Merge branch 'master' into feature/pathfinder

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

@@ -35,7 +35,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/[email protected]
         with:

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

@@ -48,7 +48,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install system dependencies
         if: runner.os == 'Linux'

.github/workflows/Test-coverage.yaml

@@ -32,7 +32,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
           workflow: Test-coverage.yml
         if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/[email protected]
       - uses: r-lib/actions/[email protected]
@@ -83,7 +83,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       NOT_CRAN: true
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/[email protected]
         with:

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

@@ -32,7 +32,7 @@ jobs:
       NOT_CRAN: true
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |

R/example.R

@@ -124,7 +124,7 @@ print_example_program <-
 #' stan_program <- "
 #' data {
 #'   int<lower=0> N;
-#'   int<lower=0,upper=1> y[N];
+#'   array[N] int<lower=0,upper=1> y;
 #' }
 #' parameters {
 #'   real<lower=0,upper=1> theta;

R/fit.R

@@ -1158,7 +1158,7 @@ CmdStanFit$set("public", name = "return_codes", value = return_codes)
 #' mcmc_program <- write_stan_file(
 #'   'data {
 #'     int<lower=0> N;
-#'     int<lower=0,upper=1> y[N];
+#'     array[N] int<lower=0,upper=1> y;
 #'   }
 #'   parameters {
 #'     real<lower=0,upper=1> theta;
@@ -1169,7 +1169,7 @@ CmdStanFit$set("public", name = "return_codes", value = return_codes)
 #'     }
 #'   }
 #'   generated quantities {
-#'     int y_rep[N];
+#'     array[N] int y_rep;
 #'     profile("gq") {
 #'       y_rep = bernoulli_rng(rep_vector(theta, N));
 #'     }

R/model.R

@@ -807,7 +807,7 @@ CmdStanModel$set("public", name = "variables", value = variables)
 #' file <- write_stan_file("
 #' data {
 #'   int N;
-#'   int y[N];
+#'   array[N] int y;
 #' }
 #' parameters {
 #'   // should have <lower=0> but omitting to demonstrate pedantic mode
@@ -933,7 +933,7 @@ CmdStanModel$set("public", name = "check_syntax", value = check_syntax)
 #' file <- write_stan_file("
 #' data {
 #'   int N;
-#'   int y[N];
+#'   array[N] int y;
 #' }
 #' parameters {
 #'   real                     lambda;
@@ -1781,7 +1781,7 @@ CmdStanModel$set("public", name = "pathfinder", value = pathfinder)
 #' mcmc_program <- write_stan_file(
 #'   "data {
 #'     int<lower=0> N;
-#'     int<lower=0,upper=1> y[N];
+#'     array[N] int<lower=0,upper=1> y;
 #'   }
 #'   parameters {
 #'     real<lower=0,upper=1> theta;
@@ -1800,13 +1800,13 @@ CmdStanModel$set("public", name = "pathfinder", value = pathfinder)
 #' gq_program <- write_stan_file(
 #'   "data {
 #'     int<lower=0> N;
-#'     int<lower=0,upper=1> y[N];
+#'     array[N] int<lower=0,upper=1> y;
 #'   }
 #'   parameters {
 #'     real<lower=0,upper=1> theta;
 #'   }
 #'   generated quantities {
-#'     int y_rep[N] = bernoulli_rng(rep_vector(theta, N));
+#'     array[N] int y_rep = bernoulli_rng(rep_vector(theta, N));
 #'   }"
 #' )
 #'

R/utils.R

@@ -816,7 +816,20 @@ get_standalone_hpp <- function(stan_file, stancflags) {
 
 get_function_name <- function(fun_start, fun_end, model_lines) {
   fun_string <- paste(model_lines[(fun_start+1):fun_end], collapse = " ")
-  fun_name <- gsub("auto ", "", fun_string, fixed = TRUE)
+  types <- c(
+    "auto",
+    "int",
+    "double",
+    "Eigen::Matrix<(.*)>",
+    "std::vector<(.*)>"
+  )
+  pattern <- paste0(
+    # Only match if the type occurs at start of string
+    "^(\\s*)?(",
+    paste0(types, collapse="|"),
+    # Only match if type followed by a function name and opening bracket
+    ")\\s*(?=\\w*\\()")
+  fun_name <- gsub(pattern, "", fun_string, perl = TRUE)
   sub("\\(.*", "", fun_name, perl = TRUE)
 }
 
@@ -864,7 +877,9 @@ get_plain_rtn <- function(fun_start, fun_end, model_lines) {
 #     that instantiates an RNG
 prep_fun_cpp <- function(fun_start, fun_end, model_lines) {
   fun_body <- paste(model_lines[fun_start:fun_end], collapse = " ")
-  fun_body <- gsub("auto", get_plain_rtn(fun_start, fun_end, model_lines), fun_body)
+  if (cmdstan_version() < "2.33") {
+    fun_body <- gsub("auto", get_plain_rtn(fun_start, fun_end, model_lines), fun_body)
+  }
   fun_body <- gsub("// [[stan::function]]", "// [[Rcpp::export]]\n", fun_body, fixed = TRUE)
   fun_body <- gsub("std::ostream\\*\\s*pstream__\\s*=\\s*nullptr", "", fun_body)
   fun_body <- gsub("boost::ecuyer1988&\\s*base_rng__", "SEXP base_rng_ptr", fun_body)

