/* NovaGenetica — design tokens for the GA/GP knowledge site.
 *
 * Brand identity:
 *   - Warm scientific paper background — calm, readable, archival
 *   - Deep indigo-violet ink — wordmark + headings (the "evolution" register)
 *   - Emerald accent — CTAs, marks, the live/growth signal
 *   - Helix-cyan as a secondary accent for diagrams and the dark band
 *   - Display serif for headlines (Playfair Display)
 *   - Inter for body text, JetBrains Mono for code/genome strings
 *
 * Adapted from the Athena/Shoreline marketing design language with a
 * distinct palette. Zero build: plain HTML + CSS, no JavaScript required.
 */

:root {
  /* Brand palette — NovaGenetica. */
  --color-ink-900: #221049;          /* Wordmark ink — deep indigo-violet */
  --color-ink-800: #382066;          /* Link ink + secondary headings */
  --color-ink-100: #e6e2ee;          /* Soft violet-tinted divider */
  --color-text: #1d1b24;
  --color-text-muted: #5c5766;
  --color-bg: #f5f3ec;               /* Warm scientific paper */
  --color-bg-card: #fcfbf6;          /* Lighter paper for cards */
  --color-border: #ddd6c8;
  --color-accent: #128a5b;           /* Emerald — primary CTAs + marks */
  --color-accent-dark: #0d6e48;      /* Emerald-on-hover */
  --color-cyan: #1f8a9c;             /* Helix cyan — diagrams + dark band */

  /* Type. */
  --font-sans: "Inter", -apple-system, BlinkMacSystemFont, "Segoe UI", system-ui, sans-serif;
  --font-serif: "Playfair Display", "EB Garamond", "Iowan Old Style", Georgia, serif;
  --font-mono: "JetBrains Mono", "SF Mono", Menlo, Consolas, monospace;
  --font-size-base: 17px;
  --line-height-base: 1.6;

  /* Layout. */
  --max-width-text: 42rem;
  --max-width-wide: 64rem;
  --space-1: 0.25rem;
  --space-2: 0.5rem;
  --space-3: 1rem;
  --space-4: 1.5rem;
  --space-5: 2.5rem;
  --space-6: 4rem;
  --space-7: 6rem;

  /* Radii + shadows. */
  --radius-sm: 4px;
  --radius-md: 8px;
  --shadow-card: 0 1px 3px rgba(34, 16, 73, 0.07), 0 1px 2px rgba(34, 16, 73, 0.04);
  --shadow-card-hover: 0 4px 14px rgba(34, 16, 73, 0.11), 0 2px 4px rgba(34, 16, 73, 0.05);
}

* {
  box-sizing: border-box;
}

html {
  scroll-behavior: smooth;
}

html,
body {
  margin: 0;
  padding: 0;
}

body {
  font-family: var(--font-sans);
  font-size: var(--font-size-base);
  line-height: var(--line-height-base);
  color: var(--color-text);
  background: var(--color-bg);
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
}

h1,
h2,
h3 {
  font-family: var(--font-serif);
  color: var(--color-ink-900);
  font-weight: 600;
  letter-spacing: -0.01em;
  line-height: 1.15;
  margin: 0 0 var(--space-3);
}

h1 {
  font-size: clamp(2.25rem, 5.5vw, 3.5rem);
  letter-spacing: -0.015em;
  font-weight: 700;
}

h2 {
  font-size: clamp(1.75rem, 3.5vw, 2.4rem);
}

h3 {
  font-size: 1.35rem;
}

h4 {
  font-family: var(--font-sans);
  color: var(--color-ink-900);
  font-weight: 700;
  letter-spacing: -0.01em;
  line-height: 1.2;
  margin: 0 0 var(--space-3);
}

p {
  margin: 0 0 var(--space-3);
  max-width: var(--max-width-text);
}

a {
  color: var(--color-accent-dark);
  text-decoration: underline;
  text-underline-offset: 2px;
}

a:hover {
  color: var(--color-ink-900);
}

code {
  font-family: var(--font-mono);
  font-size: 0.875em;
  background: var(--color-ink-100);
  padding: 0.1em 0.35em;
  border-radius: var(--radius-sm);
}

