zero pad chain IDs in file names

NEWS.md

@@ -1,5 +1,7 @@
 # cmdstanr (development version)
 
+* Chain IDs in generated filenames are now zero-padded to at least two digits, 
+for example `01` instead of `1`. (#1244)
 * When using CmdStan through WSL, paths for output, diagnostic, profile, config, 
 and metric files now remain accessible to Windows R when an explicit output 
 directory is supplied. (#1110; related: #1113)
@@ -80,7 +82,7 @@ CmdStan 2.39 or newer, and `read_cmdstan_csv()` returns these times from
 standalone generated quantities CSV files. (#1168)
 * `laplace()` no longer overwrites the internally generated optimizer CSV when
 `mode = NULL` and `output_basename` is supplied. The internally generated
-optimizer CSV now uses the filename `<output_basename>-mode-1.csv`.
+optimizer CSV now uses the filename `<output_basename>-mode-01.csv`.
 
 * CmdStanModel objects created using `compile_model_methods = TRUE` that are
 then saved and reloaded no longer error in model fitting methods. Model methods

R/fit.R

@@ -1000,7 +1000,8 @@ CmdStanFit$set("public", name = "cmdstan_diagnose", value = cmdstan_diagnose)
 #' * `basename` is the user's provided `basename` argument or, if `NULL`, the
 #'   model name;
 #' * `timestamp` is of the form `format(Sys.time(), "%Y%m%d%H%M")`;
-#' * `id` is the MCMC chain id (or `1` for non MCMC);
+#' * `id` is the MCMC chain id, zero-padded to at least two digits (or `01` for
+#'   non-MCMC);
 #' * `random` contains six random hexadecimal characters.
 #'
 #' `$save_latent_dynamics_files()` uses the pattern

R/utils.R

@@ -266,7 +266,8 @@ generate_file_names <-
       new_names <- paste0(new_names, "-", stamp)
     }
     if (!is.null(ids)) {
-      new_names <- paste0(new_names, "-", ids)
+      width <- max(2L, nchar(sprintf("%d", max(ids))))
+      new_names <- paste0(new_names, "-", sprintf("%0*d", width, ids))
     }
     if (random) {
       rand_num_pid <- as.integer(stats::runif(1, min = 0, max = 1E7)) + Sys.getpid()

tests/testthat/test-fit-shared.R

@@ -37,7 +37,7 @@ test_that("saving csv output files works", {
     should_match <- paste0("testing-output-",
                            base::format(Sys.time(), "%Y%m%d%H%M"),
                            "-",
-                           seq_len(fit$num_procs()))
+                           sprintf("%02d", seq_len(fit$num_procs())))
     for (j in seq_along(paths)) {
       expect_match(paths[j], should_match[j])
     }
@@ -72,7 +72,7 @@ test_that("saving diagnostic csv output works", {
     should_match <- paste0("testing-output-diagnostic-",
                            base::format(Sys.time(), "%Y%m%d%H%M"),
                            "-",
-                           seq_len(fit$num_procs()))
+                           sprintf("%02d", seq_len(fit$num_procs())))
 
     for (j in seq_along(paths)) {
       expect_match(paths[j], should_match[j])

tests/testthat/test-model-laplace.R

@@ -76,11 +76,11 @@ test_that("laplace() avoids output_basename conflict with internal optimize()",
     )
   )
 
-  expect_equal(basename(fit$output_files()), "custom-laplace-1.csv")
-  expect_equal(basename(fit$mode()$output_files()), "custom-laplace-mode-1.csv")
+  expect_equal(basename(fit$output_files()), "custom-laplace-01.csv")
+  expect_equal(basename(fit$mode()$output_files()), "custom-laplace-mode-01.csv")
   expect_setequal(
     list.files(output_dir, pattern = "\\.csv$"),
-    c("custom-laplace-1.csv", "custom-laplace-mode-1.csv")
+    c("custom-laplace-01.csv", "custom-laplace-mode-01.csv")
   )
 })
 

