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 <noreply@anthropic.com>

.phpcs.xml.dist

@@ -26,4 +26,9 @@
 	<rule ref="Generic.Arrays.DisallowShortArraySyntax">
 		<exclude name="Generic.Arrays.DisallowShortArraySyntax"/>
 	</rule>
+
+	<!-- Standard WordPress practice: Walker class lives in functions.php -->
+	<rule ref="WordPress.Files.FileName">
+		<exclude name="WordPress.Files.FileName.InvalidClassFileName"/>
+	</rule>
 </ruleset>

archive-peptide.php

@@ -70,4 +70,5 @@ get_header();
 	</div>
 </main>
 
-<?php get_footer();
+<?php
+get_footer();

functions.php

@@ -24,7 +24,9 @@ function peptide_starter_setup() {
 	add_theme_support( 'post-thumbnails' );
 	add_theme_support( 'responsive-embeds' );
 	add_theme_support( 'custom-logo' );
-	add_theme_support( 'html5', array(
+	add_theme_support(
+		'html5',
+		array(
 			'search-form',
 			'comment-form',
 			'comment-list',
@@ -32,13 +34,16 @@ function peptide_starter_setup() {
 			'caption',
 			'style',
 			'script',
-	) );
+		)
+	);
 
 	// Register navigation menus
-	register_nav_menus( array(
+	register_nav_menus(
+		array(
 			'primary' => esc_html__( 'Primary Menu', 'peptide-starter' ),
 			'footer'  => esc_html__( 'Footer Menu', 'peptide-starter' ),
-	) );
+		)
+	);
 
 	// Add support for wide blocks
 	add_theme_support( 'align-wide' );
@@ -60,10 +65,14 @@ function peptide_starter_scripts() {
 	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(
+	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' ) ) {
@@ -77,7 +86,9 @@ add_action( 'wp_enqueue_scripts', 'peptide_starter_scripts' );
  * 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', '
+	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,
@@ -87,7 +98,8 @@ function peptide_starter_plugin_overrides() {
 			display: block !important;
 			overflow: visible !important;
 		}
-	' );
+	'
+	);
 }
 add_action( 'wp_enqueue_scripts', 'peptide_starter_plugin_overrides', 99 );
 
@@ -95,7 +107,8 @@ add_action( 'wp_enqueue_scripts', 'peptide_starter_plugin_overrides', 99 );
  * Register widget areas
  */
 function peptide_starter_widgets_init() {
-	register_sidebar( array(
+	register_sidebar(
+		array(
 			'name'          => esc_html__( 'Footer - Column 1', 'peptide-starter' ),
 			'id'            => 'footer-1',
 			'description'   => esc_html__( 'Footer widget area 1', 'peptide-starter' ),
@@ -103,9 +116,11 @@ function peptide_starter_widgets_init() {
 			'after_widget'  => '</div>',
 			'before_title'  => '<h3 class="widget-title">',
 			'after_title'   => '</h3>',
-	) );
+		)
+	);
 
-	register_sidebar( array(
+	register_sidebar(
+		array(
 			'name'          => esc_html__( 'Footer - Column 2', 'peptide-starter' ),
 			'id'            => 'footer-2',
 			'description'   => esc_html__( 'Footer widget area 2', 'peptide-starter' ),
@@ -113,9 +128,11 @@ function peptide_starter_widgets_init() {
 			'after_widget'  => '</div>',
 			'before_title'  => '<h3 class="widget-title">',
 			'after_title'   => '</h3>',
-	) );
+		)
+	);
 
-	register_sidebar( array(
+	register_sidebar(
+		array(
 			'name'          => esc_html__( 'Footer - Column 3', 'peptide-starter' ),
 			'id'            => 'footer-3',
 			'description'   => esc_html__( 'Footer widget area 3', 'peptide-starter' ),
@@ -123,9 +140,11 @@ function peptide_starter_widgets_init() {
 			'after_widget'  => '</div>',
 			'before_title'  => '<h3 class="widget-title">',
 			'after_title'   => '</h3>',
-	) );
+		)
+	);
 
-	register_sidebar( array(
+	register_sidebar(
+		array(
 			'name'          => esc_html__( 'Footer - Column 4', 'peptide-starter' ),
 			'id'            => 'footer-4',
 			'description'   => esc_html__( 'Footer widget area 4', 'peptide-starter' ),
@@ -133,7 +152,8 @@ function peptide_starter_widgets_init() {
 			'after_widget'  => '</div>',
 			'before_title'  => '<h3 class="widget-title">',
 			'after_title'   => '</h3>',
-	) );
+		)
+	);
 }
 add_action( 'widgets_init', 'peptide_starter_widgets_init' );
 
@@ -142,93 +162,135 @@ add_action( 'widgets_init', 'peptide_starter_widgets_init' );
  */
 function peptide_starter_customize_register( $wp_customize ) {
 	// Logo section
-	$wp_customize->add_section( 'peptide_starter_branding', array(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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(
+	$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' );
 
