esc_html__( 'Primary Menu', 'peptide-starter' ),
'footer' => esc_html__( 'Footer Menu', 'peptide-starter' ),
) );
// Add support for wide blocks
add_theme_support( 'align-wide' );
// Load text domain
load_theme_textdomain( 'peptide-starter', PEPTIDE_STARTER_DIR . '/languages' );
}
add_action( 'after_setup_theme', 'peptide_starter_setup' );
/**
* Register and enqueue stylesheets and scripts
*/
function peptide_starter_scripts() {
// Register and enqueue main stylesheet
wp_enqueue_style( 'peptide-starter-style', PEPTIDE_STARTER_URI . '/style.css', array(), PEPTIDE_STARTER_VERSION );
// Add conditional scripts
wp_enqueue_script( 'peptide-starter-navigation', PEPTIDE_STARTER_URI . '/assets/js/navigation.js', array(), PEPTIDE_STARTER_VERSION, true );
wp_enqueue_script( 'peptide-starter-theme', PEPTIDE_STARTER_URI . '/assets/js/theme.js', array(), PEPTIDE_STARTER_VERSION, true );
// Pass PHP data to JavaScript
wp_localize_script( 'peptide-starter-theme', 'peptideStarterData', array(
'siteUrl' => home_url( '/' ),
'isDarkMode' => get_theme_mod( 'dark_mode_default', false ),
) );
// Dequeue comment reply script if comments are not open
if ( is_singular() && comments_open() && get_option( 'thread_comments' ) ) {
wp_enqueue_script( 'comment-reply' );
}
}
add_action( 'wp_enqueue_scripts', 'peptide_starter_scripts' );
/**
* Enqueue plugin override styles at a late priority so they load AFTER plugin stylesheets.
* This ensures theme overrides (e.g. removing line-clamp on article excerpts) beat plugin CSS.
*/
function peptide_starter_plugin_overrides() {
wp_add_inline_style( 'peptide-starter-style', '
/* Override Peptide News plugin line-clamp — show full summaries */
p.pn-article-excerpt,
.pn-article-card p.pn-article-excerpt,
body .pn-article-excerpt {
-webkit-line-clamp: unset !important;
-webkit-box-orient: unset !important;
display: block !important;
overflow: visible !important;
}
' );
}
add_action( 'wp_enqueue_scripts', 'peptide_starter_plugin_overrides', 99 );
/**
* Register widget areas
*/
function peptide_starter_widgets_init() {
register_sidebar( array(
'name' => esc_html__( 'Footer - Column 1', 'peptide-starter' ),
'id' => 'footer-1',
'description' => esc_html__( 'Footer widget area 1', 'peptide-starter' ),
'before_widget' => '',
'before_title' => '',
) );
register_sidebar( array(
'name' => esc_html__( 'Footer - Column 2', 'peptide-starter' ),
'id' => 'footer-2',
'description' => esc_html__( 'Footer widget area 2', 'peptide-starter' ),
'before_widget' => '',
'before_title' => '',
) );
register_sidebar( array(
'name' => esc_html__( 'Footer - Column 3', 'peptide-starter' ),
'id' => 'footer-3',
'description' => esc_html__( 'Footer widget area 3', 'peptide-starter' ),
'before_widget' => '',
'before_title' => '',
) );
register_sidebar( array(
'name' => esc_html__( 'Footer - Column 4', 'peptide-starter' ),
'id' => 'footer-4',
'description' => esc_html__( 'Footer widget area 4', 'peptide-starter' ),
'before_widget' => '',
'before_title' => '',
) );
}
add_action( 'widgets_init', 'peptide_starter_widgets_init' );
/**
* Register theme customizer options
*/
function peptide_starter_customize_register( $wp_customize ) {
// Logo section
$wp_customize->add_section( 'peptide_starter_branding', array(
'title' => esc_html__( 'Branding', 'peptide-starter' ),
'priority' => 30,
) );
// Hero settings section
