Merge branch 'master' into remove-deprecated

Author: jgabry

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

@@ -36,16 +36,16 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: r-lib/actions/setup-r@v2.11.2
-      - uses: r-lib/actions/setup-pandoc@v2.11.2
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.11.2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck, local::.
 
-      - uses: Vampire/setup-wsl@v5
+      - uses: Vampire/setup-wsl@v6
         with:
             distribution: Ubuntu-22.04
             wsl-version: 2
@@ -71,7 +71,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2.11.2
+      - uses: r-lib/actions/check-r-package@v2
         env:
           _R_CHECK_CRAN_INCOMING_: false
 
@@ -82,7 +82,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: wsl-backend-results
           path: check

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

@@ -11,6 +11,12 @@ name: Unit tests
   pull_request:
     branches:
       - master
+  workflow_dispatch:
+    inputs:
+      tarball_url:
+        description: 'CmdStan tarball URL to test with.'
+        required: false
+        default: ''
 
 jobs:
   R-CMD-check:
@@ -23,19 +29,21 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, r: 'devel', rtools: '', opencl: true}
-          - {os: macOS-latest, r: 'release', rtools: '', opencl: true}
-          - {os: windows-latest, r: 'devel', rtools: '44'}
-          - {os: windows-latest, r: 'release', rtools: '44'}
-          - {os: windows-latest, r: 'oldrel', rtools: '43'}
-          - {os: ubuntu-latest, r: 'devel', rtools: '', opencl: true}
-          - {os: ubuntu-latest, r: 'release', rtools: '', opencl: true}
-          - {os: ubuntu-latest, r: 'oldrel', rtools: '', opencl: true}
+          - {os: macOS-latest, r: 'devel', opencl: true}
+          - {os: macOS-latest, r: 'release', opencl: true}
+          - {os: windows-latest, r: 'devel' }
+          - {os: windows-latest, r: 'release'}
+          - {os: windows-latest, r: 'oldrel'}
+          - {os: ubuntu-latest, r: 'devel', opencl: true}
+          - {os: ubuntu-latest, r: 'release', opencl: true}
+          - {os: ubuntu-latest, r: 'oldrel', opencl: true}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       NOT_CRAN: true
       CMDSTANR_OPENCL_TESTS: ${{ matrix.config.opencl }}
+      CMDSTAN_TEST_TARBALL_URL: ${{ github.event.inputs.tarball_url }}
+      PKG_SYSREQS_DB_UPDATE_TIMEOUT: 30s
 
     steps:
       - name: cmdstan env vars
@@ -48,16 +56,21 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: r-lib/actions/setup-r@v2.11.2
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          rtools-version: ${{ matrix.config.rtools }}
 
-      - uses: r-lib/actions/setup-pandoc@v2.11.2
+      - name: Install R Package Build Dependencies on MacOS
+        if: ${{ runner.os == 'macOS' }}
+        uses: r-hub/actions/setup-r-sysreqs@v1
+        with:
+          type: 'minimal'
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.11.2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           cache: "always"
           extra-packages: any::rcmdcheck, local::.
@@ -80,7 +93,16 @@ jobs:
       - name: Install cmdstan
         run: |
           cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2)
+          tarball_url <- Sys.getenv("CMDSTAN_TEST_TARBALL_URL")
+          if (nzchar(tarball_url)) {
+            cmdstanr::install_cmdstan(
+              cores = 2,
+              overwrite = TRUE,
+              release_url = tarball_url
+            )
+          } else {
+            cmdstanr::install_cmdstan(cores = 2)
+          }
         shell: Rscript {0}
 
       - name: Session info
@@ -90,7 +112,7 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2.11.2
+      - uses: r-lib/actions/check-r-package@v2
         env:
           _R_CHECK_CRAN_INCOMING_: false
 
@@ -101,7 +123,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/Test-coverage.yaml

@@ -2,15 +2,15 @@
 # Github Actions workflow to analyze CmdStanR code, test coverage
 # yamllint disable rule:line-length
 
-name: Test coverage
-
-'on':
+on:
   push:
     branches:
       - master
   pull_request:
-    branches:
-      - master
+
+name: Test coverage
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -38,16 +38,18 @@ jobs:
       - uses: n1hility/cancel-previous-runs@v3
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          workflow: Test-coverage.yml
+          workflow: Test-coverage.yaml
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
-      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.11.2
-      - uses: r-lib/actions/setup-pandoc@v2.11.2
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2.11.2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, local::., any::covr, any::gridExtra
+          extra-packages: any::rcmdcheck, local::., any::covr, any::gridExtra, any::xml2
+          needs: coverage
 
       - name: Install cmdstan
         run: |
@@ -57,12 +59,55 @@ jobs:
 
       - name: Test coverage (Linux)
         if: runner.os == 'Linux'
-        run: covr::codecov(type = "tests")
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
+            type = "tests"
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
       - name: Test coverage (Windows)
         if: runner.os == 'Windows'
         run: |
           options(covr.gcov = 'C:/rtools44/mingw64/bin/gcov.exe');
-          covr::codecov(type = "tests", function_exclusions = "sample_mpi")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
+            type = "tests",
+            function_exclusions = "sample_mpi"
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+      - uses: codecov/codecov-action@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: 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: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v6
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package