CI updates, code formatting

.github/workflows/main.yml

@@ -8,20 +8,45 @@ on:
   workflow_dispatch: {}
 
 env:
-  CACHE_VERSION: 3
+  CACHE_VERSION: 5
 
 # only run one copy per PR
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
 jobs:
+  check-formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out github
+        uses: actions/checkout@v5
+        with:
+          submodules: recursive
+
+      - name: Set up Julia
+        uses: julia-actions/install-juliaup@v2
+        with:
+          channel: "lts"
+
+      - name: Install Formatters
+        run: |
+          sudo apt install -y clang-format black isort
+          curl --proto '=https' --tlsv1.2 -LsSf https://github.com/posit-dev/air/releases/download/0.8.0/air-installer.sh | sh
+          julia --project=clients/julia -e 'import Pkg; Pkg.add("JuliaFormatter")'
+
+      - name: Run formatting checks
+        run: |
+          make format-check || (echo "::error title=Formatting::Formatting check failed, run \`make format\` locally" && exit 1)
+
   build:
     runs-on: ${{matrix.os}}
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, ubuntu-latest, macos-latest]
+        # windows-2022 is a workaround for a julia issue as of 10/23/2025
+        # https://github.com/JuliaLang/julia/issues/59931
+        os: [windows-2022, ubuntu-latest, macos-latest]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
@@ -55,8 +80,8 @@ jobs:
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.12"]
+        os: [ubuntu-latest, macos-latest, windows-2022]
+        python-version: ["3.9", "3"]
       fail-fast: false
     steps:
       - name: Check out github
@@ -110,7 +135,7 @@ jobs:
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-2022]
       fail-fast: false
     steps:
       - name: Check out github
@@ -144,15 +169,15 @@ jobs:
           key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }}
 
       - name: Run tests
-        if: matrix.os != 'windows-latest'
+        if: matrix.os != 'windows-2022'
         run: |
           cd clients/R
           Rscript -e "devtools::test(reporter = c(\"summary\", \"fail\"))"
         env:
           TINYSTAN: ${{ github.workspace }}
 
       - name: Run tests (windows)
-        if: matrix.os == 'windows-latest'
+        if: matrix.os == 'windows-2022'
         run: |
           cd clients/R
           Rscript -e 'devtools::test(reporter = c("summary", "fail"))'
@@ -165,7 +190,7 @@ jobs:
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-2022]
         julia-version: ["1"]
       fail-fast: false
     steps:
@@ -175,9 +200,9 @@ jobs:
           submodules: recursive
 
       - name: Set up Julia
-        uses: julia-actions/setup-julia@v2
+        uses: julia-actions/install-juliaup@v2
         with:
-          version: ${{ matrix.julia-version }}
+          channel: ${{ matrix.julia-version }}
 
       - name: Restore Stan
         uses: actions/cache@v4
@@ -201,7 +226,7 @@ jobs:
 
       - name: Run tests
         run: |
-          julia --project=clients/julia -t 2 -e "using Pkg; Pkg.test()"
+          julia --project=clients/julia -t 2 --color yes -e "using Pkg; Pkg.test()"
         env:
           TINYSTAN: ${{ github.workspace }}
 

Makefile

@@ -124,13 +124,22 @@ TEST_MODEL_LIBS = $(join $(addprefix test_models/, $(TEST_MODEL_NAMES)), $(addsu
 test_models: $(TEST_MODEL_LIBS)
 
 
-.PHONY: format
+.PHONY: format format-check
 format:
 	clang-format -i src/*.cpp src/*.hpp src/*.h || true
 	isort clients/python || true
 	black clients/python || true
 	julia --project=clients/julia -e 'using JuliaFormatter; format("clients/julia/")' || true
-	Rscript -e 'formatR::tidy_dir("clients/R/", recursive=TRUE)' || true
+	air format clients/R || true
+	cd clients/typescript && npx prettier --write . || true
+
+format-check:
+	clang-format --dry-run --Werror src/*.cpp src/*.hpp src/*.h
+	isort clients/python --check
+	black clients/python --check
+	julia --project=clients/julia -e 'using JuliaFormatter; if !format("clients/julia/", overwrite=false) exit(1) end'
+	air format clients/R --check
+	cd clients/typescript && npx prettier --check .
 
