fix: address review round 3 for #7

Reviewed-on: #9

DESCRIPTION

@@ -19,6 +19,7 @@ Depends:
 Imports:
     ggplot2 (>= 4.0.0),
     jpeg,
+    jsonlite,
     png,
     stringr,
     gridExtra,

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)
@@ -41,6 +42,7 @@ export(safe_ratio)
 export(scale_color_civilytics)
 export(scale_fill_civilytics)
 export(simpleCap)
+export(stamp_logo_png)
 export(star_subs)
 export(theme_civilytics)
 export(theme_civilytics_dark)
@@ -60,8 +62,12 @@ importFrom(ggplot2,annotation_custom)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_void)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,png)
 importFrom(graphics,rasterImage)
 importFrom(grid,grid.draw)
+importFrom(grid,grid.newpage)
+importFrom(grid,grid.raster)
 importFrom(grid,rasterGrob)
 importFrom(gridExtra,arrangeGrob)
 importFrom(jpeg,readJPEG)
@@ -71,3 +77,4 @@ importFrom(stats,qnorm)
 importFrom(stats,runif)
 importFrom(stringdist,stringsim)
 importFrom(stringr,str_count)
+importFrom(utils,flush.console)

R/db.R

@@ -111,7 +111,9 @@ nvals <- function(x){
 #' simpleCap(my_string)
 simpleCap <- function(x) {
   stopifnot(class(x) == "character")
-  s <- strsplit(x, " ")[[1]]
+  sapply(x, function(word) {
+    s <- strsplit(word, " ")[[1]]
     paste(toupper(substring(s, 1, 1)), substring(s, 2),
           sep = "", collapse = " ")
+  })
 }

R/logo.R

@@ -361,3 +361,92 @@ civilytics_logo <- function(plot,
            position = position)
 }
 
+
+#' Stamp the Civilytics logo onto a saved raster (PNG) image
+#'
+#' The raster analogue of [civilytics_logo()] for outputs that are already
+#' rendered to a file rather than held as a ggplot/grob — e.g. a `flextable`
+#' exported to PNG, or any `grDevices::png()` / `ragg::agg_png()` output.
+#' Resolves the *same* brand asset that [make_logo_grob()] uses, so file-based
+#' tables stay visually consistent with logo-branded plots, and composites it
+#' into a corner of the image. Pure base-graphics + grid + png — no new
+#' package dependencies.
+#'
+#' @param path Character. Path to the PNG to stamp. The file is overwritten
+#'   in place at its original pixel dimensions.
+#' @param type Character. `"wordmark"` (default) or `"mark"`. As in
+#'   [make_logo_grob()].
+#' @param variant Character. `"light"` (default, dark logo for light
+#'   backgrounds) or `"dark"` (reverse logo for dark backgrounds).
+#' @param position Character. Corner placement: `"bottom-right"` (default),
+#'   `"bottom-left"`, `"top-right"`, or `"top-left"`.
+#' @param width_frac Numeric. Logo width as a fraction of the image width
+#'   (default `0.15`). Height follows from the logo's aspect ratio.
+#' @param margin_frac Numeric. Padding from the edges as a fraction of the
+#'   image width (default `0.02`).
+#'
+#' @return `path`, invisibly.
+#' @export
+#' @importFrom png readPNG
+#' @importFrom grid grid.newpage grid.raster
+#' @importFrom grDevices png dev.off
+#' @examples
+#' \dontrun{
+#' # Brand a table exported to PNG so it matches civilytics_logo()-branded plots
+#' ragg::agg_png("table.png", width = 8, height = 4, units = "in", res = 200)
+#' plot(flextable::flextable(head(mtcars)))
+#' dev.off()
+#' stamp_logo_png("table.png")                         # wordmark, bottom-right
+#' stamp_logo_png("table.png", type = "mark", position = "bottom-left")
+#' }
+stamp_logo_png <- function(path,
+                           type = c("wordmark", "mark"),
+                           variant = c("light", "dark"),
+                           position = c("bottom-right", "bottom-left",
+                                        "top-right", "top-left"),
+                           width_frac = 0.15,
+                           margin_frac = 0.02) {
+  type     <- match.arg(type)
+  variant  <- match.arg(variant)
+  position <- match.arg(position)
+  stopifnot(file.exists(path))
+
+  # Same asset selection as make_logo_grob() so files match branded plots.
+  img_file <- switch(
+    paste(type, variant, sep = "_"),
+    wordmark_light = "civilytics-wordmark.png",
+    wordmark_dark  = "civilytics-wordmark-reverse.png",
+    mark_light     = "civilytics-mark.png",
+    mark_dark      = "civilytics-mark-reverse.png"
+  )
+  logo_path <- system.file("img", img_file, package = "civilytics")
+  if (!nzchar(logo_path)) {
+    stop("Civilytics logo asset not found in the 'civilytics' package: ", img_file)
+  }
+
+  base_img <- png::readPNG(path)        # height x width x channels, values in [0, 1]
+  logo_img <- png::readPNG(logo_path)
+  h <- dim(base_img)[1]
+  w <- dim(base_img)[2]
+  aspect <- dim(logo_img)[1] / dim(logo_img)[2]   # logo height / width
+
+  # Sizes/margins are expressed relative to image WIDTH, then converted to the
+  # device's npc units (which scale with the viewport's own width and height).
+  lw <- width_frac
+  lh <- width_frac * aspect * (w / h)
+  mx <- margin_frac
+  my <- margin_frac * (w / h)
+
+  x <- if (grepl("right", position)) 1 - mx else mx
+  y <- if (grepl("top",   position)) 1 - my else my
+  just <- c(if (grepl("right", position)) "right" else "left",
+            if (grepl("top",   position)) "top"   else "bottom")
+
+  grDevices::png(path, width = w, height = h, units = "px")
+  on.exit(grDevices::dev.off(), add = TRUE)
+  grid::grid.newpage()
+  grid::grid.raster(base_img, width = 1, height = 1, interpolate = FALSE)
+  grid::grid.raster(logo_img, x = x, y = y, width = lw, height = lh,
+                    just = just, interpolate = TRUE)
+  invisible(path)
+}

