/* ============================================================================
   Tropism Autodecoder — Flagship CoSE (Consortium for Open Space Exploration) Theme
   Fully unified with CoSE color tokens, document rail map, responsive PDF reader,
   publication figures lightbox, and Phase 3 cross-species functional conservation.
   ========================================================================== */

:root {
  --bg: #ffffff;
  --fg: #1a2230;
  --card: #f8fafc;
  --card-hover: #f1f5f9;
  --muted: #5a6473;
  --line: #e2e8f0;
  --red: #b2182b;
  --red-pale: #fddbc7;
  --blue: #2166ac;
  --blue-pale: #d1e5f0;
  --accent: #3B6EA5;
  --accent2: #3FB6A8;
  --focus: #054a91;
  --code-bg: #f1f5f9;
  --rail: 288px;
  --maxw: 1140px;
}

/* Manual Light / Dark override & auto OS preference sync */
html[data-theme="dark"] {
  --bg: #0f141b;
  --fg: #e6ebf2;
  --card: #161d27;
  --card-hover: #1f2937;
  --muted: #9aa6b6;
  --line: #232c39;
  --code-bg: #111827;
  --blue: #6ea3d8;
  --blue-pale: #1e3a5f;
  --red: #f87171;
  --red-pale: #451a1a;
  --accent: #6ea3d8;
  --accent2: #54c9ba;
  --focus: #6ea3d8;
}

@media (prefers-color-scheme: dark) {
  :root:not([data-theme="light"]) {
    --bg: #0f141b;
    --fg: #e6ebf2;
    --card: #161d27;
    --card-hover: #1f2937;
    --muted: #9aa6b6;
    --line: #232c39;
    --code-bg: #111827;
    --blue: #6ea3d8;
    --blue-pale: #1e3a5f;
    --red: #f87171;
    --red-pale: #451a1a;
    --accent: #6ea3d8;
    --accent2: #54c9ba;
    --focus: #6ea3d8;
  }
}

* { box-sizing: border-box; }
html { -webkit-text-size-adjust: 100%; scroll-behavior: smooth; }

body {
  margin: 0;
  background: var(--bg);
  color: var(--fg);
  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Helvetica, Arial, sans-serif;
  line-height: 1.6;
  font-size: 16.5px;
  transition: background-color .2s ease, color .2s ease;
}

/* CoSE Left Rail Push Container */
.page {
  transition: margin-left .22s ease;
  min-height: 100vh;
  display: flex;
  flex-direction: column;
}
@media (min-width: 1180px) {
  body.map-open .page { margin-left: var(--rail); }
}

a { color: var(--blue); text-decoration: none; }
a:hover { color: var(--accent2); text-decoration: underline; }

:focus-visible {
  outline: 3px solid var(--focus);
  outline-offset: 2px;
}

.wrap { max-width: var(--maxw); margin: 0 auto; padding: 0 24px; width: 100%; }

/* ============================================================================
   MASTHEAD & HERO
   ========================================================================== */
header.masthead {
  border-bottom: 2px solid var(--line);
  padding: 36px 0 26px;
  background: var(--card);
  position: relative;
}
header.masthead .bar {
  height: 8px; border-radius: 4px; margin-bottom: 20px;
  background: linear-gradient(90deg, #2166ac 0%, #3FB6A8 35%, #ffffff 50%, #fddbc7 75%, #b2182b 100%);
  border: 1px solid var(--line);
}
h1 {
  font-size: 34px; margin: 0 0 10px;
  line-height: 1.2; font-weight: 800;
  letter-spacing: -0.02em; color: var(--fg);
}
.subtitle {
  color: var(--muted); font-size: 17.5px; margin: 0;
  max-width: 900px; line-height: 1.55;
}
.masthead .meta {
  margin-top: 14px; font-size: 14.5px; color: var(--muted);
}
.masthead .meta a { font-weight: 600; }

.badge {
  display: inline-flex; align-items: center; gap: 4px;
  padding: 3px 10px; border-radius: 12px; font-size: 12px; font-weight: 700;
  background: var(--blue-pale); color: var(--blue); border: 1px solid var(--line);
  letter-spacing: 0.02em;
}
.badge.accent { background: rgba(63, 182, 168, 0.16); color: var(--accent2); border-color: rgba(63, 182, 168, 0.4); }
.badge.warn { background: var(--red-pale); color: var(--red); border-color: rgba(248, 113, 113, 0.3); }

