Update from upstream

.Rbuildignore

@@ -1,4 +1,5 @@
 .+~
+BUGS
 DEVEL-README
 DEVEL-README.md
 \.Rhistory$
@@ -25,14 +26,15 @@ DEVEL-README.md
 ^TUNE.*
 ^\.git$
 ^\.github$
+^\.pre-commit-config\.yaml$
 ^check-reverse
 ^codecov\.yml$
 ^cran-comments.md$
+^devel-examples
 ^devel-tests
 ^dist\.sh$
 ^doc$
 ^docs$
-^devel-examples
 ^git_version$
 ^hooks/hook-evaluate
 ^hooks/hook-run
@@ -47,10 +49,10 @@ DEVEL-README.md
 ^revdep$
 ^scenario\.txt$
 ^scripts
-^src/iracebin/irace$
-^src/iracebin/irace.exe$
 ^src/iracebin/ablation$
 ^src/iracebin/ablation.exe$
+^src/iracebin/irace$
+^src/iracebin/irace.exe$
 ^src/iracebin/irace2pyimp$
 ^src/iracebin/irace2pyimp.exe$
 ^svn_version$
@@ -73,5 +75,5 @@ DEVEL-README.md
 ^vignettes/figure
 ^vignettes/optbib
 ^web
-_snaps
 _pkgdown\.yml$
+_snaps

.Rinstignore

@@ -1,4 +1,4 @@
-vignettes/section/irace-options.tex
-^GenericWrapper4AC
 \.github
+^GenericWrapper4AC
 _snaps
+vignettes/section/irace-options.tex

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

@@ -11,7 +11,7 @@ name: R-CMD-check
 concurrency:
   group: ${{ github.event.pull_request.number || github.run_id }}
   cancel-in-progress: true
-  
+
 env:
   R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
   _R_CHECK_FORCE_SUGGESTS_: false
@@ -29,13 +29,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-22.04, windows-latest, macos-13, macos-14 ]
-        r: [ release ]
+        os: [ windows-latest, macos-13, macos-14 ]
+        r: [ release, 4.0 ]
         include:
-          # Use 4.0 to check with rtools40's older compiler
-          - { os: windows-latest, r: '4.0' }
-          # Minimum supported version.
-          - {os: ubuntu-20.04,   r: '4.0'}
+          # 4.0 is the minimum supported version.
+          - { os: ubuntu-20.04, r: '4.0'}
+          - { os: ubuntu-22.04, r: 'release' }
           # Use latest ubuntu to make it easier to install dependencies
           - { os: ubuntu-24.04, r: 'devel', http-user-agent: 'release' }
 
@@ -53,7 +52,7 @@ jobs:
       - name: "[Linux] Install openmpi"
         if: runner.os == 'Linux'
         run: sudo apt-get update -y && sudo apt install -y libopenmpi-dev
-      
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
@@ -77,7 +76,7 @@ jobs:
           needs: check
           cache-version: 1
           install-pandoc: true
-          
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         if: runner.os == 'macOS'
         with:
@@ -88,22 +87,22 @@ jobs:
           needs: check
           cache-version: 1
           install-pandoc: true
-          
+
       - name: Check (as CRAN)
         env:
           NOT_CRAN: false
         uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual", "--as-cran")'
           build_args: 'c("--compact-vignettes=gs+qpdf")'
-      
+
       - name: Check
         env:
           NOT_CRAN: true
         uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual", "--run-donttest", "--timings")'
-          
+
       - name: Show testthat output
         if: failure()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
@@ -112,7 +111,7 @@ jobs:
   coverage:
     needs: R-CMD-check
     name: Coverage
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     continue-on-error: true
     timeout-minutes: 30
     env:
@@ -123,16 +122,17 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: release
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-tinytex@v2-branch
-        
+
       - name: Install additional LaTeX packages
         run: tlmgr install ${{ env.LATEX_PACKAGES }}
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr, mlr=?ignore, Rmpi=?ignore, local::. 
+          extra-packages: any::covr, any::xml2, mlr=?ignore, Rmpi=?ignore, local::.
           needs: coverage
           install-pandoc: true
 
