Merge branch 'main' into large-lists

Author: ms609

.Rbuildignore

@@ -9,6 +9,7 @@
 CONTRIBUTING
 README.md
 ^\.github
+^\.lintr
 cran-comments.md
 man-roxygen
 data-raw
@@ -30,5 +31,6 @@ revdep
 ^\.travis\.yml$
 ^\.zenodo\.json$
 ^\.covrignore$
+^\.vs.*$
 ^\.vscode.*$
 ^CRAN-SUBMISSION$

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

@@ -3,6 +3,7 @@
 on:
   schedule:
     - cron: "24 06 * * 1"
+  workflow_dispatch:
   push:
     branches:
       - main
@@ -48,15 +49,16 @@ jobs:
         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.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-latest, r: 'release',
+          - {os: ubuntu-24.04, r: 'release',
           rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
           - {os: ubuntu-latest, r: 'devel',
           rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
 
     env:
-      _R_CHECK_CRAN_INCOMING_: true # Seemingly not set by --as-cran
+      _R_CHECK_CRAN_INCOMING_: ${{ github.event_name == 'pull_request' }}
       _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
       R_COMPILE_AND_INSTALL_PACKAGES: 'never'
       _R_CHECK_THINGS_IN_CHECK_DIR_: false
@@ -70,18 +72,25 @@ jobs:
       - 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
         with:
           r-version: ${{ matrix.config.r }}
           extra-repositories: https://ms609.github.io/packages/
 
-      - name: Install apt packages (Linux)
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y texlive-latex-base libglpk-dev texlive-fonts-recommended
-
       - name: Set up R dependencies (Windows)
         if: runner.os == 'Windows'
         uses: r-lib/actions/setup-r-dependencies@v2
@@ -112,17 +121,30 @@ jobs:
       - name: Set up pandoc
         uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Check with incoming checks (PR)
-        if: github.event_name == 'pull_request'
+      - name: Check package
         uses: r-lib/actions/check-r-package@v2
 
-      - name: Check without incoming checks (push/schedule)
-        if: github.event_name == 'push' || github.event_name == 'schedule'
-        uses: r-lib/actions/check-r-package@v2
-        with:
-          args: "--no-incoming-check"
-
       - name: Code coverage
         if: runner.os == 'Windows'
         run: covr::codecov()
         shell: Rscript {0}
+
+      - name: Notify on failure
+        if: failure() && github.event_name == 'schedule'
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: 164,
+              body: 'Scheduled workflow has failed: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}'
+            });
+      
+            await github.rest.issues.update({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: 164,
+              state: 'open'
+            });

.github/workflows/benchmark.yml

@@ -2,19 +2,29 @@ name: Benchmark
 
 on:
   workflow_dispatch:
-  pull_request:
-    paths-ignore:
-      - "Meta**"
-      - "memcheck**"
-      - "docs**"
-      - "**.git"
-      - "**.json"
-      - "**.md"
-      - "**.yaml"
-      - "**.yml"
-      - "!**benchmark.yml"
-      - "**.R[dD]ata"
-      - "**.Rpro*"
+  workflow_run:
+    workflows: ["R-CMD-check"]
+    types:
+      - completed
+    paths:
+      - "src/**"
+      - "R/**"
+      - "**.R"
+      - "**.cpp"
+      - "**.c"
+      - "**.h"
+      - "**.hpp"
+      - "configure*"
+      - "Makevars*"
+      - "**benchmark.yml"
+      - "!memcheck**"
+      - "!docs**"
+      - "!inst**"
+      - "!man**"
+      - "!man-roxygen**"
+      - "!memcheck**"
+      - "!tests**"
+      - "!vignettes**"
 
 jobs:
   benchmark:

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

@@ -40,9 +40,11 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y texlive-latex-base libglpk-dev texlive-fonts-recommended
 
-      - name: Set up R dependencies
+      - name: Set up essential R dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          dependencies: '"hard"'
+          cache: "always"
           extra-packages: |
             ms609/TreeDistData
             devtools
@@ -58,4 +60,4 @@ jobs:
           repository: ms609/TreeTools
           path: TreeTools-source
           # This provides access to TreeTools source code for agents to inspect
-          # when debugging issues in TreeDist that may relate to TreeTools
+          # when debugging issues in TreeDist that may relate to TreeTools

.github/workflows/memcheck.yml

@@ -6,40 +6,30 @@ on:
     branches:
       - main
       - master
-    paths-ignore:
-      - "Meta**"
-      - "docs**"
-      - "**.git"
-      - "**.json"
-      - "**.md"
-      - "**.yml"
-      - "!**memcheck.yml"
-      - "**.R[dD]ata"
-      - "**.Rpro*"
+    paths:
+      - '.github/workflows/memcheck.yml'
+      - 'src/**'
+      - 'inst/include/**'
+      - 'memcheck/**'
+      - 'tests/testthat/**.R'
+      - 'vignettes/**.Rmd'
   pull_request:
     branches:
       - main
       - master
-    paths-ignore:
-      - "Meta**"
-      - "docs**"
-      - "**.git"
-      - "**.json"
-      - "**.md"
-      - "**.yml"
-      - "!**memcheck.yml"
-      - "**.R[dD]ata"
-      - "**.Rpro*"
+    paths:
+      - '.github/workflows/memcheck.yml'
+      - 'src/**'
+      - 'inst/include/**'
+      - 'memcheck/**'
+      - 'tests/testthat/**.R'
+      - 'vignettes/**.Rmd'
 
