/* ==========================================================================
   Omics with Johnson — Reader-Friendly Book Theme
   Design tokens: docs/DESIGN.md
   ========================================================================== */

/* --- Google Fonts (for HTML; PDF uses system-installed fonts) --- */
@import url('https://fonts.googleapis.com/css2?family=Fira+Code:wght@400;600&family=Inter:ital,wght@0,400;0,600;0,700;1,400&family=Lora:ital,wght@0,400;0,500;0,600;0,700;1,400;1,500;1,600;1,700&family=Outfit:wght@400;600;700;800&display=swap');

/* ==========================================================================
   Design Tokens
   ========================================================================== */
:root {
  /* Brand colors */
  --jp-primary: #3b1a54;
  --jp-primary-light: #5c357f;
  --jp-primary-lighter: #f1ebf7;
  --jp-accent: #ff6f00;
  --jp-accent-light: #fff3e0;
  --jp-accent-border: #ffe0b2;

  /* Neutrals */
  --jp-bg: #ffffff;
  --jp-surface: #f8f9fa;
  --jp-border: #dee2e6;
  --jp-text: #1a1a2e;
  --jp-text-secondary: #495057;
  --jp-text-muted: #868e96;

  /* Typography */
  --jp-font-body: 'Lora', Georgia, serif;
  --jp-font-heading: 'Outfit', sans-serif;
  --jp-font-code: 'Fira Code', 'SF Mono', 'Cascadia Code', Consolas, monospace;

  /* Spacing scale (4px base) */
  --jp-space-xs: 0.25rem;
  --jp-space-sm: 0.5rem;
  --jp-space-md: 1rem;
  --jp-space-lg: 1.5rem;
  --jp-space-xl: 2rem;
  --jp-space-2xl: 3rem;
  --jp-space-3xl: 4rem;

  /* Reading */
  --jp-line-length: 720px;
}

/* ==========================================================================
   Base Typography
   ========================================================================== */
body {
  font-family: var(--jp-font-body);
  color: var(--jp-text);
  font-size: 1.15rem;
  line-height: 1.85;
  background-color: var(--jp-bg);
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
}

/* --- Headings --- */
h1, h2, h3, h4, h5, h6 {
  font-family: var(--jp-font-heading);
  color: var(--jp-primary);
  margin-top: var(--jp-space-2xl);
  margin-bottom: var(--jp-space-md);
  line-height: 1.25;
}

h1 {
  font-size: 2.5rem;
  font-weight: 800;
  letter-spacing: -0.02em;
  margin-top: 0;
}

h2 {
  font-size: 1.75rem;
  font-weight: 700;
  letter-spacing: -0.01em;
  border-bottom: 1px solid var(--jp-border);
  padding-bottom: var(--jp-space-sm);
}

h3 {
  font-size: 1.35rem;
  font-weight: 600;
}

h4 {
  font-size: 1.1rem;
  font-weight: 600;
}

/* --- Paragraphs & Links --- */
p {
  margin-bottom: var(--jp-space-md);
}

a {
  color: var(--jp-primary-light);
  text-decoration: underline;
  text-underline-offset: 2px;
  text-decoration-thickness: 1px;
  transition: color 0.15s ease;
}

a:hover {
  color: var(--jp-primary);
}

/* ==========================================================================
   Title Block (Book & Chapter)
   ========================================================================== */
.quarto-title-block .quarto-title-banner {
  background: linear-gradient(135deg, var(--jp-primary) 0%, var(--jp-primary-light) 100%);
  color: white;
  padding: var(--jp-space-3xl) 0;
  margin-bottom: var(--jp-space-2xl);
}

.quarto-title-block .quarto-title-banner .title {
  font-family: var(--jp-font-heading);
  font-size: 3rem;
  font-weight: 800;
  letter-spacing: -0.02em;
  line-height: 1.1;
  color: white;
}

.quarto-title-block .quarto-title-banner .subtitle {
  font-size: 1.2rem;
  font-weight: 400;
  opacity: 0.9;
  margin-top: var(--jp-space-sm);
}

.quarto-title-block .quarto-title-banner .author,
.quarto-title-block .quarto-title-banner .date {
  opacity: 0.8;
  font-size: 0.9rem;
}

/* ==========================================================================
   Table of Contents
   ========================================================================== */
#TOC {
  font-family: var(--jp-font-body);
}

