/* Main custom styles */

:root {
  --primary-color: #007bff;
  --secondary-color: #6c757d;
  --light-bg: #f8f9fa;
  --list-divider-color: #e5e5e5;
  --text-primary: #333;
  --text-muted: #999;
  --text-secondary: #999;
  --text-inverse: #ffffff;
  --icon-ink: #000000;
  --icon-img-hover-filter: brightness(0);
  --surface-base: #fff;
  --surface-raised: #f8f9fa;
  --surface-sunken: #f4f4f4;
  --surface-header: #f8f9fa;
  --border: #dee2e6;
  --border-strong: #ced4da;
  --accent: #0062cc;
  --accent-link: #007bff;
  --accent-link-hover: #0056b3;
}

html {
  -webkit-text-size-adjust: 100%;
  text-size-adjust: 100%;
}

body {
  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif;
  font-size: 16px;
  line-height: 1.6;
  color: var(--text-primary);
  background-color: var(--surface-base);
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
}

.container {
  max-width: 1200px;
  margin: 0 auto;
  padding: 0 15px;
}

/* Accessibility */
.skip-link {
  position: absolute;
  top: 0;
  left: 0;
  transform: translateY(-100%);
  z-index: 10000;
  padding: 0.5rem 1rem;
  background-color: #212529;
  color: #fff;
  text-decoration: none;
}

.skip-link:focus {
  transform: translateY(0);
}

body[data-theme="dark"] .skip-link {
  background-color: #e0e0e0;
  color: #1a1a1a;
}

/* Navigation */
.navbar {
  margin-bottom: 2rem;
  box-shadow: 0 1px 3px rgba(0, 0, 0, 0.12);
  padding: 1.5rem 1rem;
}

.navbar-brand {
  display: flex;
  align-items: center;
  gap: 0.75rem;
  font-weight: bold;
  font-size: 1.4rem;
}

.navbar-brand img {
  height: 48px;
  width: auto;
}

.navbar-nav .nav-link {
  display: inline-flex;
  align-items: center;
  white-space: nowrap;
  font-size: 1.1rem;
  padding: 0.75rem 1.2rem !important;
}

.navbar-nav .nav-link.active {
  color: #212529 !important;
  font-weight: 600;
}

/* Cards */
.card {
  box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1);
  border: 1px solid transparent;
  margin-bottom: 0;
}

/* Grid-based card layout - fill columns first */
.post-grid {
  display: grid;
  grid-template-columns: repeat(3, 1fr);
  grid-template-rows: repeat(2, auto);
  grid-auto-flow: column;
  gap: 1.5rem;
  padding: 0;
  margin-right: 0;
  margin-left: 0;
}

.post-grid > .col-md-4 {
  width: 100%;
  margin-bottom: 0;
  padding: 0;
  flex: unset;
  max-width: unset;
}

@media (max-width: 992px) {
  .post-grid {
    grid-template-columns: repeat(2, 1fr);
    grid-template-rows: repeat(3, auto);
    grid-auto-flow: column;
  }
}

@media (max-width: 767px) {
  .post-grid {
    grid-template-columns: 1fr;
    grid-template-rows: auto;
    grid-auto-flow: row;
  }
}

.card-header {
  background-color: var(--surface-header);
  border-bottom: 1px solid var(--border);
  padding: 1rem;
}

.card-header h2 {
  margin: 0;
  font-size: 1.5rem;
}

.card-title {
  margin-bottom: 0.5rem;
  font-size: 1.25rem;
}

.card-subtitle {
  font-size: 0.875rem;
}

.card-body {
  padding: 1.5rem;
}

.ai-2x {
  font-size: 2em;
}

.ai-orcid:before {
  content: "\e9d9";
}

.ai-hal:before {
  content: "\e92c";
}

.ai-google-scholar:before {
  content: "\e9d4";
}

/* List separators (archive/tags) */
.archive-grid .card-body ul li {
  margin: 0;
  padding: 0.75rem 0;
}

.archive-grid .card-body ul li + li {
  border-top: 1px solid var(--list-divider-color);
}

/* Tag styling */
.badge {
  padding: 0.35rem 0.6rem;
  margin-right: 0.5rem;
  margin-bottom: 0.5rem;
  border-radius: 0.25rem;
}

.tag-badge {
  background-color: transparent;
  color: var(--accent);
  border: none;
  padding: 0;
  margin: 0;
  display: inline-block;
}

.tags-container {
  display: flex;
  flex-wrap: wrap;
  gap: 0.25rem;
}

.tags-container .tag-separator {
  color: var(--text-muted);
  margin: 0 0.25rem;
  font-size: 1.2em;
}