/* Layout primitives. */

.container {
  max-width: var(--max-width-wide);
  margin: 0 auto;
  padding: 0 var(--space-4);
}

.container-text {
  max-width: 46rem;
}

section {
  padding: var(--space-6) 0;
}

/* Site chrome. */

.site-header {
  border-bottom: 1px solid var(--color-border);
  background: rgba(245, 243, 236, 0.85);
  padding: var(--space-3) 0;
  position: sticky;
  top: 0;
  z-index: 10;
  backdrop-filter: blur(8px);
}

.site-header .container {
  display: flex;
  align-items: center;
  justify-content: space-between;
  gap: var(--space-3);
  flex-wrap: wrap;
}

.site-logo {
  display: inline-flex;
  align-items: center;
  gap: 0.6rem;
  text-decoration: none;
  line-height: 1;
}

.site-logo .mark {
  width: 2.2rem;
  height: 2.2rem;
  flex-shrink: 0;
}

.site-logo .wordmark {
  display: flex;
  flex-direction: column;
  gap: 0.22rem;
}

.site-logo .name {
  font-family: var(--font-serif);
  font-size: 1.45rem;
  font-weight: 700;
  letter-spacing: -0.005em;
  color: var(--color-ink-900);
}

.site-logo .descriptor {
  font-family: var(--font-sans);
  font-size: 0.62rem;
  font-weight: 700;
  color: var(--color-accent);
  letter-spacing: 0.22em;
  text-transform: uppercase;
}

.site-nav {
  display: flex;
  gap: var(--space-2);
  align-items: center;
  flex-wrap: wrap;
}

/* Nav links render as soft pills: plain text at rest, an emerald-tinted
   highlight on hover. */
.site-nav a:not(.btn) {
  text-decoration: none;
  color: var(--color-text-muted);
  font-size: 0.95rem;
  font-weight: 500;
  padding: 0.45em 0.85em;
  border-radius: var(--radius-md);
  transition:
    background-color 0.15s ease,
    color 0.15s ease;
}

.site-nav a:not(.btn):hover,
.site-nav a:not(.btn).active {
  color: var(--color-ink-900);
  background: rgba(18, 138, 91, 0.12);
}

.site-footer {
  border-top: 1px solid var(--color-border);
  background: var(--color-ink-100);
  padding: var(--space-5) 0 var(--space-4);
  margin-top: var(--space-7);
}

.site-footer .container {
  display: grid;
  grid-template-columns: 2fr 1fr 1fr;
  gap: var(--space-4);
}

@media (max-width: 720px) {
  .site-footer .container {
    grid-template-columns: 1fr 1fr;
  }
}

.site-footer h4 {
  font-size: 0.875rem;
  text-transform: uppercase;
  letter-spacing: 0.05em;
  color: var(--color-text-muted);
  margin-bottom: var(--space-2);
}

.site-footer ul {
  list-style: none;
  padding: 0;
  margin: 0;
  display: flex;
  flex-direction: column;
  gap: var(--space-1);
}

.site-footer a {
  color: var(--color-text);
  text-decoration: none;
  font-size: 0.9rem;
}

.site-footer a:hover {
  text-decoration: underline;
}

.site-footer .legal {
  grid-column: 1 / -1;
  border-top: 1px solid var(--color-border);
  padding-top: var(--space-3);
  margin-top: var(--space-3);
  font-size: 0.85rem;
  color: var(--color-text-muted);
}

/* Buttons / CTA. */

.btn {
  display: inline-block;
  padding: 0.75em 1.5em;
  border-radius: var(--radius-md);
  font-weight: 600;
  text-decoration: none;
  transition: background-color 0.15s, color 0.15s, transform 0.05s;
  cursor: pointer;
  border: none;
  font-size: 1rem;
  line-height: 1;
}

.btn-primary {
  background: var(--color-ink-900);
  color: var(--color-bg);
  border: 1px solid var(--color-ink-900);
}