/* Jump Navigation Pills */
.jump-nav {
  display: flex; flex-wrap: wrap; gap: 8px; margin: 20px 0 4px;
}
.jump-pill {
  display: inline-flex; align-items: center; gap: 6px;
  padding: 8px 14px; border-radius: 20px;
  background: var(--bg); border: 1.5px solid var(--line);
  color: var(--fg); font-size: 13.5px; font-weight: 600;
  transition: all .15s ease;
}
.jump-pill:hover {
  background: var(--card-hover); border-color: var(--accent2);
  color: var(--accent2); text-decoration: none; transform: translateY(-1px);
}
.jump-pill.highlight {
  background: var(--blue); color: #fff; border-color: var(--blue);
}
.jump-pill.highlight:hover {
  background: #174b80; color: #fff;
}

/* ============================================================================
   SECTIONS & COSE NUMBERED HEADINGS
   ========================================================================== */
main { padding: 16px 0 60px; flex: 1; }
section { margin: 48px 0; }
h2 {
  display: flex; align-items: center;
  font-size: 24px; margin: 0 0 18px;
  border-bottom: 2px solid var(--line); padding-bottom: 10px;
  font-weight: 700; letter-spacing: -0.01em; color: var(--fg);
}
h2 .n {
  display: inline-flex; align-items: center; justify-content: center;
  background: var(--blue-pale); color: var(--blue);
  font-size: 0.65em; font-weight: 800; border-radius: 6px;
  padding: 3px 8px; margin-right: 12px; letter-spacing: 0.04em;
  border: 1px solid var(--line); flex-shrink: 0;
}
h3 { font-size: 18.5px; margin: 22px 0 8px; font-weight: 600; color: var(--fg); }

.lede { font-size: 18.5px; color: var(--fg); line-height: 1.6; }

/* Grid & Cards */
.grid4 { display: grid; grid-template-columns: repeat(auto-fit, minmax(230px, 1fr)); gap: 16px; }
.grid2 { display: grid; grid-template-columns: repeat(auto-fit, minmax(320px, 1fr)); gap: 18px; }

.card {
  border: 1px solid var(--line); border-left: 6px solid var(--blue);
  padding: 16px 18px; border-radius: 8px; background: var(--card);
}
.card:nth-child(2) { border-left-color: var(--red); }
.card:nth-child(3) { border-left-color: var(--accent2); }
.card:nth-child(4) { border-left-color: #8b5cf6; }
.card h3 { margin: 0 0 6px; font-size: 16.5px; }
.card p { margin: 0; font-size: 14px; color: var(--muted); }

/* Key Metrics */
.stats { display: grid; grid-template-columns: repeat(auto-fit, minmax(160px, 1fr)); gap: 12px; margin-top: 14px; }
.stat {
  border: 1px solid var(--line); border-radius: 8px; padding: 14px;
  text-align: center; background: var(--card);
}
.stat .n { font-size: 26px; font-weight: 800; color: var(--blue); letter-spacing: -0.02em; }
.stat .l { font-size: 13px; color: var(--muted); margin-top: 4px; font-weight: 500; }

/* Pipeline diagram hero box */
.diagram-box {
  margin: 24px 0; border: 1px solid var(--line); border-radius: 10px;
  overflow: hidden; background: var(--card);
}
.diagram-box img { width: 100%; height: auto; display: block; cursor: pointer; }
.diagram-caption {
  padding: 12px 16px; font-size: 14px; color: var(--muted);
  border-top: 1px solid var(--line); background: var(--bg);
}

/* ============================================================================
   MANUSCRIPT PDF VIEWER
   ========================================================================== */
.pdf-viewer-section {
  border: 1px solid var(--line); border-radius: 10px;
  background: var(--card); overflow: hidden; margin-top: 18px;
}
.pdf-toolbar {
  display: flex; flex-wrap: wrap; align-items: center; justify-content: space-between;
  gap: 12px; padding: 12px 18px; background: var(--bg); border-bottom: 1px solid var(--line);
}
.pdf-meta { display: flex; align-items: center; gap: 10px; font-size: 14.5px; }
.pdf-actions { display: flex; flex-wrap: wrap; gap: 8px; align-items: center; }

