From 0a2d7aeb4a4c43fd5677cf38db00701240d242c5 Mon Sep 17 00:00:00 2001
From: peptiderepo <admin@peptiderepo.com>
Date: Wed, 8 Apr 2026 18:31:57 +0700
Subject: [PATCH] style: fix WPCS violations in config and admin classes

- Align equals signs in PSA_Config constant definitions
- Convert space indentation to tabs in PSA_Admin
---
 includes/class-psa-admin.php  | 336 +++++++++++++++++-----------------
 includes/class-psa-config.php |  15 +-
 2 files changed, 175 insertions(+), 176 deletions(-)

diff --git a/includes/class-psa-admin.php b/includes/class-psa-admin.php
index 3924dc5..c93c56a 100644
--- a/includes/class-psa-admin.php
+++ b/includes/class-psa-admin.php
@@ -7,34 +7,34 @@
  */
 
 if ( ! defined( 'ABSPATH' ) ) {
-    exit;
+	exit;
 }
 
 class PSA_Admin {
 
-    public static function init() {
-        add_action( 'admin_menu', array( __CLASS__, 'add_menu_pages' ) );
-        add_action( 'admin_init', array( __CLASS__, 'register_settings' ) );
-    }
+	public static function init() {
+		add_action( 'admin_menu', array( __CLASS__, 'add_menu_pages' ) );
+		add_action( 'admin_init', array( __CLASS__, 'register_settings' ) );
+	}
 
-    /**
-     * Add settings page under Settings menu.
-     */
-    public static function add_menu_pages() {
-        add_options_page(
-            __( 'Peptide Search AI', 'peptide-search-ai' ),
-            __( 'Peptide Search AI', 'peptide-search-ai' ),
-            'manage_options',
-            'peptide-search-ai',
-            array( __CLASS__, 'render_settings_page' )
-        );
-    }
+	/**
+	 * Add settings page under Settings menu.
+	 */
+	public static function add_menu_pages() {
+		add_options_page(
+			__( 'Peptide Search AI', 'peptide-search-ai' ),
+			__( 'Peptide Search AI', 'peptide-search-ai' ),
+			'manage_options',
+			'peptide-search-ai',
+			array( __CLASS__, 'render_settings_page' )
+		);
+	}
 
-    /**
-     * Register settings fields.
-     */
-    public static function register_settings() {
-        register_setting(
+	/**
+	 * Register settings fields.
+	 */
+	public static function register_settings() {
+		register_setting(
 			'psa_settings_group',
 			'psa_settings',
 			array(
@@ -42,28 +42,28 @@ class PSA_Admin {
 			)
 		);
 
-        // OpenRouter Section.
-        add_settings_section(
+		// OpenRouter Section.
+		add_settings_section(
 			'psa_ai_section',
 			__( 'OpenRouter API Settings', 'peptide-search-ai' ),
 			array( __CLASS__, 'render_section_description' ),
 			'peptide-search-ai'
 		);
-        add_settings_field(
+		add_settings_field(
 			'api_key',
 			__( 'API Key', 'peptide-search-ai' ),
 			array( __CLASS__, 'render_api_key_field' ),
 			'peptide-search-ai',
 			'psa_ai_section'
 		);
-        add_settings_field(
+		add_settings_field(
 			'ai_model',
 			__( 'Generation Model', 'peptide-search-ai' ),
 			array( __CLASS__, 'render_model_field' ),
 			'peptide-search-ai',
 			'psa_ai_section'
 		);
-        add_settings_field(
+		add_settings_field(
 			'validation_model',
 			__( 'Validation Model', 'peptide-search-ai' ),
 			array( __CLASS__, 'render_validation_model_field' ),
@@ -71,177 +71,177 @@ class PSA_Admin {
 			'psa_ai_section'
 		);
 
-        // Behavior Section.
-        add_settings_section(
+		// Behavior Section.
+		add_settings_section(
 			'psa_behavior_section',
 			__( 'Behavior Settings', 'peptide-search-ai' ),
 			null,
 			'peptide-search-ai'
 		);
-        add_settings_field(
+		add_settings_field(
 			'auto_publish',
 			__( 'Auto-Publish', 'peptide-search-ai' ),
 			array( __CLASS__, 'render_publish_field' ),
 			'peptide-search-ai',
 			'psa_behavior_section'
 		);
-        add_settings_field(
+		add_settings_field(
 			'use_pubchem',
 			__( 'PubChem Enrichment', 'peptide-search-ai' ),
 			array( __CLASS__, 'render_pubchem_field' ),
 			'peptide-search-ai',
 			'psa_behavior_section'
 		);
-    }
+	}
 
