Draft implementation of new SPR distance

.github/workflows/R-CMD-check.yml

@@ -15,6 +15,7 @@ on:
       - "**.git"
       - "**.json"
       - "**.md"
+      - "**.yaml"
       - "**.yml"
       - "!**R-CMD-check.yml"
       - "**.R[dD]ata"
@@ -30,6 +31,7 @@ on:
       - "**.git"
       - "**.json"
       - "**.md"
+      - "**.yaml"
       - "**.yml"
       - "!**R-CMD-check.yml"
       - "**.R[dD]ata"
@@ -38,24 +40,66 @@ on:
 name: R-CMD-check
 
 jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
+  check-release:
+    runs-on: ubuntu-24.04
+    name: ubuntu-24.04 (release)
+
+    env:
+      _R_CHECK_CRAN_INCOMING_: true # Seemingly not set by --as-cran
+      _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
+      R_COMPILE_AND_INSTALL_PACKAGES: 'never'
+      _R_CHECK_THINGS_IN_CHECK_DIR_: false
+      R_REMOTES_STANDALONE: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest"
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout git repo
+        uses: actions/checkout@v5
 
+      - name: Temporarily bump package version
+        run: |
+          old_version=$(grep "Version:" DESCRIPTION | awk '{print $2}')
+          if [[ $(echo "$old_version" | tr -cd '.' | wc -c) -eq 2 ]]; then
+            new_version="${old_version}.8888"
+            if [[ "$RUNNER_OS" == "macOS" ]]; then
+              sed -i "" "s/Version: .*/Version: ${new_version}/" DESCRIPTION
+            else
+              sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
+            fi
+          fi
+        shell: bash
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Set up R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            ms609/TreeDistData
+          needs: |
+            check
+
+      - name: Check package
+        uses: r-lib/actions/check-r-package@v2
+
+
+  check-all:
+    runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: macos-15-intel, r: 'release'} # Until Intel architecture retired 2027-11
-          - {os: ubuntu-22.04, r: '4.1',
-          rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-24.04-arm, r: "release",
-          rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
-          - {os: ubuntu-latest, r: 'devel',
-          rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
+          - {os: windows-latest, r: "release"}
+          - {os: macos-15-intel, r: "release"} # Until Intel architecture retired 2027-11
+          - {os: macOS-latest, r: "release"}
+          - {os: ubuntu-22.04, r: '4.1', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-24.04-arm, r: "release", rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
+          - {os: ubuntu-24.04, r: "devel", rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
 
     env:
       _R_CHECK_CRAN_INCOMING_: ${{ github.event_name == 'pull_request' }}
@@ -64,6 +108,7 @@ jobs:
       _R_CHECK_THINGS_IN_CHECK_DIR_: false
       R_REMOTES_STANDALONE: true
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_REALLY_FORCE_SYMBOLS: true # Until R4.3
       RSPM: ${{ matrix.config.rspm }}
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -164,3 +209,21 @@ jobs:
                 state: 'open'
               });
             }
+  rev-dep-check:
+    runs-on: ubuntu-latest
+    needs: check-release
+
+    name: revdepcheck
+
+    env:
+      R_COMPILE_AND_INSTALL_PACKAGES: 'never'
+      R_REMOTES_STANDALONE: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: ms609/actions/revdepcheck@main
+        with:
+          deps: ${{ matrix.config.deps }}
+          extra-packages: ms609/TreeDistData

.github/workflows/revdepcheck.yml

@@ -1,21 +1,14 @@
+# Now integrated into R CMD check.yml.
 name: rev-dep-check
 
 on:
   workflow_dispatch:
-  workflow_run:
-    workflows: ["R-CMD-check"]
-    types:
-      - completed
-  push:
-    paths: "**revdepcheck.yml"
-  pull_request:
-    paths: "**revdepcheck.yml"
 
 jobs:
   mem-check:
     runs-on: ubuntu-latest
 
-    name: revdepcheck
+    name: revdepcheck (manual)
 
     env:
       R_COMPILE_AND_INSTALL_PACKAGES: 'never'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TreeDist
 Type: Package
 Title: Calculate and Map Distances Between Phylogenetic Trees
-Version: 2.11.1.9001
+Version: 2.12.0
 Authors@R: c(person("Martin R.", "Smith",
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph", "prg"), 
@@ -50,7 +50,7 @@ Imports:
   Rdpack (>= 0.7),
   shiny,
   shinyjs,
-  TreeTools (>= 2.0.0.9004),
+  TreeTools (>= 2.1.0),
 Suggests:
   bookdown,
   cluster,
@@ -71,6 +71,7 @@ Suggests:
   rgl,
   Rogue,
   spelling,
+  TBRDist,
   testthat (>= 3.0),
   Ternary (>= 1.1.2),
   TreeDistData (> 0.1.0),

NAMESPACE

@@ -152,6 +152,7 @@ export(is.HPart)
 importFrom(Rdpack,reprompt)
 importFrom(TreeTools,AllAncestors)
 importFrom(TreeTools,DropTip)
+importFrom(TreeTools,FirstMatchingSplit)
 importFrom(TreeTools,KeepTip)
 importFrom(TreeTools,KeepTipPostorder)
 importFrom(TreeTools,LnRooted.int)

NEWS.md

@@ -1,12 +1,14 @@
-# TreeDist 2.11.1.9001 (2026-02-05)
-
-- Support larger trees by updating some functions to use 32-bit integers, per TreeTools v2.1.0.
-
-
-# TreeDist 2.11.1.9000 (2025-11-13)
+# TreeDist 2.12.0 (2026-02-12)
 
+- Support larger trees in some functions by updating some functions to use
+  32-bit integers, per TreeTools v2.1.0.
+
 - `AHMI()` now returns negative values (previously zeroed in error).
 
+- Experimental support for a new method of SPR distance calculation:
+  subject to change or removal.
+
+
 # TreeDist 2.11.1 (2025-10-13)
 
 - Improve robustness of `SpectralEigens()` tests.

R/RcppExports.R

@@ -1,6 +1,10 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+binary_entropy_counts <- function(inSplit, nLeaves) {
+    .Call(`_TreeDist_binary_entropy_counts`, inSplit, nLeaves)
+}
+
 COMCLUST <- function(trees) {
     .Call(`_TreeDist_COMCLUST`, trees)
 }
@@ -58,6 +62,10 @@ entropy_int <- function(n) {
     .Call(`_TreeDist_entropy_int`, n)
 }
 
+expected_mi <- function(ni, nj) {
+    .Call(`_TreeDist_expected_mi`, ni, nj)
+}
+
 lapjv <- function(x, maxX) {
     .Call(`_TreeDist_lapjv`, x, maxX)
 }
@@ -102,6 +110,10 @@ keep_and_reduce <- function(tree1, tree2, keep) {
     .Call(`_TreeDist_keep_and_reduce`, tree1, tree2, keep)
 }
 
+spr_table_7 <- function(sp1, sp2) {
+    .Call(`_TreeDist_spr_table_7`, sp1, sp2)
+}
+
 cpp_robinson_foulds_distance <- function(x, y, nTip) {
     .Call(`_TreeDist_cpp_robinson_foulds_distance`, x, y, nTip)
 }