fix(typst): ship template as partials so code blocks render (#12)

The single-file `template: civilytics-typst.typ` discarded Quarto's
auto-generated `definitions` partial, so any Typst document containing a
code block failed with `unknown variable: Skylighting`.

Ship the template as Quarto template-partials instead, so Quarto keeps its
definitions (Skylighting + token functions) and syntax-highlighted code
blocks render while the Civilytics branding still applies:

- split civilytics-typst.typ into typst-template.typ (the styling function)
  and typst-show.typ (the show/entry point, keyword-safe [ ] wrapping kept);
  remove the single-file template
- use_civilytics_theme() now copies both partials and prints the
  template-partials usage
- example report.qmd uses template-partials

Verified: a report with an R code block renders with working syntax
highlighting and full branding.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: civilytics
 Type: Package
 Title: Brand Themes, Color Palettes, and Utility Functions for Civilytics
-Version: 0.2.0
+Version: 0.3.0
 Authors@R:
     person("Jared", "E. Knowles", email = "jared@civilytics.com",
            role = c("aut", "cre"))
@@ -19,7 +19,6 @@ Depends:
 Imports:
     ggplot2 (>= 4.0.0),
     jpeg,
-    jsonlite,
     png,
     stringr,
     gridExtra,

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(beep)
 export(add_logo)
 export(add_logo_ga)
 export(agresti_coull_interval)
@@ -42,7 +41,6 @@ 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)
@@ -62,12 +60,8 @@ 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)
@@ -77,4 +71,3 @@ importFrom(stats,qnorm)
 importFrom(stats,runif)
 importFrom(stringdist,stringsim)
 importFrom(stringr,str_count)
-importFrom(utils,flush.console)

R/db.R

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

R/logo.R

@@ -361,92 +361,3 @@ 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

@@ -1,153 +0,0 @@
-#' 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/quarto.R

@@ -135,12 +135,12 @@ use_civilytics_theme <- function(path = ".", force = FALSE) {
     .copy_pkg_file(file.path("quarto/latex", f), file.path("latex", f), path, force)
   }
 
-  # Typst
+  # Typst — shipped as template-partials so Quarto keeps its Skylighting
-  .copy_pkg_file(
+  # definitions and syntax-highlighted code blocks render (see issue #12)
-    "quarto/typst/civilytics-typst.typ",
+  typst_files <- c("typst-template.typ", "typst-show.typ")
-    "typst/civilytics-typst.typ",
+  for (f in typst_files) {
-    path, force
+    .copy_pkg_file(file.path("quarto/typst", f), file.path("typst", f), path, force)
-  )
+  }
 
   # Logos — for _brand.yml (expects assets/logo/)
   .copy_logos("assets/logo", path, force)
@@ -158,7 +158,9 @@ use_civilytics_theme <- function(path = ".", force = FALSE) {
   message("    include-in-header: latex/civilytics.tex")
   message("    include-before-body: latex/civilytics-title.tex")
   message("  typst:")
-  message("    template: typst/civilytics-typst.typ")
+  message("    template-partials:")
+  message("      - typst/typst-template.typ")
+  message("      - typst/typst-show.typ")
   message("---")
   message("\nSee examples/report.qmd for a complete example.")
   invisible(NULL)

R/theme.R

@@ -36,9 +36,10 @@
 #'   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 `FALSE` (default), the plot and panel
+#' @param paper_bg Logical. If `TRUE` (default), fill the plot and panel
-#'   backgrounds are transparent (`fill = NA`). Set to `TRUE` to fill them
+#'   backgrounds with the warm `paper` color. Set to `FALSE` for a
-#'   with the warm `paper` color (the Civilytics cream canvas).
+#'   transparent background (useful for slides or overlay on colored
+#'   surfaces).
 #'
 #' @section Font size hierarchy:
 #' All text sizes are derived from `font_size` using relative scale factors.
@@ -67,29 +68,26 @@
 #' \dontrun{
 #' library(ggplot2)
 #'
-#' # Transparent background (default) — composites cleanly onto any surface
+#' # Default editorial theme
 #' 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,
@@ -104,7 +102,7 @@ theme_civilytics <- function(
     accent       = unname(civilytics_colors["ember_600"]),
     strip_color  = unname(civilytics_colors["paper_2"]),
     grid         = c("y", "x", "both", "none"),
-    paper_bg     = FALSE) {
+    paper_bg     = TRUE) {
 
