/**
 * Sequencing Portal - Modern Scientific Theme
 * Bootstrap 5 Custom Theme with Light/Dark Mode
 * Optimized for data-dense scientific applications
 */

/* ============================================
   CSS Custom Properties (CSS Variables)
   ============================================ */

:root {
    /* Scientific Color Palette - Light Mode */
    --sp-primary: #0891B2;              /* Teal/Cyan - Primary accent */
    --sp-primary-dark: #0E7490;         /* Darker teal for hover states */
    --sp-primary-light: #06B6D4;        /* Lighter teal */
    --sp-secondary: #64748B;            /* Slate gray */
    --sp-success: #10B981;              /* Emerald green */
    --sp-info: #3B82F6;                 /* Blue */
    --sp-warning: #F59E0B;              /* Amber */
    --sp-danger: #EF4444;               /* Red */
    
    /* Backgrounds - Light Mode */
    --sp-bg-primary: #FFFFFF;           /* Main background */
    --sp-bg-secondary: #F8FAFC;         /* Secondary surfaces */
    --sp-bg-tertiary: #F1F5F9;          /* Cards, panels */
    --sp-bg-hover: #E2E8F0;             /* Hover states */
    --sp-bg-active: #CBD5E1;            /* Active states */
    
    /* Text Colors - Light Mode */
    --sp-text-primary: #0F172A;         /* Primary text */
    --sp-text-secondary: #475569;       /* Secondary text */
    --sp-text-muted: #94A3B8;           /* Muted text */
    --sp-text-inverse: #FFFFFF;         /* Text on dark backgrounds */
    
    /* Borders - Light Mode */
    --sp-border-color: #E2E8F0;
    --sp-border-color-dark: #CBD5E1;
    
    /* Shadows */
    --sp-shadow-sm: 0 1px 2px 0 rgba(0, 0, 0, 0.05);
    --sp-shadow: 0 1px 3px 0 rgba(0, 0, 0, 0.1), 0 1px 2px 0 rgba(0, 0, 0, 0.06);
    --sp-shadow-md: 0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -1px rgba(0, 0, 0, 0.06);
    --sp-shadow-lg: 0 10px 15px -3px rgba(0, 0, 0, 0.1), 0 4px 6px -2px rgba(0, 0, 0, 0.05);
    
    /* Typography */
    --sp-font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif;
    --sp-font-mono: ui-monospace, SFMono-Regular, "SF Mono", Menlo, Consolas, "Liberation Mono", monospace;
    
    /* Spacing for compact tables */
    --sp-table-cell-padding-y: 0.5rem;
    --sp-table-cell-padding-x: 0.75rem;
    
    /* Transitions */
    --sp-transition: all 0.2s ease-in-out;
}

/* Dark Mode Variables */
[data-theme="dark"] {
    /* Backgrounds - Dark Mode */
    --sp-bg-primary: #0F172A;           /* Deep slate - main background */
    --sp-bg-secondary: #1E293B;         /* Slightly lighter slate */
    --sp-bg-tertiary: #334155;          /* Card backgrounds */
    --sp-bg-hover: #475569;             /* Hover states */
    --sp-bg-active: #64748B;            /* Active states */
    
    /* Text Colors - Dark Mode */
    --sp-text-primary: #F1F5F9;         /* Primary text */
    --sp-text-secondary: #CBD5E1;       /* Secondary text */
    --sp-text-muted: #94A3B8;           /* Muted text */
    --sp-text-inverse: #0F172A;         /* Text on light backgrounds */
    
    /* Borders - Dark Mode */
    --sp-border-color: #334155;
    --sp-border-color-dark: #475569;
    
    /* Adjusted shadows for dark mode */
    --sp-shadow-sm: 0 1px 2px 0 rgba(0, 0, 0, 0.3);
    --sp-shadow: 0 1px 3px 0 rgba(0, 0, 0, 0.4), 0 1px 2px 0 rgba(0, 0, 0, 0.3);
    --sp-shadow-md: 0 4px 6px -1px rgba(0, 0, 0, 0.4), 0 2px 4px -1px rgba(0, 0, 0, 0.3);
    --sp-shadow-lg: 0 10px 15px -3px rgba(0, 0, 0, 0.5), 0 4px 6px -2px rgba(0, 0, 0, 0.4);
}

