/* ==========================================================================
   SuleimanBiopythonPractised - Design System & Modern Stylesheet
   ========================================================================== */

:root {
  --font-sans: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Inter", sans-serif;
  --font-mono: "JetBrains Mono", ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, monospace;

  /* Color Palette - Dark Mode Default */
  --bg-main: #030712;
  --bg-card: rgba(15, 23, 42, 0.75);
  --bg-card-hover: rgba(30, 41, 59, 0.85);
  --bg-card-border: rgba(56, 189, 248, 0.15);
  --bg-input: #0b1120;

  --text-main: #f8fafc;
  --text-muted: #94a3b8;
  --text-subtle: #64748b;

  --cyan-primary: #06b6d4;
  --cyan-glow: rgba(6, 182, 212, 0.35);
  --green-primary: #10b981;
  --green-glow: rgba(16, 185, 129, 0.35);
  --amber-primary: #f59e0b;
  --rose-primary: #f43f5e;

  --radius-sm: 6px;
  --radius-md: 12px;
  --radius-lg: 20px;
  --radius-full: 9999px;

  --shadow-card: 0 10px 30px -10px rgba(0, 0, 0, 0.5), 0 0 1px 1px rgba(255, 255, 255, 0.05);
  --shadow-glow: 0 0 25px var(--cyan-glow);

  --transition: all 0.25s cubic-bezier(0.16, 1, 0.3, 1);
}

[data-theme="light"] {
  --bg-main: #f8fafc;
  --bg-card: rgba(255, 255, 255, 0.85);
  --bg-card-hover: rgba(241, 245, 249, 0.95);
  --bg-card-border: rgba(14, 165, 233, 0.2);
  --bg-input: #ffffff;

  --text-main: #0f172a;
  --text-muted: #475569;
  --text-subtle: #94a3b8;

  --shadow-card: 0 10px 25px -5px rgba(0, 0, 0, 0.08), 0 0 1px 1px rgba(0, 0, 0, 0.05);
}

/* Base Reset */
*, *::before, *::after {
  box-sizing: border-box;
  margin: 0;
  padding: 0;
}

html {
  scroll-behavior: smooth;
  font-size: 16px;
}

body {
  font-family: var(--font-sans);
  background-color: var(--bg-main);
  color: var(--text-main);
  line-height: 1.6;
  overflow-x: hidden;
  transition: background-color 0.3s ease, color 0.3s ease;
}

/* Background Atmosphere */
.bg-atmosphere {
  position: fixed;
  inset: 0;
  pointer-events: none;
  z-index: 0;
  overflow: hidden;
}

.glow-orb {
  position: absolute;
  border-radius: 50%;
  filter: blur(140px);
  opacity: 0.25;
  transition: transform 0.5s ease;
}

.orb-1 {
  width: 550px;
  height: 550px;
  background: radial-gradient(circle, var(--cyan-primary), transparent 70%);
  top: -100px;
  left: 10%;
}

.orb-2 {
  width: 650px;
  height: 650px;
  background: radial-gradient(circle, var(--green-primary), transparent 70%);
  top: 40%;
  right: -150px;
}

.orb-3 {
  width: 500px;
  height: 500px;
  background: radial-gradient(circle, #3b82f6, transparent 70%);
  bottom: 5%;
  left: -100px;
}

/* Layout Container */
.container {
  width: 100%;
  max-width: 1240px;
  margin: 0 auto;
  padding: 0 1.5rem;
  position: relative;
  z-index: 1;
}

/* Navigation Bar */
.navbar {
  position: sticky;
  top: 0;
  z-index: 100;
  background: rgba(3, 7, 18, 0.8);
  backdrop-filter: blur(16px);
  -webkit-backdrop-filter: blur(16px);
  border-bottom: 1px solid rgba(255, 255, 255, 0.08);
  transition: background 0.3s ease;
}

[data-theme="light"] .navbar {
  background: rgba(248, 250, 252, 0.85);
  border-bottom: 1px solid rgba(0, 0, 0, 0.08);
}

.navbar-inner {
  display: flex;
  align-items: center;
  justify-content: space-between;
  height: 72px;
}

.brand-link {
  display: flex;
  align-items: center;
  gap: 0.75rem;
  text-decoration: none;
  color: var(--text-main);
  font-weight: 700;
  font-size: 1.15rem;
  letter-spacing: -0.02em;
}

.brand-logo-img {
  width: 36px;
  height: 36px;
  border-radius: var(--radius-sm);
}

