Fix cmdstanr setup

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Renormalize line endings
+7308ea2330e787e0da8479b8a0c58547a7644b9b

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.github/workflows/touchstone-receive.yaml

@@ -1,53 +1,53 @@
-name: Continuous Benchmarks (Receive)
-
-permissions:
-  contents: read
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref }}
-  cancel-in-progress: true
-
-on:
-  pull_request:
-
-jobs:
-  prepare:
-    runs-on: ubuntu-latest
-    outputs:
-      config: ${{ steps.read_touchstone_config.outputs.config }}
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v7
-        with:
-          fetch-depth: 0
-
-      - id: read_touchstone_config
-        run: |
-          echo "config=$(jq -c . ./touchstone/config.json)" >> $GITHUB_OUTPUT
-
-  build:
-    needs: prepare
-    runs-on: ${{ matrix.config.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - ${{ fromJson(needs.prepare.outputs.config) }}
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-      R_REPOS: https://production.r-multiverse.org/2025-12-15,${{ matrix.config.rspm }}
-      RENV_CONFIG_REPOS_OVERRIDE: https://production.r-multiverse.org/2025-12-15,${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      USE_BUNDLED_LIBUV: 1
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v7
-        with:
-          fetch-depth: 0
-      - uses: lorenzwalthert/touchstone/actions/receive@main
-        with:
-          r-version: ${{ matrix.config.r }}
-          extra-repositories: |
-            https://production.r-multiverse.org/2025-12-15
-            ${{ matrix.config.rspm }}
+name: Continuous Benchmarks (Receive)
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      config: ${{ steps.read_touchstone_config.outputs.config }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+
+      - id: read_touchstone_config
+        run: |
+          echo "config=$(jq -c . ./touchstone/config.json)" >> $GITHUB_OUTPUT
+
+  build:
+    needs: prepare
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - ${{ fromJson(needs.prepare.outputs.config) }}
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      R_REPOS: https://production.r-multiverse.org/2025-12-15,${{ matrix.config.rspm }}
+      RENV_CONFIG_REPOS_OVERRIDE: https://production.r-multiverse.org/2025-12-15,${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      USE_BUNDLED_LIBUV: 1
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+      - uses: lorenzwalthert/touchstone/actions/receive@main
+        with:
+          r-version: ${{ matrix.config.r }}
+          extra-repositories: |
+            https://production.r-multiverse.org/2025-12-15
+            ${{ matrix.config.rspm }}

DESCRIPTION

@@ -44,4 +44,4 @@ Additional_repositories:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -17,8 +17,10 @@ export(stanflow_deps)
 export(stanflow_logo)
 export(stanflow_update)
 export(stdlib_funs)
-importFrom(utils,citation)
-importFrom(utils,packageDescription)
-importFrom(utils,person)
-importFrom(utils,toBibtex)
+importFrom(utils,
+  citation,
+  packageDescription,
+  person,
+  toBibtex
+)
 importFrom(withr,local_options)

NEWS.md

@@ -3,6 +3,7 @@
 * Updated posterior citation. (#39)
 * Added dry run option to see what function calls will do before execution. (#41)
 * Improved scanning performance
+* `setup_cmdstanr()` no longer auto-fixes the CmdStan toolchain (breaking).
 
 # stanflow 0.1.0
 

R/interfaces.R

@@ -236,12 +236,12 @@ setup_cmdstanr <- function(
   toolchain_ok <- tryCatch(
     {
       run_side_effect(
-        "check and fix the CmdStan toolchain",
+        "check the CmdStan toolchain",
         {
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE, quiet = quiet)
+          cmdstanr::check_cmdstan_toolchain(quiet = quiet)
         },
         code = sprintf(
-          "cmdstanr::check_cmdstan_toolchain(fix = TRUE, quiet = %s)",
+          "cmdstanr::check_cmdstan_toolchain(quiet = %s)",
           deparse1(quiet)
         )
       )
@@ -258,7 +258,7 @@ setup_cmdstanr <- function(
       c(
         "CmdStan toolchain check failed.",
         "i" = "You need a C++ compiler (RTools on Windows, Xcode on Mac) to run Stan.",
-        "i" = "Re-run {.code cmdstanr::check_cmdstan_toolchain(fix = TRUE, quiet = FALSE)} for detailed diagnostics."
+        "i" = "Re-run {.code cmdstanr::check_cmdstan_toolchain(quiet = FALSE)} for detailed diagnostics."
       )
     )
   }
@@ -405,7 +405,7 @@ setup_rstan <- function(
   run_side_effect <- dry_runner(dry_run)
 
   run_side_effect(
-    "configure {.pkg rstan}: set {.code options(mc.cores = {cores})} and {.code rstan::rstan_options(auto_write = {rstan_auto_write})}",
+    "configure {.pkg rstan}",
     {
       options(mc.cores = cores)
       rstan::rstan_options(auto_write = rstan_auto_write)
@@ -443,7 +443,7 @@ setup_brms <- function(
   brms_backend <- match.arg(brms_backend, c("cmdstanr", "rstan"))
 
   run_side_effect(
-    "configure {.pkg brms}: set {.code options(mc.cores = {cores})} and {.code options(brms.backend = '{brms_backend}')}",
+    "configure {.pkg brms}",
     {
       options(mc.cores = cores)
       options(brms.backend = brms_backend)
@@ -483,7 +483,7 @@ setup_rstanarm <- function(
 
 set_mc_cores <- function(run_side_effect, cores, pkg) {
   run_side_effect(
-    "configure {.pkg {pkg}}: set {.code options(mc.cores = {cores})}",
+    "configure {.pkg {pkg}}",
     {
       options(mc.cores = cores)
       cli::format_inline(

R/update.R

@@ -218,7 +218,7 @@ stanflow_update <- function(
   # Muffle all warnings except cannot install
   package_list <- paste0("{.pkg ", behind$package, "}", collapse = ", ")
   run_side_effect(
-    "install {package_list}",
+    paste0("install ", package_list),
     {
       withCallingHandlers(
         utils::install.packages(behind$package, repos = repos, quiet = TRUE),