Merge pull request #19 from pachadotdev/roxygen

Roxygen

Author: pachadotdev

R/register.R

@@ -77,17 +77,16 @@ cpp_register <- function(path = ".", quiet = !is_interactive(), extension = c(".
     cli::cli_alert_success("generated file {.file {basename(r_path)}}")
   }
 
-
   call_entries <- get_call_entries(path, funs$name, package)
 
   cpp_function_registration <- glue::glue_data(funs, '    {{
     "_cpp11_{name}", (DL_FUNC) &_{package}_{name}, {n_args}}}, ',
     n_args = viapply(funs$args, nrow)
   )
 
-  cpp_function_registration <- glue::glue_collapse(cpp_function_registration, sep  = "\n")
+  cpp_function_registration <- glue::glue_collapse(cpp_function_registration, sep = "\n")
 
-  extra_includes <-  character()
+  extra_includes <- character()
   if (pkg_links_to_rcpp(path)) {
     extra_includes <- c(extra_includes, "#include <cpp11/R.hpp>", "#include <Rcpp.h>", "using namespace Rcpp;")
   }
@@ -215,35 +214,75 @@ generate_init_functions <- function(funs) {
 }
 
 generate_r_functions <- function(funs, package = "cpp11", use_package = FALSE) {
-  funs <- funs[c("name", "return_type", "args")]
+  funs <- funs[c("name", "return_type", "args", "file", "line", "decoration")]
 
   if (use_package) {
     package_call <- glue::glue(', PACKAGE = "{package}"')
     package_names <- glue::glue_data(funs, '"_{package}_{name}"')
   } else {
-    package_names <- glue::glue_data(funs, '`_{package}_{name}`')
+    package_names <- glue::glue_data(funs, "`_{package}_{name}`")
     package_call <- ""
   }
 
-  funs$package <- package
   funs$package_call <- package_call
   funs$list_params <- vcapply(funs$args, glue_collapse_data, "{name}")
   funs$params <- vcapply(funs$list_params, function(x) if (nzchar(x)) paste0(", ", x) else x)
   is_void <- funs$return_type == "void"
   funs$calls <- ifelse(is_void,
-    glue::glue_data(funs, 'invisible(.Call({package_names}{params}{package_call}))'),
-    glue::glue_data(funs, '.Call({package_names}{params}{package_call})')
+    glue::glue_data(funs, "invisible(.Call({package_names}{params}{package_call}))"),
+    glue::glue_data(funs, ".Call({package_names}{params}{package_call})")
   )
 
-  out <- glue::glue_data(funs, '
-    {name} <- function({list_params}) {{
-      {calls}
-    }}
-    ')
+  # Parse and associate Roxygen comments
+  funs$roxygen_comment <- mapply(function(file, line) {
+    if (file.exists(file)) {
+      comments <- extract_roxygen_comments(file)
+      matched_comment <- ""
+      for (comment in comments) {
+        # Check if the comment directly precedes the function without gaps
+        if (line == comment$line + 1) {
+          matched_comment <- comment$text
+          break
+        }
+      }
+      matched_comment
+    } else {
+      ""
+    }
+  }, funs$file, funs$line, SIMPLIFY = TRUE)
+
+  # Generate R functions with or without Roxygen comments
+  out <- mapply(function(name, list_params, calls, roxygen_comment) {
+    if (nzchar(roxygen_comment)) {
+      glue::glue("{roxygen_comment}\n{name} <- function({list_params}) {{\n\t{calls}\n}}")
+    } else {
+      glue::glue("{name} <- function({list_params}) {{\n  {calls}\n}}")
+    }
+  }, funs$name, funs$list_params, funs$calls, funs$roxygen_comment, SIMPLIFY = TRUE)
+
+  out <- glue::trim(out)
   out <- glue::glue_collapse(out, sep = "\n\n")
   unclass(out)
 }
 