$wp_customize->add_section( 'peptide_starter_hero', array(
'title' => esc_html__( 'Hero Section', 'peptide-starter' ),
'priority' => 40,
) );
// Hero Title
$wp_customize->add_setting( 'hero_title', array(
'default' => get_bloginfo( 'name' ),
'transport' => 'postMessage',
) );
$wp_customize->add_control( 'hero_title', array(
'label' => esc_html__( 'Hero Title', 'peptide-starter' ),
'section' => 'peptide_starter_hero',
'type' => 'text',
) );
// Hero Subtitle
$wp_customize->add_setting( 'hero_subtitle', array(
'default' => esc_html__( 'A scientific peptide reference database', 'peptide-starter' ),
'transport' => 'postMessage',
) );
$wp_customize->add_control( 'hero_subtitle', array(
'label' => esc_html__( 'Hero Subtitle', 'peptide-starter' ),
'section' => 'peptide_starter_hero',
'type' => 'textarea',
) );
// Hero Search Placeholder
$wp_customize->add_setting( 'hero_search_placeholder', array(
'default' => esc_html__( 'Search peptides, sequences, or research...', 'peptide-starter' ),
'transport' => 'postMessage',
) );
$wp_customize->add_control( 'hero_search_placeholder', array(
'label' => esc_html__( 'Search Placeholder', 'peptide-starter' ),
'section' => 'peptide_starter_hero',
'type' => 'text',
) );
// Footer section
$wp_customize->add_section( 'peptide_starter_footer', array(
'title' => esc_html__( 'Footer', 'peptide-starter' ),
'priority' => 50,
) );
// Footer Copyright Text
$wp_customize->add_setting( 'footer_copyright', array(
'default' => esc_html__( 'Copyright © 2026 Peptide Repo. All rights reserved.', 'peptide-starter' ),
'transport' => 'postMessage',
) );
$wp_customize->add_control( 'footer_copyright', array(
'label' => esc_html__( 'Copyright Text', 'peptide-starter' ),
'section' => 'peptide_starter_footer',
'type' => 'textarea',
) );
// Dark mode section
$wp_customize->add_section( 'peptide_starter_theme_mode', array(
'title' => esc_html__( 'Theme Mode', 'peptide-starter' ),
'priority' => 60,
) );
// Dark mode default
$wp_customize->add_setting( 'dark_mode_default', array(
'default' => false,
'transport' => 'refresh',
) );
$wp_customize->add_control( 'dark_mode_default', array(
'label' => esc_html__( 'Enable Dark Mode by Default', 'peptide-starter' ),
'section' => 'peptide_starter_theme_mode',
'type' => 'checkbox',
) );
}
add_action( 'customize_register', 'peptide_starter_customize_register' );
/**
* Add custom logo support
*/
function peptide_starter_get_custom_logo() {
if ( function_exists( 'get_custom_logo' ) ) {
return get_custom_logo();
}
return '';
}
/**
* Navigation Menu Walker for handling active states
*/
class Peptide_Starter_Nav_Walker extends Walker_Nav_Menu {
public function start_el( &$output, $item, $depth = 0, $args = null, $id = 0 ) {
if ( isset( $args->item_spacing ) && 'discard' === $args->item_spacing ) {
$t = '';
$n = '';
} else {
$t = "\t";
$n = "\n";
}
$indent = ( $depth ) ? str_repeat( $t, $depth ) : '';
$classes = empty( $item->classes ) ? array() : (array) $item->classes;
$classes[] = 'menu-item-' . $item->ID;
if ( in_array( 'current-menu-item', $classes, true ) || in_array( 'current-menu-parent', $classes, true ) ) {
$classes[] = 'active';
}
$args = apply_filters( 'nav_menu_item_args', $args, $item, $depth );
$class_names = join( ' ', apply_filters( 'nav_menu_css_class', array_filter( $classes ), $item, $args, $depth ) );
$class_names = $class_names ? ' class="' . esc_attr( $class_names ) . '"' : '';
