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Add ReadXgroup() for TNT character-partition blocks#267

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Add ReadXgroup() for TNT character-partition blocks#267
ms609 wants to merge 2 commits into
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@ms609 ms609 commented May 15, 2026

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Summary

  • New ReadXgroup(filepath, encoding = "UTF8") parses the xgroup character-partition block of a TNT file, returning a named integer vector mapping each character (1-indexed) to its partition.
  • Returns NULL when no xread block is present; returns rep(NA_integer_, nChar) when xread is present but xgroup is not.
  • Joins the ReadCharacters doc family via @describeIn; exports .UTFLines-style encoding handling for consistency with ReadTntCharacters.
  • Sourced from a prototype that lived briefly in AutoPart; moved upstream so AutoPart and other downstream packages share a single implementation.

Bumps version to 2.3.0.9001 and adds a NEWS entry.

Test plan

  • New fixture inst/extdata/tests/tnt-xgroup.tnt (6 chars, 4 taxa, two xgroup lines)
  • 4 new tests in tests/testthat/test-ReadTntTree.R covering: well-formed xgroup parsing, NULL on missing xread, all-NA when xgroup absent, range-expansion helper .ExpandTntRange (A.B, A., A.A forms)
  • devtools::load_all() + testthat::test_file('tests/testthat/test-ReadTntTree.R') — 42 dots, no failures

🤖 Generated with Claude Code

@ms609 @claude
Add ReadXgroup() for TNT character-partition blocks
ee8bec1 
Parses the xgroup block of a TNT file into a named integer vector mapping
each character (1-indexed) to its partition; returns NULL when no xread
block is present, all-NA when xread is present but xgroup is not. Joins
the ReadCharacters family via @describeIn.

Sourced from a prototype in AutoPart, where the function originally lived;
moved upstream so AutoPart and other downstream packages can share a single
implementation. Closes that duplication.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@codecov

codecov Bot commented May 15, 2026

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Codecov Report

❌ Patch coverage is 91.66667% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.02%. Comparing base (4e5af7a) to head (ee8bec1).

Files with missing lines Patch % Lines
R/parse_files.R 91.66% 4 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #267      +/-   ##
==========================================
- Coverage   96.06%   96.02%   -0.04%     
==========================================
  Files          80       80              
  Lines        5890     5938      +48     
==========================================
+ Hits         5658     5702      +44     
- Misses        232      236       +4

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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@github-actions