+extract_roxygen_comments <- function(file) {
+  lines <- readLines(file)
+  roxygen_start <- grep("^/\\* roxygen start", lines)
+  roxygen_end <- grep("roxygen end \\*/$", lines)
+
+  if (length(roxygen_start) == 0 || length(roxygen_end) == 0) {
+    return(list())
+  }
+
+  roxygen_comments <- mapply(function(start, end) {
+    roxygen_lines <- lines[(start + 1):(end - 1)]
+    roxygen_lines <- sub("^", "#' ", roxygen_lines)
+    list(line = end, text = paste(roxygen_lines, collapse = "\n"))
+  }, roxygen_start, roxygen_end, SIMPLIFY = FALSE)
+
+  roxygen_comments
+}
+
 wrap_call <- function(name, return_type, args) {
   call <- glue::glue('{name}({list_params})', list_params = glue_collapse_data(args, "cpp11::as_cpp<cpp11::decay_t<{type}>>({name})"))
   if (return_type == "void") {

R/source.R

@@ -18,6 +18,13 @@
 #'   uses 'CXX11' if unset.
 #' @param dir The directory to store the generated source files. `tempfile()` is
 #'   used by default. The directory will be removed if `clean` is `TRUE`.
+#' @param local Passed to [dyn.load()]. If `TRUE` (the default) the shared
+#'   library is loaded with local symbols; if `FALSE` symbols are made global
+#'   (equivalent to `dyn.load(..., local = FALSE)`), which can be required when
+#'   other shared objects need to see RTTI/vtable symbols from this library.
+#' @note See the unit test that demonstrates this usage at
+#' \code{tests/testthat/test-source-local.R} (shows how `local = FALSE` exports
+#' the necessary symbols so separate shared objects can link against them).
 #' @return For [cpp_source()] and `[cpp_function()]` the results of
 #'   [dyn.load()] (invisibly). For `[cpp_eval()]` the results of the evaluated
 #'   expression.
@@ -65,7 +72,7 @@
 #' }
 #'
 #' @export
-cpp_source <- function(file, code = NULL, env = parent.frame(), clean = TRUE, quiet = TRUE, cxx_std = Sys.getenv("CXX_STD", "CXX11"), dir = tempfile()) {
+cpp_source <- function(file, code = NULL, env = parent.frame(), clean = TRUE, quiet = TRUE, cxx_std = Sys.getenv("CXX_STD", "CXX11"), dir = tempfile(), local = TRUE) {
   stop_unless_installed(c("brio", "callr", "cli", "decor", "desc", "glue", "tibble", "vctrs"))
   if (!missing(file) && !file.exists(file)) {
     stop("Can't find `file` at this path:\n", file, "\n", call. = FALSE)
@@ -145,7 +152,7 @@ cpp_source <- function(file, code = NULL, env = parent.frame(), clean = TRUE, qu
   brio::write_lines(r_functions, r_path)
   source(r_path, local = env)
 
-  dyn.load(shared_lib, local = TRUE, now = TRUE)
+  dyn.load(shared_lib, local = local, now = TRUE)
 }
 
 the <- new.env(parent = emptyenv())
@@ -183,7 +190,7 @@ generate_makevars <- function(includes, cxx_std) {
 
 #' @rdname cpp_source
 #' @export
-cpp_function <- function(code, env = parent.frame(), clean = TRUE, quiet = TRUE, cxx_std = Sys.getenv("CXX_STD", "CXX11")) {
+cpp_function <- function(code, env = parent.frame(), clean = TRUE, quiet = TRUE, cxx_std = Sys.getenv("CXX_STD", "CXX11"), local = TRUE) {
   cpp_source(code = paste(c('#include "cpp11.hpp"',
         "using namespace ::cpp11;",
         "namespace writable = ::cpp11::writable;",
@@ -193,15 +200,16 @@ cpp_function <- function(code, env = parent.frame(), clean = TRUE, quiet = TRUE,
     env = env,
     clean = clean,
     quiet = quiet,
-    cxx_std = cxx_std
+    cxx_std = cxx_std,
+    local = local
   )
 }
 
 utils::globalVariables("f")
 
