Set up Quarto website course shell and {renv}

Author: stephan-koenig

.Rprofile

@@ -0,0 +1,14 @@
+# Use Posit Package Manager
+options(
+  renv.config.pak.enabled = TRUE,
+  renv.config.ppm.enabled = TRUE,
+  renv.config.ppm.default = TRUE
+)
+
+# Use renv
+source("renv/activate.R")
+
+# Set error handler to rlang
+if (require(rlang, quietly = TRUE)) {
+  globalCallingHandlers(error = rlang::entrace)
+}

.gitignore

@@ -127,3 +127,10 @@ dmypy.json
 
 # R user settings
 .Rproj.user
+
+# Quarto project files
+/.quarto/
+
+# Jupyter Book and Quarto outputs
+/_build/
+/_site/

R/combine-pdfs.R

@@ -0,0 +1,8 @@
+library(fs)
+library(qpdf)
+
+worksheets <- path("_site", "activities", "01_analysis-review.pdf")
+output <- path("_site", "activities", "analysis.pdf")
+combined_pdf <- file_temp(ext = "pdf")
+pdf_combine(c(worksheets, output), combined_pdf)
+file_copy(combined_pdf, worksheets, overwrite = TRUE)

R/format-md-link.R

@@ -0,0 +1,4 @@
+format_md_link <- function(link) {
+  glue::glue('[{link |> stringr::str_remove("https://")}]({link})') |>
+    I()
+}

_extensions/jmbuhr/qrcode/_extension.yml

@@ -0,0 +1,6 @@
+title: Qrcode
+author: Jannik Buhr
+version: 0.0.1
+contributes:
+  shortcodes:
+    - qrcode.lua

_extensions/jmbuhr/qrcode/assets/qrcode.js

@@ -0,0 +1,107 @@
+-- for development:
+local p = quarto.log.warning
+
+---Format string like in bash or python,
+---e.g. f('Hello ${one}', {one = 'world'})
+---@param s string The string to format
+---@param kwargs {[string]: string} A table with key-value replacemen pairs
+---@return string
+local function f(s, kwargs)
+  return (s:gsub('($%b{})', function(w) return kwargs[w:sub(3, -2)] or w end))
+end
+
+
+---Merge user provided options with defaults
+---@param userOptions table
+---@return string JSON string to pass to molstar
+local function mergeOptions(url, userOptions)
+  local defaultOptions = {
+    text = url,
+    width = 128,
+    height = 128,
+    colorDark = "#000000",
+    colorLight = "#ffffff",
+  }
+  if userOptions == nil then
+    return quarto.json.encode(defaultOptions)
+  end
+
+  for k, v in pairs(userOptions) do
+    local value = pandoc.utils.stringify(v)
+    if value == 'true' then value = true end
+    if value == 'false' then value = false end
+    defaultOptions[k] = value
+  end
+
+  return quarto.json.encode(defaultOptions)
+end
+
+
+---@return string
+local function wrapInlineDiv(options)
+  return [[
+<div id="${id}" class="qrcode"></div>
+<script type="text/javascript">
+(function() {
+  var script = document.currentScript;
+  var qrcode = script.previousElementSibling;
+  qrcode.qrcode = new QRCode(qrcode, ]] .. options .. [[);
+  script.remove();
+})();
+</script>
+    ]]
+end
+
+---@return string
+local function wrapInlineTex(url, opts)
+  return [[
+\qrcode[]] .. opts .. [[]{]] .. url .. [[}
+    ]]
+end
+
+return {
+  ['qrcode'] = function(args, kwargs, _)
+    if quarto.doc.is_format("html:js") then
+      quarto.doc.add_html_dependency {
+        name = 'qrcodejs',
+        version = 'v1.0.0',
+        scripts = { './assets/qrcode.js' },
+      }
+      local url = pandoc.utils.stringify(args[1])
+      local id = ""
+      if args[2] ~= nil then
+        id = f('id="${id}" ', { id = pandoc.utils.stringify(id) })
+      end
+      local options = mergeOptions(url, kwargs)
+      local text = wrapInlineDiv(options)
+      return pandoc.RawBlock(
+        'html',
+        f(text, { id = id })
+      )
+    elseif quarto.doc.is_format("pdf") then
+      quarto.doc.use_latex_package("qrcode")
+      local url = pandoc.utils.stringify(args[1])
+      local opts = ""
+      for k, v in pairs(kwargs) do
+        if string.match(k, "^pdf") then
+          k = string.sub(k, 4)
+          opts = opts .. k .. "=" .. v .. ", "
+        end
+      end
+      for _, v in ipairs(args) do
+        if string.match(v, "^pdf") then
+          v = string.sub(v, 4)
+          opts = opts .. v .. ", "
+        end
+      end
+      if string.len(opts) then
+        opts = string.sub(opts, 1, string.len(opts) - 2)
+      end
+      local text = wrapInlineTex(url, opts)
+      return pandoc.RawBlock(
+        'tex',
+        text
+      )
+    end
+  end,
+}