 name: mem-check
 
 jobs:
   mem-check:
-    runs-on: ubuntu-20.04
-    # stringi requires libicui18n - apt get libicu-dev too recent,
-    # libicu66 deprecated in ubuntu 22.04
-    # Reinstalling stringi seems not to help
-
+    runs-on: ubuntu-24.04
     name: valgrind ${{ matrix.config.test }}, ubuntu, R release
 
     strategy:
@@ -53,61 +43,10 @@ jobs:
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       _R_CHECK_FORCE_SUGGESTS_: false
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/noble/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v5
-
-      - uses: r-lib/actions/setup-r@v2
+      - uses: ms609/actions/memcheck@main
         with:
-          r-version: release
-
-      - uses: r-lib/actions/setup-pandoc@v2
-        
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-        
-      - name: Install additional dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y texlive-latex-base texlive-fonts-recommended libglpk40 wget valgrind
-          sudo apt-get install -y valgrind texlive-latex-base
-
-      - name: Install system dependencies
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", gsub("#\\d+~(\\d{2}\\.\\d{2}).*", "\\1", Sys.info()[["version"]]))')
-      
-      - name: Cache R packages
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-          
-      - name: Install dependencies
-        run: |
-          remotes::install_github('RcppCore/Rcpp')
-          remotes::install_github('ms609/TreeTools')
-          remotes::install_github('ms609/TreeDistData')
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("devtools")
-        shell: Rscript {0}
-        
-      - name: Install TreeDist
-        run: |
-          cd ..
-          R CMD build --no-manual --no-resave-data TreeDist
-          R CMD INSTALL TreeDist*.tar.gz
-          cd TreeDist
-
-      - name: valgrind - memcheck ${{ matrix.config.test }}
-        run: |
-          R -d "valgrind --tool=memcheck --leak-check=full  --errors-for-leak-kinds=definite --error-exitcode=1" --vanilla < memcheck/${{ matrix.config.test }}.R
+          test: ${{ matrix.config.test}}

.github/workflows/rhub.yaml

@@ -1,8 +1,8 @@
-# R-hub's generic GitHub Actions workflow file. Its canonical location is at
-# https://github.com/r-hub/rhub2/blob/v1/inst/workflow/rhub.yaml
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
 # You can update this file to a newer version using the rhub2 package:
 #
-# rhub2::rhub_setup()
+# rhub::rhub_setup()
 #
 # It is unlikely that you need to modify this file manually.
 
@@ -33,7 +33,7 @@ jobs:
 
     steps:
     # NO NEED TO CHECKOUT HERE
-    - uses: r-hub/rhub2/actions/rhub-setup@v1
+    - uses: r-hub/actions/setup@v1
       with:
         config: ${{ github.event.inputs.config }}
       id: rhub-setup
@@ -51,27 +51,17 @@ jobs:
       image: ${{ matrix.config.container }}
 
     steps:
-      - name: Check distribution
-        run: |
-          echo "distribution=$(awk -F= '/^ID=/{print $2}' /etc/os-release)" \
-            >> $GITHUB_OUTPUT;
-        id: check_distribution
-      - name: apt-get install sudo (Ubuntu, for clang-asan)
-        run: apt-get install sudo
-        if: ${{ steps.check_distribution.outputs.distribution == 'ubuntu' }}
-      - uses: r-lib/actions/setup-pandoc@v2
-        if: ${{ steps.check_distribution.outputs.distribution != 'fedora' }}
-      - uses: r-hub/rhub2/actions/rhub-checkout@v1
-      - uses: r-hub/rhub2/actions/rhub-platform-info@v1
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/rhub2/actions/rhub-setup-deps@v1
+      - uses: r-hub/actions/setup-deps@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
           extra-packages: TreeDistData=?ignore-before-r=99.0.0
-      - uses: r-hub/rhub2/actions/rhub-run-check@v1
+      - uses: r-hub/actions/run-check@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
@@ -87,25 +77,21 @@ jobs:
         config: ${{ fromJson(needs.setup.outputs.platforms) }}
 
     steps:
-      - uses: teatimeguest/setup-texlive-action@v3
-        with:
-          packages: scheme-basic
-      - uses: r-lib/actions/setup-pandoc@v2
-      - uses: r-hub/rhub2/actions/rhub-checkout@v1
-      - uses: r-hub/rhub2/actions/rhub-setup-r@v1
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
-      - uses: r-hub/rhub2/actions/rhub-platform-info@v1
+      - uses: r-hub/actions/platform-info@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/rhub2/actions/rhub-setup-deps@v1
+      - uses: r-hub/actions/setup-deps@v1
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
           extra-packages: TreeDistData=?ignore-before-r=99.0.0
-      - uses: r-hub/rhub2/actions/rhub-run-check@v1
+      - uses: r-hub/actions/run-check@v1
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}