   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)
@@ -149,9 +149,6 @@ 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
@@ -159,12 +156,9 @@ race_short_names <- function(x) {
 #' @examples
 #' x <- c(2, NA, 4, 9)
 #' na_sum(x) # 15
-#' na_sum(x, quiet = TRUE) # 15 (no message)
+na_sum <- function(x) {
-na_sum <- function(x, quiet = FALSE) {
   stopifnot(is.numeric(x))
-  if (!quiet) {
+  message("Taking a sum with missing values equal to 0, be careful!")
-    message("Taking a sum with missing values equal to 0, be careful!")
-  }
   x <- na_zero(x)
   return(sum(x))
 }
@@ -283,7 +277,7 @@ get_stabbr <- function(fips) {
   fips_codes <- fips_codes[!duplicated(fips_codes),]
   if (length(fips) != 1) {
     out <- rep(NA, length(fips))
-    for (i in seq_along(fips)) {
+    for (i in length(fips)) {
       out[i] <- fips_codes[fips_codes$state_code == fips, 1]
 
     }
@@ -375,7 +369,7 @@ random_round <- function(x) {
   add = rep(as.integer(0),length(r))
   add[r>test] <- as.integer(1)
   value = v + add
-  value <- ifelse(is.na(value) | value < 0, 0, value)
+  ifelse(is.na(value) | value<0, 0, value)
   return(value)
 }
 

inst/quarto/_brand.yml

@@ -2,64 +2,65 @@
 # Optional but recommended — Quarto auto-applies these to HTML, PDF, and Revealjs.
 # https://quarto.org/docs/authoring/brand.html
 
-meta:
+brand:
-  name: Civilytics Consulting
+  meta:
-  description: Turning public data into clear, actionable analysis for public good.
+    name: Civilytics Consulting
+    description: Turning public data into clear, actionable analysis for public good.
 
-logo:
+  logo:
-  small: assets/logo/civilytics-mark.svg
+    small: assets/logo/civilytics-mark.svg
-  medium: assets/logo/civilytics-wordmark.svg
+    medium: assets/logo/civilytics-wordmark.svg
-  large: assets/logo/civilytics-wordmark.svg
+    large: assets/logo/civilytics-wordmark.svg
 
-color:
+  color:
-  palette:
+    palette:
-    paper:    "#FAF7F2"
+      paper:    "#FAF7F2"
-    paper-2:  "#F2EDE4"
+      paper-2:  "#F2EDE4"
-    ink:      "#0E1A2B"
+      ink:      "#0E1A2B"
-    ink-2:    "#2B3A52"
+      ink-2:    "#2B3A52"
-    ink-3:    "#5A6A82"
+      ink-3:    "#5A6A82"
-    navy:     "#22406A"
+      navy:     "#22406A"
-    ember:    "#C25311"
+      ember:    "#C25311"
-    ember-2:  "#923D00"
+      ember-2:  "#923D00"
-    teal:     "#1F6F70"
+      teal:     "#1F6F70"
-    plum:     "#6B3A5E"
+      plum:     "#6B3A5E"
-    moss:     "#4A6B2F"
+      moss:     "#4A6B2F"
-    brass:    "#B8751C"
+      brass:    "#B8751C"
-  background: paper
+    background: paper
-  foreground: ink
+    foreground: ink
-  primary:   navy
+    primary:   navy
-  secondary: ember
+    secondary: ember
-  success:   moss
+    success:   moss
-  info:      navy
+    info:      navy
-  warning:   "#9A5F18"
+    warning:   "#9A5F18"
-  danger:    "#A6271D"
+    danger:    "#A6271D"
-  light:     paper-2
+    light:     paper-2
-  dark:      ink
+    dark:      ink
-  link:      navy
+    link:      navy
 
