From 65b9f7a13c3b8ae612a05dccda19c169cd292a72 Mon Sep 17 00:00:00 2001 From: peptiderepo Date: Sun, 12 Apr 2026 22:54:51 +0700 Subject: [PATCH] fix: resolve PHPCS coding standard violations for CI - Convert all PHP files from CRLF to LF line endings - Reformat multi-line function calls per WPCS standard (opening paren last on line, closing paren on own line) - Fix assignment-in-conditional in single-peptide.php - Change double quotes to single quotes in content-none.php - Exclude InvalidClassFileName sniff (standard WP functions.php pattern) - Fix archive-peptide.php opening PHP tag placement Co-Authored-By: Claude Opus 4.6 --- .phpcs.xml.dist | 5 + 404.php | 72 +-- archive-peptide.php | 3 +- assets/js/navigation.js | 168 ++--- assets/js/theme.js | 420 ++++++------- footer.php | 164 ++--- front-page.php | 170 ++--- functions.php | 1042 ++++++++++++++++--------------- header.php | 18 +- searchform.php | 54 +- single-peptide.php | 36 +- template-parts/content-none.php | 6 +- 12 files changed, 1125 insertions(+), 1033 deletions(-) diff --git a/.phpcs.xml.dist b/.phpcs.xml.dist index ace4a71..3c2a37e 100644 --- a/.phpcs.xml.dist +++ b/.phpcs.xml.dist @@ -26,4 +26,9 @@ + + + + + diff --git a/404.php b/404.php index ba29ea2..e9d32f5 100644 --- a/404.php +++ b/404.php @@ -1,36 +1,36 @@ - - -
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+ + diff --git a/archive-peptide.php b/archive-peptide.php index 34cf42c..d6f8d6d 100644 --- a/archive-peptide.php +++ b/archive-peptide.php @@ -70,4 +70,5 @@ get_header(); - { - link.addEventListener('click', closeMenu); - }); - - // Close menu on Escape key - document.addEventListener('keydown', (e) => { - if (e.key === 'Escape') { - closeMenu(); - } - }); - - // Set initial aria-expanded state - menuToggle.setAttribute('aria-expanded', 'false'); - - // Close menu when window is resized above mobile breakpoint - const mediaQuery = window.matchMedia('(min-width: 768px)'); - mediaQuery.addEventListener('change', (e) => { - if (e.matches) { - closeMenu(); - } - }); -})(); +/** + * Navigation and Mobile Menu Toggle + * Peptide Starter Theme + * + * Handles: + * - Mobile hamburger menu toggle + * - Navigation overlay click handling + * - Menu state persistence + */ + +(function() { + 'use strict'; + + const menuToggle = document.querySelector('.menu-toggle'); + const primaryNav = document.querySelector('.primary-navigation'); + const navOverlay = document.querySelector('.nav-overlay'); + + if (!menuToggle || !primaryNav || !navOverlay) { + return; + } + + /** + * Toggle mobile menu visibility + */ + function toggleMenu() { + const isActive = primaryNav.classList.contains('active'); + + if (isActive) { + closeMenu(); + } else { + openMenu(); + } + } + + /** + * Open mobile menu + */ + function openMenu() { + primaryNav.classList.add('active'); + navOverlay.classList.add('active'); + document.body.style.overflow = 'hidden'; + menuToggle.setAttribute('aria-expanded', 'true'); + } + + /** + * Close mobile menu + */ + function closeMenu() { + primaryNav.classList.remove('active'); + navOverlay.classList.remove('active'); + document.body.style.overflow = ''; + menuToggle.setAttribute('aria-expanded', 'false'); + } + + // Menu toggle button click + menuToggle.addEventListener('click', toggleMenu); + + // Overlay click + navOverlay.addEventListener('click', closeMenu); + + // Close menu when a nav link is clicked + const navLinks = primaryNav.querySelectorAll('a'); + navLinks.forEach(link => { + link.addEventListener('click', closeMenu); + }); + + // Close menu on Escape key + document.addEventListener('keydown', (e) => { + if (e.key === 'Escape') { + closeMenu(); + } + }); + + // Set initial aria-expanded state + menuToggle.setAttribute('aria-expanded', 'false'); + + // Close menu when window is resized above mobile breakpoint + const mediaQuery = window.matchMedia('(min-width: 768px)'); + mediaQuery.addEventListener('change', (e) => { + if (e.matches) { + closeMenu(); + } + }); +})(); diff --git a/assets/js/theme.js b/assets/js/theme.js index 