Final check

Author: andrjohns

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

@@ -13,11 +13,11 @@ name: Unit tests - WSL Backend
       - master
 
 jobs:
-  R-CMD-check:
+  WSL-R-CMD-check:
     if: "! contains(github.event.head_commit.message, '[ci skip]')"
     runs-on: windows-latest
 
-    name: WSL1 Backend
+    name: windows-latest-WSLv1
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -65,7 +65,7 @@ jobs:
             set-as-default: 'true'
       - name: Install WSL Dependencies
         run: |
-          # Bugfix for current gzip under WSLv1:
+          # Bugfix for current gzip (for unpacking apt packages) under WSLv1:
           # https://github.com/microsoft/WSL/issues/8219#issuecomment-1110508016
           echo -en '\x10' | sudo dd of=/usr/bin/gzip count=1 bs=1 conv=notrunc seek=$((0x189))
           sudo apt-get update

.github/workflows/Test-coverage.yaml

@@ -7,7 +7,7 @@ name: Test coverage
 'on':
   push:
     branches:
-      - wsl-support
+      - master
   pull_request:
     branches:
       - master

.github/workflows/mpi.yaml

@@ -734,12 +734,14 @@ read_csv_metadata <- function(csv_file) {
   if (length(gradients) > 0) {
     csv_file_info$gradients <- gradients
   }
+
+  # Revert any WSL-updated paths before returning the metadata
   if (os_is_wsl()) {
     csv_file_info$init <- wsl_safe_path(csv_file_info$init, revert = TRUE)
     csv_file_info$profile_file <- wsl_safe_path(csv_file_info$profile_file,
-                                                  revert = TRUE)
+                                                revert = TRUE)
     csv_file_info$fitted_params <- wsl_safe_path(csv_file_info$fitted_params,
-                                                    revert = TRUE)
+                                                  revert = TRUE)
   }
   csv_file_info
 }

R/csv.R

@@ -213,7 +213,6 @@ install_cmdstan <- function(dir = NULL,
       "\nrebuild_cmdstan(cores = ...)"
     )
   }
-
   if (isTRUE(wsl)) {
     Sys.unsetenv("CMDSTANR_USE_WSL")
   }

R/install.R

@@ -1760,8 +1760,7 @@ include_paths_stanc3_args <- function(include_paths = NULL) {
   stancflags <- NULL
   if (!is.null(include_paths)) {
     checkmate::assert_directory_exists(include_paths, access = "r")
-    include_paths <- absolute_path(include_paths)
-    include_paths <- sapply(include_paths, wsl_safe_path)
+    include_paths <- sapply(absolute_path(include_paths), wsl_safe_path)
     paths_w_space <- grep(" ", include_paths)
     include_paths[paths_w_space] <- paste0("'", include_paths[paths_w_space], "'")
     include_paths <- paste0(include_paths, collapse = ",")
@@ -1782,11 +1781,12 @@ model_variables <- function(stan_file, include_paths = NULL, allow_undefined = F
     allow_undefined_arg <- NULL
   }
   out_file <- tempfile(fileext = ".json")
-  stan_file <- stan_file
   run_log <- wsl_compatible_run(
     command = stanc_cmd(),
-    args = c(wsl_safe_path(stan_file), "--info", include_paths_stanc3_args(include_paths),
-                allow_undefined_arg),
+    args = c(wsl_safe_path(stan_file),
+              "--info",
+              include_paths_stanc3_args(include_paths),
+              allow_undefined_arg),
     wd = cmdstan_path(),
     echo = FALSE,
     echo_cmd = FALSE,

R/model.R

@@ -121,6 +121,11 @@ cmdstan_default_install_path <- function(old = FALSE) {
 #' Returns the path to the installation of CmdStan with the most recent release
 #' version.
 #'
+#' For Windows systems with WSL CmdStan installs, if there are side-by-side WSL
+#' and native installs with the same version then the WSL is preferred.
+#' Otherwise, the most recent release is chosen, regardless of whether it is
+#' native or WSL.
+#'
 #' @export
 #' @keywords internal
 #' @param old See [cmdstan_default_install_path()].

R/path.R

@@ -169,7 +169,7 @@ wsl_safe_path <- function(path = NULL, revert = FALSE) {
   } else {
     path_already_safe <- grepl("^/mnt/", path)
     if (os_is_wsl() && !isTRUE(path_already_safe) && !is.na(path)) {
-      abs_path <- repair_path(path)
+      abs_path <- repair_path(utils::shortPathName(path))
       drive_letter <- tolower(strtrim(abs_path, 1))
       path <- gsub(paste0(drive_letter, ":"),
                   paste0("/mnt/", drive_letter),
@@ -180,15 +180,15 @@ wsl_safe_path <- function(path = NULL, revert = FALSE) {
   path
 }
 
+# Running commands through WSL requires using 'wsl' as the command with the
+# intended command (e.g., stanc) as the first argument. This function acts as
+# a wrapper around processx::run() to apply this change where necessary, and
+# forward all other arguments
 wsl_compatible_run <- function(...) {
   run_args <- list(...)
   if (os_is_wsl()) {
     command <- run_args$command
     run_args$command <- "wsl"
-    if (grepl("stanc", command)) {
-      run_args$args[1] <- paste0("'", run_args$args[1], "'")
-      run_args$windows_verbatim_args <- TRUE
-    }
     run_args$args <- c(command, run_args$args)
   }
   do.call(processx::run, run_args)