_extensions/jmbuhr/qrcode/qrcode.lua

@@ -0,0 +1,9 @@
+title: Include Code Files
+author: Bruno Beaufils
+version: 1.0.0
+quarto-required: ">=1.2"
+contributes:
+  filters:
+    - include-code-files.lua
+
+

_extensions/quarto-ext/include-code-files/_extension.yml

@@ -0,0 +1,130 @@
+--- include-code-files.lua – filter to include code from source files
+---
+--- Copyright: © 2020 Bruno BEAUFILS
+--- License:   MIT – see LICENSE file for details
+
+--- Dedent a line
+local function dedent(line, n)
+  return line:sub(1, n):gsub(" ", "") .. line:sub(n + 1)
+end
+
+--- Find snippet start and end.
+--
+--  Use this to populate startline and endline.
+--  This should work like pandocs snippet functionality: https://github.com/owickstrom/pandoc-include-code/tree/master
+local function snippet(cb, fh)
+  if not cb.attributes.snippet then
+    return
+  end
+
+  -- Cannot capture enum: http://lua-users.org/wiki/PatternsTutorial
+  local comment
+  local comment_stop = ""
+  if
+    string.match(cb.attributes.include, ".py$")
+    or string.match(cb.attributes.include, ".jl$")
+    or string.match(cb.attributes.include, ".r$")
+  then
+    comment = "#"
+  elseif string.match(cb.attributes.include, ".o?js$") or string.match(cb.attributes.include, ".css$") then
+    comment = "//"
+  elseif string.match(cb.attributes.include, ".lua$") then
+    comment = "--"
+  elseif string.match(cb.attributes.include, ".html$") then
+    comment = "<!%-%-"
+    comment_stop = " *%-%->"
+  else
+    -- If not known assume that it is something one or two long and not alphanumeric.
+    comment = "%W%W?"
+  end
+
+  local p_start = string.format("^ *%s start snippet %s%s", comment, cb.attributes.snippet, comment_stop)
+  local p_stop = string.format("^ *%s end snippet %s%s", comment, cb.attributes.snippet, comment_stop)
+  local start, stop = nil, nil
+
+  -- Cannot use pairs.
+  local line_no = 1
+  for line in fh:lines() do
+    if start == nil then
+      if string.match(line, p_start) then
+        start = line_no + 1
+      end
+    elseif stop == nil then
+      if string.match(line, p_stop) then
+        stop = line_no - 1
+      end
+    else
+      break
+    end
+    line_no = line_no + 1
+  end
+
+  -- Reset so nothing is broken later on.
+  fh:seek("set")
+
+  -- If start and stop not found, just continue
+  if start == nil or stop == nil then
+    return nil
+  end
+
+  cb.attributes.startLine = tostring(start)
+  cb.attributes.endLine = tostring(stop)
+end
+
+--- Filter function for code blocks
+local function transclude(cb)
+  if cb.attributes.include then
+    local content = ""
+    local fh = io.open(cb.attributes.include)
+    if not fh then
+      io.stderr:write("Cannot open file " .. cb.attributes.include .. " | Skipping includes\n")
+    else
+      local number = 1
+      local start = 1
+
+      -- change hyphenated attributes to PascalCase
+      for i, pascal in pairs({ "startLine", "endLine" }) do
+        local hyphen = pascal:gsub("%u", "-%0"):lower()
+        if cb.attributes[hyphen] then
+          cb.attributes[pascal] = cb.attributes[hyphen]
+          cb.attributes[hyphen] = nil
+        end
+      end
+
+      -- Overwrite startLine and stopLine with the snippet if any.
+      snippet(cb, fh)
+
+      if cb.attributes.startLine then
+        cb.attributes.startFrom = cb.attributes.startLine
+        start = tonumber(cb.attributes.startLine)
+      end
+
+      for line in fh:lines("L") do
+        if cb.attributes.dedent then
+          line = dedent(line, cb.attributes.dedent)
+        end
+        if number >= start then
+          if not cb.attributes.endLine or number <= tonumber(cb.attributes.endLine) then
+            content = content .. line
+          end
+        end
+        number = number + 1
+      end
+
+      fh:close()
+    end
+
+    -- remove key-value pair for used keys
+    cb.attributes.include = nil
+    cb.attributes.startLine = nil
+    cb.attributes.endLine = nil
+    cb.attributes.dedent = nil
+
+    -- return final code block
+    return pandoc.CodeBlock(content, cb.attr)
+  end
+end
+
+return {
+  { CodeBlock = transclude },
+}