/* ============================================
   Global Styles
   ============================================ */

body {
    font-family: var(--sp-font-family);
    background-color: var(--sp-bg-secondary);
    color: var(--sp-text-primary);
    transition: background-color 0.3s ease, color 0.3s ease;
    font-size: 0.9375rem; /* 15px - slightly smaller for data density */
    line-height: 1.5;
}

/* Ensure all text elements inherit proper color */
p {
    color: var(--sp-text-primary);
}

strong,
b {
    color: var(--sp-text-primary);
    font-weight: 600;
}

li {
    color: var(--sp-text-primary);
}

ul,
ol {
    color: var(--sp-text-primary);
}

/* Improved text readability */
h1, h2, h3, h4, h5, h6,
.h1, .h2, .h3, .h4, .h5, .h6 {
    color: var(--sp-text-primary) !important;
    font-weight: 600;
    letter-spacing: -0.025em;
}

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

.text-dark {
    color: var(--sp-text-primary) !important;
}

h1, .h1 { font-size: 2rem; }
h2, .h2 { font-size: 1.5rem; }
h3, .h3 { font-size: 1.25rem; }
h4, .h4 { font-size: 1.125rem; }
h5, .h5 { font-size: 1rem; }
h6, .h6 { font-size: 0.875rem; }

a {
    color: var(--sp-primary);
    text-decoration: none;
    transition: color 0.15s ease-in-out;
}

a:hover {
    color: var(--sp-primary-dark);
    text-decoration: none;
}

code {
    font-family: var(--sp-font-mono);
    background-color: var(--sp-bg-tertiary);
    color: var(--sp-primary);
    padding: 0.125rem 0.375rem;
    border-radius: 0.25rem;
    font-size: 0.875em;
}

/* ============================================
   Navbar Styles
   ============================================ */

.navbar-custom {
    background-color: var(--sp-bg-primary);
    border-bottom: 1px solid var(--sp-border-color);
    box-shadow: var(--sp-shadow-sm);
    padding: 0.75rem 1.5rem;
    position: sticky;
    top: 0;
    z-index: 1030;
}

.navbar-brand {
    font-weight: 600;
    font-size: 1.25rem;
    color: var(--sp-text-primary) !important;
    display: flex;
    align-items: center;
    gap: 0.5rem;
}

.navbar-brand i {
    color: var(--sp-primary);
    font-size: 1.5rem;
}

.nav-link {
    color: var(--sp-text-secondary) !important;
    font-weight: 500;
    padding: 0.5rem 1rem !important;
    transition: var(--sp-transition);
    border-radius: 0.375rem;
}

.nav-link:hover {
    color: var(--sp-text-primary) !important;
    background-color: var(--sp-bg-tertiary);
}

.nav-link.active {
    color: var(--sp-primary) !important;
    background-color: rgba(8, 145, 178, 0.1);
}

/* Theme Toggle Button */
.theme-toggle {
    background: none;
    border: 1px solid var(--sp-border-color);
    color: var(--sp-text-secondary);
    padding: 0.5rem 0.75rem;
    border-radius: 0.5rem;
    cursor: pointer;
    transition: var(--sp-transition);
    display: flex;
    align-items: center;
    gap: 0.5rem;
    font-size: 0.875rem;
}

.theme-toggle:hover {
    background-color: var(--sp-bg-tertiary);
    border-color: var(--sp-border-color-dark);
    color: var(--sp-text-primary);
}

/* ============================================
   Card Styles
   ============================================ */

.card {
    background-color: var(--sp-bg-primary);
    border: 1px solid var(--sp-border-color);
    border-radius: 0.5rem;
    box-shadow: var(--sp-shadow-sm);
    transition: var(--sp-transition);
}

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

.card-header {
    background-color: var(--sp-bg-secondary);
    border-bottom: 1px solid var(--sp-border-color);
    padding: 0.875rem 1.25rem;
    font-weight: 600;
    color: var(--sp-text-primary);
}

.card-body {
    padding: 1.25rem;
}

.card-text {
    color: var(--sp-text-primary);
}

.card-footer {
    background-color: var(--sp-bg-secondary);
    border-top: 1px solid var(--sp-border-color);
    padding: 0.875rem 1.25rem;
}