#TOC .nav-link {
  color: var(--jp-text-secondary);
  border-left: 2px solid transparent;
  padding: 0.3rem var(--jp-space-md);
  font-size: 0.9rem;
  transition: all 0.15s ease;
}

#TOC .nav-link:hover {
  color: var(--jp-primary);
  border-left-color: var(--jp-primary-lighter);
}

#TOC .nav-link.active {
  color: var(--jp-primary);
  border-left-color: var(--jp-primary);
  font-weight: 600;
}

/* TOC levels */
#TOC .nav > li > a {
  font-weight: 500;
}

#TOC .nav .nav > li > a {
  font-size: 0.85rem;
  padding-left: var(--jp-space-lg);
}

#TOC .nav .nav .nav > li > a {
  font-size: 0.8rem;
  padding-left: var(--jp-space-xl);
}

/* ==========================================================================
   Tables
   ========================================================================== */
.table {
  width: 100%;
  margin-bottom: var(--jp-space-lg);
  border-collapse: collapse;
  font-size: 0.9rem;
}

.table thead th {
  background-color: var(--jp-surface);
  color: var(--jp-primary);
  font-family: var(--jp-font-heading);
  font-weight: 600;
  border-bottom: 2px solid var(--jp-primary);
  padding: var(--jp-space-sm) var(--jp-space-md);
  text-align: left;
}

.table tbody td {
  padding: var(--jp-space-sm) var(--jp-space-md);
  border-bottom: 1px solid var(--jp-border);
}

.table tbody tr:hover {
  background-color: var(--jp-primary-lighter);
}

.table.table-striped tbody tr:nth-child(odd) {
  background-color: var(--jp-surface);
}

/* ==========================================================================
   Code Blocks
   ========================================================================== */
pre {
  background-color: #1e1e2e;
  color: #cdd6f4;
  border-radius: 8px;
  padding: var(--jp-space-lg);
  font-size: 0.85rem;
  line-height: 1.55;
  overflow-x: auto;
  box-shadow: 0 2px 8px rgba(0,0,0,0.08);
  margin-bottom: var(--jp-space-lg);
}

pre code {
  background: none;
  color: inherit;
  padding: 0;
  font-size: inherit;
  font-family: var(--jp-font-code);
}

pre.code {
  border-left: 4px solid var(--jp-primary);
  background-color: #1a1a24;
  border-top-left-radius: 0;
  border-bottom-left-radius: 0;
  transition: border-left-color 0.25s ease, box-shadow 0.25s ease;
}

pre.code:hover {
  border-left-color: var(--jp-accent);
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
}

/* Inline code */
code {
  background-color: var(--jp-surface);
  color: #d63384;
  padding: 0.15em 0.4em;
  border-radius: 4px;
  font-size: 0.85em;
  font-family: var(--jp-font-code);
}

/* Source code cell (not output) */
.cell-source pre {
  background-color: #f4f6f8;
  color: #1a1a2e;
  border: 1px solid var(--jp-border);
}

.cell-source code {
  color: inherit;
}

/* Code copy button */
.btn-copy {
  position: relative;
  float: right;
  opacity: 0.5;
  transition: opacity 0.15s ease;
}

pre:hover .btn-copy {
  opacity: 1;
}

/* ==========================================================================
   Figures & Images
   ========================================================================== */
.figure img,
.cell-output-display img {
  max-width: 100%;
  height: auto;
  border-radius: 8px;
  box-shadow: 0 4px 16px rgba(0,0,0,0.1);
  border: 1px solid var(--jp-border);
  transition: box-shadow 0.3s ease;
}

.figure img:hover,
.cell-output-display img:hover {
  box-shadow: 0 8px 24px rgba(0,0,0,0.15);
}

/* ==========================================================================
   Callout Blocks
   ========================================================================== */

/* --- Johnson's First Principle (custom callout) --- */
.callout-first-principles {
  border-left: 6px solid var(--jp-accent);
  background: var(--jp-accent-light);
  padding: var(--jp-space-lg) var(--jp-space-xl);
  margin: var(--jp-space-xl) 0;
  border-radius: 0 8px 8px 0;
}

.callout-first-principles::before {
  content: "JOHNSON'S FIRST PRINCIPLE";
  display: block;
  font-family: var(--jp-font-heading);
  font-size: 0.7rem;
  font-weight: 800;
  color: var(--jp-accent);
  letter-spacing: 3px;
  text-transform: uppercase;
  margin-bottom: var(--jp-space-sm);
}