$id = apply_filters( 'nav_menu_item_id', 'menu-item-' . $item->ID, $item, $args, $depth );
$id = $id ? ' id="' . esc_attr( $id ) . '"' : '';
$output .= $indent . '';
$atts = array();
$atts['title'] = ! empty( $item->attr_title ) ? $item->attr_title : '';
$atts['target'] = ! empty( $item->target ) ? $item->target : '';
$atts['rel'] = ! empty( $item->xfn ) ? $item->xfn : '';
$atts['href'] = ! empty( $item->url ) ? $item->url : '';
$atts = apply_filters( 'nav_menu_link_attributes', $atts, $item, $args, $depth );
$attributes = '';
foreach ( $atts as $attr => $value ) {
if ( ! empty( $value ) ) {
$value = ( 'href' === $attr ) ? esc_url( $value ) : esc_attr( $value );
$attributes .= ' ' . $attr . '="' . $value . '"';
}
}
$title = apply_filters( 'nav_menu_item_title', $item->title, $item, $args, $depth );
$title = apply_filters( 'nav_menu_item_title', $title, $item, $args, $depth );
$link = $args->before;
$link .= '';
$link .= $args->link_before . $title . $args->link_after;
$link .= '';
$link .= $args->after;
$output .= apply_filters( 'nav_menu_item_title', $link, $item, $args, $depth );
$output .= '' . $n;
}
}
/**
* Display custom logo
*/
function peptide_starter_the_custom_logo() {
if ( function_exists( 'the_custom_logo' ) ) {
the_custom_logo();
} else {
$site_name = get_bloginfo( 'name' );
echo '' . esc_html( $site_name ) . '';
}
}
/**
* Get hero title
*/
function peptide_starter_get_hero_title() {
return get_theme_mod( 'hero_title', get_bloginfo( 'name' ) );
}
/**
* Get hero subtitle
*/
function peptide_starter_get_hero_subtitle() {
return get_theme_mod( 'hero_subtitle', esc_html__( 'A scientific peptide reference database', 'peptide-starter' ) );
}
/**
* Get search placeholder
*/
function peptide_starter_get_search_placeholder() {
return get_theme_mod( 'hero_search_placeholder', esc_html__( 'Search peptides, sequences, or research...', 'peptide-starter' ) );
}
/**
* Get footer copyright text
*/
function peptide_starter_get_footer_copyright() {
return get_theme_mod( 'footer_copyright', esc_html__( 'Copyright © 2026 Peptide Repo. All rights reserved.', 'peptide-starter' ) );
}
/**
* Apply dark mode class to body if enabled
*/
function peptide_starter_dark_mode_body_class( $classes ) {
if ( get_theme_mod( 'dark_mode_default', false ) ) {
$classes[] = 'dark-mode-default';
}
return $classes;
}
add_filter( 'body_class', 'peptide_starter_dark_mode_body_class' );
/**
* Register pagination function
*/
function peptide_starter_pagination() {
global $wp_query;
if ( $wp_query->max_num_pages <= 1 ) {
return;
}
$current_page = max( 1, get_query_var( 'paged' ) );
$total_pages = $wp_query->max_num_pages;
echo '';
}
/**
* Get the excerpt
*/
function peptide_starter_get_excerpt( $post_id = 0, $length = 20 ) {
if ( ! $post_id ) {
$post_id = get_the_ID();
}
$excerpt = get_the_excerpt( $post_id );
if ( ! $excerpt ) {
$excerpt = wp_trim_words( get_the_content( $post_id ), $length );
}
return $excerpt;
}
/**
* Check if we should show footer newsletter signup
*/
function peptide_starter_show_newsletter_form() {
return apply_filters( 'peptide_starter_show_newsletter', true );
}
/**
* Enqueue inline script for dark mode toggle (output in footer)
*/
function peptide_starter_inline_dark_mode_script() {
$default_dark = get_theme_mod( 'dark_mode_default', false ) ? 'dark' : 'light';
?>