-    /**
-     * Sanitize settings input.
-     *
-     * @param array $input Raw input from the form.
-     * @return array Sanitized settings.
-     */
-    public static function sanitize_settings( $input ) {
-        return array(
-            'api_key'          => sanitize_text_field( $input['api_key'] ?? '' ),
-            'ai_model'         => sanitize_text_field( $input['ai_model'] ?? '' ),
-            'validation_model' => sanitize_text_field( $input['validation_model'] ?? '' ),
-            'auto_publish'     => sanitize_text_field( $input['auto_publish'] ?? 'draft' ),
-            // Checkbox: if key is absent in POST, it was unchecked → '0'.
-            'use_pubchem'      => ! empty( $input['use_pubchem'] ) ? '1' : '0',
-        );
-    }
+	/**
+	 * Sanitize settings input.
+	 *
+	 * @param array $input Raw input from the form.
+	 * @return array Sanitized settings.
+	 */
+	public static function sanitize_settings( $input ) {
+		return array(
+			'api_key'          => sanitize_text_field( $input['api_key'] ?? '' ),
+			'ai_model'         => sanitize_text_field( $input['ai_model'] ?? '' ),
+			'validation_model' => sanitize_text_field( $input['validation_model'] ?? '' ),
+			'auto_publish'     => sanitize_text_field( $input['auto_publish'] ?? 'draft' ),
+			// Checkbox: if key is absent in POST, it was unchecked → '0'.
+			'use_pubchem'      => ! empty( $input['use_pubchem'] ) ? '1' : '0',
+		);
+	}
 
-    // -------------------------------------------------------------------------
-    // Field renderers
-    // -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
+	// Field renderers
+	// -------------------------------------------------------------------------
 
-    public static function render_section_description() {
-        ?>
-        <p>
-            <?php
-            printf(
-                __( 'This plugin uses <a href="%s" target="_blank" rel="noopener">OpenRouter</a> to access AI models. OpenRouter provides a unified API for hundreds of models including open-source options like Gemini Flash, Llama, Mistral, Qwen, and DeepSeek, as well as commercial models.', 'peptide-search-ai' ),
-                escourl( 'https://openrouter.ai/' )
-            );
-            ?>
-        </p>
-        <?php
-    }
+	public static function render_section_description() {
+		?>
+		<p>
+			<?php
+			printf(
+				__( 'This plugin uses <a href="%s" target="_blank" rel="noopener">OpenRouter</a> to access AI models. OpenRouter provides a unified API for hundreds of models including open-source options like Gemini Flash, Llama, Mistral, Qwen, and DeepSeek, as well as commercial models.', 'peptide-search-ai' ),
+				esc_url( 'https://openrouter.ai/' )
+			);
+			?>
+		</p>
+		<?php
+	}
 
