/* DiffBio Documentation Custom Styles */
/* Scientific/Bioinformatics documentation enhancements for differentiable pipelines */

/* Scientific equation styling */
.arithmatex {
  margin: 1em 0;
}

/* Code block enhancements for scientific computing */
.highlight .hll {
  background-color: #ffffcc
}

.highlight .c {
  color: #408080;
  font-style: italic
}

/* Comment */
.highlight .k {
  color: #008000;
  font-weight: bold
}

/* Keyword */
.highlight .o {
  color: #666666
}

/* Operator */
.highlight .cm {
  color: #408080;
  font-style: italic
}

/* Comment.Multiline */
.highlight .cp {
  color: #BC7A00
}

/* Comment.Preproc */
.highlight .c1 {
  color: #408080;
  font-style: italic
}

/* Comment.Single */
.highlight .cs {
  color: #408080;
  font-style: italic
}

/* Comment.Special */

/* Scientific/ML array styling */
.highlight .nd {
  color: #AA22FF
}

/* Name.Decorator */
.highlight .nf {
  color: #0000FF
}

/* Name.Function */
.highlight .nn {
  color: #0000FF;
  font-weight: bold
}

/* Name.Namespace */

/* Mathematical symbols and bioinformatics notation */
.math {
  font-family: 'Computer Modern', 'Latin Modern Math', serif;
}

/* Enhanced admonition styling for bioinformatics content */
.md-typeset .admonition.note {
  border-left: 4px solid #448aff;
}

.md-typeset .admonition.tip {
  border-left: 4px solid #00c853;
}

.md-typeset .admonition.warning {
  border-left: 4px solid #ff9100;
}

.md-typeset .admonition.danger {
  border-left: 4px solid #ff5252;
}

/* Bioinformatics-specific styling */
.pipeline-info {
  background: linear-gradient(135deg, #4f46e5, #6366f1);
  color: white;
  padding: 1em;
  border-radius: 4px;
  margin: 1em 0;
}

.performance-warning {
  background: linear-gradient(135deg, #dc2626, #ef4444);
  color: white;
  padding: 1em;
  border-radius: 4px;
  margin: 1em 0;
}

.differentiability-note {
  background: linear-gradient(135deg, #4f46e5, #818cf8);
  color: white;
  padding: 1em;
  border-radius: 4px;
  margin: 1em 0;
}

/* Differentiability rating badges */
.diff-high {
  background: linear-gradient(135deg, #059669, #10b981);
  color: white;
  padding: 0.5em 1em;
  border-radius: 4px;
  font-weight: bold;
  display: inline-block;
  margin: 0.25em;
}

.diff-medium {
  background: linear-gradient(135deg, #d97706, #f59e0b);
  color: white;
  padding: 0.5em 1em;
  border-radius: 4px;
  font-weight: bold;
  display: inline-block;
  margin: 0.25em;
}

.diff-low {
  background: linear-gradient(135deg, #dc2626, #ef4444);
  color: white;
  padding: 0.5em 1em;
  border-radius: 4px;
  font-weight: bold;
  display: inline-block;
  margin: 0.25em;
}

/* Operator type badges */
.operator-alignment {
  background: linear-gradient(135deg, #4f46e5, #6366f1);
  color: white;
  padding: 0.5em 1em;
  border-radius: 4px;
  font-weight: bold;
  display: inline-block;
  margin: 0.25em;
}

.operator-pileup {
  background: linear-gradient(135deg, #6366f1, #8b5cf6);
  color: white;
  padding: 0.5em 1em;
  border-radius: 4px;
  font-weight: bold;
  display: inline-block;
  margin: 0.25em;
}

.operator-variant {
  background: linear-gradient(135deg, #0891b2, #06b6d4);
  color: white;
  padding: 0.5em 1em;
  border-radius: 4px;
  font-weight: bold;
  display: inline-block;
  margin: 0.25em;
}

.operator-filter {
  background: linear-gradient(135deg, #7c3aed, #a855f7);
  color: white;
  padding: 0.5em 1em;
  border-radius: 4px;
  font-weight: bold;
  display: inline-block;
  margin: 0.25em;
}

/* Pipeline/architecture diagrams */
.pipeline-diagram {
  text-align: center;
  margin: 2em 0;
}

.pipeline-diagram svg {
  max-width: 100%;
  height: auto;
}

/* ── Stat cards (display-only, non-interactive) ── */
.stat-grid {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(150px, 1fr));
  gap: 1em;
  margin: 1em 0;
}

.stat-card {
  background: color-mix(in srgb, var(--md-primary-fg-color) 8%, var(--md-default-bg-color));
  border-radius: 8px;
  padding: 1.2em 1em;
  text-align: center;
}