R/notifications.R

@@ -0,0 +1,153 @@
+#' 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")) {
+    system2("notify-send", args = c(status, msg),
+            stdout = TRUE, stderr = TRUE)
+    return(invisible(NULL))
+  }
+
+  # macOS: osascript
+  if (.has_command("osascript")) {
+    system2("osascript",
+            args = c("-e",
+                     paste0("display notification \"", msg,
+                            "\" with title \"", status, "\"")),
+            stdout = TRUE, 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 system2() for maximum compatibility (no extra R deps).
+  # system2() passes arguments directly to the executable without shell
+  # interpolation, avoiding command injection.
+  if (.has_command("curl")) {
+    system2("curl",
+            args = c("-s", "-X", "POST",
+                     "-H", "Content-Type: application/json",
+                     "-d", payload,
+                     url,
+                     "--max-time", as.character(timeout)),
+            stdout = TRUE, stderr = TRUE)
+  } else if (.has_command("wget")) {
+    system2("wget",
+            args = c("-q", "-O", "/dev/null",
+                     paste0("--post-data=", payload),
+                     paste0("--header=Content-Type: application/json"),
+                     paste0("--timeout=", timeout),
+                     url),
+            stdout = TRUE, 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/theme.R

@@ -36,10 +36,9 @@
 #'   to [civilytics_colors]`["paper_2"]` (`#F2EDE4`).
 #' @param grid Character. Which major gridlines to draw: `"y"` (default,
 #'   horizontal only), `"x"` (vertical only), `"both"`, or `"none"`.
-#' @param paper_bg Logical. If `TRUE` (default), fill the plot and panel
+#' @param paper_bg Logical. If `FALSE` (default), the plot and panel
-#'   backgrounds with the warm `paper` color. Set to `FALSE` for a
+#'   backgrounds are transparent (`fill = NA`). Set to `TRUE` to fill them
-#'   transparent background (useful for slides or overlay on colored
+#'   with the warm `paper` color (the Civilytics cream canvas).
-#'   surfaces).
 #'
 #' @section Font size hierarchy:
 #' All text sizes are derived from `font_size` using relative scale factors.
@@ -68,26 +67,29 @@
 #' \dontrun{
 #' library(ggplot2)
 #'
-#' # Default editorial theme
+#' # Transparent background (default) — composites cleanly onto any surface
 #' ggplot(mpg, aes(displ, hwy)) +
 #'   geom_point() +
 #'   theme_civilytics()
 #'
+#' # Warm paper canvas (opt-in)
+#' ggplot(mpg, aes(displ, hwy)) +
+#'   geom_point() +
+#'   theme_civilytics(paper_bg = TRUE)
+#'
 #' # With both gridlines and brand colors
 #' ggplot(mpg, aes(displ, hwy, colour = class)) +
 #'   geom_point() +
 #'   scale_color_civilytics() +
 #'   theme_civilytics(grid = "both")
 #'
-#' # Transparent background for embedding
-#' ggplot(mpg, aes(displ, hwy)) +
-#'   geom_point() +
-#'   theme_civilytics(paper_bg = FALSE)
-#'
 #' # Larger text for poster or display
 #' ggplot(mpg, aes(displ, hwy)) +
 #'   geom_point() +
 #'   theme_civilytics(font_size = 18)
+#'
+#' # Note: for fully-transparent PNGs, also set a transparent device
+#' # background (e.g. `ggsave("plot.png", bg = NA)`).
 #' }
 theme_civilytics <- function(
     font_size    = 14,
@@ -102,7 +104,7 @@ theme_civilytics <- function(
     accent       = unname(civilytics_colors["ember_600"]),