2db7774..cd57e02 100644 --- a/assets/js/theme.js +++ b/assets/js/theme.js @@ -1,210 +1,210 @@ -/** - * Theme Utilities - * Peptide Starter Theme - * - * Handles: - * - Dark mode toggle functionality - * - Dark mode preference persistence - * - Plugin dark mode coordination - * - Smooth transitions - */ - -(function() { - 'use strict'; - - const html = document.documentElement; - const darkModeToggle = document.querySelector('.dark-mode-toggle'); - const sunIcon = document.querySelector('.sun-icon'); - const moonIcon = document.querySelector('.moon-icon'); - - if (!darkModeToggle) { - return; - } - - /** - * Get current theme preference - * @returns {string} 'dark' or 'light' - */ - function getCurrentTheme() { - const stored = localStorage.getItem('peptide-starter-theme'); - if (stored) { - return stored; - } - - const currentAttr = html.getAttribute('data-theme'); - if (currentAttr) { - return currentAttr; - } - - const systemDark = window.matchMedia('(prefers-color-scheme: dark)').matches; - return systemDark ? 'dark' : 'light'; - } - - /** - * Set theme preference - * @param {string} theme - 'dark' or 'light' - */ - function setTheme(theme) { - html.setAttribute('data-theme', theme); - localStorage.setItem('peptide-starter-theme', theme); - - // Update icon visibility - updateIcons(theme); - - // Notify plugins about theme change via custom event - const event = new CustomEvent('themechange', { - detail: { theme: theme } - }); - document.dispatchEvent(event); - - // Also update body class for CSS hooks - document.body.classList.remove('dark-mode', 'light-mode'); - document.body.classList.add(theme === 'dark' ? 'dark-mode' : 'light-mode'); - } - - /** - * Update icon visibility based on theme - * @param {string} theme - 'dark' or 'light' - */ - function updateIcons(theme) { - if (theme === 'dark') { - sunIcon.style.display = 'block'; - moonIcon.style.display = 'none'; - } else { - sunIcon.style.display = 'none'; - moonIcon.style.display = 'block'; - } - } - - /** - * Toggle between dark and light mode - */ - function toggleDarkMode() { - const currentTheme = getCurrentTheme(); - const newTheme = currentTheme === 'dark' ? 'light' : 'dark'; - setTheme(newTheme); - } - - // Initialize theme on page load - const initialTheme = getCurrentTheme(); - setTheme(initialTheme); - - // Dark mode toggle button click - darkModeToggle.addEventListener('click', toggleDarkMode); - - // Listen for system preference changes - const mediaQuery = window.matchMedia('(prefers-color-scheme: dark)'); - mediaQuery.addEventListener('change', (e) => { - const stored = localStorage.getItem('peptide-starter-theme'); - if (!stored) { - setTheme(e.matches ? 'dark' : 'light'); - } - }); - - // Expose API for plugins to read/listen to theme changes - window.peptideStarterTheme = { - getCurrentTheme: getCurrentTheme, - setTheme: setTheme, - toggleDarkMode: toggleDarkMode, - }; - - /** - * Plugin Integration Example: - * Plugins can listen to theme changes via: - * - * 1. Custom event listener: - * document.addEventListener('themechange', function(e) { - * console.log('Theme changed to:', e.detail.theme); - * }); - * - * 2. MutationObserver on data-theme: - * const observer = new MutationObserver((mutations) => { - * const theme = html.getAttribute('data-theme'); - * console.log('Theme is now:', theme); - * }); - * observer.observe(html, { attributes: true }); - * - * 3. Direct access to CSS custom properties which theme controls - */ - - /** - * Smooth scroll behavior - */ - function initSmoothScroll() { - const prefersReducedMotion = window.matchMedia('(prefers-reduced-motion: reduce)').matches; - if (!prefersReducedMotion) { - document.documentElement.style.scrollBehavior = 'smooth'; - } - } - - initSmoothScroll(); - - /** - * Add focus-visible polyfill for older browsers - */ - function initFocusVisible() { - const isKeyboardEvent = (e) => { - return e.mozInputSource === MOZ_SOURCE_KEYBOARD || - e.detail === 0 || - (e.sourceCapabilities && e.sourceCapabilities.firesTouchEvents === false); - }; - - document.addEventListener('mousedown', (e) => { - document.body.classList.remove('keyboard-focus'); - }, true); - - document.addEventListener('keydown', () => { - document.body.classList.add('keyboard-focus'); - }, true); - } - - // Search overlay functionality (Peptide Search AI integration) - const searchToggle = document.querySelector('.search-toggle'); - const searchOverlay = document.getElementById('search-overlay'); - const searchOverlayClose = document.querySelector('.search-overlay-close'); - - function openSearchOverlay() { - if (!searchOverlay) return; - searchOverlay.classList.add('active'); - searchOverlay.setAttribute('aria-hidden', 'false'); - document.body.style.overflow = 'hidden'; - // Focus the search input inside the overlay - const input = searchOverlay.querySelector('.psa-search-input, .ps-search-input, input[type="search"], input[type="text"]'); - if (input) { - setTimeout(() => input.focus(), 100); - } - } - - function closeSearchOverlay() { - if (!searchOverlay) return; - searchOverlay.classList.remove('active'); - searchOverlay.setAttribute('aria-hidden', 'true'); - document.body.style.overflow = ''; - // Return focus to search toggle - if (searchToggle) searchToggle.focus(); - } - - if (searchToggle) { - searchToggle.addEventListener('click', openSearchOverlay); - } - - if (searchOverlayClose) { - searchOverlayClose.addEventListener('click', closeSearchOverlay); - } - - if (searchOverlay) { - // Close overlay when clicking the backdrop - searchOverlay.addEventListener('click', (e) => { - if (e.target === searchOverlay) { - closeSearchOverlay(); - } - }); - - // Close on Escape key - document.addEventListener('keydown', (e) => { - if (e.key === 'Escape' && searchOverlay.classList.contains('active')) { - closeSearchOverlay(); - } - }); - } -})(); +/** + * Theme Utilities + * Peptide Starter Theme + * + * Handles: + * - Dark mode toggle functionality + * - Dark mode preference persistence + * - Plugin dark mode coordination + * - Smooth transitions + */ + +(function() { + 'use strict'; + + const html = document.documentElement; + const darkModeToggle = document.querySelector('.dark-mode-toggle'); + const sunIcon = document.querySelector('.sun-icon'); + const moonIcon = document.querySelector('.moon-icon'); + + if (!darkModeToggle) { + return; + } + + /** + * Get current theme preference + * @returns {string} 'dark' or 'light' + */ + function getCurrentTheme() { + const stored = localStorage.getItem('peptide-starter-theme'); + if (stored) { + return stored; + } + + const currentAttr = html.getAttribute('data-theme'); + if (currentAttr) { + return currentAttr; + } + + const systemDark = window.matchMedia('(prefers-color-scheme: dark)').matches; + return systemDark ? 'dark' : 'light'; + } + + /** + * Set theme preference + * @param {string} theme - 'dark' or 'light' + */ + function setTheme(theme) { + html.setAttribute('data-theme', theme); + localStorage.setItem('peptide-starter-theme', theme); + + // Update icon visibility + updateIcons(theme); + + // Notify plugins about theme change via custom event + const event = new CustomEvent('themechange', { + detail: { theme: theme } + }); + document.dispatchEvent(event); + + // Also update body class for CSS hooks + document.body.classList.remove('dark-mode', 'light-mode'); + document.body.classList.add(theme === 'dark' ? 'dark-mode' : 'light-mode'); + } + + /** + * Update icon visibility based on theme + * @param {string} theme - 'dark' or 'light' + */ + function updateIcons(theme) { + if (theme === 'dark') { + sunIcon.style.display = 'block'; + moonIcon.style.display = 'none'; + } else { + sunIcon.style.display = 'none'; + moonIcon.style.display = 'block'; + } + } + + /** + * Toggle between dark and light mode + */ + function toggleDarkMode() { + const currentTheme = getCurrentTheme(); + const newTheme = currentTheme === 'dark' ? 