/* PhyloFlask — light, modern "biotech SaaS" theme.
   Loaded after the HTML5UP main.css on every tool/doc page; it flips the dark
   template to a clean light, card-based look and styles all shared components. */
:root {
  --bg: #eaeef6;
  --bg-2: #f6f8fc;
  --surface: #ffffff;
  --surface-2: #f3f5fa;
  --text: #0e1726;
  --text-2: #586074;
  --text-3: #8b93a5;
  --line: rgba(18, 28, 54, 0.10);
  --line-2: rgba(18, 28, 54, 0.16);
  --ink: #111827;            /* black pill buttons */
  --accent: #2f6bff;         /* links / active */
  --accent-soft: #e7eeff;
  --teal: #0bb39a;
  --radius: 16px;
  --radius-sm: 11px;
  --pill: 999px;
  --shadow: 0 10px 30px rgba(20, 30, 60, 0.08);
  --shadow-hover: 0 16px 40px rgba(20, 30, 60, 0.14);
  --tool-accent: var(--accent);
  --tool-line: var(--line);
  --tool-text: var(--text);
  --tool-muted: var(--text-2);
  --font: "Inter", "Segoe UI", system-ui, -apple-system, "Helvetica Neue", Arial, sans-serif;
  --font-display: "Space Grotesk", "Inter", system-ui, sans-serif;
}
h1, h2, h3, h4 { font-family: var(--font-display) !important; }

/* ---- Global flip: light background, dark text ---- */
html, body { background: var(--bg) !important; }
body {
  color: var(--text) !important;
  font-family: var(--font) !important;
  margin: 0 !important; padding: 0 !important; min-width: 0 !important;
  background-image: radial-gradient(1200px 600px at 80% -10%, #dfe7fb 0%, rgba(223,231,251,0) 60%) !important;
}
#wrapper, #wrapper > section, .wrapper, section.wrapper, .wrapper.style1, .wrapper.style1-alt, .wrapper.style2 {
  background-color: transparent !important;
  color: var(--text) !important;
}
.wrapper.fullscreen { min-height: auto; padding-top: 2.5rem; padding-bottom: 2.5rem; }
h1, h2, h3, h4, h5, h6 { color: var(--text) !important; font-family: var(--font) !important; letter-spacing: -0.01em; }
h1 { font-weight: 800; }
p, li, dd, dt, span, label, td, th, summary, div { color: inherit; }
a { color: var(--accent); }
a:hover { color: #1b4fd6; }
code { background: var(--surface-2); color: #b4275e; padding: 1px 6px; border-radius: 6px; }
.text-warning, .text-info, .text-muted, .text-light { color: var(--text-2) !important; }
strong, b { color: var(--text) !important; font-weight: 700; }   /* HTML5UP makes bold white — keep it dark */

/* ---- Top navbar (HTML5UP #sidebar) ---- */
#sidebar { background: transparent; }
#sidebar .inner {
  background: rgba(255, 255, 255, 0.75);
  backdrop-filter: saturate(160%) blur(10px);
  -webkit-backdrop-filter: saturate(160%) blur(10px);
  border-bottom: 1px solid var(--line);
}
#sidebar .brand {
  display: inline-flex; align-items: center; gap: 8px;
  font-weight: 800; font-size: 1.15rem; letter-spacing: -0.02em;
  color: var(--text) !important; text-decoration: none; padding: 12px 0 4px;
}
#sidebar .brand i { color: var(--accent); }
#sidebar nav ul { display: flex; flex-wrap: wrap; gap: 2px 6px; }
#sidebar nav ul li a {
  color: var(--text-2) !important; font-weight: 500;
  border-radius: var(--pill); padding: 7px 13px !important;
  transition: background 0.15s, color 0.15s;
}
#sidebar nav ul li a:hover { color: var(--text) !important; background: var(--surface-2); }
#sidebar nav ul li a.active { color: var(--accent) !important; background: var(--accent-soft); }