.pdf-btn {
  display: inline-flex; align-items: center; gap: 6px;
  font-size: 13.5px; font-weight: 600; padding: 7px 12px; border-radius: 6px;
  border: 1px solid var(--line); background: var(--card); color: var(--fg);
  cursor: pointer; text-decoration: none; transition: all .15s ease;
}
.pdf-btn:hover { background: var(--card-hover); border-color: var(--blue); color: var(--blue); text-decoration: none; }
.pdf-btn.primary { background: var(--blue); color: #fff; border-color: var(--blue); }
.pdf-btn.primary:hover { background: #174b80; color: #fff; }

.pdf-frame-wrap {
  position: relative; width: 100%; height: 800px; background: #525659;
}
.pdf-frame-wrap iframe, .pdf-frame-wrap object {
  width: 100%; height: 100%; border: 0; display: block;
}

/* Fullscreen mode for PDF */
.pdf-frame-wrap.fullscreen {
  position: fixed; inset: 0; width: 100vw; height: 100vh;
  z-index: 99999; border-radius: 0;
}
.pdf-fullscreen-exit {
  display: none; position: fixed; top: 16px; right: 24px; z-index: 100000;
  background: #111; color: #fff; border: 1px solid #444; border-radius: 6px;
  padding: 8px 14px; font-weight: 600; cursor: pointer;
}
.pdf-frame-wrap.fullscreen + .pdf-fullscreen-exit { display: block; }

.pdf-mobile-fallback {
  display: none; padding: 18px; text-align: center; background: var(--card);
  border-top: 1px solid var(--line); font-size: 14.5px;
}
@media (max-width: 768px) {
  .pdf-frame-wrap { height: 480px; }
  .pdf-mobile-fallback { display: block; }
}

/* ============================================================================
   PUBLICATION FIGURE GALLERY & LIGHTBOX
   ========================================================================== */
.gallery-grid {
  display: grid; grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
  gap: 18px; margin-top: 18px;
}
.gallery-card {
  border: 1px solid var(--line); border-radius: 8px; background: var(--card);
  overflow: hidden; display: flex; flex-direction: column; cursor: pointer;
  transition: transform .18s ease, box-shadow .18s ease, border-color .18s ease;
}
.gallery-card:hover {
  transform: translateY(-2px); border-color: var(--accent2);
  box-shadow: 0 6px 18px rgba(0,0,0,.08);
}
.gallery-thumb-wrap {
  width: 100%; height: 210px; background: var(--bg); display: flex;
  align-items: center; justify-content: center; overflow: hidden;
  border-bottom: 1px solid var(--line);
}
.gallery-card img {
  max-width: 100%; max-height: 100%; object-fit: contain; display: block;
}
.gallery-card-body {
  padding: 12px 14px; flex: 1; display: flex; flex-direction: column;
}
.gallery-tag { font-size: 12px; font-weight: 700; color: var(--blue); text-transform: uppercase; letter-spacing: .04em; }
.gallery-title { font-size: 15px; font-weight: 600; margin: 4px 0 6px; line-height: 1.35; color: var(--fg); }
.gallery-desc { font-size: 13.5px; color: var(--muted); margin: 0; line-height: 1.45; }

/* Lightbox Modal */
.lightbox-modal {
  position: fixed; inset: 0; z-index: 10000; background: rgba(0,0,0,.85);
  display: none; align-items: center; justify-content: center; padding: 20px;
}
.lightbox-modal.active { display: flex; }
.lightbox-content {
  background: var(--bg); border-radius: 10px; max-width: 95vw; max-height: 94vh;
  overflow-y: auto; display: flex; flex-direction: column; position: relative;
  border: 1px solid var(--line); box-shadow: 0 12px 36px rgba(0,0,0,.4);
}
.lightbox-img-wrap {
  max-height: 72vh; display: flex; align-items: center; justify-content: center;
  background: #fff; padding: 14px; overflow: hidden;
}
.lightbox-img-wrap img { max-width: 100%; max-height: 70vh; object-fit: contain; }
.lightbox-caption-wrap {
  padding: 16px 20px; border-top: 1px solid var(--line); background: var(--card);
}
.lightbox-caption-wrap h4 { margin: 0 0 6px; font-size: 17px; }
.lightbox-caption-wrap p { margin: 0; font-size: 14px; color: var(--muted); line-height: 1.5; }
.lightbox-close {
  position: absolute; top: 10px; right: 12px; z-index: 2;
  background: rgba(0,0,0,.65); color: #fff; border: 0; border-radius: 50%;
  width: 32px; height: 32px; font-size: 20px; cursor: pointer; display: flex;
  align-items: center; justify-content: center;
}
.lightbox-close:hover { background: #000; }

