Fix issues #1, #3, #5: misc improvements

- #5: Unwrap _brand.yml for Quarto 1.9+ compatibility (remove top-level
  brand: wrapper so meta/logo/color/typography are at the top level)
- #1: Add quiet parameter to na_sum() to suppress warnings in loops/pipelines
- #3: Add beep() function for CLI beep, desktop notifications, and webhook
  alerts (supports type=beep|notify|webhook|all)

R/notifications.R

@@ -0,0 +1,151 @@
+#' Send a CLI beep / desktop notification
+#'
+#' Plays an audible beep in the terminal and/or sends a desktop notification
+#' when a long-running R script completes or reaches a milestone.
+#'
+#' @param msg Character. Optional message to include in the notification.
+#'   When `type = "notify"`, this becomes the notification body.
+#' @param type Character. Notification method:
+#'   - `"beep"` (default): emit a terminal bell character (`\007`).
+#'     Works in any terminal that supports the bell.
+#'   - `"notify"`: send a desktop notification via `notify-send` (Linux) or
+#'     `osascript` (macOS). Falls back to `"beep"` if neither tool is found.
+#'   - `"webhook"`: POST a JSON payload to a URL. Requires `url` argument.
+#'   - `"all"`: play beep + send desktop notification (webhook only if `url`
+#'     is provided).
+#' @param url Character. Webhook URL for `type = "webhook"` or `"all"`.
+#'   A JSON payload is POSTed with keys `message`, `status`, and `timestamp`.
+#' @param status Character. Status label for the notification (default `"done"`).
+#'   Used in the notification title and webhook payload.
+#' @param timeout Numeric. Seconds to wait for the webhook POST to complete
+#'   (default `5`). Ignored for non-webhook types.
+#' @param quiet Logical. If `TRUE`, suppress the terminal beep even when
+#'   `type` includes `"beep"`. Useful for silent background runs.
+#'
+#' @return Invisible `NULL`.
+#'
+#' @section Requirements:
+#' - `type = "notify"` requires `notify-send` (Linux) or `osascript` (macOS).
+#' - `type = "webhook"` requires network access to the provided URL.
+#'
+#' @section Examples:
+#' \preformatted{
+#' # Simple terminal beep
+#' beep()
+#'
+#' # Desktop notification with message
+#' beep("Analysis complete!", type = "notify")
+#'
+#' # Send to a webhook (e.g., Slack, Discord, custom endpoint)
+#' beep("Job finished", type = "webhook",
+#'      url = "https://hooks.slack.com/services/...")
+#'
+#' # Beep + desktop notification
+#' beep("Processing done", type = "all")
+#' }
+#'
+#' @export
+#'
+beep <- function(msg = "done",
+                 type = c("beep", "notify", "webhook", "all"),
+                 url = NULL,
+                 status = "done",
+                 timeout = 5,
+                 quiet = FALSE) {
+  type <- match.arg(type)
+
+  # -- Terminal beep ----------------------------------------------------------
+  if (!quiet && grepl("beep", type)) {
+    cat("\007")
+    flush.console()
+  }
+
+  # -- Desktop notification ---------------------------------------------------
+  if (grepl("notify", type)) {
+    .send_desktop_notify(msg, status)
+  }
+
+  # -- Webhook ----------------------------------------------------------------
+  if (grepl("webhook", type) && !is.null(url)) {
+    .send_webhook(url, msg, status, timeout)
+  }
+
+  invisible(NULL)
+}
+
+
+# -- Internal helpers ---------------------------------------------------------
+
+#' Send a desktop notification via notify-send or osascript
+#'
+#' @param msg Message body
+#' @param status Status label for the title
+#' @keywords internal
+.send_desktop_notify <- function(msg, status) {
+  # Linux: notify-send
+  if (.has_command("notify-send")) {
+    cmd <- paste0("notify-send '", status, "' '", gsub("'", "'\\''", msg), "'")
+    system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE)
+    return(invisible(NULL))
+  }
+
+  # macOS: osascript
+  if (.has_command("osascript")) {
+    escaped_msg <- gsub('"', '\\"', msg)
+    escaped_status <- gsub('"', '\\"', status)
+    cmd <- paste0(
+      "osascript -e 'display notification \"", escaped_msg,
+      "\" with title \"", escaped_status, "\"'"
+    )
+    system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE)
+    return(invisible(NULL))
+  }
+
+  # Neither tool available — silently skip
+  invisible(NULL)
+}
+
+
+#' POST a JSON payload to a webhook URL
+#'
+#' @param url Webhook URL
+#' @param msg Message body
+#' @param status Status label
+#' @param timeout Seconds to wait for the request
+#' @keywords internal
+.send_webhook <- function(url, msg, status, timeout) {
+  payload <- jsonlite::toJSON(list(
+    message   = msg,
+    status    = status,
+    timestamp = format(Sys.time(), "%Y-%m-%dT%H:%M:%S%z")
+  ), auto_unbox = TRUE)
+
+  # Use curl via system() for maximum compatibility (no extra R deps)
+  if (.has_command("curl")) {
+    cmd <- paste0(
+      "curl -s -X POST -H 'Content-Type: application/json' ",
+      "-d '", payload, "' '", url, "' ",
+      "--max-time ", timeout
+    )
+    system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE)
+  } else if (.has_command("wget")) {
+    cmd <- paste0(
+      "wget -q -O /dev/null --post-data='", payload,
+      "' --header='Content-Type: application/json' ",
+      "--timeout=", timeout, " '", url, "'"
+    )
+    system(cmd, ignore.stdout = TRUE, ignore.stderr = TRUE)
+  }
+
+  invisible(NULL)
+}
+
+
+#' Check if a command exists on the system PATH
+#'
+#' @param cmd Command name
+#' @return Logical
+#' @keywords internal
+.has_command <- function(cmd) {
+  Sys.which(cmd) != ""
+}