 .PHONY: clean
 clean:

clients/R/R/compile.R

@@ -3,26 +3,36 @@ MAKE <- Sys.getenv("MAKE", "make")
 
 
 verify_tinystan_path <- function(path) {
-    suppressWarnings({
-        folder <- normalizePath(path)
-    })
-    if (!dir.exists(folder)) {
-        stop(paste0("TinyStan folder '", folder, "' does not exist!\n", "If you need to set a different location, call 'set_tinystan_path()'"))
-    }
-    makefile <- file.path(folder, "Makefile")
-    if (!file.exists(makefile)) {
-        stop(paste0("TinyStan folder '", folder, "' does not contain file 'Makefile',",
-            " please ensure it is built properly!\n", "If you need to set a different location, call 'set_tinystan_path()'"))
-    }
+  suppressWarnings({
+    folder <- normalizePath(path)
+  })
+  if (!dir.exists(folder)) {
+    stop(paste0(
+      "TinyStan folder '",
+      folder,
+      "' does not exist!\n",
+      "If you need to set a different location, call 'set_tinystan_path()'"
+    ))
+  }
+  makefile <- file.path(folder, "Makefile")
+  if (!file.exists(makefile)) {
+    stop(paste0(
+      "TinyStan folder '",
+      folder,
+      "' does not contain file 'Makefile',",
+      " please ensure it is built properly!\n",
+      "If you need to set a different location, call 'set_tinystan_path()'"
+    ))
+  }
 }
 
 #' @title Function `set_tinystan_path()`
 #' @description Set the path to TinyStan.
 #' @details This should point to the top-level folder of the repository.
 #' @export
 set_tinystan_path <- function(path) {
-    verify_tinystan_path(path)
-    Sys.setenv(TINYSTAN = normalizePath(path))
+  verify_tinystan_path(path)
+  Sys.setenv(TINYSTAN = normalizePath(path))
 }
 
 #' Get the path to TinyStan.
@@ -36,21 +46,28 @@ set_tinystan_path <- function(path) {
 #'
 #' @seealso [set_tinystan_path]
 get_tinystan_path <- function() {
-    # try to get from environment
-    path <- Sys.getenv("TINYSTAN", unset = "")
-    if (path == "") {
-        path <- CURRENT_TINYSTAN
-        tryCatch({
-            verify_tinystan_path(path)
-        }, error = function(e) {
-            print(paste0("TinyStan not found at location specified by $TINYSTAN ",
-                "environment variable, downloading version ", packageVersion("tinystan"),
-                " to ", path))
-            get_tinystan_src()
-        })
-    }
+  # try to get from environment
+  path <- Sys.getenv("TINYSTAN", unset = "")
+  if (path == "") {
+    path <- CURRENT_TINYSTAN
+    tryCatch(
+      {
+        verify_tinystan_path(path)
+      },
+      error = function(e) {
+        print(paste0(
+          "TinyStan not found at location specified by $TINYSTAN ",
+          "environment variable, downloading version ",
+          packageVersion("tinystan"),
+          " to ",
+          path
+        ))
+        get_tinystan_src()
+      }
+    )
+  }
 