     strip_color  = unname(civilytics_colors["paper_2"]),
     grid         = c("y", "x", "both", "none"),
-    paper_bg     = TRUE) {
+    paper_bg     = FALSE) {
 
   grid <- match.arg(grid)
   half_line  <- font_size / 2

R/utils.R

@@ -31,7 +31,7 @@ safe_max <- function(x) {
 #' pretty_per(0.2, ndigit = 1)
 #' pretty_per(c(0.2, 0.332423, 0.4, 0.342342), ndigit = 2)
 pretty_per <- function(x, ndigit = 1) {
-  if (any(x >= 100) & !all(is.na(x))) {
+  if (any(x >= 100) && !all(is.na(x))) {
     message("Values over 100 found, did you mean to use proportions?")
   }
   x <- format(round(x, digits = ndigit + 2) * 100, nsmall = ndigit)
@@ -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))
 }
@@ -277,7 +283,7 @@ get_stabbr <- function(fips) {
   fips_codes <- fips_codes[!duplicated(fips_codes),]
   if (length(fips) != 1) {
     out <- rep(NA, length(fips))
-    for (i in length(fips)) {
+    for (i in seq_along(fips)) {
       out[i] <- fips_codes[fips_codes$state_code == fips, 1]
 
     }
@@ -369,7 +375,7 @@ random_round <- function(x) {
   add = rep(as.integer(0),length(r))
   add[r>test] <- as.integer(1)
   value = v + add
-  ifelse(is.na(value) | value<0, 0, value)
+  value <- ifelse(is.na(value) | value < 0, 0, value)
   return(value)
 }
 

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.

man/beep.Rd

@@ -0,0 +1,71 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/notifications.R
+\name{beep}
+\alias{beep}
+\title{Send a CLI beep / desktop notification}
+\usage{
+beep(
+  msg = "done",
+  type = c("beep", "notify", "webhook", "all"),
+  url = NULL,
+  status = "done",
+  timeout = 5,
+  quiet = FALSE
+)
+}
+\arguments{
+\item{msg}{Character. Optional message to include in the notification.
+When \code{type = "notify"}, this becomes the notification body.}
+
+\item{type}{Character. Notification method:
+\itemize{
+\item \code{"beep"} (default): emit a terminal bell character.
+Works in any terminal that supports the bell.
+\item \code{"notify"}: send a desktop notification via \code{notify-send} (Linux) or
+\code{osascript} (macOS). Falls back to \code{"beep"} if neither tool is found.
+\item \code{"webhook"}: POST a JSON payload to a URL. Requires \code{url} argument.
+\item \code{"all"}: play beep + send desktop notification (webhook only if \code{url}
+is provided).
+}}
+
+\item{url}{Character. Webhook URL for \code{type = "webhook"} or \code{"all"}.
+A JSON payload is POSTed with keys \code{message}, \code{status}, and \code{timestamp}.}
+
+\item{status}{Character. Status label for the notification (default \code{"done"}).
+Used in the notification title and webhook payload.}
+
+\item{timeout}{Numeric. Seconds to wait for the webhook POST to complete
+(default \code{5}). Ignored for non-webhook types.}
+
+\item{quiet}{Logical. If \code{TRUE}, suppress the terminal beep even when
+\code{type} includes \code{"beep"}. Useful for silent background runs.}
+}
+\value{
+Invisible \code{NULL}.
+}
+\description{
+Plays an audible beep in the terminal and/or sends a desktop notification
+when a long-running R script completes or reaches a milestone.
+}
+\section{Requirements}{
+\itemize{
+\item \code{type = "notify"} requires \code{notify-send} (Linux) or \code{osascript} (macOS).
+\item \code{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")
+}
+}