.stat-card .stat-value {
  font-size: 1.8em;
  font-weight: 700;
  color: var(--md-primary-fg-color);
  line-height: 1.2;
}

.stat-card .stat-label {
  font-size: 0.85em;
  color: var(--md-default-fg-color--light);
  margin-top: 0.3em;
}

/* ── Nav cards (clickable, link to other pages) ── */
.nav-grid {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
  gap: 1em;
  margin: 1em 0;
}

.nav-card {
  background: var(--md-default-bg-color);
  border: 1px solid var(--md-default-fg-color--lightest);
  border-left: 4px solid var(--md-primary-fg-color);
  border-radius: 8px;
  padding: 1.5em 2.5em 1.5em 1.5em;
  text-align: left;
  box-shadow: 0 2px 4px rgba(0, 0, 0, 0.06);
  transition: box-shadow 0.2s ease, transform 0.2s ease, border-color 0.2s ease;
  cursor: pointer;
  position: relative;
}

.nav-card:hover {
  box-shadow: 0 8px 20px rgba(0, 0, 0, 0.1);
  transform: translateY(-3px);
  border-left-color: var(--md-accent-fg-color);
}

.nav-card::after {
  content: "\2192";
  position: absolute;
  right: 1em;
  top: 50%;
  transform: translateY(-50%);
  font-size: 1.3em;
  color: var(--md-default-fg-color--lighter);
  transition: color 0.2s ease, transform 0.2s ease;
}

.nav-card:hover::after {
  color: var(--md-accent-fg-color);
  transform: translateY(-50%) translateX(3px);
}

.nav-card a {
  text-decoration: none;
  color: inherit;
  display: block;
}

.nav-card .nav-title {
  font-size: 1.4em;
  font-weight: 700;
  color: var(--md-primary-fg-color);
  line-height: 1.2;
}

.nav-card:hover .nav-title {
  color: var(--md-accent-fg-color);
}

.nav-card .nav-description {
  font-size: 0.85em;
  color: var(--md-default-fg-color--light);
  margin-top: 0.3em;
}

/* ── Legacy metric-card fallback ── */
.performance-metrics {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
  gap: 1em;
  margin: 1em 0;
}

.metric-card {
  background: var(--md-default-bg-color);
  border: 1px solid var(--md-default-fg-color--lightest);
  border-radius: 8px;
  padding: 1.5em 1em;
  text-align: center;
}

.metric-value {
  font-size: 2em;
  font-weight: bold;
  color: var(--md-primary-fg-color);
}

.metric-label {
  font-size: 0.9em;
  color: var(--md-default-fg-color--light);
  margin-top: 0.5em;
}

/* Alignment quality indicators */
.quality-high {
  color: #059669;
  font-weight: bold;
}

.quality-medium {
  color: #d97706;
  font-weight: bold;
}

.quality-low {
  color: #dc2626;
  font-weight: bold;
}

/* Results table styling */
.results-table {
  width: 100%;
  border-collapse: collapse;
  margin: 1em 0;
}

.results-table th,
.results-table td {
  padding: 0.75em;
  text-align: left;
  border-bottom: 1px solid var(--md-default-fg-color--lightest);
}

.results-table th {
  background: var(--md-default-bg-color--light);
  font-weight: bold;
}

.results-table .metric-name {
  font-family: 'Roboto Mono', monospace;
  font-weight: bold;
  color: var(--md-primary-fg-color);
}

.results-table .value {
  font-family: 'Roboto Mono', monospace;
}

/* Operator architecture styling */
.architecture-block {
  background: var(--md-code-bg-color);
  border: 1px solid var(--md-default-fg-color--lightest);
  border-radius: 4px;
  padding: 1em;
  margin: 0.5em 0;
}

.architecture-block .block-title {
  font-weight: bold;
  color: var(--md-primary-fg-color);
  margin-bottom: 0.5em;
}

.architecture-block .block-description {
  font-size: 0.9em;
  color: var(--md-default-fg-color--light);
}

/* Framework badges */
.framework-jax {
  background: #d97706;
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

.framework-flax {
  background: #6366f1;
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

.framework-datarax {
  background: #4f46e5;
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

/* Code annotation enhancements */
.md-typeset .md-annotation {
  font-size: 0.8em;
  line-height: 1.4;
}

/* Bioinformatics badge styling */
.bio-badge {
  display: inline-block;
  padding: 0.25rem 0.5rem;
  border-radius: 0.25rem;
  font-size: 0.75rem;
  font-weight: 600;
  text-transform: uppercase;
  letter-spacing: 0.05em;
  margin: 0.125rem;
}