/* Stat Cards */
.stat-card {
    border: 2px solid transparent;
    transition: transform 0.2s ease, box-shadow 0.2s ease;
}

.stat-card:hover {
    transform: translateY(-4px);
    box-shadow: var(--sp-shadow-md);
}

.stat-card.border-primary {
    border-color: var(--sp-primary);
}

.stat-card .display-4 {
    opacity: 0.8;
}

/* ============================================
   Table Styles - Optimized for Data Density
   ============================================ */

.table {
    color: var(--sp-text-primary) !important;
    margin-bottom: 0;
    font-size: 0.875rem; /* Compact font size */
    background-color: transparent !important;
}

.table thead th {
    background-color: var(--sp-bg-secondary) !important;
    color: var(--sp-text-primary) !important;
    font-weight: 600;
    border-bottom: 2px solid var(--sp-border-color-dark);
    padding: var(--sp-table-cell-padding-y) var(--sp-table-cell-padding-x);
    position: sticky;
    top: 0;
    z-index: 10;
    white-space: nowrap;
    text-transform: uppercase;
    font-size: 0.75rem;
    letter-spacing: 0.05em;
}

.table tbody td {
    padding: var(--sp-table-cell-padding-y) var(--sp-table-cell-padding-x);
    vertical-align: middle;
    border-bottom: 1px solid var(--sp-border-color);
    color: var(--sp-text-primary) !important;
    background-color: transparent !important;
}

.table tbody tr {
    background-color: transparent !important;
}

.table-borderless tbody td,
.table-borderless thead th {
    border: 0 !important;
    background-color: transparent !important;
}

.table-hover tbody tr:hover {
    background-color: var(--sp-bg-hover);
    transition: background-color 0.15s ease;
}

.table-striped tbody tr:nth-of-type(odd) {
    background-color: var(--sp-bg-secondary);
}

/* Sticky table headers for scrolling */
.table-responsive {
    max-height: 70vh;
    overflow-y: auto;
    overflow-x: auto;
    border-radius: 0.5rem;
}

.table-responsive::-webkit-scrollbar {
    width: 8px;
    height: 8px;
}

.table-responsive::-webkit-scrollbar-track {
    background: var(--sp-bg-secondary);
}

.table-responsive::-webkit-scrollbar-thumb {
    background: var(--sp-border-color-dark);
    border-radius: 4px;
}

.table-responsive::-webkit-scrollbar-thumb:hover {
    background: var(--sp-text-muted);
}

/* Row actions dropdown */
.table .btn-group {
    opacity: 0.7;
    transition: opacity 0.15s ease;
}

.table tr:hover .btn-group {
    opacity: 1;
}

/* ============================================
   Button Styles
   ============================================ */

.btn {
    font-weight: 500;
    padding: 0.5rem 1rem;
    border-radius: 0.375rem;
    transition: var(--sp-transition);
    font-size: 0.875rem;
}

.btn-primary {
    background-color: var(--sp-primary);
    border-color: var(--sp-primary);
    color: white;
}

.btn-primary:hover {
    background-color: var(--sp-primary-dark);
    border-color: var(--sp-primary-dark);
    transform: translateY(-1px);
    box-shadow: var(--sp-shadow);
}

.btn-outline-primary {
    color: var(--sp-primary);
    border-color: var(--sp-primary);
}

.btn-outline-primary:hover {
    background-color: var(--sp-primary);
    border-color: var(--sp-primary);
    color: white;
}

.btn-secondary {
    background-color: var(--sp-secondary);
    border-color: var(--sp-secondary);
    color: white;
}

.btn-outline-secondary {
    color: var(--sp-text-secondary);
    border-color: var(--sp-border-color-dark);
}

.btn-outline-secondary:hover {
    background-color: var(--sp-bg-tertiary);
    border-color: var(--sp-border-color-dark);
    color: var(--sp-text-primary);
}

.btn-sm {
    padding: 0.375rem 0.75rem;
    font-size: 0.8125rem;
}

.btn-group .btn {
    border-right-width: 0;
}

.btn-group .btn:last-child {
    border-right-width: 1px;
}

/* ============================================
   Badge Styles
   ============================================ */

.badge {
    font-weight: 500;
    padding: 0.35em 0.65em;
    font-size: 0.75rem;
    border-radius: 0.375rem;
}

