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)

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(beep)
 export(add_logo)
 export(add_logo_ga)
 export(agresti_coull_interval)

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) != ""
+}

R/utils.R

@@ -149,6 +149,9 @@ race_short_names <- function(x) {
 #' Sum a numeric that contains missing values and ignore missing values
 #'
 #' @param x a numeric vector
+#' @param quiet Logical. If `TRUE` (default `FALSE`), suppress the warning
+#'   message. Useful when calling `na_sum()` inside a loop or `dplyr` pipeline
+#'   where the message would be emitted repeatedly.
 #'
 #' @return the sum, ignoring any missing values
 #' @export
@@ -156,9 +159,12 @@ race_short_names <- function(x) {
 #' @examples
 #' x <- c(2, NA, 4, 9)
 #' na_sum(x) # 15
-na_sum <- function(x) {
+#' na_sum(x, quiet = TRUE) # 15 (no message)
+na_sum <- function(x, quiet = FALSE) {
   stopifnot(is.numeric(x))
+  if (!quiet) {
     message("Taking a sum with missing values equal to 0, be careful!")
+  }
   x <- na_zero(x)
   return(sum(x))
 }

inst/quarto/_brand.yml

@@ -2,7 +2,6 @@
 # Optional but recommended — Quarto auto-applies these to HTML, PDF, and Revealjs.
 # https://quarto.org/docs/authoring/brand.html
 
-brand:
 meta:
   name: Civilytics Consulting
   description: Turning public data into clear, actionable analysis for public good.

tests/testthat/test_notifications.R

@@ -0,0 +1,22 @@
+# Test beep / notification function
+
+context("Test beep() function")
+
+test_that("beep() returns invisibly", {
+  expect_invisible(beep())
+  expect_invisible(beep("test", type = "beep"))
+  expect_invisible(beep("test", type = "all"))
+})
+
+test_that("beep() with quiet=TRUE produces no output", {
+  expect_silent(beep("test", type = "beep", quiet = TRUE))
+})
+
+test_that("beep() with type=notify is silent when no tools available", {
+  # When notify-send and osascript are both absent, should be silent
+  expect_silent(beep("test", type = "notify"))
+})
+
+test_that("beep() with type=webhook and no URL is silent", {
+  expect_silent(beep("test", type = "webhook"))
+})

tests/testthat/test_utils.R

@@ -58,6 +58,12 @@ test_that("na_sum fails with non-numerics", {
   expect_error(na_sum(as.factor(1:10)))
 })
 
+test_that("na_sum quiet=TRUE suppresses the message", {
+  expect_message(na_sum(c(1:10, NA)), "Taking a sum")
+  expect_silent(na_sum(c(1:10, NA), quiet = TRUE))
+  expect_equal(na_sum(c(1:10, NA), quiet = TRUE), 55)
+})
+
 
 context("Test Utilities - Pretty Count")