_extensions/quarto-ext/include-code-files/include-code-files.lua

@@ -0,0 +1,91 @@
+project:
+  type: website
+  output-dir: _site
+  preview:
+    port: 4200
+    browser: false
+  render:
+    - "*.qmd"
+    - "slides"
+    - "!quarto"
+    - "!tools"
+    - "!about"
+    - "!getting-started"
+    - "!notes"
+
+  post-render:
+    - R/combine-pdfs.R
+
+website:
+  title: "{{< var course.full-title >}}"
+  description: >
+    Course website for {{< var course.code >}} of the Department of Computer Science at the
+    University of British Columbia
+  open-graph: true
+  twitter-card: true
+  site-url: "https://ubc-cs.github.io/cpsc203"
+  repo-url: "https://github.com/UBC-CS/cpsc203"
+  repo-actions: [source, edit, issue]
+  bread-crumbs: false
+
+  page-footer:
+    left: >
+      CPSC 203 was created by
+      [Dr. Cinda Heeren](https://www.cs.ubc.ca/people/cinda-heeren),
+      then adapted by [Dr. Firas Moosvi](https://firas.moosvi.com), and further
+      refined by [Dr. Ian Mitchell](https://www.cs.ubc.ca/~mitchell/).
+      The website and slides were converted to [Quarto](https://quarto.org/) by
+      [Dr. Stephan Koenig](https://stephankoenig.io).
+    center: >
+      UBC's Point Grey Campus is located on the traditional, ancestral, and
+      unceded territory of the [xʷməθkʷəy̓ə
+      (Musqueam)](https://www.musqueam.bc.ca/) people.
+    right: >
+      Unless specified otherwise, all content on this site is licensed under
+      [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0)
+      {{< iconify fa6-brands creative-commons >}}
+      {{< iconify fa6-brands creative-commons-by >}}
+      {{< iconify fa6-brands creative-commons-sa >}}
+
+  search:
+    location: sidebar
+    type: overlay
+
+  sidebar:
+    style: floating
+    search: true
+    contents:
+      - section: "Course information"
+        contents:
+          - href: announcements.qmd
+            text: "Announcements"
+          - href: syllabus.qmd
+            text: "Syllabus"
+          - href: index.qmd
+            text: "Schedule"
+      - section: "Resources"
+        contents:
+          - href: formatting.qmd
+            text: "Formatting"
+          - href: "https://canvas.ubc.ca/courses/130127"
+            text: "Canvas"
+          - href: "https://ca.prairielearn.com/pl/course_instance/6665"
+            text: "PrairieLearn"
+
+  # comments:
+  #   giscus:
+  #     repo: UBC-CS/cpsc203
+  #     repo-id:
+  #     category: announcements
+  #     category-id:
+  #     mapping: title
+  #     reactions-enabled: true
+  #     loading: lazy
+
+format:
+  html:
+    theme: [cosmo, styles/theme.scss]
+    css: styles/styles.css
+    toc: true
+
+freeze: auto