.bg-primary {
    background-color: var(--sp-primary) !important;
    color: white !important;
}

.bg-secondary {
    background-color: var(--sp-secondary) !important;
    color: white !important;
}

.bg-success {
    background-color: var(--sp-success) !important;
    color: white !important;
}

.bg-info {
    background-color: var(--sp-info) !important;
    color: white !important;
}

.bg-warning {
    background-color: var(--sp-warning) !important;
    color: white !important;
}

.bg-danger {
    background-color: var(--sp-danger) !important;
    color: white !important;
}

.bg-light {
    background-color: var(--sp-bg-tertiary) !important;
    color: var(--sp-text-primary) !important;
}

.badge.bg-light {
    border: 1px solid var(--sp-border-color-dark);
}

/* Badge with counts - show inline with filters */
.filter-badge {
    display: inline-flex;
    align-items: center;
    gap: 0.375rem;
}

/* ============================================
   Form Styles
   ============================================ */

.form-label {
    font-weight: 500;
    color: var(--sp-text-primary);
    margin-bottom: 0.5rem;
    font-size: 0.875rem;
}

.form-check-label {
    color: var(--sp-text-primary);
}

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

.form-control,
.form-select {
    background-color: var(--sp-bg-primary);
    border: 1px solid var(--sp-border-color);
    color: var(--sp-text-primary);
    padding: 0.5rem 0.75rem;
    border-radius: 0.375rem;
    transition: var(--sp-transition);
    font-size: 0.875rem;
}

.form-control:focus,
.form-select:focus {
    background-color: var(--sp-bg-primary);
    border-color: var(--sp-primary);
    color: var(--sp-text-primary);
    box-shadow: 0 0 0 0.2rem rgba(8, 145, 178, 0.25);
}

.form-control::placeholder {
    color: var(--sp-text-muted);
}

/* Form validation */
.form-control.is-valid {
    border-color: var(--sp-success);
}

.form-control.is-invalid {
    border-color: var(--sp-danger);
}

.valid-feedback {
    color: var(--sp-success);
}

.invalid-feedback {
    color: var(--sp-danger);
}

/* ============================================
   Alert Styles
   ============================================ */

.alert {
    border-radius: 0.5rem;
    border: 1px solid transparent;
    padding: 0.875rem 1.25rem;
    margin-bottom: 1rem;
    color: var(--sp-text-primary);
}

.alert-info {
    background-color: rgba(59, 130, 246, 0.1);
    border-color: rgba(59, 130, 246, 0.3);
    color: #3B82F6;
}

[data-theme="dark"] .alert-info {
    color: #60A5FA;
}

.alert-success {
    background-color: rgba(16, 185, 129, 0.1);
    border-color: rgba(16, 185, 129, 0.3);
    color: #10B981;
}

[data-theme="dark"] .alert-success {
    color: #34D399;
}

.alert-warning {
    background-color: rgba(245, 158, 11, 0.1);
    border-color: rgba(245, 158, 11, 0.3);
    color: #F59E0B;
}

[data-theme="dark"] .alert-warning {
    color: #FBBF24;
}

.alert-danger {
    background-color: rgba(239, 68, 68, 0.1);
    border-color: rgba(239, 68, 68, 0.3);
    color: #EF4444;
}

[data-theme="dark"] .alert-danger {
    color: #F87171;
}

.alert-light {
    background-color: var(--sp-bg-tertiary);
    border-color: var(--sp-border-color);
    color: var(--sp-text-primary);
}

/* ============================================
   Modal Styles
   ============================================ */

.modal-content {
    background-color: var(--sp-bg-primary);
    border: 1px solid var(--sp-border-color);
    border-radius: 0.5rem;
}

.modal-header {
    border-bottom: 1px solid var(--sp-border-color);
    background-color: var(--sp-bg-secondary);
}

.modal-body {
    color: var(--sp-text-primary);
}

.modal-footer {
    border-top: 1px solid var(--sp-border-color);
    background-color: var(--sp-bg-secondary);
}

.modal-title {
    color: var(--sp-text-primary);
}

.btn-close {
    filter: var(--sp-btn-close-filter, none);
}

[data-theme="dark"] .btn-close {
    --sp-btn-close-filter: invert(1) grayscale(100%) brightness(200%);
    filter: var(--sp-btn-close-filter);
}