.btn-primary:hover {
  background: var(--color-ink-800);
  color: var(--color-bg);
  border-color: var(--color-ink-800);
}

.btn-secondary {
  background: transparent;
  color: var(--color-ink-900);
  border: 1px solid var(--color-ink-900);
}

.btn-secondary:hover {
  background: var(--color-ink-900);
  color: var(--color-bg);
}

.btn-accent {
  background: var(--color-accent);
  color: #fff;
  border: 1px solid var(--color-accent);
}

.btn-accent:hover {
  background: var(--color-accent-dark);
  color: #fff;
  border-color: var(--color-accent-dark);
}

/* Cards. */

.card {
  background: var(--color-bg-card);
  border: 1px solid var(--color-border);
  border-radius: var(--radius-md);
  padding: var(--space-4);
  box-shadow: var(--shadow-card);
  transition: box-shadow 0.15s ease, transform 0.05s ease;
}

.card:hover {
  box-shadow: var(--shadow-card-hover);
}

.card h3 {
  margin-top: var(--space-2);
}

.card-icon {
  width: 2.4rem;
  height: 2.4rem;
  color: var(--color-accent);
}

/* Card that is itself a link. */
a.card {
  display: block;
  text-decoration: none;
  color: inherit;
}

a.card:hover {
  transform: translateY(-2px);
}

a.card h3 {
  color: var(--color-ink-900);
}

a.card .card-more {
  color: var(--color-accent-dark);
  font-weight: 600;
  font-size: 0.9rem;
}

/* Hero. */

.hero {
  padding: var(--space-7) 0 var(--space-6);
  background: var(--color-bg);
  border-bottom: 1px solid var(--color-border);
  position: relative;
  overflow: hidden;
}

.hero .container {
  position: relative;
  z-index: 1;
}

.hero h1 {
  margin-bottom: var(--space-3);
  max-width: 20ch;
}

.hero h1 .accent {
  color: var(--color-accent);
}

.hero-tagline {
  font-size: 1.25rem;
  color: var(--color-text-muted);
  margin-bottom: var(--space-4);
  max-width: 42rem;
}

.hero-ctas {
  display: flex;
  gap: var(--space-3);
  flex-wrap: wrap;
}

/* Decorative helix that floats at the right of the hero. */
.hero-helix {
  position: absolute;
  top: 50%;
  right: -2rem;
  transform: translateY(-50%);
  width: 22rem;
  height: 22rem;
  opacity: 0.5;
  pointer-events: none;
  z-index: 0;
}

@media (max-width: 900px) {
  .hero-helix {
    display: none;
  }
}

/* Tag — small uppercase label above section headings. */

.tag {
  display: inline-block;
  padding: 0.2em 0.75em;
  background: transparent;
  color: var(--color-accent);
  border: 1px solid var(--color-accent);
  border-radius: 999px;
  font-size: 0.75rem;
  font-weight: 600;
  letter-spacing: 0.08em;
  text-transform: uppercase;
  margin-bottom: var(--space-3);
}

/* Stat / counters. */

.stat-row {
  display: grid;
  grid-template-columns: repeat(4, 1fr);
  gap: var(--space-4);
  margin: var(--space-5) 0 0;
}

@media (max-width: 720px) {
  .stat-row {
    grid-template-columns: repeat(2, 1fr);
  }
}

.stat-value {
  font-family: var(--font-serif);
  font-size: 2.4rem;
  font-weight: 700;
  color: var(--color-ink-800);
  line-height: 1;
}

.stat-label {
  font-size: 0.9rem;
  color: var(--color-text-muted);
  margin-top: var(--space-1);
}

/* Column grids. */

.two-up {
  display: grid;
  grid-template-columns: repeat(2, 1fr);
  gap: var(--space-4);
}

.three-up {
  display: grid;
  grid-template-columns: repeat(3, 1fr);
  gap: var(--space-4);
}

@media (max-width: 900px) {
  .three-up {
    grid-template-columns: 1fr;
  }
}

@media (max-width: 720px) {
  .two-up {
    grid-template-columns: 1fr;
  }
}

.four-up {
  display: grid;
  grid-template-columns: repeat(2, 1fr);
  gap: var(--space-4);
}