.callout-first-principles p:last-child {
  margin-bottom: 0;
}

/* --- Standard Quarto callout overrides --- */
.callout {
  border-radius: 8px;
  border-left-width: 6px !important;
  box-shadow: 0 2px 8px rgba(0,0,0,0.04);
  margin: var(--jp-space-xl) 0;
}

.callout.callout-warning {
  border-left-color: var(--jp-accent) !important;
}

.callout.callout-important {
  border-left-color: #d32f2f !important;
}

.callout.callout-note {
  border-left-color: var(--jp-primary) !important;
}

.callout.callout-tip {
  border-left-color: #2e7d32 !important;
}

.callout-header {
  font-family: var(--jp-font-heading);
  font-weight: 700;
  font-size: 0.8rem;
  letter-spacing: 1px;
  text-transform: uppercase;
}

/* ==========================================================================
   Blockquotes
   ========================================================================== */
blockquote {
  border-left: 4px solid var(--jp-primary-light);
  background: var(--jp-surface);
  padding: var(--jp-space-md) var(--jp-space-lg);
  margin: var(--jp-space-lg) 0;
  border-radius: 0 8px 8px 0;
  color: var(--jp-text-secondary);
  font-style: italic;
}

blockquote p:last-child {
  margin-bottom: 0;
}

/* ==========================================================================
   Content Dividers
   ========================================================================== */
hr {
  border: none;
  height: 2px;
  background: linear-gradient(to right, transparent, var(--jp-border), transparent);
  margin: var(--jp-space-2xl) 0;
}

/* ==========================================================================
   Navigation & Footer
   ========================================================================== */
.navbar {
  background-color: rgba(255, 255, 255, 0.85) !important;
  backdrop-filter: blur(12px);
  -webkit-backdrop-filter: blur(12px);
  border-bottom: 1px solid rgba(0,0,0,0.05);
  padding: 0.8rem 0;
}

.navbar-brand {
  font-family: var(--jp-font-heading);
  font-size: 1.4rem;
  font-weight: 700;
  color: var(--jp-primary) !important;
  letter-spacing: -0.5px;
}

.navbar .nav-link,
[data-bs-theme="dark"] .navbar .nav-link {
  font-size: 0.95rem;
  color: var(--jp-text-secondary) !important;
  font-weight: 500;
  transition: color 0.15s ease;
}

.navbar .nav-link:hover,
[data-bs-theme="dark"] .navbar .nav-link:hover {
  color: var(--jp-primary-light) !important;
}

.navbar .nav-link.active,
[data-bs-theme="dark"] .navbar .nav-link.active {
  color: var(--jp-primary) !important;
  font-weight: 600;
}

/* Sidebar */
.sidebar {
  font-family: var(--jp-font-body);
  font-size: 0.9rem;
}

.sidebar .sidebar-item {
  padding: 0.2rem 0;
}

/* Footer */
.nav-footer {
  border-top: 1px solid var(--jp-border);
  margin-top: var(--jp-space-3xl);
  padding-top: var(--jp-space-lg);
  font-size: 0.85rem;
  color: var(--jp-text-muted);
}

/* ==========================================================================
   Page Layout
   ========================================================================== */
/* Constrain main content width for readability */
.page-columns {
  --page-columns-main: 720px;
}

@media (min-width: 992px) {
  .page-columns {
    grid-template-columns:
      [screen-start] 1fr
      [screen-start-inset] 1.5rem
      [page-start] minmax(0, 1fr)
      [column-start] var(--jp-line-length)
      [column-end] minmax(0, 1fr)
      [page-end] 1.5rem
      [screen-end-inset] 1fr
      [screen-end];
  }
}

/* ==========================================================================
   Print / PDF Styles
   ========================================================================== */
@media print {
  @page {
    size: letter;
    margin: 1in 1.25in;
  }

  body {
    font-size: 11pt;
    line-height: 1.6;
    color: black;
    background: white;
  }

