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Merge branch 'main' into transfer-consensus
2 parents 9e01c6e + a971e42 commit dca5918

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‎.github/workflows/ASan.yml‎

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ASAN_OPTIONS: detect_container_overflow=1:verify_asan_link_order=0
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Initialize ASan configuration
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run: |

‎.github/workflows/R-CMD-check.yml‎

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steps:
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- name: Checkout git repo
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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- name: Temporarily bump package version
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run: |
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steps:
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- name: Checkout git repo
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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- name: Temporarily bump package version
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run: |
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steps:
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- name: Checkout PR branch
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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path: pr
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- name: Checkout target branch
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uses: actions/checkout@v5
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uses: actions/checkout@v6
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with:
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ref: ${{ github.event.pull_request.base.ref || 'main' }}
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path: main
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- name: Upload PR benchmark results
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if: failure()
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v6
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with:
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name: pr-benchmark-results
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path: pr/pr-benchmark-results/*.bench.Rds
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- name: Upload main benchmark results
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if: failure()
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v6
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with:
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name: main-benchmark-results
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path: pr/main-benchmark-results/*.bench.Rds

‎.github/workflows/copilot-setup-steps.yml‎

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# If you do not check out your code, Copilot will do this for you.
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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check
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- name: Checkout TreeTools source (for debugging support)
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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with:
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repository: ms609/TreeTools
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path: TreeTools-source

‎.github/workflows/pkgdown.yml‎

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- name: Export Shinylive app
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shell: Rscript {0}
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run: |
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# ── Pin shiny to pre-otel version ──
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# otel (OpenTelemetry) became a hard Import of shiny in 1.12.0,
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# but otel is not yet available as a WebAssembly binary on
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# repo.r-wasm.org. shinylive resolves deps from the LOCAL
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# library, so the installed shiny's otel dep causes a download
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# failure. Pin to the last CRAN release without otel.
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#
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# TODO: Remove this pin once otel appears at
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# http://repo.r-wasm.org/bin/emscripten/contrib/4.4/PACKAGES
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# ── Use dev shinylive for R 4.5 WASM support ──
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# CRAN shinylive 0.3.0 targets webR R 4.4.1.
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# The dev version (0.3.0.9000) targets R 4.5.1, where:
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# - otel is available on repo.r-wasm.org
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# - R-universe has a fixed TreeTools (no RCurl dep)
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# TODO: Switch back to CRAN shinylive once 0.4.0 ships.
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remotes::install_github("posit-dev/r-shinylive", quiet = TRUE)
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# ── Install TreeTools and TreeDist from R-universe ──
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# repo.r-wasm.org has TreeTools 2.0.0 (still imports RCurl) for
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# both R 4.4 and 4.5. R-universe has 2.2.0.9001 (RCurl moved to
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# Suggests) compiled for R 4.5. Setting Repository to the
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# R-universe URL makes shinylive fetch the WASM binary from there.
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# Similarly, installing TreeDist from R-universe avoids the version
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# mismatch warning (local dev != WASM 2.9.2 on repo.r-wasm.org).
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# TODO: Remove once TreeTools >= 2.2.0 and TreeDist >= 2.13.0
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# are on CRAN and r-wasm.org has rebuilt them.
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install.packages(
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"https://cran.r-project.org/src/contrib/Archive/shiny/shiny_1.11.1.tar.gz",
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repos = NULL, type = "source"
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c("TreeTools", "TreeDist"),
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repos = c("https://ms609.r-universe.dev",
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"https://cloud.r-project.org")
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)
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# ── Work around shinylive bug (coatless/quarto-webr#228) ──
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)
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# ── Export ──
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if (!requireNamespace("shinylive", quietly = TRUE)) {
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install.packages("shinylive")
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}
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tryCatch(
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shinylive::export(appdir = app_dir, destdir = "docs/app"),
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error = function(e) {
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msg <- conditionMessage(e)
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message("\n===== shinylive::export() failed =====")
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message(msg)
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message("This is often caused by a dependency that is not")
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message("available as a WebAssembly binary. Check:")
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message(" http://repo.r-wasm.org/bin/emscripten/contrib/4.4/PACKAGES")
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message("This is often caused by a dependency not available")
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message("as a WebAssembly binary. Check both:")
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message(" https://repo.r-wasm.org/bin/emscripten/contrib/4.5/PACKAGES")
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message(" https://ms609.r-universe.dev/bin/emscripten/contrib/4.5/PACKAGES")
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stop(e)
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}
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)

