Fix for bare cli args like --cascade to be TRUE, not NA

Author: michaelhallquist

R/cli_functions.R

@@ -191,6 +191,9 @@ parse_cli_args <- function(args, sep = "/", type_values = TRUE) {
   # always collapse into a single string to avoid continuation errors in args_to_df
   if (length(args) > 1L) args <- paste(args, collapse = " ")
   df <- args_to_df(args)
+  # Treat bare options (e.g. "--flag") as logical TRUE.
+  bare_flag_idx <- !df$has_equals & is.na(df$rhs)
+  if (any(bare_flag_idx)) df$rhs[bare_flag_idx] <- "TRUE"
   assignments <- paste(df$lhs, df$rhs, sep="=")
   set_nested_values(assignments, sep = sep, type_values = type_values)
 }

inst/upd_job_status.R

@@ -41,7 +41,7 @@ args <- BrainGnomes::parse_cli_args(tmp)
 if (isTRUE(args$job_id == "NULL")) args$job_id <- NULL
 if (isTRUE(args$sqlite_db == "NULL")) args$sqlite_db <- NULL
 if (isTRUE(args$status == "NULL")) args$status <- NULL
-if (isTRUE(args$cascade == "NULL") | isTRUE(is.null(args$cascade))) args$cascade <- FALSE
+args$cascade <- isTRUE(args$cascade)
 if (isTRUE(args$output_dir == "NULL")) args$output_dir <- NULL
 
 # Capture output manifest if status is COMPLETED and output_dir is provided

tests/testthat/test-cli_utils.R

@@ -33,6 +33,17 @@ test_that("parse_cli_args handles embedded equals signs", {
   expect_equal(res$bar, "a = b")
 })
 
+test_that("parse_cli_args treats bare flags as TRUE", {
+  res <- parse_cli_args(c("--status FAILED", "--cascade"))
+  expect_equal(res$status, "FAILED")
+  expect_true(isTRUE(res$cascade))
+})
+
+test_that("parse_cli_args respects explicit FALSE and NULL for flags", {
+  expect_false(parse_cli_args(c("--cascade=FALSE"))$cascade)
+  expect_null(parse_cli_args(c("--cascade=NULL"))$cascade)
+})
+
 # nested_list_to_args round-trips with parse_cli_args
 
 test_that("nested_list_to_args creates expected CLI strings", {
@@ -53,4 +64,3 @@ test_that("set_cli_options updates and adds options", {
   # expect_equal(result, c("--foo=3", "--bar=2", "--baz=4"))
   expect_equal(result, c("--foo=3 --baz=4 --bar=2"))
 })
-