  .navbar,
  #TOC,
  .sidebar,
  .btn-copy {
    display: none !important;
  }

  h1, h2, h3, h4, h5, h6 {
    color: black;
    page-break-after: avoid;
  }

  h2 {
    border-bottom-color: #ccc;
  }

  p, li {
    orphans: 3;
    widows: 3;
  }

  pre {
    background: #f5f5f5 !important;
    color: black !important;
    border: 1px solid #ddd;
    box-shadow: none;
    white-space: pre-wrap;
    word-break: break-all;
    font-size: 9pt;
  }

  code {
    background: #f0f0f0 !important;
    color: #333 !important;
  }

  a {
    color: black;
    text-decoration: none;
  }

  .figure img,
  .cell-output-display img {
    box-shadow: none;
    border: 1px solid #ddd;
    max-width: 100% !important;
  }

  .table td,
  .table th {
    border-color: #ccc;
  }

  .table thead th {
    background: #f0f0f0;
    color: black;
  }

  .callout {
    box-shadow: none;
    border: 1px solid #ddd;
    border-left-width: 6px !important;
  }

  .callout-first-principles {
    background: #fafafa;
    border: 1px solid #ddd;
    border-left: 6px solid var(--jp-accent);
  }

  img {
    page-break-inside: avoid;
  }

  table {
    page-break-inside: avoid;
  }
}

/* Bold text hover pen-underline effect */
strong, b {
  display: inline;
  background-image: linear-gradient(120deg, var(--jp-accent) 0%, var(--jp-accent) 100%);
  background-repeat: no-repeat;
  background-size: 0% 3px;
  background-position: 100% 100%;
  transition: background-size 0.3s ease-out;
  padding-bottom: 2px;
}

strong:hover, b:hover {
  background-size: 100% 3px;
  background-position: 0% 100%;
}

/* ==========================================================================
   Dark Mode
   ========================================================================== */
@media (prefers-color-scheme: dark) {
  :root {
    --jp-bg: #1a1a2e;
    --jp-surface: #252540;
    --jp-border: #363650;
    --jp-text: #e8e8f0;
    --jp-text-secondary: #b0b0c8;
    --jp-text-muted: #707088;
    --jp-primary-lighter: #2e1e3b;
    --jp-accent-light: #2a1a00;
    --jp-accent-border: #5a3a00;
  }

  body {
    background-color: var(--jp-bg);
    color: var(--jp-text);
  }

  h1, h2, h3, h4, h5, h6 {
    color: #c5a3e8;
  }

  h2 {
    border-bottom-color: var(--jp-border);
  }

  a {
    color: #a277d6;
  }

  a:hover {
    color: #c5a3e8;
  }

  .navbar {
    background-color: rgba(26, 26, 46, 0.9) !important;
    border-bottom-color: rgba(255,255,255,0.05);
  }

  .navbar-brand {
    color: #c5a3e8 !important;
  }

  .navbar .nav-link,
  [data-bs-theme="dark"] .navbar .nav-link {
    color: var(--jp-text-secondary) !important;
  }

  .navbar .nav-link:hover,
  [data-bs-theme="dark"] .navbar .nav-link:hover {
    color: #c5a3e8 !important;
  }

  .navbar .nav-link.active,
  [data-bs-theme="dark"] .navbar .nav-link.active {
    color: #c5a3e8 !important;
  }

  #TOC .nav-link {
    color: var(--jp-text-secondary);
  }

  #TOC .nav-link.active {
    color: #c5a3e8;
  }

  .quarto-title-block .quarto-title-banner {
    background: linear-gradient(135deg, #1f0e2b 0%, #32164c 100%);
  }

  pre {
    background-color: #12121e;
    color: #cdd6f4;
  }

  pre.code {
    border-left-color: #c5a3e8;
    background-color: #0f0f18;
  }

  pre.code:hover {
    border-left-color: var(--jp-accent);
  }

  .cell-source pre {
    background-color: #1e1e30;
    border-color: var(--jp-border);
    color: var(--jp-text);
  }

  code {
    background-color: var(--jp-surface);
  }

  .table thead th {
    background-color: var(--jp-surface);
    color: #c5a3e8;
  }

  .table tbody tr:hover {
    background-color: var(--jp-primary-lighter);
  }

  .table.table-striped tbody tr:nth-child(odd) {
    background-color: var(--jp-surface);
  }

  .callout-first-principles {
    background: #1a1200;
  }

  blockquote {
    background: var(--jp-surface);
    border-left-color: #a277d6;
  }

  .figure img,
  .cell-output-display img {
    border-color: var(--jp-border);
    box-shadow: 0 4px 16px rgba(0,0,0,0.3);
  }

  hr {
    background: linear-gradient(to right, transparent, var(--jp-border), transparent);
  }
}