-typography:
+  typography:
-  fonts:
+    fonts:
-    - family: "Source Serif 4"
+      - family: "Source Serif 4"
-      source: google
+        source: google
-    - family: "Inter"
+      - family: "Inter"
-      source: google
+        source: google
-    - family: "JetBrains Mono"
+      - family: "JetBrains Mono"
-      source: google
+        source: google
-    - family: "Libre Franklin"
+      - family: "Libre Franklin"
-      source: google
+        source: google
-  base:
+    base:
-    family: Inter
+      family: Inter
-    size: 1rem
+      size: 1rem
-    line-height: 1.65
+      line-height: 1.65
-  headings:
+    headings:
-    family: "Libre Franklin"
+      family: "Libre Franklin"
-    weight: 800
+      weight: 800
-    style: normal
+      style: normal
-    line-height: 1.08
+      line-height: 1.08
-    color: ink
+      color: ink
-  monospace:
+    monospace:
-    family: "JetBrains Mono"
+      family: "JetBrains Mono"
-    size: 0.92em
+      size: 0.92em
-  link:
+    link:
-    color: navy
+      color: navy
-    decoration: underline
+      decoration: underline

inst/quarto/examples/report.qmd

@@ -19,7 +19,9 @@ format:
     toc: true
     toc-location: right
   typst:
-    template: ../typst/civilytics-typst.typ
+    template-partials:
+      - ../typst/typst-template.typ
+      - ../typst/typst-show.typ
   pdf:
     include-in-header: ../latex/civilytics.tex
     include-before-body: ../latex/civilytics-title.tex

inst/quarto/examples/slides.qmd

@@ -62,4 +62,4 @@ Civilytics Research, 2026
 Questions?
 
 - jared@civilytics.com
-- civilytics.consulting
+- civilytics.com

inst/quarto/latex/civilytics-title.tex

@@ -2,6 +2,11 @@
 % Replaces Quarto's default \maketitle. Uses values from YAML
 % (\thetitle, \theauthor, \thedate) plus an \ifabstract block.
 
+% Guard: \thesubtitle is normally defined by civilytics.tex's subtitle
+% capture; provide a fallback so this partial degrades gracefully if used
+% without that preamble. See civilyticsR issue #13.
+\providecommand{\thesubtitle}{}
+
 \begin{titlepage}
   \pagecolor{paper}
   \color{ink}
@@ -33,8 +38,6 @@
 
   % Pulse mark, in ember
   \begin{center}
-    \begin{tikzpicture}[overlay, remember picture]
-    \end{tikzpicture}
     {\color{ember}\rule{40pt}{2pt}}
   \end{center}
 \end{titlepage}

inst/quarto/latex/civilytics.tex

@@ -40,17 +40,40 @@
 \color{ink}
 
 % --- Fonts (require local install or fontspec lookup) ---
+% Bold uses the family's native Bold weight (present in every Source Serif 4
+% install). Do NOT hard-require a "SemiBold" face: the package installs no
+% system fonts for the PDF path, and standard Source Serif 4 ships only
+% Regular/Bold/Italic/BoldItalic. See civilyticsR issue #14.
 \setmainfont{Source Serif 4}[
   UprightFont = *,
   ItalicFont = * Italic,
-  BoldFont = * SemiBold,
-  BoldItalicFont = * SemiBold Italic,
   Ligatures = TeX,
 ]
 \setsansfont{Inter}[Ligatures = TeX]
 \setmonofont{JetBrains Mono}[Scale = 0.92]
 \newfontfamily\displayfont{Libre Franklin}[Ligatures = TeX]
 
+% --- Subtitle capture ---
+% Quarto/pandoc defines \subtitle (which appends to \@title) but never
+% \thesubtitle, which the title page uses. This preamble is emitted before
+% pandoc's \providecommand{\subtitle}, so our definition wins: capture the
+% subtitle into \thesubtitle instead. See civilyticsR issue #13.
+\makeatletter
+\providecommand{\thesubtitle}{}
+\def\subtitle#1{\renewcommand{\thesubtitle}{#1}}
+\makeatother
+
+% --- Use the Civilytics title page, not pandoc's default ---
+% civilytics-title.tex (include-before-body) IS the title page. Quarto emits
+% its default \maketitle + abstract *before* include-before-body, which would
+% print a second, unstyled title. Neutralise both here, in the preamble
+% (runs at \begin{document}, before the default title). The branded title page
+% does not display the abstract. See civilyticsR issue #13.
+\AtBeginDocument{%
+  \renewcommand{\maketitle}{}%
+  \renewenvironment{abstract}{\setbox0=\vbox\bgroup}{\egroup}%
+}
+
 % --- Hyperlinks ---
 \hypersetup{
   colorlinks = true,
@@ -77,7 +100,7 @@
 \renewcommand{\footrulewidth}{0pt}
 \fancyhead[L]{\sffamily\scriptsize\color{ink3}\MakeUppercase{Civilytics Consulting}}
 \fancyhead[R]{\sffamily\scriptsize\color{ink3}\thetitle}
-\fancyfoot[L]{\sffamily\scriptsize\color{ink3}civilytics.consulting}
+\fancyfoot[L]{\sffamily\scriptsize\color{ink3}civilytics.com}
 \fancyfoot[C]{\sffamily\scriptsize\color{ink3}\thepage}
 \fancyfoot[R]{\sffamily\scriptsize\color{ink3}\textcopyright\ 2026}
 