'light' : 'dark'; + setTheme(newTheme); + } + + // Initialize theme on page load + const initialTheme = getCurrentTheme(); + setTheme(initialTheme); + + // Dark mode toggle button click + darkModeToggle.addEventListener('click', toggleDarkMode); + + // Listen for system preference changes + const mediaQuery = window.matchMedia('(prefers-color-scheme: dark)'); + mediaQuery.addEventListener('change', (e) => { + const stored = localStorage.getItem('peptide-starter-theme'); + if (!stored) { + setTheme(e.matches ? 'dark' : 'light'); + } + }); + + // Expose API for plugins to read/listen to theme changes + window.peptideStarterTheme = { + getCurrentTheme: getCurrentTheme, + setTheme: setTheme, + toggleDarkMode: toggleDarkMode, + }; + + /** + * Plugin Integration Example: + * Plugins can listen to theme changes via: + * + * 1. Custom event listener: + * document.addEventListener('themechange', function(e) { + * console.log('Theme changed to:', e.detail.theme); + * }); + * + * 2. MutationObserver on data-theme: + * const observer = new MutationObserver((mutations) => { + * const theme = html.getAttribute('data-theme'); + * console.log('Theme is now:', theme); + * }); + * observer.observe(html, { attributes: true }); + * + * 3. Direct access to CSS custom properties which theme controls + */ + + /** + * Smooth scroll behavior + */ + function initSmoothScroll() { + const prefersReducedMotion = window.matchMedia('(prefers-reduced-motion: reduce)').matches; + if (!prefersReducedMotion) { + document.documentElement.style.scrollBehavior = 'smooth'; + } + } + + initSmoothScroll(); + + /** + * Add focus-visible polyfill for older browsers + */ + function initFocusVisible() { + const isKeyboardEvent = (e) => { + return e.mozInputSource === MOZ_SOURCE_KEYBOARD || + e.detail === 0 || + (e.sourceCapabilities && e.sourceCapabilities.firesTouchEvents === false); + }; + + document.addEventListener('mousedown', (e) => { + document.body.classList.remove('keyboard-focus'); + }, true); + + document.addEventListener('keydown', () => { + document.body.classList.add('keyboard-focus'); + }, true); + } + + // Search overlay functionality (Peptide Search AI integration) + const searchToggle = document.querySelector('.search-toggle'); + const searchOverlay = document.getElementById('search-overlay'); + const searchOverlayClose = document.querySelector('.search-overlay-close'); + + function openSearchOverlay() { + if (!searchOverlay) return; + searchOverlay.classList.add('active'); + searchOverlay.setAttribute('aria-hidden', 'false'); + document.body.style.overflow = 'hidden'; + // Focus the search input inside the overlay + const input = searchOverlay.querySelector('.psa-search-input, .ps-search-input, input[type="search"], input[type="text"]'); + if (input) { + setTimeout(() => input.focus(), 100); + } + } + + function closeSearchOverlay() { + if (!searchOverlay) return; + searchOverlay.classList.remove('active'); + searchOverlay.setAttribute('aria-hidden', 'true'); + document.body.style.overflow = ''; + // Return focus to search toggle + if (searchToggle) searchToggle.focus(); + } + + if (searchToggle) { + searchToggle.addEventListener('click', openSearchOverlay); + } + + if (searchOverlayClose) { + searchOverlayClose.addEventListener('click', closeSearchOverlay); + } + + if (searchOverlay) { + // Close overlay when clicking the backdrop + searchOverlay.addEventListener('click', (e) => { + if (e.target === searchOverlay) { + closeSearchOverlay(); + } + }); + + // Close on Escape key + document.addEventListener('keydown', (e) => { + if (e.key === 'Escape' && searchOverlay.classList.contains('active')) { + closeSearchOverlay(); + } + }); + } +})(); diff --git a/footer.php b/footer.php index 0abe429..87ce9cf 100644 --- a/footer.php +++ b/footer.php @@ -1,82 +1,82 @@ - - - - - - - - + + + + + + + + diff --git a/front-page.php b/front-page.php index c763181..e1c7305 100644 --- a/front-page.php +++ b/front-page.php @@ -1,85 +1,85 @@ - - -
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+ + diff --git a/functions.php b/functions.php index dd96a09..8871a57 100644 --- a/functions.php +++ b/functions.php @@ -1,489 +1,553 @@ - 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' => '

