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)
@@ -72,4 +71,3 @@ importFrom(stats,qnorm)
 importFrom(stats,runif)
 importFrom(stringdist,stringsim)
 importFrom(stringr,str_count)
-importFrom(utils,flush.console)

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
-  .copy_pkg_file(
-    "quarto/typst/civilytics-typst.typ",
-    "typst/civilytics-typst.typ",
-    path, force
-  )
+  # Typst — shipped as template-partials so Quarto keeps its Skylighting
+  # definitions and syntax-highlighted code blocks render (see issue #12)
+  typst_files <- c("typst-template.typ", "typst-show.typ")
+  for (f in typst_files) {
+    .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/utils.R

@@ -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, quiet = FALSE) {
+na_sum <- function(x) {
   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

@@ -2,6 +2,7 @@
 # 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.

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)
 }

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_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")