@@ -143,21 +143,29 @@ jobs:
         run: |
           options(covr.fix_parallel_mcexit = TRUE)
           coverage <- covr::package_coverage(type = "all",
-                                             quiet = FALSE, clean = FALSE,
-                                             install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package"),
-                                             commentDonttest = FALSE)
+                 quiet = FALSE, clean = FALSE,
+                 install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
+                 commentDonttest = FALSE)
           print(coverage)
-          covr::codecov(coverage = coverage)
+          covr::to_cobertura(coverage)
+          #covr::codecov(coverage = coverage)
         shell: Rscript {0}
 
-
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
           find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
-        
+
       - name: Show failures
         if: failure()
         run: |
@@ -167,7 +175,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
@@ -193,7 +201,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          
+
       - uses: r-lib/actions/setup-tinytex@v2-branch
 
       - name: Install additional LaTeX packages
@@ -204,7 +212,7 @@ jobs:
           extra-packages: any::pkgdown, mlr=?ignore, Rmpi=?ignore, any::remotes
           needs: website
           install-pandoc: true
-          
+
       - name: Install package with vignettes
         run: |
           remotes::install_local(".", build = TRUE, upgrade = "never", force = TRUE, build_opts = c("--no-resave-data"), build_manual = TRUE, build_vignettes = TRUE)

.github/workflows/revdepcheck.yml

@@ -0,0 +1,21 @@
+on:
+  workflow_dispatch:
+    inputs:
+      which:
+        type: choice
+        description: Which dependents to check
+        options:
+          - strong
+          - most
+
+name: Reverse dependency check
+
+jobs:
+  revdep_check:
+    name: Reverse check ${{ inputs.which }} dependents
+    uses: r-devel/recheck/.github/workflows/recheck.yml@v1
+    with:
+      which: ${{ inputs.which }}
+      subdirectory: '' # set if your R package is in a subdir of the git repo
+      repository: '' # set to recheck an R package from another git repo
+      ref: '' # set to recheck a custom tag/branch from another repo

.gitignore

@@ -63,7 +63,7 @@ docs/
 /vignettes/*.bbl
 /vignettes/*.fls
 /vignettes/*.synctex*
-/vignettes/irace-options.tex
+/vignettes/section/irace-options.tex
 /vignettes/irace-package.tex
 /vignettes/irace-package.pdf
 /vignettes/irace-package.R

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3.9003
+    hooks:
+      - id: parsable-R
+      - id: no-browser-statement
+      - id: no-debug-statement
+      - id: deps-in-desc
+        exclude: '\.Rnw$'
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: check-merge-conflict
+        args: [ --assume-in-merge ]
+      - id: check-added-large-files
+        args: ['--maxkb=200']
+      - id: file-contents-sorter
+        files: '^(\.Rbuildignore|\.Rinstignore)$'
+      - id: end-of-file-fixer
+        exclude: '(\.Rd|python/doc/source/reference/.*|test-doctest-.*)'

DESCRIPTION

@@ -7,7 +7,7 @@ Description: Iterated race is an extension of the Iterated F-race method for
              settings given a set of instances of an optimization problem.
              M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
              and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
-Version: 3.9.0.9000
+Version: 4.2.0.9000
 Authors@R: c(person("Manuel", "López-Ibáñez", role = c("aut", "cre"),
                               email = "manuel.lopez-ibanez@manchester.ac.uk",
                               comment = c(ORCID = "0000-0001-9974-1295")),
@@ -20,17 +20,17 @@ Authors@R: c(person("Manuel", "López-Ibáñez", role = c("aut", "cre"),
              person("Nguyen", "Dang", role = "ctb", email = "nttd@st-andrews.ac.uk"))
 Depends: R (>= 4.0.0)
 Imports:
-        stats,
-        utils,
+        R6,
+        codetools,
         compiler,
-        fs,
         data.table (>= 1.15.0),
-        matrixStats,
-        R6,
+        fs,
+        matrixStats (>= 1.4.1),
         spacefillr,
+        stats,
+        utils,
         withr
 Suggests:
-    ParamHelpers,
     Rmpi (>= 0.6.0),
     highr,
     knitr,