github-actions Bot commented May 15, 2026 •
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⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call Status Change Time (ms)
as.Splits(bigTrees) ⚪ NSD 3.04% 23 →
22.4, 21.2
as.Splits(someTrees) ⚪ NSD -1.51% 11 →
11.2, 11.2
Consensus(forest1k.888, check = FALSE) ⚪ NSD 3.89% 104 →
100, 97.2
Consensus(forest201.80, check = FALSE) ⚪ NSD 0.05% 4.08 →
4.12, 4.02
Consensus(forest21.260, 0.5, FALSE) ⚪ NSD 1.09% 1.26 →
1.26, 1.24
Consensus(forest21.260) ⚪ NSD 1.55% 1.28 →
1.27, 1.25
Consensus(forestMaj, 0.5, FALSE) ⚪ NSD -0.01% 2.98 →
3, 2.93
DropTip(tr2000, 5) ⚪ NSD -0.37% 16.6 →
16.5, 16.8
DropTip(tr80, 5) ⚪ NSD 0% 0.104 →
0.104, 0.104
DropTip(unlen2k, 5) ⚪ NSD 2.04% 0.215 →
0.206, 0.214
DropTip(unlen80, 5) ⚪ NSD 1.32% 0.041 →
0.0397, 0.0411
lapply(bigSplits, as.phylo) ⚪ NSD -0.33% 29.3 →
29.3, 29.6
lapply(someSplits, as.phylo) ⚪ NSD -0.37% 13.6 →
13.7, 13.7
PathLengths(tr2000, full = TRUE) ⚪ NSD 0.66% 16 →
15.8, 15.9
PathLengths(tr80, full = TRUE) ⚪ NSD -1.39% 0.0982 →
0.0982, 0.102
PathLengths(tr80Unif, full = TRUE) ⚪ NSD -0.55% 0.101 →
0.1, 0.104
RootTree(tr2000, 5) ⚪ NSD -0.54% 0.394 →
0.397, 0.395
RootTree(tr80, c("t3", "t36")) ⚪ NSD 0.39% 0.0715 →
0.071, 0.0714
RootTree(tr80, "t3") ⚪ NSD 0.71% 0.0505 →
0.0502, 0.0502
RootTree(tr80, "t30") ⚪ NSD 0.43% 0.0507 →
0.0503, 0.0508
RootTree(unlen2k, 5) ⚪ NSD 2.67% 0.351 →
0.33, 0.349
RootTree(unlen80, c("t3", "t36")) ⚪ NSD 0.09% 0.067 →
0.0652, 0.0682
RootTree(unlen80, "t3") ⚪ NSD 1.95% 0.0448 →
0.0429, 0.0446
RootTree(unlen80, "t30") ⚪ NSD 0.84% 0.0451 →
0.0434, 0.0457
TreeDist::RobinsonFoulds(forest201.80) ⚪ NSD 3.76% 17 →
16.1, 16.7
TreeDist::RobinsonFoulds(forest21.888) ⚪ NSD 1.56% 3.54 →
3.39, 3.53
TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE) ⚪ NSD -3.56% 0.0874 →
0.089, 0.0922
TreeTools:::postorder_order(bal40) ⚪ NSD -0.59% 0.00166 →
0.00166, 0.00168
TreeTools:::postorder_order(bal40k) ⚪ NSD 0.18% 0.429 →
0.428, 0.429
TreeTools:::postorder_order(dbal40) ⚪ NSD -1.68% 0.00171 →
0.00174, 0.00174
TreeTools:::postorder_order(dbal40k) ⚪ NSD -1.08% 2 →
2.02, 2.02
TreeTools:::postorder_order(dpec40) ⚪ NSD -0.43% 0.00253 →
0.00254, 0.00255
TreeTools:::postorder_order(dpec40k) 🟣 ~same -0.47% 3300 →
3310, 3310
TreeTools:::postorder_order(drnd80) ⚪ NSD 0.27% 0.00405 →
0.00407, 0.00402
TreeTools:::postorder_order(nbal40) ⚪ NSD -0.49% 0.00206 →
0.00207, 0.00206
TreeTools:::postorder_order(nbal40k) ⚪ NSD -0.7% 2.18 →
2.19, 2.2
TreeTools:::postorder_order(npec40) ⚪ NSD -0.31% 0.00286 →
0.00286, 0.00288
TreeTools:::postorder_order(npec40k) ⚪ NSD -0.15% 3320 →
3320, 3330
TreeTools:::postorder_order(nrnd80) ⚪ NSD -0.66% 0.00458 →
0.00462, 0.0046
TreeTools:::postorder_order(pec40) ⚪ NSD -1.84% 0.00164 →
0.00166, 0.00168
TreeTools:::postorder_order(pec40k) ⚪ NSD -0.58% 0.428 →
0.428, 0.431
TreeTools:::postorder_order(rnd80) ⚪ NSD -2.01% 0.00209 →
0.00214, 0.00213

@ms609 @claude
Add coverage tests for unlabelled xgroup and malformed dimension
aeb35c5 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@ms609 ms609 closed this May 15, 2026
@ms609 ms609 deleted the xgroup branch May 15, 2026 12:59
@github-actions

github-actions Bot commented May 15, 2026

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Performance benchmark results