/* Configuration YAML highlighting */
.config-structure {
  background: var(--md-code-bg-color);
  border-left: 4px solid var(--md-primary-fg-color);
  padding: 1em;
  margin: 1em 0;
  font-family: 'Roboto Mono', monospace;
}

/* Improve code block readability */
.md-typeset code {
  font-size: 0.85em;
}

/* Better spacing for API documentation */
.md-typeset .doc-contents {
  padding-left: 1rem;
}

/* Improve table of contents */
.md-nav__link {
  font-size: 0.9em;
}

/* Better heading hierarchy */
.md-typeset h1 {
  color: var(--md-primary-fg-color);
}

.md-typeset h2 {
  border-bottom: 1px solid var(--md-default-fg-color--lightest);
  padding-bottom: 0.3rem;
}

/* Sequence type badges */
.seq-dna {
  background: linear-gradient(135deg, #4f46e5, #6366f1);
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

.seq-rna {
  background: linear-gradient(135deg, #6366f1, #8b5cf6);
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

.seq-protein {
  background: linear-gradient(135deg, #0891b2, #06b6d4);
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

/* Algorithm category badges */
.algo-alignment {
  background: #4f46e5;
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

.algo-variant {
  background: #dc2626;
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

.algo-assembly {
  background: #7c3aed;
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

.algo-quantification {
  background: #0891b2;
  color: white;
  padding: 0.25em 0.5em;
  border-radius: 4px;
  font-size: 0.8em;
  font-weight: bold;
}

/* Responsive design for mobile */
@media screen and (max-width: 768px) {
  .performance-metrics {
    grid-template-columns: 1fr;
  }

  .pipeline-diagram {
    overflow-x: auto;
  }

  .results-table {
    font-size: 0.9em;
  }

  .bio-badge {
    font-size: 0.7em;
    padding: 0.2rem 0.4rem;
  }
}

/* Dark mode specific adjustments */
[data-md-color-scheme="slate"] {
  .pipeline-info {
    background: linear-gradient(135deg, #4338ca, #4f46e5);
  }

  .performance-warning {
    background: linear-gradient(135deg, #b91c1c, #dc2626);
  }

  .differentiability-note {
    background: linear-gradient(135deg, #4338ca, #6366f1);
  }

  .stat-card {
    background: color-mix(in srgb, var(--md-primary-fg-color) 12%, var(--md-default-bg-color));
  }

  .nav-card {
    background: var(--md-code-bg-color);
    box-shadow: 0 2px 4px rgba(0, 0, 0, 0.2);
  }

  .nav-card:hover {
    box-shadow: 0 8px 20px rgba(0, 0, 0, 0.35);
  }

  .metric-card {
    background: var(--md-code-bg-color);
  }

  .architecture-block {
    background: var(--md-code-bg-color);
  }
}

/* Print styles for documentation */
@media print {

  .md-header,
  .md-tabs,
  .md-footer {
    display: none;
  }

  .md-content {
    margin: 0;
  }

  .pipeline-diagram {
    page-break-inside: avoid;
  }

  .results-table {
    page-break-inside: avoid;
  }

  .architecture-block {
    page-break-inside: avoid;
  }
}

/* Benchmark result styling */
.benchmark-results {
  margin: 1em 0;
  padding: 1em;
  background: var(--md-code-bg-color);
  border-radius: 4px;
  border-left: 4px solid var(--md-primary-fg-color);
}

.benchmark-title {
  font-weight: bold;
  color: var(--md-primary-fg-color);
  margin-bottom: 0.5em;
}

/* Gradient flow visualization */
.gradient-flow {
  background: linear-gradient(90deg, #dc2626 0%, #d97706 25%, #059669 50%, #0891b2 75%, #6366f1 100%);
  height: 4px;
  border-radius: 2px;
  margin: 1em 0;
}

/* Differentiability technique cards */
.technique-card {
  background: var(--md-code-bg-color);
  border: 1px solid var(--md-default-fg-color--lightest);
  border-radius: 8px;
  padding: 1.5em;
  margin: 1em 0;
}

.technique-card .technique-name {
  font-size: 1.2em;
  font-weight: bold;
  color: var(--md-primary-fg-color);
  margin-bottom: 0.5em;
}

.technique-card .technique-description {
  color: var(--md-default-fg-color--light);
  margin-bottom: 1em;
}

.technique-card .technique-use-cases {
  font-size: 0.9em;
  background: var(--md-default-bg-color);
  padding: 0.5em 1em;
  border-radius: 4px;
}