Support compilation inside R code

.github/workflows/main.yaml

@@ -216,12 +216,6 @@ jobs:
           path: ./test_models/
           key: ${{ hashFiles('**/*.stan', 'src/*', 'stan/src/stan/version.hpp', 'Makefile') }}-${{ matrix.os }}-v${{ env.CACHE_VERSION }}
 
-      # needed for R tests until they have compilation utilities and can set this themselves.
-      - name: Set up TBB
-        if: matrix.os == 'windows-latest'
-        run: |
-          Add-Content $env:GITHUB_PATH "$(pwd)/stan/lib/stan_math/lib/tbb"
-
       - name: Run tests
         if: matrix.os != 'windows-latest'
         run: |
@@ -231,6 +225,8 @@ jobs:
           Rscript -e "devtools::test(reporter = c(\"summary\", \"fail\"))"
           Rscript -e "install.packages(getwd(), repos=NULL, type=\"source\")"
           Rscript example.R
+        env:
+          BRIDGESTAN: ${{ github.workspace }}
 
       - name: Run tests (windows)
         if: matrix.os == 'windows-latest'
@@ -241,6 +237,8 @@ jobs:
           Rscript -e 'devtools::test(reporter = c(\"summary\", \"fail\"))'
           Rscript -e 'install.packages(getwd(), repos=NULL, type=\"source\")'
           Rscript example.R
+        env:
+          BRIDGESTAN: ${{ github.workspace }}
 
   rust:
     needs: [build]

R/NAMESPACE

@@ -1,3 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
 export(StanModel)
+export(compile_model)
+export(set_bridgestan_path)

R/R/bridgestan.R

@@ -15,6 +15,7 @@ StanModel <- R6::R6Class("StanModel",
     #' @return A new StanModel.
     initialize = function(lib, data, seed) {
       if (.Platform$OS.type == "windows"){
+        windows_path_setup()
         lib_old <- lib
         lib <- paste0(tools::file_path_sans_ext(lib), ".dll")
         file.copy(from=lib_old, to=lib)
@@ -75,7 +76,8 @@ StanModel <- R6::R6Class("StanModel",
         PACKAGE = private$lib_name
       )$info_out
     },
-
+    #' @description
+    #' Get the version of BridgeStan used in the compiled model.
     model_version= function() {
       .C("bs_version_R",
         major = as.integer(0),
@@ -345,7 +347,7 @@ handle_error <- function(lib_name, err_msg, err_ptr, function_name) {
 #' StanRNG
 #'
 #' RNG object for use with `StanModel$param_constrain()`
-#' @field rng The pointer to the RNG object.
+#' @field ptr The pointer to the RNG object.
 #' @keywords internal
 StanRNG <- R6::R6Class("StanRNG",
   public = list(