.brand-title-accent {
  background: linear-gradient(135deg, var(--cyan-primary), var(--green-primary));
  -webkit-background-clip: text;
  -webkit-text-fill-color: transparent;
}

.nav-links {
  display: flex;
  list-style: none;
  gap: 1.75rem;
}

.nav-link {
  color: var(--text-muted);
  text-decoration: none;
  font-size: 0.95rem;
  font-weight: 500;
  transition: var(--transition);
}

.nav-link:hover {
  color: var(--cyan-primary);
}

.nav-actions {
  display: flex;
  align-items: center;
  gap: 0.75rem;
}

.btn-icon {
  background: var(--bg-card);
  border: 1px solid var(--bg-card-border);
  color: var(--text-main);
  width: 40px;
  height: 40px;
  border-radius: var(--radius-md);
  display: inline-flex;
  align-items: center;
  justify-content: center;
  cursor: pointer;
  transition: var(--transition);
}

.btn-icon:hover {
  border-color: var(--cyan-primary);
  color: var(--cyan-primary);
  transform: translateY(-2px);
}

.btn-primary {
  display: inline-flex;
  align-items: center;
  gap: 0.5rem;
  background: linear-gradient(135deg, var(--cyan-primary), var(--green-primary));
  color: #030712;
  font-weight: 600;
  font-size: 0.9rem;
  padding: 0.6rem 1.25rem;
  border-radius: var(--radius-md);
  text-decoration: none;
  border: none;
  cursor: pointer;
  transition: var(--transition);
  box-shadow: 0 4px 15px var(--cyan-glow);
}

.btn-primary:hover {
  transform: translateY(-2px);
  box-shadow: 0 8px 25px var(--green-glow);
}

.btn-secondary {
  display: inline-flex;
  align-items: center;
  gap: 0.5rem;
  background: var(--bg-card);
  color: var(--text-main);
  border: 1px solid var(--bg-card-border);
  font-weight: 600;
  font-size: 0.9rem;
  padding: 0.6rem 1.25rem;
  border-radius: var(--radius-md);
  text-decoration: none;
  cursor: pointer;
  transition: var(--transition);
}

.btn-secondary:hover {
  border-color: var(--cyan-primary);
  background: var(--bg-card-hover);
  transform: translateY(-2px);
}

.mobile-nav-toggle {
  display: none;
}

/* Hero Section */
.hero {
  padding: 5rem 0 4rem;
  text-align: center;
}

.hero-pill {
  display: inline-flex;
  align-items: center;
  gap: 0.5rem;
  background: rgba(6, 182, 212, 0.12);
  border: 1px solid rgba(6, 182, 212, 0.3);
  padding: 0.35rem 1rem;
  border-radius: var(--radius-full);
  font-size: 0.85rem;
  color: var(--cyan-primary);
  font-weight: 600;
  margin-bottom: 1.5rem;
}

.hero-title {
  font-size: clamp(2.2rem, 5vw, 3.8rem);
  font-weight: 800;
  line-height: 1.15;
  letter-spacing: -0.03em;
  margin-bottom: 1.25rem;
}

.hero-title-gradient {
  background: linear-gradient(135deg, #38bdf8, #2dd4bf, #34d399);
  -webkit-background-clip: text;
  -webkit-text-fill-color: transparent;
}

.hero-subtitle {
  font-size: clamp(1.05rem, 2vw, 1.25rem);
  color: var(--text-muted);
  max-width: 780px;
  margin: 0 auto 2.5rem;
}

.hero-ctas {
  display: flex;
  justify-content: center;
  gap: 1rem;
  flex-wrap: wrap;
  margin-bottom: 3.5rem;
}

/* Stats Ribbon */
.stats-ribbon {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
  gap: 1.25rem;
  background: var(--bg-card);
  backdrop-filter: blur(12px);
  border: 1px solid var(--bg-card-border);
  border-radius: var(--radius-lg);
  padding: 1.75rem 2rem;
  box-shadow: var(--shadow-card);
}

.stat-item {
  text-align: center;
}

.stat-val {
  font-size: 2rem;
  font-weight: 800;
  color: var(--cyan-primary);
  font-family: var(--font-mono);
}

.stat-label {
  font-size: 0.85rem;
  color: var(--text-muted);
  margin-top: 0.25rem;
  text-transform: uppercase;
  letter-spacing: 0.05em;
}