-    return(path)
+  return(path)
 }
 
 
@@ -73,52 +90,67 @@ get_tinystan_path <- function() {
 #' @seealso [tinystan::set_tinystan_path()]
 #' @export
 compile_model <- function(stan_file, stanc_args = NULL, make_args = NULL) {
-    verify_tinystan_path(get_tinystan_path())
-    suppressWarnings({
-        file_path <- normalizePath(stan_file)
-    })
-    if (tools::file_ext(file_path) != "stan") {
-        stop(paste0("File '", file_path, "' does not end with '.stan'"))
-    }
-    if (!file.exists(file_path)) {
-        stop(paste0("File '", file_path, "' does not exist!"))
-    }
+  verify_tinystan_path(get_tinystan_path())
+  suppressWarnings({
+    file_path <- normalizePath(stan_file)
+  })
+  if (tools::file_ext(file_path) != "stan") {
+    stop(paste0("File '", file_path, "' does not end with '.stan'"))
+  }
+  if (!file.exists(file_path)) {
+    stop(paste0("File '", file_path, "' does not exist!"))
+  }
 
-    output <- paste0(tools::file_path_sans_ext(file_path), "_model.so")
-    stancflags <- paste("--include-paths=.", paste(stanc_args, collapse = " "))
+  output <- paste0(tools::file_path_sans_ext(file_path), "_model.so")
+  stancflags <- paste("--include-paths=.", paste(stanc_args, collapse = " "))
 
-    flags <- c(paste("-C", get_tinystan_path()), make_args, paste0("STANCFLAGS=\"",
-        stancflags, "\""), output)
+  flags <- c(
+    paste("-C", get_tinystan_path()),
+    make_args,
+    paste0("STANCFLAGS=\"", stancflags, "\""),
+    output
+  )
 
-    suppressWarnings({
-        res <- system2(MAKE, args = flags, stdout = TRUE, stderr = TRUE)
-    })
-    res_attrs <- attributes(res)
-    if ("status" %in% names(res_attrs) && res_attrs$status != 0) {
-        stop(paste0("Compilation failed with error code ", res_attrs$status, "\noutput:\n",
-            paste(res, collapse = "\n")))
-    }
+  suppressWarnings({
+    res <- system2(MAKE, args = flags, stdout = TRUE, stderr = TRUE)
+  })
+  res_attrs <- attributes(res)
+  if ("status" %in% names(res_attrs) && res_attrs$status != 0) {
+    stop(paste0(
+      "Compilation failed with error code ",
+      res_attrs$status,
+      "\noutput:\n",
+      paste(res, collapse = "\n")
+    ))
+  }
 
-    return(output)
+  return(output)
 }
 
 tbb_found <- function() {
-    suppressWarnings(out <- system2("where.exe", "tbb.dll", stdout = NULL, stderr = NULL))
-    return(out == 0)
+  suppressWarnings(
+    out <- system2("where.exe", "tbb.dll", stdout = NULL, stderr = NULL)
+  )
+  return(out == 0)
 }
 
 WINDOWS_PATH_SET <- FALSE
 
 windows_dll_path_setup <- function() {
-    if (.Platform$OS.type == "windows" && !WINDOWS_PATH_SET) {
-
-        if (tbb_found()) {
-            assign("WINDOWS_PATH_SET", TRUE, envir = .GlobalEnv)
-        } else {
-            tbb_path <- file.path(get_tinystan_path(), "stan", "lib", "stan_math",
-                "lib", "tbb")
-            Sys.setenv(PATH = paste(tbb_path, Sys.getenv("PATH"), sep = ";"))
-            assign("WINDOWS_PATH_SET", tbb_found(), envir = .GlobalEnv)
-        }
+  if (.Platform$OS.type == "windows" && !WINDOWS_PATH_SET) {
+    if (tbb_found()) {
+      assign("WINDOWS_PATH_SET", TRUE, envir = .GlobalEnv)
+    } else {
+      tbb_path <- file.path(
+        get_tinystan_path(),
+        "stan",
+        "lib",
+        "stan_math",
+        "lib",
+        "tbb"
+      )
+      Sys.setenv(PATH = paste(tbb_path, Sys.getenv("PATH"), sep = ";"))
+      assign("WINDOWS_PATH_SET", tbb_found(), envir = .GlobalEnv)
     }
+  }
 }