Merge remote-tracking branch 'origin/master' into gq-timing

Author: jgabry

.github/CONTRIBUTING.md

@@ -54,3 +54,5 @@ new to you.
 Please note that the cmdstanr project follows the Stan project's 
 [Code of Conduct](https://discourse.mc-stan.org/t/announcing-our-new-stan-code-of-conduct/23764).
 By contributing to this project you agree to abide by its terms.
+
+All contributions must follow the [Stan AI Contribution Policy](https://github.com/stan-dev/stan/wiki/AI-Contribution-Policy).

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

@@ -30,12 +30,7 @@ jobs:
       CMDSTANR_OPENCL_TESTS: true
 
     steps:
-      - name: cmdstan env vars
-        run: |
-          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
-        shell: bash
-
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-pandoc@v2
@@ -44,7 +39,7 @@ jobs:
         with:
           extra-packages: any::rcmdcheck, local::.
 
-      - uses: Vampire/setup-wsl@v6
+      - uses: Vampire/setup-wsl@v7
         with:
             distribution: Ubuntu-22.04
             wsl-version: 2
@@ -55,12 +50,18 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y build-essential libopenmpi-dev ocl-icd-opencl-dev pocl-opencl-icd
+          sudo chmod 755 /root
         shell: wsl-bash {0}
 
       - name: Install cmdstan
         run: |
           cmdstanr::check_cmdstan_toolchain()
           cmdstanr::install_cmdstan(cores = 2, wsl = TRUE, overwrite = TRUE)
+          cat(
+            paste0("CMDSTAN=", cmdstanr::cmdstan_path(), "\n"),
+            file = Sys.getenv("GITHUB_ENV"),
+            append = TRUE
+          )
         shell: Rscript {0}
 
       - name: Session info

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

@@ -44,6 +44,7 @@ jobs:
           - {os: ubuntu-latest, r: 'devel', opencl: true}
           - {os: ubuntu-latest, r: 'release', opencl: true}
           - {os: ubuntu-latest, r: 'oldrel', opencl: true}
+          - {os: windows-11-arm, r: 'release'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -56,9 +57,13 @@ jobs:
       - name: cmdstan env vars
         run: |
           echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
+          # GHA Windows ARM containers configured with RTOOLS45_HOME instead of RTOOLS45_AARCH64_HOME
+          if [[ "${{ matrix.config.os }}" == "windows-11-arm" ]]; then
+            echo "RTOOLS45_AARCH64_HOME=C:/rtools45-aarch64" >> $GITHUB_ENV
+          fi
         shell: bash
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -75,7 +80,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           cache: "always"
-          extra-packages: any::rcmdcheck, local::.
+          extra-packages: any::rcmdcheck, local::., ${{ matrix.config.os == 'windows-11-arm' && 'RcppCore/RcppParallel' || '' }}
 
       - name: Debug Windows toolchain resolution
         if: ${{ runner.os == 'Windows' }}

.github/workflows/Test-coverage.yaml

@@ -43,7 +43,7 @@ jobs:
           workflow: Test-coverage.yaml
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-pandoc@v2
@@ -87,7 +87,7 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v5
+      - uses: codecov/codecov-action@v7
         with:
           # Fail if error if not on PR, or if on PR and token is given
           fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -24,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-pandoc@v2
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cmdstanr
 Title: R Interface to 'CmdStan'
-Version: 0.9.0.9000
+Version: 0.9.0.9001
 Date: 2025-03-30
 Authors@R:
     c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),
@@ -20,7 +20,8 @@ Authors@R:
       person(given = "Jacob", family = "Socolar", role = "ctb"),
       person(given = "Martin", family = "Modrák", role = "ctb"),
       person(given = "Ven", family = "Popov", role = "ctb"),
-      person("Visruth", "Srimath Kandali", role = "ctb")
+      person("Visruth", "Srimath Kandali", role = "ctb"),
+      person("Aki", "Vehtari", role = "ctb")
       )
 Description: A lightweight interface to 'Stan' <https://mc-stan.org>.
     The 'CmdStanR' interface is an alternative to 'RStan' that calls the command
@@ -33,15 +34,14 @@ URL: https://mc-stan.org/cmdstanr/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/cmdstanr/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE, r6 = FALSE)
 SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
 Depends:
     R (>= 4.0.0)
 Imports:
     checkmate,
     data.table,
-    jsonlite (>= 1.2.0),
+    jsonlite (>= 1.8.7),
     posterior (>= 1.5.0),
     processx (>= 3.5.0),
     R6 (>= 2.4.0),
@@ -55,6 +55,8 @@ Suggests:
     loo (>= 2.0.0),
     qs2,
     rmarkdown,
-    testthat (>= 2.1.0),
+    testthat (>= 3.3.0),
     Rcpp
 VignetteBuilder: knitr
+Config/testthat/edition: 3
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -37,6 +37,7 @@ export(draws_to_csv)
 export(eng_cmdstan)
 export(install_cmdstan)
 export(print_example_program)
+export(print_stan_file)
 export(read_cmdstan_csv)
 export(rebuild_cmdstan)
 export(register_knitr_engine)

NEWS.md

@@ -1,11 +1,19 @@
 # cmdstanr (development version)
 
+* `pathfinder()` now respects `save_single_paths = TRUE` instead of always
+passing `0` to CmdStan.
+* `pathfinder()` now uses `threads` argument (`num_threads` is deprecated),
+to be consistent with other methods.
 * Informative error when exposing functions using names that are reserved 
 keywords (@VisruthSK, #1154)
 * `save_cmdstan_config` and `save_metric` default to `FALSE` but can be 
 set to `TRUE` for an entire R session via new global options. (#1159)
+* `save_metric_files()` now gives an informative error when metric files were not created and keeps saved metric files after the fitted model is garbage-collected. (#1021)
 * `cmdstan_model()` no longer fails when `MAKEFLAGS` enables directory-printing 
 output while reading `STANCFLAGS` from `make`. (#1163)
+* `laplace()` no longer overwrites the internally generated optimizer CSV when
+`mode = NULL` and `output_basename` is supplied. The internally generated
+optimizer CSV now uses the filename `<output_basename>-mode-1.csv`.
 
 * CmdStanModel objects created using `compile_model_methods = TRUE` that are
 then saved and reloaded no longer error in model fitting methods. Model methods