Call Status Change Time (ms)
as.Splits(bigTrees) ⚪ NSD -3.15% 32.4 →
38.2, 31.6
as.Splits(someTrees) ⚪ NSD 2.06% 10.9 →
10.8, 10.6
Consensus(forest1k.888, check = FALSE) 🟣 ~same 3.08% 97.8 →
94.9, 94.7
Consensus(forest201.80, check = FALSE) ⚪ NSD 1.93% 4.33 →
4.3, 4.2
Consensus(forest21.260, 0.5, FALSE) ⚪ NSD 0.96% 1.18 →
1.17, 1.17
Consensus(forest21.260) ⚪ NSD 1.18% 1.19 →
1.17, 1.18
Consensus(forestMaj, 0.5, FALSE) ⚪ NSD 0.43% 2.98 →
2.98, 2.96
DropTip(tr2000, 5) ⚪ NSD -0.38% 16 →
16, 16.1
DropTip(tr80, 5) ⚪ NSD 0.25% 0.0879 →
0.0878, 0.0875
DropTip(unlen2k, 5) ⚪ NSD -10.07% 0.187 →
0.277, 0.185
DropTip(unlen80, 5) ⚪ NSD -0.17% 0.0361 →
0.0359, 0.0364
lapply(bigSplits, as.phylo) 🟣 ~same -2.49% 29.3 →
30.2, 29.7
lapply(someSplits, as.phylo) ⚪ NSD 0.06% 13.6 →
13.7, 13.6
PathLengths(tr2000, full = TRUE) ⚪ NSD 0.35% 15.3 →
15.2, 15.3
PathLengths(tr80, full = TRUE) ⚪ NSD -3.33% 0.0971 →
0.1, 0.101
PathLengths(tr80Unif, full = TRUE) ⚪ NSD -2.95% 0.0998 →
0.103, 0.103
RootTree(tr2000, 5) ⚪ NSD -0.49% 0.344 →
0.342, 0.35
RootTree(tr80, c("t3", "t36")) ⚪ NSD -0.11% 0.0608 →
0.0606, 0.0612
RootTree(tr80, "t3") ⚪ NSD -0.27% 0.0444 →
0.0441, 0.0448
RootTree(tr80, "t30") ⚪ NSD -0.71% 0.044 →
0.044, 0.0446
RootTree(unlen2k, 5) ⚪ NSD 2.43% 0.304 →
0.298, 0.295
RootTree(unlen80, c("t3", "t36")) ⚪ NSD 0.68% 0.0564 →
0.056, 0.0561
RootTree(unlen80, "t3") ⚪ NSD -0.21% 0.0383 →
0.0383, 0.0384
RootTree(unlen80, "t30") ⚪ NSD 0.59% 0.0387 →
0.0383, 0.0387
TreeDist::RobinsonFoulds(forest201.80) ⚪ NSD 1.46% 17.4 →
17.2, 16.6
TreeDist::RobinsonFoulds(forest21.888) ⚪ NSD -0.21% 3.19 →
3.22, 3.17
TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE) ⚪ NSD 0.93% 0.093 →
0.0921, 0.0923
TreeTools:::postorder_order(bal40) ⚪ NSD 0.01% 0.00162 →
0.00163, 0.00161
TreeTools:::postorder_order(bal40k) ⚪ NSD 0.17% 0.37 →
0.37, 0.368
TreeTools:::postorder_order(dbal40) ⚪ NSD 0.59% 0.00171 →
0.00173, 0.00166
TreeTools:::postorder_order(dbal40k) ⚪ NSD -0.58% 2.12 →
2.14, 2.13
TreeTools:::postorder_order(dpec40) ⚪ NSD -1.18% 0.00254 →
0.0026, 0.00253
TreeTools:::postorder_order(dpec40k) ⚪ NSD 0.3% 2870 →
2860, 2860
TreeTools:::postorder_order(drnd80) ⚪ NSD 0.76% 0.00394 →
0.00391, 0.00391
TreeTools:::postorder_order(nbal40) ⚪ NSD -0.99% 0.00201 →
0.00205, 0.002
TreeTools:::postorder_order(nbal40k) ⚪ NSD -0.53% 2.32 →
2.34, 2.32
TreeTools:::postorder_order(npec40) ⚪ NSD -1.1% 0.00282 →
0.00288, 0.00282
TreeTools:::postorder_order(npec40k) ⚪ NSD 0.05% 2860 →
2860, 2860
TreeTools:::postorder_order(nrnd80) ⚪ NSD -1.1% 0.00452 →
0.0046, 0.00453
TreeTools:::postorder_order(pec40) ⚪ NSD 0.01% 0.00162 →
0.00165, 0.00159
TreeTools:::postorder_order(pec40k) ⚪ NSD -2.11% 0.37 →
0.392, 0.371
TreeTools:::postorder_order(rnd80) ⚪ NSD 3.46% 0.00205 →
0.00197, 0.00201

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