man/na_sum.Rd

@@ -4,10 +4,14 @@
 \alias{na_sum}
 \title{Sum a numeric that contains missing values and ignore missing values}
 \usage{
-na_sum(x)
+na_sum(x, quiet = FALSE)
 }
 \arguments{
 \item{x}{a numeric vector}
+
+\item{quiet}{Logical. If \code{TRUE} (default \code{FALSE}), suppress the warning
+message. Useful when calling \code{na_sum()} inside a loop or \code{dplyr} pipeline
+where the message would be emitted repeatedly.}
 }
 \value{
 the sum, ignoring any missing values
@@ -18,4 +22,5 @@ Sum a numeric that contains missing values and ignore missing values
 \examples{
 x <- c(2, NA, 4, 9)
 na_sum(x) # 15
+na_sum(x, quiet = TRUE) # 15 (no message)
 }

man/stamp_logo_png.Rd

@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/logo.R
+\name{stamp_logo_png}
+\alias{stamp_logo_png}
+\title{Stamp the Civilytics logo onto a saved raster (PNG) image}
+\usage{
+stamp_logo_png(
+  path,
+  type = c("wordmark", "mark"),
+  variant = c("light", "dark"),
+  position = c("bottom-right", "bottom-left", "top-right", "top-left"),
+  width_frac = 0.15,
+  margin_frac = 0.02
+)
+}
+\arguments{
+\item{path}{Character. Path to the PNG to stamp. The file is overwritten
+in place at its original pixel dimensions.}
+
+\item{type}{Character. `"wordmark"` (default) or `"mark"`. As in
+[make_logo_grob()].}
+
+\item{variant}{Character. `"light"` (default, dark logo for light
+backgrounds) or `"dark"` (reverse logo for dark backgrounds).}
+
+\item{position}{Character. Corner placement: `"bottom-right"` (default),
+`"bottom-left"`, `"top-right"`, or `"top-left"`.}
+
+\item{width_frac}{Numeric. Logo width as a fraction of the image width
+(default `0.15`). Height follows from the logo's aspect ratio.}
+
+\item{margin_frac}{Numeric. Padding from the edges as a fraction of the
+image width (default `0.02`).}
+}
+\value{
+`path`, invisibly.
+}
+\description{
+The raster analogue of [civilytics_logo()] for outputs that are already
+rendered to a file rather than held as a ggplot/grob — e.g. a `flextable`
+exported to PNG, or any `grDevices::png()` / `ragg::agg_png()` output.
+Resolves the *same* brand asset that [make_logo_grob()] uses, so file-based
+tables stay visually consistent with logo-branded plots, and composites it
+into a corner of the image. Pure base-graphics + grid + png — no new
+package dependencies.
+}
+\examples{
+\dontrun{
+# Brand a table exported to PNG so it matches civilytics_logo()-branded plots
+ragg::agg_png("table.png", width = 8, height = 4, units = "in", res = 200)
+plot(flextable::flextable(head(mtcars)))
+dev.off()
+stamp_logo_png("table.png")                         # wordmark, bottom-right
+stamp_logo_png("table.png", type = "mark", position = "bottom-left")
+}
+}