/* ---- Buttons (modern pills) ---- */
.button, .futuristic-btn, .futuristic-btn-secondary, .btn {
  display: inline-flex; align-items: center; gap: 8px;
  border-radius: var(--pill) !important; font-weight: 600;
  padding: 11px 22px !important; font-size: 0.95rem; cursor: pointer;
  border: 1px solid transparent !important; transition: transform 0.12s, box-shadow 0.15s, background 0.15s;
  text-decoration: none; line-height: 1;
}
.button, .button.primary, .futuristic-btn, .btn-primary {
  background: var(--ink) !important; color: #fff !important; box-shadow: 0 6px 18px rgba(17, 24, 39, 0.18);
}
.button:hover, .futuristic-btn:hover, .btn-primary:hover { transform: translateY(-1px); box-shadow: 0 12px 26px rgba(17, 24, 39, 0.26); color: #fff !important; }
.futuristic-btn-secondary, .btn-success, .button.secondary {
  background: var(--surface) !important; color: var(--text) !important; border-color: var(--line-2) !important; box-shadow: var(--shadow);
}
.futuristic-btn-secondary:hover, .button.secondary:hover { transform: translateY(-1px); border-color: var(--accent) !important; color: var(--text) !important; }
.futuristic-btn:disabled, .futuristic-btn-secondary:disabled, button:disabled, .button.disabled {
  background: var(--surface-2) !important; background-image: none !important; color: var(--text-3) !important;
  cursor: not-allowed; transform: none; box-shadow: none; border: 1px solid var(--line) !important;
}

/* ---- Inputs & selects ---- */
.futuristic-input, .futuristic-select, input[type="text"], input[type="file"], select, textarea, .form-control, .form-select {
  width: 100%; background: var(--surface) !important; border: 1px solid var(--line-2) !important;
  color: var(--text) !important; border-radius: var(--radius-sm) !important; padding: 10px 12px; font-size: 0.95rem;
  transition: border-color 0.15s, box-shadow 0.15s;
}
.futuristic-input:focus, .futuristic-select:focus, input:focus, select:focus, .form-control:focus {
  outline: none; border-color: var(--accent) !important; box-shadow: 0 0 0 3px rgba(47, 107, 255, 0.18) !important;
}
.futuristic-input::file-selector-button {
  margin-right: 12px; border: 1px solid var(--line-2); background: var(--surface-2); color: var(--text);
  border-radius: 8px; padding: 6px 12px; cursor: pointer; font-weight: 500;
}

/* ---- Drop-zone ---- */
.dropzone {
  background: var(--surface); border: 1.5px dashed var(--line-2); border-radius: var(--radius);
  padding: 1.9rem 1.25rem; text-align: center; cursor: pointer; box-shadow: var(--shadow);
  transition: border-color 0.15s, box-shadow 0.15s, transform 0.15s;
}
.dropzone:hover { border-color: var(--accent); transform: translateY(-1px); box-shadow: var(--shadow-hover); }
.dropzone.is-dragover { border-color: var(--accent); background: var(--accent-soft); }
.dropzone .dz-icon { font-size: 1.9rem; color: var(--accent); transition: transform 0.2s; }
.dropzone:hover .dz-icon { transform: translateY(-3px); }
.dropzone .dz-title { margin: 10px 0 2px; font-weight: 700; color: var(--text); }
.dropzone .dz-hint { margin: 0; font-size: 0.85rem; color: var(--text-3); }
.dropzone input[type="file"] { display: none; }

.file-pill {
  display: inline-flex; align-items: center; gap: 8px; margin-top: 12px;
  background: var(--surface-2); border: 1px solid var(--line); border-radius: var(--pill);
  padding: 6px 14px; font-size: 0.85rem; color: var(--text);
}

/* ---- Status banner + progress + loader + note ---- */
.tool-status { display: none; margin-top: 1rem; padding: 11px 15px; border-radius: var(--radius-sm); font-size: 0.95rem; border: 1px solid transparent; }
.tool-status.show { display: block; }
.tool-status.is-info { background: var(--accent-soft); color: #1c44b8; border-color: rgba(47,107,255,0.2); }
.tool-status.is-error { background: #fdecef; color: #b4275e; border-color: rgba(180,39,94,0.18); }
.tool-status.is-success { background: #e6f7f0; color: #0a7f63; border-color: rgba(11,179,154,0.22); }
.tool-progress { height: 5px; margin-top: 10px; background: rgba(18,28,54,0.10); border-radius: var(--pill); overflow: hidden; }
.tool-progress > span { display: block; width: 35%; height: 100%; background: var(--accent); animation: tool-indet 1.2s ease-in-out infinite; }
@keyframes tool-indet { 0% { margin-left: -35%; } 100% { margin-left: 100%; } }