/* ============================================================================
   INTERACTIVE TOOL (Multi-Species & Phase 3)
   ========================================================================== */
.tool { border: 2px solid var(--line); border-radius: 12px; padding: 24px; background: var(--bg); box-shadow: 0 2px 8px rgba(0,0,0,.04); }

/* Species picker button pills */
.species-picker {
  display: flex; flex-wrap: wrap; gap: 8px; margin: 12px 0 18px; align-items: center;
}
.species-label {
  display: inline-flex; align-items: center; gap: 6px;
  padding: 7px 14px; border-radius: 20px;
  background: var(--card); border: 1.5px solid var(--line);
  font-size: 13.5px; font-weight: 600; cursor: pointer;
  transition: all .15s ease; color: var(--fg);
}
.species-label:hover {
  border-color: var(--accent2); background: var(--card-hover);
}
.species-label input[type="radio"] {
  margin: 0; accent-color: var(--accent2);
}
.species-label:has(input:checked) {
  border-color: var(--accent2);
  background: rgba(63, 182, 168, 0.15);
  color: var(--fg);
}

#drop {
  border: 2.5px dashed var(--blue);
  border-radius: 10px; padding: 30px 20px; text-align: center;
  background: var(--card); transition: background-color .2s ease;
}
#drop.drag { background: var(--blue-pale); border-color: var(--accent2); }
#drop p { margin: 6px 0; }

.controls { display: flex; flex-wrap: wrap; gap: 10px; align-items: center; margin-top: 16px; }

.btn {
  font: inherit; font-weight: 600; font-size: 14px;
  background: var(--fg); color: var(--bg);
  border: 2px solid var(--fg); border-radius: 6px;
  padding: 8px 16px; cursor: pointer; transition: all .15s ease;
}
.btn:hover { background: var(--bg); color: var(--fg); }
.btn.secondary { background: var(--card); color: var(--fg); border-color: var(--line); }
.btn.secondary:hover { background: var(--card-hover); border-color: var(--accent2); color: var(--accent2); }
.btn:focus-visible { outline: 3px solid var(--focus); outline-offset: 2px; }

label.file-label {
  display: inline-block; font-weight: 600; font-size: 14.5px;
  background: var(--blue); color: #fff;
  border: 2px solid var(--blue); border-radius: 6px;
  padding: 8px 16px; cursor: pointer;
}
label.file-label:hover { background: #174b80; border-color: #174b80; }
input[type=file] { position: absolute; width: 1px; height: 1px; opacity: 0; }

.field { display: inline-flex; align-items: center; gap: 8px; }
.field input {
  font: inherit; padding: 6px 9px; width: 64px;
  border: 1.5px solid var(--line); border-radius: 5px;
  background: var(--bg); color: var(--fg);
}

.method-choice {
  margin-top: 18px; border: 1.5px solid var(--line); border-radius: 8px;
  padding: 12px 16px; background: var(--card);
}
.method-choice legend { font-weight: 700; padding: 0 8px; color: var(--fg); }
.method-choice label { display: block; margin: 6px 0; cursor: pointer; font-size: 14.5px; }
.method-choice input[type="radio"] { margin-right: 6px; accent-color: var(--blue); }
.method-choice input[disabled] + span, .method-choice label:has(input[disabled]) { color: var(--muted); }
.method-choice .muted { color: var(--muted); }
p.muted { color: var(--muted); }

.status {
  margin-top: 14px; padding: 12px 14px; border-radius: 6px; font-size: 14.5px;
  border: 1.5px solid var(--line); background: var(--card); line-height: 1.5;
}
.status.ok { border-color: var(--accent2); background: rgba(63, 182, 168, 0.12); color: var(--fg); }
.status.warn { border-color: var(--red); background: var(--red-pale); }
.status.err { border-color: var(--red); background: var(--red-pale); font-weight: 600; }

#results { margin-top: 26px; }
#figure { overflow-x: auto; border: 1px solid var(--line); border-radius: 8px; padding: 8px; background: #fff; }
#figure svg { max-width: 100%; height: auto; display: block; }