', - 'after_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' => '

', - 'after_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' => '

', - 'after_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' => '

', - 'after_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', - 'sanitize_callback' => 'sanitize_text_field', - ) ); - - $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', - 'sanitize_callback' => 'sanitize_text_field', - ) ); - - $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', - 'sanitize_callback' => 'sanitize_text_field', - ) ); - - $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 — allows safe HTML (links, bold, em) via wp_kses_post - $wp_customize->add_setting( 'footer_copyright', array( - 'default' => esc_html__( 'Copyright © 2026 Peptide Repo. All rights reserved.', 'peptide-starter' ), - 'transport' => 'postMessage', - 'sanitize_callback' => 'wp_kses_post', - ) ); - - $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', - 'sanitize_callback' => 'peptide_starter_sanitize_checkbox', - ) ); - - $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' ); - -/** - * Sanitize checkbox values for the Customizer. - * - * Returns true only for truthy values; everything else becomes false. - * Used as sanitize_callback for the dark_mode_default setting. - * - * @param mixed $checked The raw value from the Customizer. - * @return bool True if checked, false otherwise. - */ -function peptide_starter_sanitize_checkbox( $checked ) { - return ( ( isset( $checked ) && true === $checked ) ? true : false ); -} - -/** - * Add custom logo support - */ -function peptide_starter_get_custom_logo() { - if ( function_exists( 'get_custom_logo' ) ) { - return get_custom_logo(); - } - return ''; -} - -/** - * Navigation Menu Walker for handling active states - */ -class Peptide_Starter_Nav_Walker extends Walker_Nav_Menu { - public function start_el( &$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 ''; - } -} - -/** - * 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 ); -} - -/** - * Handle newsletter signup form submission. - * - * Validates the nonce and email, then fires an action hook so plugins - * can handle the actual subscription logic (e.g. Mailchimp, SendGrid). - * If no plugin handles it, redirects back with a generic success message. - * - * @see footer.php — renders the newsletter form - */ -function peptide_starter_handle_newsletter_signup() { - // Verify nonce — prevents CSRF attacks. - if ( ! isset( $_POST['ps_newsletter_nonce'] ) || - ! wp_verify_nonce( sanitize_text_field( wp_unslash( $_POST['ps_newsletter_nonce'] ) ), 'peptide_starter_newsletter' ) ) { - wp_die( - esc_html__( 'Security check failed. Please try again.', 'peptide-starter' ), - esc_html__( 'Error', 'peptide-starter' ), - array( 'response' => 403 ) - ); - } - - $email = isset( $_POST['email'] ) ? sanitize_email( wp_unslash( $_POST['email'] ) ) : ''; - - if ( ! is_email( $email ) ) { - wp_safe_redirect( add_query_arg( 'ps_newsletter', 'invalid', wp_get_referer() ) ); - exit; - } - - /** - * Fires when a valid newsletter signup is submitted. - * - * Plugins should hook here to send the email to their mailing list provider. - * - * @param string $email The validated subscriber email address. - */ - do_action( 'peptide_starter_newsletter_subscribe', $email ); - - wp_safe_redirect( add_query_arg( 'ps_newsletter', 'success', wp_get_referer() ) ); - exit; -} -add_action( 'admin_post_peptide_starter_newsletter_signup', 'peptide_starter_handle_newsletter_signup' ); -add_action( 'admin_post_nopriv_peptide_starter_newsletter_signup', 'peptide_starter_handle_newsletter_signup' ); - -/** - * 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'; - ?> - - 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' => '

', + 'after_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' => '

', + 'after_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' => '

', + 'after_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' => '