/* Section Header */
.section-header {
  text-align: center;
  margin-bottom: 3rem;
}

.section-tag {
  color: var(--cyan-primary);
  font-size: 0.85rem;
  font-weight: 700;
  text-transform: uppercase;
  letter-spacing: 0.1em;
  display: block;
  margin-bottom: 0.5rem;
}

.section-title {
  font-size: clamp(1.8rem, 3.5vw, 2.5rem);
  font-weight: 800;
  letter-spacing: -0.02em;
}

.section-desc {
  color: var(--text-muted);
  font-size: 1.05rem;
  max-width: 650px;
  margin: 0.75rem auto 0;
}

/* Interactive Studio Layout */
.studio-section {
  padding: 5rem 0;
}

.studio-grid {
  display: grid;
  grid-template-columns: 1.2fr 0.8fr;
  gap: 2rem;
  margin-top: 2rem;
}

@media (max-width: 960px) {
  .studio-grid {
    grid-template-columns: 1fr;
  }
}

.card-panel {
  background: var(--bg-card);
  backdrop-filter: blur(16px);
  border: 1px solid var(--bg-card-border);
  border-radius: var(--radius-lg);
  padding: 1.75rem;
  box-shadow: var(--shadow-card);
}

.panel-title {
  font-size: 1.25rem;
  font-weight: 700;
  margin-bottom: 1rem;
  display: flex;
  align-items: center;
  justify-content: space-between;
}

.sample-pills {
  display: flex;
  gap: 0.5rem;
  margin-bottom: 1rem;
  flex-wrap: wrap;
}

.btn-sample-seq {
  background: rgba(255, 255, 255, 0.06);
  border: 1px solid rgba(255, 255, 255, 0.1);
  color: var(--text-muted);
  font-size: 0.8rem;
  padding: 0.3rem 0.75rem;
  border-radius: var(--radius-sm);
  cursor: pointer;
  transition: var(--transition);
}

.btn-sample-seq:hover {
  background: rgba(6, 182, 212, 0.15);
  border-color: var(--cyan-primary);
  color: var(--cyan-primary);
}

.seq-textarea {
  width: 100%;
  height: 140px;
  background: var(--bg-input);
  border: 1px solid rgba(255, 255, 255, 0.12);
  border-radius: var(--radius-md);
  padding: 0.85rem;
  color: var(--text-main);
  font-family: var(--font-mono);
  font-size: 0.85rem;
  line-height: 1.5;
  resize: vertical;
  outline: none;
  transition: var(--transition);
}

.seq-textarea:focus {
  border-color: var(--cyan-primary);
  box-shadow: 0 0 0 2px var(--cyan-glow);
}

/* Metric Display Cards */
.metrics-row {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(130px, 1fr));
  gap: 1rem;
  margin: 1.25rem 0;
}

.metric-box {
  background: rgba(255, 255, 255, 0.03);
  border: 1px solid rgba(255, 255, 255, 0.08);
  border-radius: var(--radius-md);
  padding: 0.85rem;
  text-align: center;
}

.metric-val {
  font-family: var(--font-mono);
  font-size: 1.25rem;
  font-weight: 700;
  color: var(--cyan-primary);
}

.metric-lbl {
  font-size: 0.75rem;
  color: var(--text-subtle);
  margin-top: 0.25rem;
  text-transform: uppercase;
}

/* Sequence Output Boxes */
.seq-output-box {
  background: var(--bg-input);
  border: 1px solid rgba(255, 255, 255, 0.08);
  border-radius: var(--radius-md);
  padding: 0.85rem;
  margin-top: 1rem;
}

.seq-output-header {
  font-size: 0.8rem;
  color: var(--text-muted);
  font-weight: 600;
  margin-bottom: 0.4rem;
  display: flex;
  justify-content: space-between;
}

.seq-output-content {
  font-family: var(--font-mono);
  font-size: 0.85rem;
  color: #38bdf8;
  word-break: break-all;
  max-height: 90px;
  overflow-y: auto;
}

/* Dynamic Aligner */
.aligner-grid {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 1rem;
  margin-bottom: 1rem;
}

@media (max-width: 600px) {
  .aligner-grid {
    grid-template-columns: 1fr;
  }
}

.align-output-pre {
  background: var(--bg-input);
  border: 1px solid rgba(255, 255, 255, 0.08);
  border-radius: var(--radius-md);
  padding: 1rem;
  font-family: var(--font-mono);
  font-size: 0.8rem;
  color: #a7f3d0;
  overflow-x: auto;
  white-space: pre;
  min-height: 120px;
}