R/R/compile.R

@@ -0,0 +1,110 @@
+IS_WINDOWS <- isTRUE(.Platform$OS.type == "windows")
+MAKE <- Sys.getenv("MAKE", ifelse(IS_WINDOWS, "mingw32-make", "make"))
+
+
+#' Get the path to BridgeStan.
+#'
+#' By default this is set to the value of the environment
+#' variable `BRIDGESTAN`.
+#'
+#' If there is no path set, this function will download
+#' a matching version of BridgeStan to a folder called
+#' `.bridgestan` in the user's home directory.
+#'
+#' See also `set_bridgestan_path`
+verify_bridgestan_path <- function(path) {
+    suppressWarnings({
+        folder <- normalizePath(path)
+    })
+    if (!dir.exists(folder)) {
+        stop(paste0("BridgeStan folder '", folder, "' does not exist!\n", "If you need to set a different location, call 'set_bridgestan_path()'"))
+    }
+    makefile <- file.path(folder, "Makefile")
+    if (!file.exists(makefile)) {
+        stop(paste0("BridgeStan folder '", folder, "' does not contain file 'Makefile',",
+            " please ensure it is built properly!\n", "If you need to set a different location, call 'set_bridgestan_path()'"))
+    }
+}
+
+#' Set the path to BridgeStan.
+#'
+#' This should point to the top-level folder of the repository.
+#' @export
+set_bridgestan_path <- function(path) {
+    verify_bridgestan_path(path)
+    Sys.setenv(BRIDGESTAN = normalizePath(path))
+}
+
+get_bridgestan_path <- function() {
+    # try to get from environment
+    path <- Sys.getenv("BRIDGESTAN")
+    if (path == "") {
+        path <- CURRENT_BRIDGESTAN
+        tryCatch({
+            verify_bridgestan_path(path)
+        }, error = function(e) {
+            print(paste0("Bridgestan not found at location specified by $BRIDGESTAN ",
+                "environment variable, downloading version ", packageVersion("bridgestan"),
+                " to ", path))
+            get_bridgestan_src()
+        })
+    }
+
+    return(path)
+}
+
+
+#' Run BridgeStan's Makefile on a `.stan` file, creating the `.so`
+#' used by the StanModel class.
+#' This function assumes that the path to BridgeStan is valid.
+#' This can be set with `set_bridgestan_path`.
+#'
+#' @param stan_file A path to a Stan model file.
+#' @param stanc_arg A list of arguments to pass to stanc3.
+#' For example, `c('--O1')` will enable compiler optimization level 1.
+#' @param make_args A list of additional arguments to pass to Make.
+#' For example, `c('STAN_THREADS=True')` will enable
+#' threading for the compiled model. If the same flags are defined
+#' in `make/local`, the versions passed here will take precedent.
+#' @return Path to the compiled model.
+#' @export
+compile_model <- function(stan_file, stanc_args = NULL, make_args = NULL) {
+    verify_bridgestan_path(get_bridgestan_path())
+    suppressWarnings({
+        file_path <- normalizePath(stan_file)
+    })
+    if (tools::file_ext(file_path) != "stan") {
+        stop(paste0("File '", file_path, "' does not end with '.stan'"))
+    }
+    if (!file.exists(file_path)) {
+        stop(paste0("File '", file_path, "' does not exist!"))
+    }
+
+    output <- paste0(tools::file_path_sans_ext(file_path), "_model.so")
+    stancflags <- paste("--include-paths=.", paste(stanc_args, collapse = " "))
+
+    flags <- c(paste("-C", get_bridgestan_path()), make_args, paste0("STANCFLAGS=\"",
+        stancflags, "\""), output)
+
+    suppressWarnings({
+        res <- system2(MAKE, args = flags, stdout = TRUE, stderr = TRUE)
+    })
+    res_attrs <- attributes(res)
+    if ("status" %in% names(res_attrs) && res_attrs$status != 0) {
+        stop(paste0("Compilation failed with error code ", res_attrs$status, "\noutput:\n",
+            paste(res, collapse = "\n")))
+    }
+
+    return(output)
+}
+
+windows_path_setup <- function() {
+    if (.Platform$OS.type == "windows") {
+        suppressWarnings(out <- system2("where.exe", "tbb.dll", stdout = NULL, stderr = NULL))
+        if (out != 0) {
+            tbb_path <- file.path(get_bridgestan_path(), "stan", "lib", "stan_math",
+                "lib", "tbb")
+            Sys.setenv(PATH = paste(tbb_path, Sys.getenv("PATH"), sep = ";"))
+        }
+    }
+}