@media (max-width: 720px) {
  .four-up {
    grid-template-columns: 1fr;
  }
}

/* Two-column layouts. */

.split {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: var(--space-5);
  align-items: start;
}

@media (max-width: 720px) {
  .split {
    grid-template-columns: 1fr;
  }
}

/* Step list. */

.steps {
  counter-reset: step;
  list-style: none;
  padding: 0;
  margin: var(--space-4) 0;
  display: grid;
  gap: var(--space-4);
}

.steps li {
  counter-increment: step;
  display: grid;
  grid-template-columns: auto 1fr;
  gap: var(--space-3);
  align-items: start;
}

.steps li::before {
  content: counter(step);
  width: 2em;
  height: 2em;
  background: var(--color-accent);
  color: white;
  border-radius: 50%;
  display: grid;
  place-items: center;
  font-weight: 700;
  font-size: 0.95rem;
}

.steps strong {
  display: block;
  margin-bottom: var(--space-1);
  color: var(--color-ink-900);
}

/* Dark band — flips to deep indigo so a section stands apart. */

.dark-band {
  background: var(--color-ink-900);
  border-top: 1px solid var(--color-ink-800);
  border-bottom: 1px solid var(--color-ink-800);
}

.dark-band h2,
.dark-band h3 {
  color: var(--color-bg-card);
}

.dark-band p {
  color: #c9c3d6;
}

.dark-band .tag {
  color: #5bd6a6;
  border-color: #5bd6a6;
}

.dark-band .card {
  background: #2c1a55;
  border-color: #3c2770;
  box-shadow: none;
}

.dark-band .card h3 {
  color: var(--color-bg-card);
}

.dark-band .card p {
  color: #c9c3d6;
}

.dark-band .card-icon {
  color: #5bd6a6;
}

.dark-band .materials {
  font-family: var(--font-mono);
  font-size: 0.8rem;
  color: #5bd6a6;
  letter-spacing: 0.06em;
  text-transform: uppercase;
}

/* Resource / reading lists. */

.resource-list {
  list-style: none;
  padding: 0;
  margin: var(--space-4) 0 0;
  display: grid;
  gap: var(--space-3);
}

.resource-list > li {
  background: var(--color-bg-card);
  border: 1px solid var(--color-border);
  border-radius: var(--radius-md);
  padding: var(--space-3) var(--space-4);
  box-shadow: var(--shadow-card);
}

.resource-list .res-title {
  font-weight: 700;
  color: var(--color-ink-900);
  font-size: 1.05rem;
  margin: 0 0 var(--space-1);
}

.resource-list .res-title a {
  text-decoration: none;
}

.resource-list .res-title a:hover {
  text-decoration: underline;
}

.resource-list .res-meta {
  font-size: 0.85rem;
  color: var(--color-text-muted);
  margin: 0 0 var(--space-2);
}

.resource-list .res-meta .res-type {
  display: inline-block;
  font-family: var(--font-mono);
  font-size: 0.7rem;
  letter-spacing: 0.05em;
  text-transform: uppercase;
  color: var(--color-cyan);
  border: 1px solid currentColor;
  border-radius: 999px;
  padding: 0.05em 0.6em;
  margin-right: 0.5em;
  vertical-align: middle;
}

.resource-list .res-desc {
  margin: 0;
  font-size: 0.95rem;
  color: var(--color-text);
  max-width: none;
}

/* Definition / concept blocks. */

.concept {
  border-left: 3px solid var(--color-accent);
  padding: var(--space-1) 0 var(--space-1) var(--space-4);
  margin: var(--space-4) 0;
}

.concept h3 {
  margin-bottom: var(--space-2);
}

/* Prose article wrapper. */

.prose h2 {
  margin-top: var(--space-5);
}

.prose h3 {
  margin-top: var(--space-4);
}

.prose ul,
.prose ol {
  max-width: var(--max-width-text);
  padding-left: 1.3em;
}