Makefile

@@ -30,7 +30,8 @@ help:
 	@echo "install        install the package"
 	@echo "build          build the package as a tar.gz file"
 	@echo "check          build the package and run 'R CMD check'"
-	@echo "check TEST=x   run test called test-x.R"
+	@echo "test           run all tests under testthat"
+	@echo "test TEST=x    run test called test-x.R"
 	@echo "rsync          copy the package and install it on $(RNODE)"
 	@echo "cran           build the package and run 'R CMD check --as-cran'"
 	@echo "winbuild       submit the package to the WINDOWS builder service"
@@ -47,12 +48,13 @@ install: build
 	cd $(BINDIR) && R CMD INSTALL $(INSTALL_FLAGS) $(PACKAGE)_$(PACKAGEVERSION).tar.gz
 
 quick-install:
-	cd $(BINDIR) &&	R CMD build $(BUILD_FLAGS) $(NO_BUILD_VIGNETTES) $(PACKAGEDIR) && R CMD INSTALL $(INSTALL_FLAGS) $(PACKAGE)_$(PACKAGEVERSION).tar.gz
+	R CMD INSTALL $(INSTALL_FLAGS) --no-docs $(PACKAGEDIR)
 
 genoptions: R/irace-options.R vignettes/section/irace-options.tex
 
 R/irace-options.R vignettes/section/irace-options.tex: scripts/irace_options.json scripts/generate-options.R
 	cd scripts && R --slave -f generate-options.R && cd ..
+	touch R/irace-options.R vignettes/section/irace-options.tex
 
 gendoc:
 	$(Reval) 'devtools::document()'
@@ -61,7 +63,7 @@ pkgdown: gendoc
 	$(Reval) 'pkgdown::build_site()'
 	@$(MAKE) clean
 
-build: 
+build:
 	@$(MAKE) genoptions
 	$(MAKE) releasevignette
 	@if grep -q @ $(PACKAGEDIR)/vignettes/$(PACKAGE)-package.bib; then true; \
@@ -107,18 +109,18 @@ releasecheck: cran
 	$(MAKE) macbuild
 
 check: build
-ifdef TEST
-	_R_CHECK_FORCE_SUGGESTS_=false NOT_CRAN=true $(Reval) 'devtools::test(filter="$(TEST)", stop_on_failure = TRUE)'
-else
 	test -d ./GenericWrapper4AC/build || (cd GenericWrapper4AC && python3 setup.py install --user)
 	cd $(BINDIR) && (_R_CHECK_FORCE_SUGGESTS_=false NOT_CRAN=true R CMD check --run-donttest --timings --install-args="$(INSTALL_FLAGS)" $(PACKAGE)_$(PACKAGEVERSION).tar.gz; cat $(PACKAGE).Rcheck/$(PACKAGE)-Ex.timings)
-endif
 
-# Using testthat nicer output
+# Using testthat nicer output.
 test: clean
+ifdef TEST
+	_R_CHECK_FORCE_SUGGESTS_=false NOT_CRAN=true $(Reval) 'devtools::test(filter="$(TEST)", stop_on_failure = TRUE)'
+else
 	_R_CHECK_FORCE_SUGGESTS_=false NOT_CRAN=true $(Reval) 'testthat::test_local(stop_on_failure = TRUE)'
+endif
 
-clean: 
+clean:
 	cd $(PACKAGEDIR) && (./cleanup; make -C src -f Makevars clean)
 
 ## FIXME: building the vignettes is a bit complicated and sometimes fails.
@@ -178,8 +180,8 @@ macbuild: releasebuild
 	$(Reval) "rhub::check(platform='macos-highsierra-release-cran', $(RHUB_COMMON_ARGS))"
 
 winbuild: releasebuild
-	$(Reval) "devtools::check_win_release()"
-	$(Reval) "devtools::check_win_devel()"
+	$(Reval) "devtools::check_win_release(args = '--compact-vignettes=both')"
+	$(Reval) "devtools::check_win_devel(args = '--compact-vignettes=both')"
 	$(Reval) "rhub::check_on_windows($(RHUB_COMMON_ARGS))"
 
 examples: quick-install

NAMESPACE

@@ -62,11 +62,9 @@ export(target_runner_default)
 export(testConfigurations)
 export(testing_fromfile)
 export(testing_fromlog)
-import(compiler)
 import(data.table)
 import(matrixStats)
 import(stats)
-import(utils)
 import(withr)
 importFrom(R6,R6Class)
 importFrom(graphics,abline)
@@ -79,3 +77,4 @@ importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(graphics,strwidth)
 importFrom(spacefillr,generate_sobol_set)
+importFrom(utils,str)