@@ -382,7 +444,8 @@ function peptide_starter_pagination() {
 	$total_pages  = $wp_query->max_num_pages;
 
 	echo '<nav class="ps-pagination">';
-	echo paginate_links( array(
+	echo paginate_links(
+		array(
 			'base'      => get_pagenum_link( 1 ) . '%_%',
 			'format'    => 'page/%#%/',
 			'current'   => $current_page,
@@ -390,7 +453,8 @@ function peptide_starter_pagination() {
 			'prev_text' => esc_html__( '← Previous', 'peptide-starter' ),
 			'next_text' => esc_html__( 'Next →', 'peptide-starter' ),
 			'type'      => 'plain',
-	) );
+		)
+	);
 	echo '</nav>';
 }
 

header.php

@@ -29,14 +29,16 @@
 		<!-- Primary Navigation -->
 		<nav class="primary-navigation">
 			<?php
-			wp_nav_menu( array(
+			wp_nav_menu(
+				array(
 					'theme_location' => 'primary',
 					'fallback_cb'     => 'peptide_starter_primary_menu_fallback',
 					'walker'          => new Peptide_Starter_Nav_Walker(),
 					'depth'           => 2,
 					'container'       => false,
 					'items_wrap'      => '<ul>%3$s</ul>',
-			) );
+				)
+			);
 			?>
 		</nav>
 

single-peptide.php

@@ -39,25 +39,45 @@ get_header();
 					<!-- Meta Information -->
 					<div class="peptide-meta" style="margin-top: var(--spacing-3xl); padding-top: var(--spacing-2xl); border-top: 1px solid var(--color-border-default);">
 						<dl>
-							<?php if ( $formula = get_post_meta( get_the_ID(), 'peptide_formula', true ) ) { ?>
+							<?php
+							$formula = get_post_meta( get_the_ID(), 'peptide_formula', true );
+							if ( $formula ) {
+								?>
 								<dt><strong><?php esc_html_e( 'Molecular Formula:', 'peptide-starter' ); ?></strong></dt>
 								<dd><code><?php echo esc_html( $formula ); ?></code></dd>
-							<?php } ?>
+								<?php
+							}
+							?>
 
-							<?php if ( $sequence = get_post_meta( get_the_ID(), 'peptide_sequence', true ) ) { ?>
+							<?php
+							$sequence = get_post_meta( get_the_ID(), 'peptide_sequence', true );
+							if ( $sequence ) {
+								?>
 								<dt><strong><?php esc_html_e( 'Sequence:', 'peptide-starter' ); ?></strong></dt>
 								<dd><code><?php echo esc_html( $sequence ); ?></code></dd>
-							<?php } ?>
+								<?php
+							}
+							?>
 
-							<?php if ( $molecular_weight = get_post_meta( get_the_ID(), 'peptide_molecular_weight', true ) ) { ?>
+							<?php
+							$molecular_weight = get_post_meta( get_the_ID(), 'peptide_molecular_weight', true );
+							if ( $molecular_weight ) {
+								?>
 								<dt><strong><?php esc_html_e( 'Molecular Weight:', 'peptide-starter' ); ?></strong></dt>
 								<dd><?php echo esc_html( $molecular_weight ); ?> Da</dd>
-							<?php } ?>
+								<?php
+							}
+							?>
 
-							<?php if ( $therapeutic_use = get_post_meta( get_the_ID(), 'peptide_therapeutic_use', true ) ) { ?>
+							<?php
+							$therapeutic_use = get_post_meta( get_the_ID(), 'peptide_therapeutic_use', true );
+							if ( $therapeutic_use ) {
+								?>
 								<dt><strong><?php esc_html_e( 'Therapeutic Use:', 'peptide-starter' ); ?></strong></dt>
 								<dd><?php echo esc_html( $therapeutic_use ); ?></dd>
-							<?php } ?>
+								<?php
+							}
+							?>
 						</dl>
 					</div>
 

template-parts/content-none.php

@@ -15,7 +15,7 @@
 		<?php
 		if ( is_search() ) {
 			?>
-			<p><?php esc_html_e( "Sorry, but nothing matched your search terms. Please try again with some different keywords.", 'peptide-starter' ); ?></p>
+			<p><?php esc_html_e( 'Sorry, but nothing matched your search terms. Please try again with some different keywords.', 'peptide-starter' ); ?></p>
 			<?php
 			get_search_form();
 		} elseif ( is_home() && current_user_can( 'publish_posts' ) ) {
@@ -38,11 +38,11 @@
 			<?php
 		} elseif ( is_archive() ) {
 			?>
-			<p><?php esc_html_e( "It looks like there are no posts for this archive. Try a different category or date.", 'peptide-starter' ); ?></p>
+			<p><?php esc_html_e( 'It looks like there are no posts for this archive. Try a different category or date.', 'peptide-starter' ); ?></p>
 			<?php
 		} else {
 			?>
-			<p><?php esc_html_e( "It seems we can't find what you're looking for. Perhaps searching can help.", 'peptide-starter' ); ?></p>
+			<p><?php esc_html_e( 'It seems we can\'t find what you\'re looking for. Perhaps searching can help.', 'peptide-starter' ); ?></p>
 			<?php
 			get_search_form();
 		}