R/R/download.R

@@ -0,0 +1,35 @@
+current_version <- packageVersion("bridgestan")
+HOME_BRIDGESTAN <- path.expand(file.path("~", ".bridgestan"))
+CURRENT_BRIDGESTAN <- file.path(HOME_BRIDGESTAN, paste0("bridgestan-", current_version))
+
+RETRIES <- 5
+
+get_bridgestan_src <- function() {
+    url <- paste0("https://github.com/roualdes/bridgestan/releases/download/", "v",
+        current_version, "/bridgestan-", current_version, ".tar.gz")
+
+    dir.create(HOME_BRIDGESTAN, showWarnings = FALSE, recursive = TRUE)
+    temp <- tempfile()
+    err_text <- paste("Failed to download Bridgestan", current_version, "from github.com.")
+    for (i in 1:RETRIES) {
+        tryCatch({
+            download.file(url, destfile = temp, mode = "wb", quiet = TRUE, method = "auto")
+        }, error = function(e) {
+            cat(err_text, "\n")
+            if (i == RETRIES) {
+                stop(err_text, call. = FALSE)
+            } else {
+                cat("Retrying (", i + 1, "/", RETRIES, ")...\n", sep = "")
+                Sys.sleep(1)
+            }
+        })
+    }
+
+    tryCatch({
+        untar(temp, exdir = HOME_BRIDGESTAN)
+    }, error = function(e) {
+        stop(paste("Failed to unpack", url, "during installation"), call. = FALSE)
+    })
+
+    unlink(temp)
+}

R/tests/testthat.R

@@ -1,11 +1,3 @@
-# This file is part of the standard setup for testthat.
-# It is recommended that you do not modify it.
-#
-# Where should you do additional test configuration?
-# Learn more about the roles of various files in:
-# * https://r-pkgs.org/tests.html
-# * https://testthat.r-lib.org/reference/test_package.html#special-files
-
 library(testthat)
 library(bridgestan)
 

R/tests/testthat/setup.R

@@ -0,0 +1,15 @@
+base = "../../.."
+
+load_model <- function(name, include_data = TRUE) {
+    if (include_data) {
+        data = file.path(base, "test_models", name, paste0(name, ".data.json"))
+    } else {
+        data = ""
+    }
+    model <- StanModel$new(file.path(base, "test_models", name, paste0(name, "_model.so")),
+        data, 1234)
+    return(model)
+}
+
+simple <- load_model("simple")
+bernoulli <- load_model("bernoulli")

R/tests/testthat/test_collisions.R

@@ -0,0 +1,13 @@
+
+test_that("loading another library didn't break prior ones", {
+    if (.Platform$OS.type == "windows") {
+        dll = "./test_collisions.dll"
+    } else {
+        dll = "./test_collisions.so"
+    }
+    if (file.exists(dll)) {
+        dyn.load(dll)
+        expect_equal(bernoulli$name(), "bernoulli_model")
+        expect_equal(simple$name(), "simple_model")
+    }
+})

R/tests/testthat/test_compile.R

@@ -0,0 +1,37 @@
+
+
+test_that("compilation works", {
+    name <- "multi"
+    file <- file.path(base, "test_models", name, paste0(name, ".stan"))
+
+    lib <- file.path(base, "test_models", name, paste0(name, "_model.so"))
+    unlink(lib, force = TRUE)
+
+    out <- compile_model(file, stanc_args = c("--O1"))
+
+    expect_true(file.exists(lib))
+    expect_equal(normalizePath(lib), normalizePath(out))
+
+    unlink(lib, force = TRUE)
+
+    out <- compile_model(file, make_args = c("STAN_THREADS=True"))
+})
+
+test_that("compilation fails on non-stan file", {
+    expect_error(compile_model(file.path(base, "test_models", "simple", "simple.data.json")),
+        "does not end with '.stan'")
+})
+
+test_that("compilation fails on missing file", {
+    expect_error(compile_model("badpath.stan"), "does not exist!")
+})
+
+test_that("compilation fails on bad syntax", {
+    expect_error(compile_model(file.path(base, "test_models", "syntax_error", "syntax_error.stan")),
+        "Compilation failed")
+})
+
+test_that("bad paths fail", {
+    expect_error(set_bridgestan_path("badpath"), "does not exist!")
+    expect_error(set_bridgestan_path(file.path(base, "test_models")), "does not contain file 'Makefile'")
+})