.tool-loader { display: none; align-items: center; gap: 12px; margin-top: 1rem; padding: 14px 16px; border-radius: var(--radius-sm); background: var(--surface); border: 1px solid var(--line); box-shadow: var(--shadow); }
.tool-loader.show { display: flex; }
.tool-loader .spinner { width: 22px; height: 22px; flex: 0 0 22px; border: 3px solid var(--surface-2); border-top-color: var(--accent); border-radius: 50%; animation: tool-spin 0.8s linear infinite; }
@keyframes tool-spin { to { transform: rotate(360deg); } }
.tool-loader .caption { font-size: 0.95rem; color: var(--text); }
.tool-loader .caption small { display: block; color: var(--text-3); font-size: 0.8rem; margin-top: 2px; }

.tool-note { margin-top: 1rem; padding: 11px 15px; border-radius: var(--radius-sm); font-size: 0.9rem; background: var(--accent-soft); color: #1c44b8; }
.tool-note.is-warn { background: #fdecef; color: #b4275e; }

/* ---- Workflow stepper ---- */
.tool-stepper { display: flex; align-items: center; gap: 8px; margin-bottom: 1.5rem; flex-wrap: wrap; }
.tool-step { display: flex; align-items: center; gap: 8px; font-size: 0.85rem; color: var(--text-3); }
.tool-step .dot { width: 24px; height: 24px; border-radius: 50%; display: flex; align-items: center; justify-content: center; font-size: 0.8rem; font-weight: 700; background: var(--surface-2); color: var(--text-3); }
.tool-step.done .dot { background: #e6f7f0; color: #0a7f63; }
.tool-step.active .dot { background: var(--accent); color: #fff; }
.tool-step.active { color: var(--text); font-weight: 600; }
.tool-stepper .bar { flex: 1; min-width: 16px; height: 1px; background: var(--line); }

/* ---- Cards ---- */
.doc-card, .about, .card {
  background: var(--surface); border: 1px solid var(--line); border-radius: var(--radius);
  box-shadow: var(--shadow); transition: transform 0.15s, box-shadow 0.15s;
}
.doc-card:hover { transform: translateY(-2px); box-shadow: var(--shadow-hover); }

/* ---- Pill tags (biotech keyword chips) ---- */
.pill-tags { display: flex; flex-wrap: wrap; gap: 10px; }
.pill-tag {
  display: inline-flex; align-items: center; gap: 8px; background: var(--surface);
  border: 1px solid var(--line); border-radius: var(--pill); padding: 9px 18px;
  font-size: 0.9rem; font-weight: 500; color: var(--text); box-shadow: var(--shadow);
}
.pill-tag i { color: var(--accent); }

/* ---- Stat cards ---- */
.stat-card { background: var(--ink); color: #fff; border-radius: var(--radius); padding: 1.1rem 1.25rem; }
.stat-card .n { font-size: 1.9rem; font-weight: 800; letter-spacing: -0.02em; }
.stat-card .l { font-size: 0.8rem; color: rgba(255,255,255,0.7); }

/* ---- Visualisation containers on light ---- */
#graph { background: var(--surface) !important; border: 1px solid var(--line) !important; }
#tree-svg { background: var(--surface) !important; border: 1px solid var(--line) !important; }
#cy-tooltip, #tree-tooltip { background: #111827 !important; color: #fff !important; border-color: rgba(255,255,255,0.18) !important; }
.search-bubble { box-shadow: var(--shadow); }

/* ---- Footer ---- */
#footer, #footer .inner { background: transparent !important; }
#footer .menu li, #footer a { color: var(--text-2) !important; }

img, svg, canvas { max-width: 100%; }

/* ---- Animations ---- */
@keyframes tool-fade-in { from { opacity: 0; transform: translateY(8px); } to { opacity: 1; transform: none; } }
.inner > h1, .tool-stepper, .doc-card, .faq details, .dropzone, .pill-tags, .stat-card { animation: tool-fade-in 0.4s ease both; }

/* ---- Responsive ---- */
@media screen and (max-width: 980px) {
  #sidebar .inner nav ul { overflow-x: auto; flex-wrap: nowrap; -webkit-overflow-scrolling: touch; }
}
@media screen and (max-width: 736px) {
  .tool-stepper { font-size: 0.78rem; gap: 6px; }
  .dropzone { padding: 1.4rem 0.9rem; }
  #graph { height: 60vh !important; }
  .futuristic-btn, .futuristic-btn-secondary, .button { width: auto; justify-content: center; }
}
@media (prefers-reduced-motion: reduce) {
  *, *::before, *::after { animation-duration: 0.001ms !important; transition-duration: 0.001ms !important; }
}