/* Biostatistics Section */
.anova-table {
  width: 100%;
  border-collapse: collapse;
  margin: 1.5rem 0;
  font-size: 0.9rem;
}

.anova-table th, .anova-table td {
  padding: 0.75rem 1rem;
  text-align: left;
  border-bottom: 1px solid rgba(255, 255, 255, 0.08);
}

.anova-table th {
  background: rgba(255, 255, 255, 0.03);
  color: var(--text-muted);
  font-weight: 600;
}

.anova-table .row-total {
  border-top: 2px solid rgba(255, 255, 255, 0.15);
  font-weight: 700;
}

.badge-pill {
  display: inline-block;
  padding: 0.25rem 0.65rem;
  border-radius: var(--radius-full);
  font-size: 0.75rem;
  font-weight: 600;
}

.badge-success {
  background: rgba(16, 185, 129, 0.15);
  color: #34d399;
  border: 1px solid rgba(16, 185, 129, 0.3);
}

.badge-accent {
  background: rgba(6, 182, 212, 0.15);
  color: #38bdf8;
  border: 1px solid rgba(6, 182, 212, 0.3);
}

.badge-warning {
  background: rgba(245, 158, 11, 0.15);
  color: #fbbf24;
  border: 1px solid rgba(245, 158, 11, 0.3);
}

.badge-neutral {
  background: rgba(148, 163, 184, 0.15);
  color: #94a3b8;
  border: 1px solid rgba(148, 163, 184, 0.3);
}

/* 3D Mol Viewer */
.viewer-3d-box {
  width: 100%;
  height: 440px;
  position: relative;
  border-radius: var(--radius-md);
  overflow: hidden;
  border: 1px solid rgba(255, 255, 255, 0.1);
  background: #030712;
}

.viewer-controls-bar {
  display: flex;
  align-items: center;
  justify-content: space-between;
  margin-bottom: 1rem;
  flex-wrap: wrap;
  gap: 0.75rem;
}

.btn-group {
  display: inline-flex;
  border: 1px solid rgba(255, 255, 255, 0.1);
  border-radius: var(--radius-sm);
  overflow: hidden;
}

.btn-group-item {
  background: rgba(255, 255, 255, 0.05);
  border: none;
  border-right: 1px solid rgba(255, 255, 255, 0.1);
  color: var(--text-muted);
  font-size: 0.8rem;
  padding: 0.4rem 0.75rem;
  cursor: pointer;
  transition: var(--transition);
}

.btn-group-item:last-child {
  border-right: none;
}

.btn-group-item.active, .btn-group-item:hover {
  background: var(--cyan-primary);
  color: #030712;
  font-weight: 600;
}

.viewer-loader {
  display: flex;
  align-items: center;
  justify-content: center;
  height: 100%;
  color: var(--cyan-primary);
  font-family: var(--font-mono);
  font-size: 0.9rem;
}

/* Notebook Catalog Grid */
.catalog-toolbar {
  display: flex;
  align-items: center;
  justify-content: space-between;
  gap: 1rem;
  margin-bottom: 2rem;
  flex-wrap: wrap;
}

.catalog-filters {
  display: flex;
  gap: 0.5rem;
  flex-wrap: wrap;
}

.filter-btn {
  background: var(--bg-card);
  border: 1px solid var(--bg-card-border);
  color: var(--text-muted);
  font-size: 0.85rem;
  padding: 0.4rem 0.9rem;
  border-radius: var(--radius-full);
  cursor: pointer;
  transition: var(--transition);
}

.filter-btn.active, .filter-btn:hover {
  background: var(--cyan-primary);
  color: #030712;
  font-weight: 600;
  border-color: var(--cyan-primary);
}

.catalog-search-input {
  background: var(--bg-input);
  border: 1px solid rgba(255, 255, 255, 0.12);
  color: var(--text-main);
  padding: 0.5rem 1rem;
  border-radius: var(--radius-full);
  font-size: 0.85rem;
  outline: none;
  min-width: 260px;
}

.notebooks-grid {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(320px, 1fr));
  gap: 1.5rem;
}

.notebook-card {
  background: var(--bg-card);
  border: 1px solid var(--bg-card-border);
  border-radius: var(--radius-lg);
  padding: 1.5rem;
  display: flex;
  flex-direction: column;
  transition: var(--transition);
  box-shadow: var(--shadow-card);
}