‎.github/workflows/update-csl.yml‎

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update-csl:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: actions/checkout@v6
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- name: Download latest CSL file
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run: |

‎DESCRIPTION‎

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Package: TreeDist
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Title: Calculate and Map Distances Between Phylogenetic Trees
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Version: 2.13.0
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Version: 2.13.0.9001
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Authors@R: c(person("Martin R.", "Smith",
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email = "martin.smith@durham.ac.uk",
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role = c("aut", "cre", "cph", "prg"),

‎NEWS.md‎

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<!-- AI-generated branch summary (2026-03-22) -->
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# Branch: `expose-lapjv` → merge target: `master`
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# Branch: `transfer-consensus` → merge target: `main`
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This branch exposes the LAPJV (Jonker–Volgenant) linear assignment solver
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via C++ headers so that downstream packages can link to it (`LinkingTo`),
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`Rcpp::stop()` / `Rf_error()` calls out of C++ implementation code
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into R-level input validation.
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# TreeDist 2.13.0.9000
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# TreeDist 2.13.0.9001
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This branch implements transfer consensus trees (`TransferConsensus()`) and
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a corresponding transfer distance metric (`TransferDist()`), providing a
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implementation code.
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<!-- end AI-generated summary -->
2020

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## Performance
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- `RobinsonFoulds()` now uses a fast C++ batch path for cross-distance
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computations (tree list vs tree list), matching the existing all-pairs
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batch performance. Previously, cross-distance calls fell through to
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per-pair R dispatch (~27× slower per pair); the new path achieves ~21×
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speedup on typical inputs (e.g. 50 × 250 trees, 50 tips).
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# TreeDist 2.13.0 (2026-03-17)
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## New features

‎R/RcppExports.R‎

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.Call(`_TreeDist_robinson_foulds_all_pairs`, tables)
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}
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robinson_foulds_cross_pairs <- function(tables_a, tables_b) {
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.Call(`_TreeDist_robinson_foulds_cross_pairs`, tables_a, tables_b)
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}
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consensus_info <- function(trees, phylo, p) {
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.Call(`_TreeDist_consensus_info`, trees, phylo, p)
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}

‎R/tree_distance_rf.R‎

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class = "dist")
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}
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} else {
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unnormalized <- CalculateTreeDistance(RobinsonFouldsSplits, tree1, tree2,
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reportMatching)
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if (similarity) {
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unnormalized <- .MaxValue(tree1, tree2, NSplits) - unnormalized
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# Fast cross-pairs path: batch C++ via ClusterTable (Day 1985).
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# Only applicable when both inputs are lists of trees with matching
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# tip labels and reportMatching is not requested.
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fast <- NULL
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if (!reportMatching &&
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!inherits(tree1, c("phylo", "Splits")) &&
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!inherits(tree2, c("phylo", "Splits")) &&
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is.null(getOption("TreeDist-cluster"))) {
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lab1 <- TipLabels(tree1)
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lab2 <- TipLabels(tree2)
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if (is.list(lab1)) lab1 <- lab1[[1]]
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if (is.list(lab2)) lab2 <- lab2[[1]]
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if (setequal(lab1, lab2)) {
164+
ct1 <- as.ClusterTable(tree1, tipLabels = lab1)
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ct2 <- as.ClusterTable(tree2, tipLabels = lab1)
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shared <- robinson_foulds_cross_pairs(
167+
if (is.list(ct1)) ct1 else list(ct1),
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if (is.list(ct2)) ct2 else list(ct2)
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)
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splits1 <- NSplits(tree1)
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splits2 <- NSplits(tree2)
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if (similarity) {
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fast <- shared + shared
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} else {
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fast <- outer(splits1, splits2, "+") - shared - shared
176+
}
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dimnames(fast) <- list(names(tree1), names(tree2))
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}
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}
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if (is.null(fast)) {
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unnormalized <- CalculateTreeDistance(RobinsonFouldsSplits, tree1, tree2,
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reportMatching)
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if (similarity) {
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unnormalized <- .MaxValue(tree1, tree2, NSplits) - unnormalized
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}
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} else {
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unnormalized <- fast
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}
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}
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‎R/tree_information.R‎

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#' }
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#'
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#' @template MRS
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#' @family summary trees
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#' @importFrom TreeTools as.Splits SplitFrequency
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#' @export
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MCITree <- function(trees, info = "phylogenetic", check.tips = TRUE) {

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