/* ============================================
   Sidebar Styles (if used)
   ============================================ */

.sidebar {
    background-color: var(--sp-bg-primary);
    border-right: 1px solid var(--sp-border-color);
    min-height: 100vh;
    transition: var(--sp-transition);
}

.sidebar .nav-link {
    color: var(--sp-text-secondary);
    padding: 0.625rem 1rem;
    border-radius: 0.375rem;
    margin-bottom: 0.25rem;
    transition: var(--sp-transition);
}

.sidebar .nav-link:hover {
    background-color: var(--sp-bg-tertiary);
    color: var(--sp-text-primary);
}

.sidebar .nav-link.active {
    background-color: rgba(8, 145, 178, 0.15);
    color: var(--sp-primary);
    font-weight: 600;
}

.sidebar .nav-link i {
    width: 1.25rem;
    margin-right: 0.5rem;
}

/* ============================================
   Filter Panel Styles
   ============================================ */

.filter-panel {
    background-color: var(--sp-bg-primary);
    border: 1px solid var(--sp-border-color);
    border-radius: 0.5rem;
    padding: 1rem;
    margin-bottom: 1.5rem;
}

.filter-panel .form-label {
    font-size: 0.8125rem;
    margin-bottom: 0.375rem;
}

/* ============================================
   Pagination Styles
   ============================================ */

.pagination {
    margin-bottom: 0;
}

.page-link {
    color: var(--sp-primary);
    background-color: var(--sp-bg-primary);
    border: 1px solid var(--sp-border-color);
    padding: 0.375rem 0.75rem;
    transition: var(--sp-transition);
}

.page-link:hover {
    background-color: var(--sp-bg-tertiary);
    border-color: var(--sp-border-color-dark);
    color: var(--sp-primary-dark);
}

.page-item.active .page-link {
    background-color: var(--sp-primary);
    border-color: var(--sp-primary);
    color: white;
}

.page-item.disabled .page-link {
    color: var(--sp-text-muted);
    background-color: var(--sp-bg-secondary);
    border-color: var(--sp-border-color);
}

/* ============================================
   Utility Classes
   ============================================ */

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

.text-primary {
    color: var(--sp-primary) !important;
}

.text-secondary {
    color: var(--sp-text-secondary) !important;
}

.text-success {
    color: var(--sp-success) !important;
}

.text-info {
    color: var(--sp-info) !important;
}

.text-warning {
    color: var(--sp-warning) !important;
}

.text-danger {
    color: var(--sp-danger) !important;
}

/* Ensure small text inherits proper color */
.small,
small {
    color: inherit;
}

.bg-light {
    background-color: var(--sp-bg-secondary) !important;
}

.border {
    border-color: var(--sp-border-color) !important;
}

/* ============================================
   Dropdown Menus
   ============================================ */

.dropdown-menu {
    background-color: var(--sp-bg-primary);
    border: 1px solid var(--sp-border-color);
    box-shadow: var(--sp-shadow-md);
    border-radius: 0.5rem;
}

.dropdown-item {
    color: var(--sp-text-primary);
    padding: 0.5rem 1rem;
    transition: var(--sp-transition);
}

.dropdown-item:hover {
    background-color: var(--sp-bg-tertiary);
    color: var(--sp-text-primary);
}

.dropdown-divider {
    border-top: 1px solid var(--sp-border-color);
}

/* ============================================
   Loading States
   ============================================ */

.spinner-border {
    border-color: var(--sp-primary);
    border-right-color: transparent;
}

/* ============================================
   Responsive Adjustments
   ============================================ */

@media (max-width: 768px) {
    .table {
        font-size: 0.8125rem;
    }
    
    .table thead th {
        padding: 0.375rem 0.5rem;
        font-size: 0.6875rem;
    }
    
    .table tbody td {
        padding: 0.375rem 0.5rem;
    }
    
    .btn {
        padding: 0.375rem 0.75rem;
        font-size: 0.8125rem;
    }
}

/* ============================================
   Print Styles
   ============================================ */

@media print {
    body {
        background-color: white;
        color: black;
    }
    
    .navbar,
    .sidebar,
    .btn,
    .theme-toggle {
        display: none;
    }
    
    .card {
        border: 1px solid #000;
        box-shadow: none;
    }
}