🔄 synced local '_extensions/rostools/r3-theme/' with remote '_extensi…

…ons/r3-theme/'

_extensions/rostools/r3-theme/_extension.yml

@@ -4,6 +4,10 @@ version: 1.0.6
 quarto-required: ">=1.5.0"
 contributes:
   format:
+    common:
+      shortcodes:
+        - debruine/glossary
+        - quarto-ext/fontawesome
     html:
       highlight-style: a11y
       fig-dpi: 72
@@ -34,10 +38,14 @@ contributes:
       execute: project
 
     book:
+      navbar:
+        logo: "favicon.ico"
+        logo-alt: "Graphic of a capital R with a 3 as a superscript."
+        search: true
+        pinned: true
       favicon: "favicon.ico"
       repo-branch: main
       repo-actions: [edit, issue, source]
-      search: true
 
     csl: vancouver.csl
 
@@ -49,3 +57,8 @@ contributes:
 
     execute:
       freeze: auto
+
+    knitr:
+      opts_chunk:
+        R.options:
+          width: 72

_extensions/rostools/r3-theme/_extensions/debruine/glossary/_extension.yml

@@ -0,0 +1,7 @@
+title: Glossary
+author: Lisa DeBruine
+version: 1.0.0
+quarto-required: ">=1.2.0"
+contributes:
+  shortcodes:
+    - glossary.lua

_extensions/rostools/r3-theme/_extensions/debruine/glossary/glossary.css

@@ -0,0 +1,56 @@
+.glossary {
+  color: purple;
+  text-decoration: underline;
+  cursor: help;
+  position: relative;
+  border: none;
+  padding: 0;
+}
+
+/* only needed for popup = "click" */
+/* popup-definition */
+.glossary .def {
+  display: none;
+  position: absolute;
+  z-index: 1;
+  width: 200px;
+  bottom: 100%;
+  left: 50%;
+  margin-left: -100px;
+  background-color: #333;
+  color: white;
+  padding: 5px;
+  border-radius: 6px;
+}
+/* show on click */
+.glossary:active .def {
+  display: inline-block;
+}
+/* triangle arrow */
+.glossary:active .def::after {
+  content: ' ';
+  position: absolute;
+  top: 100%;
+  left: 50%;
+  margin-left: -5px;
+  border-width: 5px;
+  border-style: solid;
+  border-color: #333 transparent transparent transparent;
+}
+
+/* glossary table styles */
+.glossary_table td {
+  vertical-align: top;
+}
+
+.glossary_table td:first-child {
+  padding-right: 1em;
+}
+
+.glossary_table tr {
+  border-bottom: 1px solid #ddd;
+}
+
+.glossary_table tr:nth-child(even) {
+  background-color: #99999933;
+}

