Merge branch 'stan-dev:master' into expose_new_stan_args

Author: venpopov

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

@@ -37,11 +37,11 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.7.2
+      - uses: r-lib/actions/setup-r@v2.8.2
         with:
           r-version: 'release'
           rtools-version: '42'
-      - uses: r-lib/actions/setup-pandoc@v2.7.2
+      - uses: r-lib/actions/setup-pandoc@v2.8.2
 
       - name: Query dependencies
         run: |

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

@@ -57,11 +57,11 @@ jobs:
           sudo apt-get install -y libcurl4-openssl-dev || true
           sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
 
-      - uses: r-lib/actions/setup-r@v2.7.2
+      - uses: r-lib/actions/setup-r@v2.8.2
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
-      - uses: r-lib/actions/setup-pandoc@v2.7.2
+      - uses: r-lib/actions/setup-pandoc@v2.8.2
 
       - name: Query dependencies
         run: |

.github/workflows/Test-coverage.yaml

@@ -34,8 +34,8 @@ jobs:
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.7.2
-      - uses: r-lib/actions/setup-pandoc@v2.7.2
+      - uses: r-lib/actions/setup-r@v2.8.2
+      - uses: r-lib/actions/setup-pandoc@v2.8.2
 
       - name: Install Ubuntu dependencies
         run: |
@@ -85,12 +85,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2.7.2
+      - uses: r-lib/actions/setup-r@v2.8.2
         with:
           r-version: 'release'
           rtools-version: '42'
 
-      - uses: r-lib/actions/setup-pandoc@v2.7.2
+      - uses: r-lib/actions/setup-pandoc@v2.8.2
 
       - name: Query dependencies
         run: |

.github/workflows/cmdstan-tarball-check.yaml

@@ -40,12 +40,12 @@ jobs:
           sudo apt-get install -y libcurl4-openssl-dev || true
           sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
 
-      - uses: r-lib/actions/setup-r@v2.7.2
+      - uses: r-lib/actions/setup-r@v2.8.2
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
 
-      - uses: r-lib/actions/setup-pandoc@v2.7.2
+      - uses: r-lib/actions/setup-pandoc@v2.8.2
 
       - name: Query dependencies
         run: |

man-roxygen/model-common-args.R

@@ -56,10 +56,11 @@
 #'   method.
 #'
 #' @param output_dir (string) A path to a directory where CmdStan should write
-#'   its output CSV files. For interactive use this can typically be left at
-#'   `NULL` (temporary directory) since CmdStanR makes the CmdStan output
-#'   (posterior draws and diagnostics) available in \R via methods of the fitted
-#'   model objects. The behavior of `output_dir` is as follows:
+#'   its output CSV files. For MCMC there will be one file per chain; for other
+#'   methods there will be a single file. For interactive use this can typically
+#'   be left at `NULL` (temporary directory) since CmdStanR makes the CmdStan
+#'   output (posterior draws and diagnostics) available in \R via methods of the
+#'   fitted model objects. The behavior of `output_dir` is as follows:
 #'   * If `NULL` (the default), then the CSV files are written to a temporary
 #'   directory and only saved permanently if the user calls one of the `$save_*`
 #'   methods of the fitted model object (e.g.,