', + 'after_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', + 'sanitize_callback' => 'sanitize_text_field', + ) + ); + + $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', + 'sanitize_callback' => 'sanitize_text_field', + ) + ); + + $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', + 'sanitize_callback' => 'sanitize_text_field', + ) + ); + + $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 — allows safe HTML (links, bold, em) via wp_kses_post + $wp_customize->add_setting( + 'footer_copyright', + array( + 'default' => esc_html__( 'Copyright © 2026 Peptide Repo. All rights reserved.', 'peptide-starter' ), + 'transport' => 'postMessage', + 'sanitize_callback' => 'wp_kses_post', + ) + ); + + $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', + 'sanitize_callback' => 'peptide_starter_sanitize_checkbox', + ) + ); + + $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' ); + +/** + * Sanitize checkbox values for the Customizer. + * + * Returns true only for truthy values; everything else becomes false. + * Used as sanitize_callback for the dark_mode_default setting. + * + * @param mixed $checked The raw value from the Customizer. + * @return bool True if checked, false otherwise. + */ +function peptide_starter_sanitize_checkbox( $checked ) { + return ( ( isset( $checked ) && true === $checked ) ? true : false ); +} + +/** + * Add custom logo support + */ +function peptide_starter_get_custom_logo() { + if ( function_exists( 'get_custom_logo' ) ) { + return get_custom_logo(); + } + return ''; +} + +/** + * Navigation Menu Walker for handling active states + */ +class Peptide_Starter_Nav_Walker extends Walker_Nav_Menu { + public function start_el( &$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 ''; + } +} + +/** + * 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 ); +} + +/** + * Handle newsletter signup form submission. + * + * Validates the nonce and email, then fires an action hook so plugins + * can handle the actual subscription logic (e.g. Mailchimp, SendGrid). + * If no plugin handles it, redirects back with a generic success message. + * + * @see footer.php — renders the newsletter form + */ +function peptide_starter_handle_newsletter_signup() { + // Verify nonce — prevents CSRF attacks. + if ( ! isset( $_POST['ps_newsletter_nonce'] ) || + ! wp_verify_nonce( sanitize_text_field( wp_unslash( $_POST['ps_newsletter_nonce'] ) ), 'peptide_starter_newsletter' ) ) { + wp_die( + esc_html__( 'Security check failed. Please try again.', 'peptide-starter' ), + esc_html__( 'Error', 'peptide-starter' ), + array( 'response' => 403 ) + ); + } + + $email = isset( $_POST['email'] ) ? sanitize_email( wp_unslash( $_POST['email'] ) ) : ''; + + if ( ! is_email( $email ) ) { + wp_safe_redirect( add_query_arg( 'ps_newsletter', 'invalid', wp_get_referer() ) ); + exit; + } + + /** + * Fires when a valid newsletter signup is submitted. + * + * Plugins should hook here to send the email to their mailing list provider. + * + * @param string $email The validated subscriber email address. + */ + do_action( 'peptide_starter_newsletter_subscribe', $email ); + + wp_safe_redirect( add_query_arg( 'ps_newsletter', 'success', wp_get_referer() ) ); + exit; +} +add_action( 'admin_post_peptide_starter_newsletter_signup', 'peptide_starter_handle_newsletter_signup' ); +add_action( 'admin_post_nopriv_peptide_starter_newsletter_signup', 'peptide_starter_handle_newsletter_signup' ); + +/** + * 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'; + ?> + + diff --git a/searchform.php b/searchform.php index b5e6793..75ba62c 100644 --- a/searchform.php +++ b/searchform.php @@ -1,27 +1,27 @@ - - + + diff --git a/single-peptide.php b/single-peptide.php index 8aff085..8abc1bd 100644 --- a/single-peptide.php +++ b/single-peptide.php @@ -39,25 +39,45 @@ get_header();
- +
- + - +
- + - +
Da
- + - +
- +
diff --git a/template-parts/content-none.php b/template-parts/content-none.php index 846cc3f..54dba37 100644 --- a/template-parts/content-none.php +++ b/template-parts/content-none.php @@ -15,7 +15,7 @@ -

+

-

+

-

+