_extensions/rostools/r3-theme/_extensions/debruine/glossary/glossary.lua

@@ -0,0 +1,174 @@
+-- Glossary.lua
+-- Author: Lisa DeBruine
+
+-- Global glossary table
+globalGlossaryTable = {}
+
+-- Helper Functions
+
+local function addHTMLDeps()
+  -- add the HTML requirements for the library used
+    quarto.doc.add_html_dependency({
+    name = 'glossary',
+    stylesheets = {'glossary.css'}
+  })
+end
+
+local function kwExists(kwargs, keyword)
+    for key, value in pairs(kwargs) do
+        if key == keyword then
+            return true
+        end
+    end
+    return false
+end
+
+-- Function to sort a Lua table by keys
+function sortByKeys(tbl)
+    local sortedKeys = {}
+
+    -- Extract keys from the table and store them in the 'sortedKeys' array
+    for key, _ in pairs(tbl) do
+        table.insert(sortedKeys, key)
+    end
+
+    -- Sort the keys alphabetically
+    table.sort(sortedKeys)
+
+    -- Create a new table with the sorted keys
+    local sortedTable = {}
+    for _, key in pairs(sortedKeys) do
+        sortedTable[key] = tbl[key]
+    end
+
+    return sortedTable
+end
+
+local function read_metadata_file(fname)
+  local metafile = io.open(fname, 'r')
+  local content = metafile:read("*a")
+  metafile:close()
+  local metadata = pandoc.read(content, "markdown").meta
+  return metadata
+end
+
+local function readGlossary(path)
+  local f = io.open(path, "r")
+  if not f then
+    io.stderr:write("Cannot open file " .. path)
+  else
+    local lines = f:read("*all")
+    f:close()
+    return(lines)
+  end
+end
+
+---Merge user provided options with defaults
+---@param userOptions table
+local function mergeOptions(userOptions, meta)
+  local defaultOptions = {
+    path = "glossary.yml",
+    popup = "hover",
+    show = true,
+    add_to_table = true
+  }
+
+  -- override with meta values first
+  if meta.glossary ~= nil then
+    for k, v in pairs(meta.glossary) 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
+  end
+
+  -- then override with function keyword values
+  if userOptions ~= nil then
+    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
+  end
+
+  return defaultOptions
+end
+
+
+-- Main Glossary Function Shortcode
+
+return {
+
+["glossary"] = function(args, kwargs, meta)
+
+  -- this will only run for HTML documents
+  if not quarto.doc.isFormat("html:js") then
+    return pandoc.Null()
+  end
+
+  addHTMLDeps()
+
+  -- create glossary table
+  if kwExists(kwargs, "table") then
+    local gt = "<table class='glossary_table'>\n"
+    gt = gt .. "<tr><th> Term </th><th> Definition </th></tr>\n"
+
+    local sortedTable = sortByKeys(globalGlossaryTable)
+
+    for key, value in pairs(sortedTable) do
+        gt = gt .. "<tr><td>" .. key
+        gt = gt .. "</td><td>" .. value .. "</td></tr>\n"
+    end
+    gt = gt .. "</table>"
+
+    return pandoc.RawBlock('html', gt)
+  end
+
+  -- or set up in-text term
+  local options = mergeOptions(kwargs, meta)
+
+  local display = pandoc.utils.stringify(args[1])
+  local term = string.lower(display)
+
+  if kwExists(kwargs, "display") then
+    display = pandoc.utils.stringify(kwargs.display)
+  end
+
+  -- get definition
+  local def = ""
+  if kwExists(kwargs, "def") then
+    def = pandoc.utils.stringify(kwargs.def)
+  else
+    local metafile = io.open(options.path, 'r')
+    local content = "---\n" .. metafile:read("*a") .. "\n---\n"
+    metafile:close()
+    local glossary = pandoc.read(content, "markdown").meta
+    for key, value in pairs(glossary) do
+      glossary[string.lower(key)] = value
+    end
+    -- quarto.log.output()
+    if kwExists(glossary, term) then
+      def = pandoc.utils.stringify(glossary[term])
+    end
+  end
+
+  -- add to global table
+  if options.add_to_table then
+    globalGlossaryTable[term] = def
+  end
+
+  if options.popup == "hover" then
+    glosstext = "<button class='glossary' title='" .. def .."'>" .. display .. "</button>"
+  elseif options.popup == "click" then
+    glosstext = "<button class='glossary'><span class='def'>" .. def .."</span>" .. display .. "</button>"
+  elseif options.popup == "none" then
+    glosstext = "<button class='glossary'>" .. display .. "</button>"
+  end
+
+  return pandoc.RawInline("html", glosstext)
+
+end
+
+}

_extensions/rostools/r3-theme/_extensions/quarto-ext/fontawesome/_extension.yml

@@ -0,0 +1,7 @@
+title: Font Awesome support
+author: Carlos Scheidegger
+version: 1.2.0
+quarto-required: ">=1.2.269"
+contributes:
+  shortcodes:
+    - fontawesome.lua