-    public static function render_api_key_field() {
-        if ( defined( 'PSA_OPENROUTER_KEY' ) && PSA_OPENROUTER_KEY ) {
-            ?>
-            <span class="dashicons dashicons-yes-alt" style="color:#46b450;"></span>
-            <strong><?php esc_html_e( 'Configured via wp-config.php', 'peptide-search-ai' ); ?></strong>
-            <p class="description"><?php esc_html_e( 'The API key is securely set using the PSA_OPENROUTER_KEY constant in wp-config.php. This is the recommended approach.', 'peptide-search-ai' ); ?></p>
-            <?php
-        } else {
-            $value = self::get_setting( 'api_key', '' );
-            ?>
-            <input type="password" name="psa_settings[api_key]" value="<?php echo esc_attr( $value ); ?>" class="regular-text" autocomplete="off" />
-            <p class="description">
-                <?php esc_html_e( 'Your OpenRouter API key. Get one at', 'peptide-search-ai' ); ?>
-                <a href="https://openrouter.ai/settings/keys" target="_blank" rel="noopener">openrouter.ai/settings/keys</a>.<br />
-                <strong><?php esc_html_e( 'Recommended:', 'peptide-search-ai' ); ?></strong> <?php esc_html_e( 'For better security, add', 'peptide-search-ai' ); ?> <code>define( 'PSA_OPENROUTER_KEY', 'your-key-here' );</code> <?php esc_html_e( 'to your wp-config.php instead.', 'peptide-search-ai' ); ?>
-            </p>
-            <?php
-        }
-    }
+	public static function render_api_key_field() {
+		if ( defined( 'PSA_OPENROUTER_KEY' ) && PSA_OPENROUTER_KEY ) {
+			?>
+			<span class="dashicons dashicons-yes-alt" style="color:#46b450;"></span>
+			<strong><?php esc_html_e( 'Configured via wp-config.php', 'peptide-search-ai' ); ?></strong>
+			<p class="description"><?php esc_html_e( 'The API key is securely set using the PSA_OPENROUTER_KEY constant in wp-config.php. This is the recommended approach.', 'peptide-search-ai' ); ?></p>
+			<?php
+		} else {
+			$value = self::get_setting( 'api_key', '' );
+			?>
+			<input type="password" name="psa_settings[api_key]" value="<?php echo esc_attr( $value ); ?>" class="regular-text" autocomplete="off" />
+			<p class="description">
+				<?php esc_html_e( 'Your OpenRouter API key. Get one at', 'peptide-search-ai' ); ?>
+				<a href="https://openrouter.ai/settings/keys" target="_blank" rel="noopener">openrouter.ai/settings/keys</a>.<br />
+				<strong><?php esc_html_e( 'Recommended:', 'peptide-search-ai' ); ?></strong> <?php esc_html_e( 'For better security, add', 'peptide-search-ai' ); ?> <code>define( 'PSA_OPENROUTER_KEY', 'your-key-here' );</code> <?php esc_html_e( 'to your wp-config.php instead.', 'peptide-search-ai' ); ?>
+			</p>
+			<?php
+		}
+	}
 
-    public static function render_model_field() {
-        $value = self::get_setting( 'ai_model', '' );
-        ?>
-        <input type="text" name="psa_settings[ai_model]" value="<?php echo esc_attr( $value ); ?>" class="regular-text" placeholder="<?php esc_attr_e( 'Leave blank for default', 'peptide-search-ai' ); ?>" />
-        <p class="description">
-            <?php esc_html_e( 'Model for full content generation. Default:', 'peptide-search-ai' ); ?> <code>google/gemini-2.5-flash</code>.<br />
-            <?php esc_html_e( 'Browse models at', 'peptide-search-ai' ); ?> <a href="https://openrouter.ai/models" target="_blank" rel="noopener">openrouter.ai/models</a>.
-            <?php esc_html_e( 'Examples:', 'peptide-search-ai' ); ?> <code>meta-llama/llama-4-maverick</code>, <code>deepseek/deepseek-chat-v3-0324</code>, <code>qwen/qwen-2.5-72b-instruct</code>.
-        </p>
-        <?php
-    }
+	public static function render_model_field() {
+		$value = self::get_setting( 'ai_model', '' );
+		?>
+		<input type="text" name="psa_settings[ai_model]" value="<?php echo esc_attr( $value ); ?>" class="regular-text" placeholder="<?php esc_attr_e( 'Leave blank for default', 'peptide-search-ai' ); ?>" />
+		<p class="description">
+			<?php esc_html_e( 'Model for full content generation. Default:', 'peptide-search-ai' ); ?> <code>google/gemini-2.5-flash</code>.<br />
+			<?php esc_html_e( 'Browse models at', 'peptide-search-ai' ); ?> <a href="https://openrouter.ai/models" target="_blank" rel="noopener">openrouter.ai/models</a>.
+			<?php esc_html_e( 'Examples:', 'peptide-search-ai' ); ?> <code>meta-llama/llama-4-maverick</code>, <code>deepseek/deepseek-chat-v3-0324</code>, <code>qwen/qwen-2.5-72b-instruct</code>.
+		</p>
+		<?php
+	}
 
