init: add quarto rendering files

_environment

+QUARTO_PYTHON="/opt/conda/envs/igfl_python/bin/python3"

_extensions/custom-callout/_extension.yml

+title: custom-callout
+author: James Joseph Balamuta
+version: 0.0.0-dev.1
+quarto-required: ">=1.5.0"
+contributes:
+  filters:
+    - customcallout.lua
+    - fa.lua
+

_extensions/custom-callout/customcallout.lua

+-- customcallout.lua
+local customCallouts = {}
+
+local fa = require("fa")
+
+-- Function to convert color to rgba
+local function colorToRgba(color, alpha)
+  if color:sub(1,1) == "#" then
+    local r = tonumber(color:sub(2,3), 16)
+    local g = tonumber(color:sub(4,5), 16)
+    local b = tonumber(color:sub(6,7), 16)
+    return string.format("rgba(%d, %d, %d, %.2f)", r, g, b, alpha)
+  else
+    -- For named colors, we use the functional notation of rgba()
+    return string.format("rgb(from %s r g b / %.0f%%)", color, alpha * 100)
+  end
+end
+
+-- Function to check if a string starts with "fa-"
+local function isFontAwesomeIcon(icon)
+  return icon ~= nil and icon:sub(1, 3) == "fa-"
+end
+
+-- Generate CSS for custom callouts
+local function generateCustomCSS()
+  local css = ""
+
+  -- Translate YAML callout information for custom callouts
+  for type, callout in pairs(customCallouts) do
+    if callout.color then
+      local color = pandoc.utils.stringify(callout.color)
+      
+      -- Base color
+      css = css .. string.format("div.callout-%s.callout {\n", type)
+      css = css .. string.format("  border-left-color: %s;\n", color)
+      css = css .. "}\n"
+      
+      -- Header background
+      css = css .. string.format("div.callout-%s.callout-style-default > .callout-header {\n", type)
+      css = css .. string.format("  background-color: %s;\n", colorToRgba(color, 0.13))
+      css = css .. "}\n"
+
+      -- Collapse Icon
+      css = css .. string.format("div.callout-%s .callout-toggle::before {", type)
+      css = css .. "  background-image: url('data:image/svg+xml,<svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"rgb(33, 37, 41)\" class=\"bi bi-chevron-down\" viewBox=\"0 0 16 16\"><path fill-rule=\"evenodd\" d=\"M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z\"/></svg>');"
+      css = css .. "}\n"
+      
+      -- Icon Styling
+      css = css .. string.format("div.callout-%s.callout-style-default .callout-icon::before, div.callout-%s.callout-titled .callout-icon::before {\n", type, type)
+
+      if callout.icon_symbol then
+        local icon_symbol_str = pandoc.utils.stringify(callout.icon_symbol)
+        if isFontAwesomeIcon(icon_symbol_str) then
+          quarto.log.output("icon_symbol_str is a Font Awesome icon")
+          -- Font Awesome icon
+          css = css .. string.format("  font-family: 'Font Awesome 6 Free';\n")
+          css = css .. string.format("  content: '%s';\n", fa.fa_unicode(icon_symbol_str))         
+        else 
+          -- Custom icon symbol
+          css = css .. string.format("  content: '%s';\n", icon_symbol_str)
+        end
+        css = css .. "  background-image: none;\n"
+      else 
+        css = css .. string.format("  background-image: url('data:image/svg+xml,<svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"%s\" class=\"bi bi-exclamation-triangle\" viewBox=\"0 0 16 16\"><path d=\"M7.938 2.016A.13.13 0 0 1 8.002 2a.13.13 0 0 1 .063.016.146.146 0 0 1 .054.057l6.857 11.667c.036.06.035.124.002.183a.163.163 0 0 1-.054.06.116.116 0 0 1-.066.017H1.146a.115.115 0 0 1-.066-.017.163.163 0 0 1-.054-.06.176.176 0 0 1 .002-.183L7.884 2.073a.147.147 0 0 1 .054-.057zm1.044-.45a1.13 1.13 0 0 0-1.96 0L.165 13.233c-.457.778.091 1.767.98 1.767h13.713c.889 0 1.438-.99.98-1.767L8.982 1.566z\"/></svg>');\n", escapedColor)
+      end 
+
+      css = css .. "}\n"
+
+    end
+  end
+  return css
+end
+
+
+-- Parse YAML and extract custom callout definitions
+local function parseCustomCallouts(meta)
+  if not meta['custom-callout'] then return end
+
+  for k, v in pairs(meta['custom-callout']) do
+    if type(v) == "table" then
+      customCallouts[k] = {
+        type = k,
+        title = v.title or k:gsub("^%l", string.upper),
+        icon = v.icon == 'true' or nil,
+        appearance = v.appearance or nil,
+        collapse = v.collapse or nil,
+        icon_symbol = v['icon-symbol'] or nil,
+        color = v.color or nil,
+        background_color = v['background-color'] or nil
+      }
+    end
+  end
+
+
+  -- Generate and add custom CSS to the document
+  local customCSS = generateCustomCSS()
+  if customCSS ~= "" then
+    quarto.doc.include_text('in-header', '<style>\n' .. customCSS .. '</style>')
+  end
+
+end
+
+
+-- Convert div to custom callout if it matches a defined custom callout
+local function convertToCustomCallout(div)
+  -- Check if the div has classes
+  for _, class in ipairs(div.classes) do
+    
+    -- Check if the class matches a custom callout
+    local callout = customCallouts[class]
+
+    if callout then 
+
+      -- Create a new Callout with the custom callout parameters
+      local calloutParams = {
+        type = callout.type,
+        content = div.content,
+        title = div.attributes.title or callout.title,
+        icon = div.attributes.icon or callout.icon,
+        appearance = div.attributes.appearance or callout.appearance,
+        collapse = div.attributes.collapse or callout.collapse
+      }
+      
+      return quarto.Callout(calloutParams)
+    end
+  end
+  
+
+  return div
+end
+
+-- Main filter function
+local function customCalloutFilter(doc)
+
+  -- Walk the AST and process divs
+  doc.blocks = doc.blocks:walk({
+    Div = convertToCustomCallout
+  })
+  
+  -- Return the modified document
+  return doc
+end
+
+-- Return the Pandoc filter
+return {
+  Meta = parseCustomCallouts,
+  Pandoc = customCalloutFilter
+}
\ No newline at end of file

