Merge branch 'master' into pr/839

stan-dev · Sep 13, 2023 · 7daf92b · 7daf92b
2 parents f0812a1 + b29374e
commit 7daf92b
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diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.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:

diff --git a/.github/workflows/R-CMD-check.yaml b/.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'

diff --git a/.github/workflows/Test-coverage.yaml b/.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:

diff --git a/.github/workflows/cmdstan-tarball-check.yaml b/.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: |

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: cmdstanr
 Title: R Interface to 'CmdStan'
-Version: 0.6.0.9000
-Date: 2023-07-25
+Version: 0.6.1.9000
+Date: 2023-08-25
 Authors@R:
     c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),
            email = "[email protected]"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,19 @@
-# cmdstanr 0.6.0.9000
+# cmdstanr 0.6.1.9000
+
+# cmdstanr 0.6.1
+
+* Store return codes instead of always querying exit status by @jgabry in #798
+* enable jacobian argument for optimization by @jgabry in #799
+* Fix init_model_methods for models with no data by @andrjohns in #801
+* Document a CmdStan-focused way to pre-compile Stan models in R packages by @wlandau in #809
+* Describe how to efficiently save model fit objects by @wlandau in #816
+* fix errors in doc for new methods by @jgabry in #823
+* Give informative error when exposing stan functions with precompiled model by @andrjohns in #831
+* Bugfixes in .stanfunctions, hessian model method, and exposing RNG functions by @andrjohns in #811
+* Fix variable_skeleton() with containers by @andrjohns in #832
+* Improve handling of user header by @martinmodrak in #818
+* change duplicate stdout_file to stderr_file by @jgabry in #834
 
-Items for next release
 
 # cmdstanr 0.6.0
 

diff --git a/R/example.R b/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;

diff --git a/R/fit.R b/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));
 #'     }

diff --git a/R/model.R b/R/model.R
@@ -190,6 +190,12 @@ cmdstan_model <- function(stan_file = NULL, exe_file = NULL, compile = TRUE, ...
 #'  [`$save_hpp_file()`][model-method-compile] |  Save the `.hpp` file containing the generated C++ code. |
 #'  [`$expose_functions()`][model-method-expose_functions] |  Expose Stan functions for use in R. |
 #'
+#'  ## Diagnostics
+#'
+#'  |**Method**|**Description**|
+#'  |:----------|:---------------|
+#'  [`$diagnose()`][model-method-diagnose] |  Run CmdStan's `"diagnose"` method to test gradients, return [`CmdStanDiagnose`] object. |
+#'
 #'  ## Model fitting
 #'
 #'  |**Method**|**Description**|
@@ -800,7 +806,7 @@ CmdStanModel$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
@@ -926,7 +932,7 @@ CmdStanModel$set("public", name = "check_syntax", value = check_syntax)
 #' file <- write_stan_file("
 #' data {
 #'   int N;
-#'   int y[N];
+#'   array[N] int y;
 #' }
 #' parameters {
 #'   real                     lambda;
@@ -1653,7 +1659,7 @@ CmdStanModel$set("public", name = "variational", value = variational)
 #' 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;
@@ -1672,13 +1678,13 @@ CmdStanModel$set("public", name = "variational", value = variational)
 #' 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));
 #'   }"
 #' )
 #'

diff --git a/R/run.R b/R/run.R
@@ -560,8 +560,8 @@ CmdStanRun$set("private", name = "run_variational_", value = .run_other)
     if (file.exists(stdout_file)) {
       cat(readLines(stdout_file), sep = "\n")
     }
-    if (file.exists(stdout_file)) {
-      cat(readLines(stdout_file), sep = "\n")
+    if (file.exists(stderr_file)) {
+      cat(readLines(stderr_file), sep = "\n")
     }
     stop(
       "Diagnose failed with the status code ", ret$status, "!\n",

diff --git a/R/utils.R b/R/utils.R
@@ -821,7 +821,20 @@ 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)
 }
 
@@ -869,7 +882,9 @@ 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)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -72,7 +72,6 @@ articles:
       - cmdstanr-internals
       - posterior
       - r-markdown
-      - deprecations
       - profiling
       - articles-online-only/opencl
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html