tests/testthat/test-model-output_dir.R

@@ -47,7 +47,7 @@ test_that("WSL output paths stay host-native until command composition", {
           output_basename = "model"
         )
       })
-      output_files <- file.path(host_dirs, "model-1.csv")
+      output_files <- file.path(host_dirs, "model-01.csv")
       expect_equal(
         vapply(args, function(x) x$output_dir, character(1)),
         host_dirs
@@ -62,15 +62,15 @@ test_that("WSL output paths stay host-native until command composition", {
         )
         sub("file=", "", command_args[grepl("^file=", command_args)], fixed = TRUE)
       }, character(1))
-      expect_equal(cmdstan_output_files, file.path(wsl_dirs, "model-1.csv"))
+      expect_equal(cmdstan_output_files, file.path(wsl_dirs, "model-01.csv"))
 
       command_args <- args[[1]]$compose_all_args(
         output_file = output_files[1],
-        profile_file = file.path(host_dirs[1], "model-profile-1.csv"),
-        latent_dynamics_file = file.path(host_dirs[1], "model-diagnostic-1.csv")
+        profile_file = file.path(host_dirs[1], "model-profile-01.csv"),
+        latent_dynamics_file = file.path(host_dirs[1], "model-diagnostic-01.csv")
       )
-      expect_in("diagnostic_file=/mnt/c/output/model-diagnostic-1.csv", command_args)
-      expect_in("profile_file=/mnt/c/output/model-profile-1.csv", command_args)
+      expect_in("diagnostic_file=/mnt/c/output/model-diagnostic-01.csv", command_args)
+      expect_in("profile_file=/mnt/c/output/model-profile-01.csv", command_args)
 
       # Omitting output_dir must still use the faster WSL-native temp directory.
       default_args <- CmdStanArgs$new(
@@ -82,7 +82,7 @@ test_that("WSL output paths stay host-native until command composition", {
       )
       expect_equal(default_args$output_dir, "//wsl$/Ubuntu/tmp/cmdstanr")
       expect_in(
-        "file=/tmp/cmdstanr/model-1.csv",
+        "file=/tmp/cmdstanr/model-01.csv",
         default_args$compose_all_args(
           output_file = default_args$new_files("output")
         )
@@ -145,7 +145,7 @@ test_that("all fitting methods work with output_dir", {
     fit <- testing_fit("bernoulli", method = method, seed = 123,
                        output_basename = "custom")
     n_files <- length(fit$output_files())
-    files <- paste0("custom-", 1:n_files, ".csv")
+    files <- sprintf("custom-%02d.csv", seq_len(n_files))
     expect_equal(basename(fit$output_files()), files)
   }
 

tests/testthat/test-model-pathfinder.R

@@ -169,9 +169,9 @@ test_that("pathfinder() saves single path outputs", {
     )
   )
 
-  expect_equal(basename(fit$output_files()), "pathfinder-1.csv")
+  expect_equal(basename(fit$output_files()), "pathfinder-01.csv")
   single_path_files <- file.path(output_dir, paste0(
-    "pathfinder-1_path_",
+    "pathfinder-01_path_",
     rep(1:2, each = 2),
     c(".csv", ".json")
   ))

tests/testthat/test-utils.R

@@ -182,6 +182,30 @@ test_that("get_standalone_hpp() suggests formatting deprecated syntax", {
 
 # misc --------------------------------------------------------------------
 
+test_that("generate_file_names() zero-pads IDs for lexicographic sorting", {
+  expect_equal(
+    generate_file_names(
+      basename = "output",
+      ids = 1:10,
+      timestamp = FALSE,
+      random = FALSE
+    ),
+    paste0("output-", sprintf("%02d", 1:10), ".csv")
+  )
+
+  file_names <- generate_file_names(
+    basename = "output",
+    ids = 1:100,
+    timestamp = FALSE,
+    random = FALSE
+  )
+  expect_equal(
+    file_names[c(1, 9, 10, 100)],
+    paste0("output-", c("001", "009", "010", "100"), ".csv")
+  )
+  expect_equal(sort(file_names), file_names)
+})
+
 test_that("copy_temp_files retains sources if any copy fails", {
   source_dir <- withr::local_tempdir()
   destination_dir <- withr::local_tempdir()