tests/testthat/test_logo.R

@@ -0,0 +1,30 @@
+test_that("stamp_logo_png preserves image dimensions and returns the path invisibly", {
+  p <- tempfile(fileext = ".png")
+  on.exit(unlink(p), add = TRUE)
+  grDevices::png(p, width = 600, height = 240); plot(1:5); grDevices::dev.off()
+  in_dim <- dim(png::readPNG(p))[1:2]
+
+  expect_invisible(out <- stamp_logo_png(p))
+  expect_identical(out, p)
+  expect_identical(dim(png::readPNG(p))[1:2], in_dim)  # overwritten at same size
+})
+
+test_that("stamp_logo_png runs for every type/variant/position combination", {
+  p <- tempfile(fileext = ".png")
+  on.exit(unlink(p), add = TRUE)
+  grDevices::png(p, width = 500, height = 200); plot(1:5); grDevices::dev.off()
+
+  for (ty in c("wordmark", "mark")) {
+    for (va in c("light", "dark")) {
+      for (pos in c("bottom-right", "bottom-left", "top-right", "top-left")) {
+        expect_no_error(stamp_logo_png(p, type = ty, variant = va, position = pos))
+      }
+    }
+  }
+})
+
+test_that("stamp_logo_png validates its inputs", {
+  expect_error(stamp_logo_png(tempfile(fileext = ".png")))  # file does not exist
+  # invalid type is rejected by match.arg() before the file is touched
+  expect_error(stamp_logo_png(tempfile(fileext = ".png"), type = "banner"))
+})

tests/testthat/test_notifications.R

@@ -0,0 +1,56 @@
+# 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"))
+})
+
+test_that("beep(type='all') exercises both beep and notify paths", {
+  # type="all" should trigger the terminal beep (unless quiet) and
+  # attempt a desktop notification. We verify by checking that the
+  # function returns invisibly and does not error when notify-send
+  # is absent (which is the case in CI).
+  expect_invisible(beep("all-test", type = "all"))
+  expect_invisible(beep("all-test", type = "all", quiet = TRUE))
+})
+
+test_that("notification helpers use system2() to prevent command injection", {
+  # Security regression: .send_webhook and .send_desktop_notify must
+  # use system2() with separate args, never system() with shell
+  # interpolation.  system2() passes arguments directly to the
+  # executable without going through a shell, so shell metacharacters
+  # in msg, status, url, or payload are treated as literal data.
+
+  webhook_body <- deparse(body(.send_webhook))
+  notify_body  <- deparse(body(.send_desktop_notify))
+
+  # Must use system2
+  expect_true(any(grepl("system2", webhook_body)),
+              info = ".send_webhook() must use system2() to avoid shell injection")
+  expect_true(any(grepl("system2", notify_body)),
+              info = ".send_desktop_notify() must use system2() to avoid shell injection")
+
+  # Must NOT use system( with string interpolation (system("curl ..."))
+  # We look for system( followed by a string literal (the old pattern).
+  # system2 calls look like system2("curl", args = ...) which is fine.
+  expect_false(any(grepl('system\\(\\s*"', webhook_body)),
+               info = ".send_webhook() must not use system() with interpolated strings")
+  expect_false(any(grepl('system\\(\\s*"', notify_body)),
+               info = ".send_desktop_notify() must not use system() with interpolated strings")
+})

tests/testthat/test_theme.R

@@ -133,9 +133,17 @@ test_that("theme_civilytics uses brand ink color for text", {
   expect_equal(th$text$colour, unname(civilytics_colors["ink"]))
 })
 
-test_that("theme_civilytics uses brand paper color for plot background", {
+test_that("theme_civilytics has transparent background by default", {
   th <- theme_civilytics()
+  expect_true(is.na(th$plot.background$fill))
+  expect_true(is.na(th$panel.background$fill))
+  expect_null(th$legend.background$fill)
+})
+
+test_that("theme_civilytics paper_bg=TRUE opt-in fills with cream", {
+  th <- theme_civilytics(paper_bg = TRUE)
   expect_equal(th$plot.background$fill, unname(civilytics_colors["paper"]))
+  expect_equal(th$panel.background$fill, unname(civilytics_colors["paper"]))
 })
 
 test_that("theme_civilytics uses paper_2 for strip background by default", {

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")