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fix: resolve PHPCS coding standard violations for CI

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- 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>
This commit is contained in:
peptiderepo
2026-04-12 22:54:51 +07:00
parent 7226a08719
commit 65b9f7a13c
12 changed files with 1125 additions and 1033 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
.phpcs.xml.dist
View File

@@ -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>

3
archive-peptide.php
View File

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

324
functions.php
View File

@@ -24,21 +24,26 @@ function peptide_starter_setup() {
add_theme_support( 'post-thumbnails' );
add_theme_support( 'responsive-embeds' );
add_theme_support( 'custom-logo' );
add_theme_support( 'html5', array(
'search-form',
'comment-form',
'comment-list',
'gallery',
'caption',
'style',
'script',
) );
add_theme_support(
'html5',
array(
'search-form',
'comment-form',
'comment-list',
'gallery',
'caption',
'style',
'script',
)
);
// Register navigation menus
register_nav_menus( array(
'primary' => esc_html__( 'Primary Menu', 'peptide-starter' ),
'footer' => esc_html__( 'Footer Menu', 'peptide-starter' ),
) );
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(
'siteUrl' => home_url( '/' ),
'isDarkMode' => get_theme_mod( 'dark_mode_default', false ),
) );
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 );
@@ -95,45 +107,53 @@ 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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'after_widget' => '</div>',
'before_title' => '<h3 class="widget-title">',
'after_title' => '</h3>',
) );
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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'after_widget' => '</div>',
'before_title' => '<h3 class="widget-title">',
'after_title' => '</h3>',
)
);
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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'after_widget' => '</div>',
'before_title' => '<h3 class="widget-title">',
'after_title' => '</h3>',
) );
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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'after_widget' => '</div>',
'before_title' => '<h3 class="widget-title">',
'after_title' => '</h3>',
)
);
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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'after_widget' => '</div>',
'before_title' => '<h3 class="widget-title">',
'after_title' => '</h3>',
) );
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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'after_widget' => '</div>',
'before_title' => '<h3 class="widget-title">',
'after_title' => '</h3>',
)
);
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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'after_widget' => '</div>',
'before_title' => '<h3 class="widget-title">',
'after_title' => '</h3>',
) );
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' => '<div id="%1$s" class="widget %2$s footer-widget">',
'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(
'title' => esc_html__( 'Branding', 'peptide-starter' ),
'priority' => 30,
) );
$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,
) );
$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_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',
) );
$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_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',
) );
$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_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',
) );
$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,
) );
$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_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',
) );
$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,
) );
$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_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',
) );
$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' );
@@ -382,15 +444,17 @@ function peptide_starter_pagination() {
$total_pages = $wp_query->max_num_pages;
echo '<nav class="ps-pagination">';
echo paginate_links( array(
'base' => get_pagenum_link( 1 ) . '%_%',
'format' => 'page/%#%/',
'current' => $current_page,
'total' => $total_pages,
'prev_text' => esc_html__( '← Previous', 'peptide-starter' ),
'next_text' => esc_html__( 'Next →', 'peptide-starter' ),
'type' => 'plain',
) );
echo paginate_links(
array(
'base' => get_pagenum_link( 1 ) . '%_%',
'format' => 'page/%#%/',
'current' => $current_page,
'total' => $total_pages,
'prev_text' => esc_html__( '← Previous', 'peptide-starter' ),
'next_text' => esc_html__( 'Next →', 'peptide-starter' ),
'type' => 'plain',
)
);
echo '</nav>';
}

18
header.php
View File

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

36
single-peptide.php
View File

@@ -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>

6
template-parts/content-none.php
View File

@@ -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();
}