inst/quarto/typst/typst-show.typ

@@ -0,0 +1,17 @@
+// Civilytics — Typst show/entry partial for Quarto (typst-show.typ).
+// Pairs with typst-template.typ. Quarto appends the rendered document body
+// after this partial, so this file intentionally ends with the show rule and
+// no trailing body token. (Do not write that token in a comment here: Quarto
+// interpolates its template variables even inside comments.)
+// Title/subtitle/date are wrapped in [ ] so arbitrary text (including words
+// that are Typst keywords like "for"/"in") is treated as content, not code.
+// See civilyticsR issue #12.
+#show: doc => civilytics(
+  title: [$title$],
+  $if(subtitle)$subtitle: [$subtitle$],$endif$
+  $if(by-author)$authors: ($for(by-author)$"$it.name.literal$",$endfor$),$endif$
+  $if(date)$date: [$date$],$endif$
+  $if(abstract)$abstract: [$abstract$],$endif$
+  toc: $if(toc)$true$else$false$endif$,
+  doc
+)

inst/quarto/typst/typst-template.typ

@@ -1,9 +1,15 @@
 // =============================================================
-// Civilytics — Typst template for Quarto PDF
+// Civilytics — Typst template partial for Quarto PDF (typst-template.typ).
+// Shipped as a Quarto template-partial (paired with typst-show.typ) rather
+// than a full `template:` so Quarto keeps its own `definitions` partial —
+// which defines Skylighting/token functions needed for syntax-highlighted
+// code blocks. See civilyticsR issue #12.
 // Usage in YAML:
 //   format:
 //     typst:
-//       template: quarto/typst/civilytics-typst.typ
+//       template-partials:
+//         - quarto/typst/typst-template.typ
+//         - quarto/typst/typst-show.typ
 // =============================================================
 
 #let paper-bg   = rgb("#FAF7F2")
@@ -54,7 +60,7 @@
       grid(
         columns: (1fr, auto, 1fr),
         align: (left, center, right),
-        [civilytics.consulting],
+        [civilytics.com],
         counter(page).display("1 / 1", both: true),
         [© 2026]
       )
@@ -229,16 +235,3 @@
 
   doc
 }
-
-// Quarto entry point
-#show: doc => civilytics(
-  title: $title$,
-  $if(subtitle)$subtitle: $subtitle$,$endif$
-  $if(by-author)$authors: ($for(by-author)$"$it.name.literal$",$endfor$),$endif$
-  $if(date)$date: $date$,$endif$
-  $if(abstract)$abstract: [$abstract$],$endif$
-  toc: $if(toc)$true$else$false$endif$,
-  doc
-)
-
-$body$

man/beep.Rd

@@ -1,71 +0,0 @@
-% 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

@@ -4,14 +4,10 @@
 \alias{na_sum}
 \title{Sum a numeric that contains missing values and ignore missing values}
 \usage{
-na_sum(x, quiet = FALSE)
+na_sum(x)
 }
 \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
@@ -22,5 +18,4 @@ 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

@@ -1,56 +0,0 @@
-% 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

@@ -1,30 +0,0 @@
-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

@@ -1,56 +0,0 @@
-# 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

@@ -133,17 +133,9 @@ test_that("theme_civilytics uses brand ink color for text", {
   expect_equal(th$text$colour, unname(civilytics_colors["ink"]))
 })
 
-test_that("theme_civilytics has transparent background by default", {
+test_that("theme_civilytics uses brand paper color for plot background", {
   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

@@ -58,12 +58,6 @@ 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")