.project-github {
  color: var(--accent-link);
  font-size: 0.9em;
}

.project-github:hover {
  color: var(--accent-link-hover);
}

.card-footer {
  padding: 0.75rem 1.25rem;
  background-color: var(--surface-header) !important;
  border-top: 1px solid var(--border);
}


.tag-cloud {
  margin-bottom: 2rem;
}

.tag-cloud .badge {
  background-color: #8a9199;
  border: none;
  color: #ffffff;
}

/* Code highlighting */
pre {
  background-color: var(--surface-sunken);
  border: 1px solid var(--border);
  border-radius: 4px;
  padding: 12px;
  overflow-x: auto;
}

pre code {
  font-family: 'Courier New', Courier, monospace;
  font-size: 0.9rem;
}

code {
  background-color: var(--surface-sunken);
  padding: 2px 4px;
  border-radius: 3px;
  font-family: 'Courier New', Courier, monospace;
}

pre code {
  background-color: transparent;
  padding: 0;
  border-radius: 0;
}

/* Footer */
footer {
  margin-top: 3rem;
  padding-top: 2rem;
  border-top: 1px solid #eee;
  text-align: center;
  font-size: 0.875rem;
}

.blog-footer {
  padding: 2.5rem 0;
  color: var(--text-secondary);
  text-align: center;
  background-color: var(--surface-raised);
  border-top: 0.05rem solid var(--list-divider-color);
}

.nav-footer {
  display: flex;
  flex-flow: row wrap;
}

.nav-footer .nav-link {
  display: flex;
  align-items: center;
  justify-content: center;
}

.footericon {
  color: var(--text-muted);
  transition: transform 0.3s ease;
}

.footericon-img {
  height: 2em;
  width: 2em;
  display: inline-block;
  transition: transform 0.3s ease;
}

.footericon:hover {
  transform: scale(1.5);
}

.nav-footer a:hover .footericon-img {
  transform: scale(1.5);
  filter: var(--icon-img-hover-filter);
}

.nav-footer a[href*="seqera.io"]:hover .footericon-img {
  filter: brightness(0) saturate(100%) invert(63%) sepia(62%) saturate(1738%) hue-rotate(127deg) brightness(94%) contrast(90%);
}

.nav-footer a:hover {
  text-decoration: none !important;
}

.nav-footer .ai-google-scholar:hover { color: #4885ed; }
.nav-footer .ai-orcid:hover { color: #a6ce39; }
.nav-footer .ai-hal:hover { color: var(--icon-ink); }
.nav-footer .fa-bluesky:hover { color: #1185fe; }
.nav-footer .fa-github:hover { color: var(--icon-ink); }
.nav-footer .fa-instagram:hover { color: var(--icon-ink); }
.nav-footer .fa-keybase:hover { color: #3763eaff; }
.nav-footer .fa-linkedin-in:hover { color: #007bb6; }
.nav-footer .fa-mastodon:hover { color: #3088d4; }
.nav-footer .fa-reddit-alien:hover { color: #ff4500; }
.nav-footer .fa-researchgate:hover { color: #00d0b0; }
.nav-footer .fa-square-rss:hover { color: #ff6600; }
.nav-footer .fa-stack-overflow:hover { color: #F47F24; }
.nav-footer .fa-x-twitter:hover { color: var(--icon-ink); }
.nav-footer .fa-youtube:hover { color: #ff0000; }

footer a {
  color: var(--accent-link);
  text-decoration: none;
}

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

/* Card layouts */
.card-deck {
  display: flex;
  flex-wrap: wrap;
  gap: 1.5rem;
}

.card-deck .card {
  flex: 1 1 calc(50% - 0.75rem);
  min-width: 300px;
}

/* Responsive */
@media (max-width: 768px) {
  .card-deck {
    flex-direction: column;
  }

  .card-deck .card {
    flex: 1 1 100%;
  }

  .navbar-brand {
    font-size: 1rem;
  }

  .card-header h2 {
    font-size: 1.25rem;
  }
}

/* Links */
a {
  color: var(--accent-link);
  text-decoration: none;
}

a:hover {
  color: var(--accent-link-hover);
  text-decoration: underline;
}

/* Custom utility classes */
.only-one-column {
  column-count: 1;
}

.card-columns {
  display: contents;
}

@supports (display: grid) {
  /* Modern browser support for better card layouts */
  .card-columns {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
    gap: 1.5rem;
  }

  .card-columns.only-one-column {
    display: grid;
    grid-template-columns: 1fr;
    gap: 1.5rem;
  }
}

/* Theme dropdown */
.theme-dropdown {
  position: relative;
  display: flex;
}

.theme-dropdown-menu {
  display: none;
  position: absolute;
  top: 100%;
  right: 0;
  margin-top: 0.5rem;
  background: var(--surface-base);
  border: 1px solid #ddd;
  border-radius: 8px;
  padding: 0.5rem 0;
  min-width: 150px;
  z-index: 200;
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
}