_quarto.yml

+project:
+  type: book
+  output-dir: public
+  resources: 
+    - chapters/1_basics/data/proteins.tab
+    - chapters/2_numpy/data/blobs.tif
+    - chapters/2_numpy/data/coords_P.dat
+    - chapters/3_pandas/data/pod5_inspect.csv
+
+book:
+  title: "Python for beginners"
+  author:
+    - "Laurent Gilquin [laurent.gilquin@ens-lyon.fr](mailto:laurent.gilquin@ens-lyon.fr)"
+    - "Hugo Blanc [hugo.blanc@ens-lyon.fr](mailto:hugo.blanc@ens-lyon.fr)"
+    - "Bernard Billoud [bernard.billoud@ens-lyon.fr](mailto:bernard.billoud@ens-lyon.fr)"
+  date: "2025-03-01"
+  chapters:
+    - index.qmd
+    - preamble/preamble.qmd
+    - part: "Chapters"
+    - chapters/1_basics/main.qmd
+    - chapters/2_numpy/main.qmd
+    - chapters/3_pandas/main.qmd
+    - chapters/4_visualisation/main.qmd
+  appendices:
+    - appendix/files.qmd
+    - appendix/numpy.qmd
+  page-footer: "License: Creative Commons [CC-BY-SA-4.0](http://creativecommons.org/licenses/by-sa/4.0/).  Made with [Quarto](https://quarto.org/)."
+  navbar:
+    title: "Python for beginners"
+    search: true
+    logo: assets/image/python.svg
+    right:
+      - icon: git
+        href: https://gitbio.ens-lyon.fr/lgilquin/python-basis
+        text: Sources
+
+  sidebar:
+    style: docked
+  reader-mode: true
+
+format:
+  html:
+    toc-depth: 4
+    crossrefs-hover: false
+    include-in-header:
+      - file: _includes/fontawesome.html
+      - file: _includes/mathjax.html
+      - file: _includes/iconify.html
+      - file: _includes/jquery.html
+    include-after-body:
+      - file: _includes/hide_df.html
+    html-math-method:
+      method: mathjax
+      url: "https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-mml-chtml.js"
+    theme:
+      light: [flatly, _sass/main-light.scss]
+      dark: [darkly, _sass/main-dark.scss]
+
+execute:
+  cache: false
+  freeze: auto

chapters/2_numpy/main.qmd

@@ -783,7 +783,7 @@ print("image1_bis is a copy:", image1_bis.base is None)
 Despite the nice features of array views, it is sometimes useful to instead explicitly copy the data within an array or a subarray. This can be done with the `copy` method:
 ```{python}
 new_arr = image1[:, 0].copy()
-print("view is a copy:", new_arr.base is None)
+print("new_arr is a copy:", new_arr.base is None)
 new_arr[:] = 1
 print(image1)
 ```