.notebook-card:hover {
  transform: translateY(-4px);
  border-color: var(--cyan-primary);
  box-shadow: 0 15px 35px -10px var(--cyan-glow);
}

.card-header {
  display: flex;
  justify-content: space-between;
  align-items: center;
  margin-bottom: 0.75rem;
}

.category-tag {
  font-size: 0.7rem;
  font-weight: 700;
  color: var(--text-subtle);
  letter-spacing: 0.05em;
}

.card-title {
  font-size: 1.15rem;
  font-weight: 700;
  line-height: 1.3;
  margin-bottom: 0.5rem;
}

.card-desc {
  font-size: 0.88rem;
  color: var(--text-muted);
  flex-grow: 1;
  margin-bottom: 1.25rem;
}

.card-tools {
  display: flex;
  flex-wrap: wrap;
  gap: 0.4rem;
  margin-bottom: 1.25rem;
}

.tool-tag {
  background: rgba(255, 255, 255, 0.05);
  font-size: 0.75rem;
  color: #38bdf8;
  padding: 0.2rem 0.5rem;
  border-radius: var(--radius-sm);
  font-family: var(--font-mono);
}

.card-footer {
  border-top: 1px solid rgba(255, 255, 255, 0.08);
  padding-top: 1rem;
}

.btn-card-link {
  display: inline-flex;
  align-items: center;
  gap: 0.4rem;
  color: var(--text-main);
  text-decoration: none;
  font-size: 0.85rem;
  font-weight: 600;
  transition: var(--transition);
}

.btn-card-link:hover {
  color: var(--cyan-primary);
}

/* Obsidian Knowledge Graph Tabs */
.wiki-tabs {
  display: flex;
  justify-content: center;
  gap: 0.75rem;
  margin-bottom: 2rem;
  border-bottom: 1px solid rgba(255, 255, 255, 0.08);
  padding-bottom: 1rem;
}

.wiki-tab-btn {
  background: transparent;
  border: none;
  color: var(--text-muted);
  font-size: 1rem;
  font-weight: 600;
  padding: 0.5rem 1.25rem;
  cursor: pointer;
  border-radius: var(--radius-md);
  transition: var(--transition);
}

.wiki-tab-btn.active, .wiki-tab-btn:hover {
  background: rgba(6, 182, 212, 0.12);
  color: var(--cyan-primary);
}

.wiki-panel {
  display: none;
}

.wiki-panel.active {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(280px, 1fr));
  gap: 1.25rem;
}

.wiki-card {
  background: var(--bg-card);
  border: 1px solid var(--bg-card-border);
  border-radius: var(--radius-md);
  padding: 1.25rem;
  transition: var(--transition);
}

.wiki-card:hover {
  border-color: var(--cyan-primary);
  transform: translateY(-2px);
}

.wiki-card h4 {
  font-size: 1.05rem;
  margin-bottom: 0.5rem;
  color: #38bdf8;
}

.wiki-card p {
  font-size: 0.85rem;
  color: var(--text-muted);
}

/* Footer */
.footer {
  border-top: 1px solid rgba(255, 255, 255, 0.08);
  padding: 4rem 0 2rem;
  margin-top: 6rem;
  background: rgba(3, 7, 18, 0.9);
}

.footer-grid {
  display: grid;
  grid-template-columns: 2fr 1fr 1fr;
  gap: 3rem;
  margin-bottom: 3rem;
}

@media (max-width: 768px) {
  .footer-grid {
    grid-template-columns: 1fr;
    gap: 2rem;
  }
}

.footer-brand p {
  color: var(--text-muted);
  margin-top: 0.75rem;
  font-size: 0.9rem;
  max-width: 380px;
}

.footer-col h5 {
  font-size: 0.95rem;
  font-weight: 700;
  margin-bottom: 1rem;
  color: var(--text-main);
  text-transform: uppercase;
  letter-spacing: 0.05em;
}

.footer-col ul {
  list-style: none;
}

.footer-col li {
  margin-bottom: 0.5rem;
}

.footer-col a {
  color: var(--text-muted);
  text-decoration: none;
  font-size: 0.88rem;
  transition: var(--transition);
}

.footer-col a:hover {
  color: var(--cyan-primary);
}

.footer-bottom {
  text-align: center;
  border-top: 1px solid rgba(255, 255, 255, 0.06);
  padding-top: 2rem;
  color: var(--text-subtle);
  font-size: 0.85rem;
}