawnlaffan

  committed
  f04a819

Commits on Mar 10, 2024

• Indices: _calc_pe_lists: call _calc_pe if needed to populate cache

  Show description for 113cd2f
  shawnlaffan

  committed
  113cd2f