.legend-box {
  margin-top: 18px; border: 1px solid var(--line); border-left: 6px solid var(--accent2);
  border-radius: 6px; padding: 14px 16px; background: var(--card);
}
.legend-box h3 { margin-top: 0; }
#legend { white-space: pre-wrap; font-size: 14.5px; margin: 0; font-family: Georgia, "Times New Roman", serif; color: var(--fg); }

.downloads { display: flex; flex-wrap: wrap; gap: 10px; margin-top: 16px; }

details { border: 1px solid var(--line); border-radius: 6px; padding: 6px 14px; margin: 12px 0; background: var(--card); }
summary { cursor: pointer; font-weight: 600; padding: 6px 0; }

table.spec { border-collapse: collapse; width: 100%; font-size: 14px; }
table.spec th, table.spec td { border: 1px solid var(--line); padding: 8px 12px; text-align: left; vertical-align: middle; }
table.spec th { background: var(--card); font-weight: 700; color: var(--fg); }

code { background: var(--code-bg); padding: 2px 6px; border-radius: 4px; font-size: 0.9em; font-family: ui-monospace, Menlo, Monaco, Consolas, monospace; }
pre {
  background: var(--code-bg); border: 1px solid var(--line); border-radius: 6px;
  padding: 12px; overflow-x: auto; font-size: 13.5px;
  font-family: ui-monospace, Menlo, Monaco, Consolas, monospace;
}

.callout { border: 1.5px solid var(--blue); background: var(--blue-pale); border-radius: 8px; padding: 14px 16px; }
.callout.warn { border-color: var(--red); background: var(--red-pale); }
.callout.accent { border-color: var(--accent2); background: rgba(63, 182, 168, 0.12); }

/* ============================================================================
   RESEARCHER & COSE SUITE
   ========================================================================== */
.researcher-card {
  display: flex; flex-wrap: wrap; gap: 20px; align-items: flex-start;
  border: 1px solid var(--line); border-radius: 10px; padding: 24px;
  background: var(--card); margin-top: 14px;
}
.researcher-avatar {
  width: 90px; height: 90px; border-radius: 50%; background: rgba(63, 182, 168, 0.18);
  display: flex; align-items: center; justify-content: center; font-size: 40px;
  border: 2px solid var(--accent2); flex-shrink: 0;
}
.researcher-info { flex: 1; min-width: 260px; }
.researcher-name { font-size: 22px; font-weight: 800; margin: 0 0 4px; color: var(--fg); }
.researcher-title { font-size: 15px; color: var(--muted); margin: 0 0 10px; }
.researcher-links { display: flex; flex-wrap: wrap; gap: 10px; margin-top: 14px; }

.suite-grid {
  display: grid; grid-template-columns: repeat(auto-fit, minmax(240px, 1fr));
  gap: 14px; margin-top: 14px;
}
.suite-card {
  border: 1px solid var(--line); border-radius: 8px; padding: 16px;
  background: var(--card); transition: all .18s ease; display: block;
}
.suite-card:hover {
  border-color: var(--accent2); transform: translateY(-2px); text-decoration: none;
  box-shadow: 0 4px 12px rgba(0,0,0,.06);
}
.suite-card h4 { margin: 0 0 6px; font-size: 16px; color: var(--fg); }
.suite-card p { margin: 0; font-size: 13.5px; color: var(--muted); line-height: 1.45; }

/* Citation box */
.citation-box {
  position: relative; margin-top: 16px; border: 1px solid var(--line);
  border-radius: 8px; background: var(--code-bg); padding: 16px;
}
.copy-btn {
  position: absolute; top: 12px; right: 12px; font-size: 13px; font-weight: 600;
  padding: 6px 12px; border-radius: 5px; border: 1px solid var(--line);
  background: var(--bg); color: var(--fg); cursor: pointer; transition: all .15s ease;
}
.copy-btn:hover { border-color: var(--accent2); color: var(--accent2); }

footer {
  border-top: 2px solid var(--line); padding: 28px 0 48px;
  font-size: 14px; color: var(--muted); background: var(--card);
}

.skip { position: absolute; left: -999px; }
.skip:focus { left: 12px; top: 12px; background: var(--bg); border: 2px solid var(--fg); padding: 8px 12px; z-index: 100; border-radius: 6px; }

@media (max-width: 640px) {
  h1 { font-size: 26px; }
  h2 { font-size: 21px; }
  body { font-size: 16px; }
  .tool { padding: 16px; }
}