.prose li {
  margin-bottom: var(--space-2);
}

.prose pre {
  background: var(--color-ink-900);
  color: #e8e3f2;
  border-radius: var(--radius-md);
  padding: var(--space-4);
  overflow-x: auto;
  font-family: var(--font-mono);
  font-size: 0.85rem;
  line-height: 1.5;
  max-width: var(--max-width-text);
}

.prose pre code {
  background: none;
  padding: 0;
  color: inherit;
  font-size: inherit;
}

.prose blockquote {
  margin: var(--space-4) 0;
  padding: var(--space-1) 0 var(--space-1) var(--space-4);
  border-left: 3px solid var(--color-cyan);
  color: var(--color-text-muted);
  font-style: italic;
}

/* Breadcrumb. */

.breadcrumb {
  font-size: 0.85rem;
  color: var(--color-text-muted);
  margin-bottom: var(--space-3);
}

.breadcrumb a {
  color: var(--color-text-muted);
  text-decoration: none;
}

.breadcrumb a:hover {
  color: var(--color-ink-900);
  text-decoration: underline;
}

/* Pagefoot prev/next links for learning flow. */

.page-nav {
  display: flex;
  justify-content: space-between;
  gap: var(--space-3);
  flex-wrap: wrap;
  margin-top: var(--space-5);
  border-top: 1px solid var(--color-border);
  padding-top: var(--space-4);
}

/* Contact / link-out card. */

.contact-card {
  background: var(--color-bg-card);
  border: 1px solid var(--color-border);
  border-radius: var(--radius-md);
  padding: var(--space-5);
  box-shadow: var(--shadow-card);
  text-align: center;
}

.contact-card p {
  margin-left: auto;
  margin-right: auto;
}

.contact-email {
  font-family: var(--font-serif);
  font-size: clamp(1.3rem, 3vw, 1.9rem);
  font-weight: 600;
}

/* Author / profile block. */

.profile {
  display: grid;
  grid-template-columns: auto 1fr;
  gap: var(--space-4);
  align-items: start;
}

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

.profile .avatar {
  width: 7rem;
  height: 7rem;
  border-radius: 50%;
  background: var(--color-ink-900);
  display: grid;
  place-items: center;
  color: #5bd6a6;
  font-family: var(--font-serif);
  font-size: 2.4rem;
  font-weight: 700;
}

/* Pills row (tags on project page). */

.pill-row {
  display: flex;
  gap: var(--space-2);
  flex-wrap: wrap;
  margin: var(--space-3) 0;
}

.pill {
  font-family: var(--font-mono);
  font-size: 0.72rem;
  letter-spacing: 0.04em;
  text-transform: uppercase;
  color: var(--color-cyan);
  border: 1px solid currentColor;
  border-radius: 999px;
  padding: 0.2em 0.7em;
}

/* Figure / diagram caption. */

.figure {
  margin: var(--space-4) 0;
}

.figure figcaption {
  font-size: 0.85rem;
  color: var(--color-text-muted);
  margin-top: var(--space-2);
  text-align: center;
}

/* Layered-stack diagram for the SEED-Nav page. */

.layer-stack {
  list-style: none;
  padding: 0;
  margin: var(--space-4) 0;
  display: grid;
  gap: var(--space-1);
  max-width: var(--max-width-text);
}

.layer-stack li {
  background: var(--color-bg-card);
  border: 1px solid var(--color-border);
  border-left: 4px solid var(--color-accent);
  border-radius: var(--radius-sm);
  padding: var(--space-2) var(--space-3);
  font-size: 0.95rem;
}

.layer-stack li strong {
  color: var(--color-ink-900);
  font-family: var(--font-mono);
  font-size: 0.8rem;
  margin-right: 0.5em;
}

/* Utility. */

.muted {
  color: var(--color-text-muted);
}

.small {
  font-size: 0.875em;
}

.center {
  text-align: center;
}

.section-lead {
  font-size: 1.15rem;
  color: var(--color-text-muted);
  max-width: var(--max-width-text);
}

.lede {
  font-size: 1.2rem;
  color: var(--color-text);
  max-width: var(--max-width-text);
}