 #' @rdname cpp_source
 #' @export
-cpp_eval <- function(code, env = parent.frame(), clean = TRUE, quiet = TRUE, cxx_std = Sys.getenv("CXX_STD", "CXX11")) {
+cpp_eval <- function(code, env = parent.frame(), clean = TRUE, quiet = TRUE, cxx_std = Sys.getenv("CXX_STD", "CXX11"), local = TRUE) {
   cpp_source(code = paste(c('#include "cpp11.hpp"',
         "using namespace ::cpp11;",
         "namespace writable = ::cpp11::writable;",
@@ -214,7 +222,8 @@ cpp_eval <- function(code, env = parent.frame(), clean = TRUE, quiet = TRUE, cxx
     env = env,
     clean = clean,
     quiet = quiet,
-    cxx_std = cxx_std
+    cxx_std = cxx_std,
+    local = local
   )
   f()
 }

README.md

@@ -78,3 +78,13 @@ Please note that the cpp11 project is released with a [Contributor Code of Condu
 
 cpp11 would not exist without Rcpp.
 Thanks to the Rcpp authors, Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates and John Chambers for their work writing and maintaining Rcpp.
+
+## Clang format
+
+To match GHA, use clang-format-12 to format C++ code. With systems that provide clang-format-14 or newer, you can use Docker:
+
+```bash
+docker run --rm -v "$PWD":/work -w /work ubuntu:22.04 bash -lc "\
+  apt-get update && apt-get install -y clang-format-12 && \
+  find . -name '*.cpp' -o -name '*.hpp' -o -name '*.h' | xargs -r clang-format-12 -i"
+```

cpp11test/DESCRIPTION

@@ -20,4 +20,4 @@ Suggests:
     xml2
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2

cpp11test/NAMESPACE

@@ -1,5 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+export(roxcpp2_)
+export(roxcpp3_)
+export(roxcpp4_)
+export(roxcpp5_)
+export(roxcpp7_)
 export(run_tests)
 exportPattern("_$")
 importFrom(Rcpp,sourceCpp)

cpp11test/R/cpp11.R

@@ -156,6 +156,63 @@ rcpp_release_ <- function(n) {
   invisible(.Call(`_cpp11test_rcpp_release_`, n))
 }
 
+notroxcpp1_ <- function(x) {
+  .Call(`_cpp11test_notroxcpp1_`, x)
+}
+
+#' @title Roxygenise C++ function II
+#' @param x numeric value
+#' @description Dummy function to test roxygen2. It adds 2.0 to a double.
+#' @export
+#' @examples roxcpp2_(1.0)
+roxcpp2_ <- function(x) {
+	.Call(`_cpp11test_roxcpp2_`, x)
+}
+
+#' @title Roxygenise C++ function III
+#' @param x numeric value
+#' @description Dummy function to test roxygen2. It adds 3.0 to a double.
+#' @export
+#' @examples roxcpp3_(1.0)
+roxcpp3_ <- function(x) {
+	.Call(`_cpp11test_roxcpp3_`, x)
+}
+
+#' @title Roxygenise C++ function IV
+#' @param x numeric value
+#' @description Dummy function to test roxygen2. It adds 4.0 to a double.
+#' @export
+#' @examples roxcpp4_(1.0)
+roxcpp4_ <- function(x) {
+	.Call(`_cpp11test_roxcpp4_`, x)
+}
+
+#' @title Roxygenise C++ function V
+#' @param x numeric value
+#' @description Dummy function to test roxygen2. It adds 5.0 to a double.
+#' @export
+#' @examples roxcpp5_(1.0)
+roxcpp5_ <- function(x) {
+	.Call(`_cpp11test_roxcpp5_`, x)
+}
+
+notroxcpp6_ <- function(x) {
+  .Call(`_cpp11test_notroxcpp6_`, x)
+}
+
+#' @title Roxygenise C++ function VII
+#' @param x numeric value
+#' @description Dummy function to test roxygen2. It adds 7.0 to a double.
+#' @export
+#' @examples
+#' my_fun <- function(x) {
+#'   roxcpp7_(x)
+#' }
+#' @seealso \code{\link{roxcpp1_}}
+roxcpp7_ <- function(x) {
+	.Call(`_cpp11test_roxcpp7_`, x)
+}
+
 cpp11_safe_ <- function(x_sxp) {
   .Call(`_cpp11test_cpp11_safe_`, x_sxp)
 }
@@ -168,6 +225,26 @@ string_push_back_ <- function() {
   .Call(`_cpp11test_string_push_back_`)
 }
 