/* ============================================================
   Site chrome — clean top navbar + content + footer
   (replaces the old HTML5UP vertical sidebar on tool pages)
   ============================================================ */
.site-nav { position: sticky; top: 0; z-index: 50; }
.site-nav-inner {
  max-width: 1180px; margin: 0 auto; padding: 13px 22px;
  display: flex; align-items: center; gap: 8px;
  background: rgba(255,255,255,0.78); backdrop-filter: saturate(160%) blur(12px);
  -webkit-backdrop-filter: saturate(160%) blur(12px);
  border-bottom: 1px solid var(--line);
}
.site-nav .logo { display: inline-flex; align-items: center; gap: 9px; font-family: var(--font-display);
  font-weight: 700; font-size: 1.22rem; letter-spacing: -0.02em; color: var(--text); text-decoration: none; margin-right: 12px; }
.site-nav .logo i { color: var(--accent); }
.site-nav .links { display: flex; flex-wrap: wrap; gap: 2px; }
.site-nav .links a { color: var(--text-2); text-decoration: none; font-weight: 500; font-size: 0.92rem;
  padding: 8px 13px; border-radius: var(--pill); transition: background .15s, color .15s; white-space: nowrap; }
.site-nav .links a:hover { color: var(--text); background: var(--surface-2); }
.site-nav .links a.active { color: var(--accent); background: var(--accent-soft); }
.site-nav .spacer { flex: 1; }
.site-nav .cta { display: inline-flex; align-items: center; gap: 7px; background: var(--ink); color: #fff;
  border-radius: var(--pill); padding: 9px 18px; font-weight: 600; font-size: 0.9rem; text-decoration: none;
  box-shadow: 0 6px 16px rgba(17,24,39,.2); transition: transform .12s, box-shadow .15s; }
.site-nav .cta:hover { transform: translateY(-1px); color: #fff; box-shadow: 0 12px 24px rgba(17,24,39,.28); }

.site-main { max-width: 1180px; margin: 0 auto; padding: 8px 22px 40px; }
/* Center & constrain tool/doc content; drop the HTML5UP fullscreen empties. */
.site-main .wrapper, .site-main section.wrapper { padding: 1.5rem 0 !important; min-height: 0 !important; }
.fade-up, .fade-up.is-visible { opacity: 1 !important; transform: none !important; }  /* no scroll-JS dependency */
.site-main .inner { max-width: 980px; margin: 0 auto; width: 100%; }

/* Beautiful footer */
.site-footer { background: var(--surface); border-top: 1px solid var(--line); margin-top: 24px; }
.site-footer .cols { max-width: 1180px; margin: 0 auto; padding: 40px 22px 22px;
  display: grid; grid-template-columns: 1.6fr 1fr 1fr; gap: 30px; }
.site-footer h4 { font-size: 0.78rem; text-transform: uppercase; letter-spacing: 0.06em; color: var(--text-3); margin: 0 0 12px; }
.site-footer .brand { display: inline-flex; align-items: center; gap: 9px; font-family: var(--font-display);
  font-weight: 700; font-size: 1.2rem; color: var(--text); text-decoration: none; margin-bottom: 10px; }
.site-footer .brand i { color: var(--accent); }
.site-footer p { color: var(--text-2); font-size: 0.92rem; line-height: 1.6; max-width: 360px; margin: 0; }
.site-footer ul { list-style: none; margin: 0; padding: 0; }
.site-footer ul li { margin-bottom: 8px; }
.site-footer ul a { color: var(--text-2); text-decoration: none; font-size: 0.92rem; }
.site-footer ul a:hover { color: var(--accent); }
.site-footer .bottom { border-top: 1px solid var(--line); }
.site-footer .bottom div { max-width: 1180px; margin: 0 auto; padding: 16px 22px; display: flex;
  flex-wrap: wrap; gap: 10px; justify-content: space-between; color: var(--text-3); font-size: 0.85rem; }

@media (max-width: 820px) {
  .site-nav .links { display: none; }
  .site-footer .cols { grid-template-columns: 1fr; gap: 22px; }
}