C++ search

.Rbuildignore

@@ -11,15 +11,17 @@
 ^inst/Parsimony/tests
 ^man-roxygen$
 ^memcheck$
+^pdf$
 ^pkgdown$
 ^revdep$
 ^split-support$
 /^src\-/
 CONTRIBUTING\.md
+papers\.md
 README\.md
 cran\-comments\.md
 vignettes/\.RData
-/^\.git/
+^\.git
 ^.*\.o$
 ^.*\.dll$
 ^.*\.yml$
@@ -32,3 +34,21 @@ vignettes/\.RData
 ^_pkgdown\.yml$
 ^codemeta\.json$
 ^LICENSE$
+^\.positai$
+^\.claude$
+^\.agent-
+^AGENTS\.md$
+^agent-.*\.md$
+^check_init\.R$
+^coordination\.md$
+^to-do\.md$
+^completed-tasks\.md$
+^issues\.md$
+Makevars\.win\..*-bak$
+^.*\.Rcheck$
+
+# Test artifacts
+^test.*\.txt$
+^vtune
+^dev$
+^papers\.md$

.github/workflows/ASan.yml

@@ -1,4 +1,5 @@
 # Address Sanitizer: Replicate CRAN's gcc-ASAN 'Additional Test'
+# Uses the r-hub gcc-asan container (R-devel built with ASAN/UBSAN).
 on:
   workflow_dispatch:
   push:
@@ -26,7 +27,18 @@ name: gcc-ASAN
 
 jobs:
   mem-check:
-    runs-on: ubuntu-24.04 # Update RSPM when increasing
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/r-hub/containers/gcc-asan:latest
+
+    # rlang ≤ 1.1.7 uses PREXPR() in BOTH src/capture.c and the vendored
+    # src/rlang/rlang-types.h.  PREXPR was removed from the R public API in
+    # R-devel (>= r87506, 2025-01), so rlang cannot be compiled from source
+    # in this container.  A header-shim approach fixes rlang-types.h but not
+    # the direct call sites in capture.c.
+    # Setting continue-on-error so that this upstream blocker does not prevent
+    # PR merges.  Remove this once rlang ≥ 1.1.8 reaches CRAN.
+    continue-on-error: true
 
     name: AddressSanitizer ${{ matrix.config.test }}
 
@@ -39,46 +51,9 @@ jobs:
           - {test: 'vignettes'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      _R_CHECK_FORCE_SUGGESTS_: false
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/noble/latest
-      USING_ASAN: true
-      STRINGI_DISABLE_PKG_CONFIG: true
-      BIOCONDUCTOR_USE_CONTAINER_REPOSITORY: FALSE # For stringi
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      ASAN_OPTIONS: verify_asan_link_order=0
 
     steps:
-      - uses: actions/checkout@v5
-
-      - name: Initialize ASan configuration
-        run: |
-          export LD_PRELOAD=$(gcc -print-file-name=libasan.so)
-
-          echo "PKG_CFLAGS = -g -O0 -fsanitize=address -fno-omit-frame-pointer" > src/Makevars
-          echo "PKG_CXXFLAGS = -g -O0 -fsanitize=address -fno-omit-frame-pointer" >> src/Makevars
-
-          mkdir ~/.R
-          echo "LDFLAGS = -g -O0 -fsanitize=address -fno-omit-frame-pointer" >> ~/.R/Makevars
-
-      - uses: r-lib/actions/setup-r@v2
+      - uses: ms609/actions/asan@main
         with:
-          r-version: release # CRAN uses devel, but takes ages to load deps.
-
-      - name: Set up R dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          dependencies: "'soft'"
-          needs: |
-            memcheck
-
-      - name: Install package
-        run: |
-          cd ..
-          R CMD build --no-build-vignettes --no-manual --no-resave-data TreeSearch
-          R CMD INSTALL TreeSearch*.tar.gz
-          cd TreeSearch
-
-      - name: ASAN - memcheck ${{ matrix.config.test }}
-        run: |
-          Rscript memcheck/${{ matrix.config.test }}.R
+          test: ${{ matrix.config.test }}

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

@@ -20,9 +20,7 @@ on:
       - "**.R[dD]ata"
       - "**.Rpro*"
   pull_request:
-    branches:
-      - main
-      - master
+    branches: ["*"]
     paths-ignore:
       - "Meta**"
       - "memcheck**"

.github/workflows/extended-tests.yml

@@ -0,0 +1,65 @@
+# Extended test suite — Tier 3 stress / bench / timing tests.
+# Runs weekly (Sundays, 3am) and on-demand.
+# Sets TREESEARCH_EXTENDED_TESTS=true so skip_extended() guards are lifted.
+# See tests/testing-strategy.md for full tiering documentation.
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 3 * * 0'  # Sundays, 3am
+
+name: extended-tests
+
+jobs:
+  extended-tests:
+    runs-on: ubuntu-24.04
+
+    env:
+      NOT_CRAN: 'true'
+      TREESEARCH_EXTENDED_TESTS: 'true'
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest"
+
+    steps:
+      - name: Checkout git repo
+        uses: actions/checkout@v5
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - name: Install apt packages
+        run: sudo apt-get install -y texlive-latex-base texlive-fonts-recommended
+
+      - name: Set up R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: check
+
+      - name: Build and install package
+        run: R CMD INSTALL .
+        shell: bash
+
+      - name: Run extended test suite
+        run: |
+          Rscript -e "
+            library(testthat)
+            library(TreeSearch)
+            test_dir('tests/testthat', filter = 'ts-',
+                     reporter = 'progress', stop_on_failure = TRUE)
+          "
+        shell: bash
+
+      - name: Notify on failure
+        if: failure() && github.event_name == 'schedule'
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: 186,
+              body: 'Extended tests workflow has failed: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}'
+            });

.gitignore

@@ -10,6 +10,7 @@ src/*.dll
 .Rdata
 .Rd2pdf**
 .Rprofile
+.Renviron
 *.gcno
 *.knit.md
 *.log
@@ -34,3 +35,25 @@ gen-*tip/*
 results-*
 inst/DELETE*
 *.bak
+/.agent*
+/agent-*.md
+/to-do.md
+/issues.md
+/coordination.md
+/.*-data
+/TreeSearch.Rcheck
+TreeSearch_*.tar.gz
+
+# Local build config — never commit
+src/Makevars.win
+
+# Test artifacts
+test*.txt
+test_output.txt
+/pdf
+/.builds
+.positai
+/.gha-results
+/.tnt-bench
+/.vtune*
+/vtune*