+grow_strings_cpp11_ <- function(n, seed) {
+  .Call(`_cpp11test_grow_strings_cpp11_`, n, seed)
+}
+
+grow_strings_rcpp_ <- function(n, seed) {
+  .Call(`_cpp11test_grow_strings_rcpp_`, n, seed)
+}
+
+grow_strings_manual_ <- function(n, seed) {
+  .Call(`_cpp11test_grow_strings_manual_`, n, seed)
+}
+
+assign_cpp11_ <- function(n, seed) {
+  .Call(`_cpp11test_assign_cpp11_`, n, seed)
+}
+
+assign_rcpp_ <- function(n, seed) {
+  .Call(`_cpp11test_assign_rcpp_`, n, seed)
+}
+
 sum_dbl_for_ <- function(x) {
   .Call(`_cpp11test_sum_dbl_for_`, x)
 }
@@ -236,6 +313,14 @@ rcpp_push_and_truncate_ <- function(size_sxp) {
   .Call(`_cpp11test_rcpp_push_and_truncate_`, size_sxp)
 }
 
+nullable_extptr_1 <- function() {
+  .Call(`_cpp11test_nullable_extptr_1`)
+}
+
+nullable_extptr_2 <- function() {
+  .Call(`_cpp11test_nullable_extptr_2`)
+}
+
 test_destruction_inner <- function() {
   invisible(.Call(`_cpp11test_test_destruction_inner`))
 }

cpp11test/bench/strings.R

@@ -0,0 +1,35 @@
+pkgload::load_all("cpp11test")
+
+bench::press(len = as.integer(10^(0:6)), {
+  bench::mark(
+    assign_cpp11_(n = len, 123L),
+    assign_rcpp_(n = len, 123L),
+    iterations = 20
+  )
+})[c("expression", "len", "min", "mem_alloc", "n_itr", "n_gc")]
+
+# Longer benchmark, lots of gc
+len <- as.integer(10^7)
+bench::mark(
+  cpp11 = cpp11_push_and_truncate_(len),
+  rcpp = rcpp_push_and_truncate_(len),
+  min_iterations = 200
+)[c("expression", "min", "mem_alloc", "n_itr", "n_gc")]
+
+bench::press(len = as.integer(10^(0:6)), {
+  bench::mark(
+    grow_strings_cpp11_(len, 123L),
+    grow_strings_rcpp_(len, 123L),
+    grow_strings_manual_(len, 123L),
+    iterations = 20
+  )
+})[c("expression", "len", "min", "mem_alloc", "n_itr", "n_gc")]
+
+# Longer benchmark, lots of gc
+len <- as.integer(10^7)
+bench::mark(
+  cpp11 = cpp11_grow_strings_(len),
+  rcpp = rcpp_grow_strings_(len),
+  manual = manual_grow_strings_(len),
+  min_iterations = 200
+)[c("expression", "min", "mem_alloc", "n_itr", "n_gc")]