.theme-dropdown.open .theme-dropdown-menu {
  display: flex;
  flex-direction: column;
}

.theme-option {
  display: flex;
  align-items: center;
  gap: 0.5rem;
  background: none;
  border: none;
  color: var(--text-primary);
  cursor: pointer;
  font-size: 0.9rem;
  padding: 0.5rem 1rem;
  text-align: left;
  width: 100%;
  transition: background 0.2s, color 0.2s;
}

.theme-option:hover {
  background: #f0f0f0;
}

.theme-option.active {
  font-weight: 600;
}

/* Dark mode — leverage Bootstrap 5.3 native data-bs-theme support.
   Bootstrap handles all component-level dark mode automatically.
   Only custom properties and non-Bootstrap elements need overrides. */
[data-bs-theme="dark"] {
  --text-primary: #e0e0e0;
  --text-muted: #a3a3a3;
  --text-secondary: #b0b0b0;
  --text-inverse: #ffffff;
  --icon-ink: #ffffff;
  --icon-img-hover-filter: brightness(0) invert(1);
  --surface-base: #1a1a1a;
  --surface-raised: #2d2d2d;
  --surface-sunken: #2a2a2a;
  --surface-header: #333;
  --border: #444;
  --border-strong: #555;
  --accent-link: #4da3ff;
  --accent-link-hover: #6db3ff;
  --list-divider-color: var(--border);
  background-color: var(--surface-base);
  color: var(--text-primary);
}

[data-bs-theme="dark"] .container {
  background-color: var(--surface-base);
}

[data-bs-theme="dark"] .publications-list li + li {
  border-top-color: var(--list-divider-color);
}

[data-bs-theme="dark"] .cv-date {
  color: var(--text-primary);
}

[data-bs-theme="dark"] .cv-page .card-body,
[data-bs-theme="dark"] .cv-page .card-body h6,
[data-bs-theme="dark"] .cv-page .card-body p,
[data-bs-theme="dark"] .cv-page .text-muted {
  color: var(--text-primary);
}

[data-bs-theme="dark"] .tag-badge {
  color: var(--accent-link);
}

[data-bs-theme="dark"] .tag-separator {
  color: #777;
}

[data-bs-theme="dark"] .blog-footer {
  background-color: #1f1f1f;
  border-top: 1px solid var(--border);
}

[data-bs-theme="dark"] .footericon {
  color: var(--text-muted);
}

[data-bs-theme="dark"] .theme-dropdown-menu {
  background: var(--surface-raised);
  border-color: var(--border);
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.4);
}

[data-bs-theme="dark"] .theme-option {
  color: var(--text-primary);
}

[data-bs-theme="dark"] .theme-option:hover {
  background: var(--surface-header);
}

[data-bs-theme="dark"] .tag-cloud .badge {
  background-color: #6c757d !important;
  border: none;
  color: var(--text-inverse);
}

/* Bootstrap utility classes set hardcoded light colors that don't
   respond to data-bs-theme. Override them explicitly for dark mode. */
[data-bs-theme="dark"] .navbar.bg-light {
  background-color: var(--surface-raised) !important;
}

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

[data-bs-theme="dark"] .card.bg-light,
[data-bs-theme="dark"] .card.bg-light .card-text,
[data-bs-theme="dark"] .card.bg-light .card-text.text-muted,
[data-bs-theme="dark"] .card.bg-light h6,
[data-bs-theme="dark"] .card.bg-light a,
[data-bs-theme="dark"] .card.bg-light a:hover {
  background-color: var(--surface-header) !important;
  color: var(--text-primary) !important;
}

[data-bs-theme="dark"] .card.bg-light a {
  color: var(--accent-link) !important;
}

[data-bs-theme="dark"] .card.bg-light a:hover {
  color: var(--accent-link-hover) !important;
}

[data-bs-theme="dark"] .alert {
  background-color: var(--surface-header) !important;
  border-color: var(--border) !important;
  color: var(--text-primary) !important;
}

[data-bs-theme="dark"] .alert-primary {
  background-color: #2c3e50 !important;
  border-color: #34495e !important;
}

[data-bs-theme="dark"] .alert a {
  color: var(--accent-link) !important;
}

[data-bs-theme="dark"] .badge.text-bg-light {
  background-color: var(--border) !important;
  color: var(--text-primary) !important;
}

[data-bs-theme="dark"] code {
  background-color: var(--surface-sunken);
  color: var(--text-primary);
}

[data-bs-theme="dark"] pre {
  background-color: var(--surface-sunken);
  color: var(--text-primary);
  border: 1px solid var(--border);
}