_pkgdown.yml

@@ -72,7 +72,6 @@ articles:
       - cmdstanr-internals
       - posterior
       - r-markdown
-      - deprecations
       - profiling
       - articles-online-only/opencl
 

tests/testthat/test-data.R

@@ -339,7 +339,7 @@ test_that("process_data() corrrectly casts integers and floating point numbers",
 
   stan_file <- write_stan_file("
   data {
-    int<lower=0> k[3,3];
+    array[3,3] int<lower=0> k;
   }
   ")
   mod <- cmdstan_model(stan_file, compile = FALSE)

tests/testthat/test-example.R

@@ -23,7 +23,7 @@ test_that("cmdstanr_example works", {
 stan_program <- "
   data {
     int<lower=0> N;
-    int<lower=0,upper=1> y[N];
+    array[N] int<lower=0,upper=1> y;
   }
   parameters {
     real<lower=0,upper=1> theta;

tests/testthat/test-fit-mle.R

@@ -53,7 +53,7 @@ test_that("time is reported after optimization", {
 
 test_that("no error when checking estimates after failure", {
   fit <- cmdstanr_example("schools", method = "optimize", seed = 123) # optim ålways fails for this
-  expect_silent(fit$summary()) # no error
+  expect_error(fit$summary(), "Fitting failed. Unable to retrieve the draws.")
 })
 
 test_that("draws() works for different formats", {

tests/testthat/test-fit-shared.R

@@ -308,7 +308,7 @@ test_that("sig_figs works with all methods", {
   m <- "data {
     int<lower=0> N;
     int<lower=0> K;
-    int<lower=0,upper=1> y[N];
+    array[N] int<lower=0,upper=1> y;
     matrix[N, K] X;
   }
   parameters {

tests/testthat/test-model-compile.R

@@ -278,7 +278,7 @@ test_that("compile() works with pedantic=TRUE", {
   }
   ")
   expect_message(
-    mod_pedantic_warn <- cmdstan_model(stan_file, pedantic = TRUE),
+    mod_pedantic_warn <- cmdstan_model(stan_file, pedantic = TRUE, force_recompile = TRUE),
     "The parameter x was declared but was not used",
     fixed = TRUE
   )
@@ -387,13 +387,10 @@ test_that("check_syntax() works with pedantic=TRUE", {
     fixed = TRUE
   )
 
-  expect_output(
-    expect_message(
-      mod_pedantic_warn$check_syntax(pedantic = TRUE),
-      "The parameter x was declared but was not used",
-      fixed = TRUE
-    ),
-    regexp = NA
+  expect_message(
+    mod_pedantic_warn$check_syntax(pedantic = TRUE),
+    "The parameter x was declared but was not used",
+    fixed = TRUE
   )
 })
 
@@ -424,14 +421,14 @@ test_that("check_syntax() works with pedantic=TRUE", {
   "
   stan_file <- write_stan_file(model_code)
   mod_dep_warning <- cmdstan_model(stan_file, compile = FALSE)
-  expect_message(
+  expect_error(
     mod_dep_warning$compile(),
-    "deprecated in the Stan language",
+    "An error occured during compilation! See the message above for more information.",
     fixed = TRUE
   )
-  expect_message(
+  expect_error(
     mod_dep_warning$check_syntax(),
-    "deprecated in the Stan language",
+    "Syntax error found! See the message above for more information.",
     fixed = TRUE
   )
 })
@@ -690,13 +687,9 @@ test_that("format() works", {
   stan_file_tmp <- write_stan_file(code)
   mod_1 <- cmdstan_model(stan_file_tmp, compile = FALSE)
 
-  expect_output(
-    expect_message(
-      mod_1$format(),
-      "is deprecated",
-      fixed = TRUE
-    ),
-    "target += normal_log(y, 0, 1);",
+  expect_error(
+    mod_1$format(),
+    "Syntax error found! See the message above for more information.",
     fixed = TRUE
   )
 
@@ -710,13 +703,9 @@ test_that("format() works", {
     "target += normal_lpdf(y | 0, 1);",
     fixed = TRUE
   )
-  expect_output(
-    expect_message(
-      mod_1$format(canonicalize = list("includes")),
-      "is deprecated",
-      fixed = TRUE
-    ),
-    "target += normal_log(y, 0, 1);",
+  expect_error(
+    mod_1$format(),
+    "Syntax error found! See the message above for more information.",
     fixed = TRUE
   )
 

tests/testthat/test-model-expose-functions.R

@@ -192,7 +192,8 @@ test_that("Exposing functions with precompiled model gives meaningful error", {
     parameters { real x; }
     model { x ~ std_normal(); }
   ")
-  mod1 <- cmdstan_model(stan_file, compile_standalone = TRUE)
+  mod1 <- cmdstan_model(stan_file, compile_standalone = TRUE,
+                        force_recompile = TRUE)
   expect_equal(7.5, mod1$functions$a_plus_b(5, 2.5))
 
   mod2 <- cmdstan_model(stan_file)

tests/testthat/test-model-sample_mpi.R

@@ -4,15 +4,15 @@ test_that("sample_mpi() works", {
   skip_if(!mpi_toolchain_present())
   mpi_file <- write_stan_file("
   functions {
-    vector test(vector beta, vector theta, real[] x, int[] y) {
+    vector test(vector beta, vector theta, array[] real x, array[] int y) {
       return theta;
     }
   }
   transformed data {
     vector[4] a;
-    vector[5] b[4] = {[1,1,1,1,1]', [2,2,2,2,2]', [3,3,3,3,3]', [4,4,4,4,4]'};
-    real x[4,4];
-    int y[4,4];
+    array[4] vector[5] b = {[1,1,1,1,1]', [2,2,2,2,2]', [3,3,3,3,3]', [4,4,4,4,4]'};
+    array[4,4] real x;
+    array[4,4] int y;
   }
   parameters {
     real beta;