-    public static function render_validation_model_field() {
-        $value = self::get_setting( 'validation_model', '' );
-        ?>
-        <input type="text" name="psa_settings[validation_model]" value="<?php echo esc_attr( $value ); ?>" class="regular-text" placeholder="<?php esc_attr_e( 'Leave blank for default (fast/cheap model)', 'peptide-search-ai' ); ?>" />
-        <p class="description">
-            <?php esc_html_e( 'Lighter model for peptide name validation. Default:', 'peptide-search-ai' ); ?> <code>google/gemini-2.0-flash-001</code>.<br />
-            <?php esc_html_e( 'Use a fast, cheap model here to keep validation quick. Examples:', 'peptide-search-ai' ); ?> <code>meta-llama/llama-4-scout</code>, <code>mistralai/mistral-small-3.1-24b-instruct</code>.
-        </p>
-        <?php
-    }
+	public static function render_validation_model_field() {
+		$value = self::get_setting( 'validation_model', '' );
+		?>
+		<input type="text" name="psa_settings[validation_model]" value="<?php echo esc_attr( $value ); ?>" class="regular-text" placeholder="<?php esc_attr_e( 'Leave blank for default (fast/cheap model)', 'peptide-search-ai' ); ?>" />
+		<p class="description">
+			<?php esc_html_e( 'Lighter model for peptide name validation. Default:', 'peptide-search-ai' ); ?> <code>google/gemini-2.0-flash-001</code>.<br />
+			<?php esc_html_e( 'Use a fast, cheap model here to keep validation quick. Examples:', 'peptide-search-ai' ); ?> <code>meta-llama/llama-4-scout</code>, <code>mistralai/mistral-small-3.1-24b-instruct</code>.
+		</p>
+		<?php
+	}
 
-    public static function render_publish_field() {
-        $value = self::get_setting( 'auto_publish', 'draft' );
-        ?>
-        <select name="psa_settings[auto_publish]">
-            <option value="draft" <?php selected( $value, 'draft' ); ?>><?php esc_html_e( 'Save as Draft (review before publishing)', 'peptide-search-ai' ); ?></option>
-            <option value="publish" <?php selected( $value, 'publish' ); ?>><?php esc_html_e( 'Publish Immediately', 'peptide-search-ai' ); ?></option>
-        </select>
-        <p class="description"><?php esc_html_e( 'Whether AI-generated peptides are published immediately or saved as drafts for review.', 'peptide-search-ai' ); ?></p>
-        <?php
-    }
+	public static function render_publish_field() {
+		$value = self::get_setting( 'auto_publish', 'draft' );
+		?>
+		<select name="psa_settings[auto_publish]">
+			<option value="draft" <?php selected( $value, 'draft' ); ?>><?php esc_html_e( 'Save as Draft (review before publishing)', 'peptide-search-ai' ); ?></option>
+			<option value="publish" <?php selected( $value, 'publish' ); ?>><?php esc_html_e( 'Publish Immediately', 'peptide-search-ai' ); ?></option>
+		</select>
+		<p class="description"><?php esc_html_e( 'Whether AI-generated peptides are published immediately or saved as drafts for review.', 'peptide-search-ai' ); ?></p>
+		<?php
+	}
 
-    public static function render_pubchem_field() {
-        $value = self::get_setting( 'use_pubchem', '1' );
-        ?>
-        <label>
-            <input type="checkbox" name="psa_settings[use_pubchem]" value="1" <?php checked( $value, '1' ); ?> />
-            <?php esc_html_e( 'Cross-reference with PubChem for verified molecular data', 'peptide-search-ai' ); ?>
-        </label>
-        <p class="description"><?php esc_html_e( 'When enabled, the plugin queries PubChem\'s free API to validate molecular weight, formula, and other properties.', 'peptide-search-ai' ); ?></p>
-        <?php
-    }
+	public static function render_pubchem_field() {
+		$value = self::get_setting( 'use_pubchem', '1' );
+		?>
+		<label>
+			<input type="checkbox" name="psa_settings[use_pubchem]" value="1" <?php checked( $value, '1' ); ?> />
+			<?php esc_html_e( 'Cross-reference with PubChem for verified molecular data', 'peptide-search-ai' ); ?>
+		</label>
+		<p class="description"><?php esc_html_e( 'When enabled, the plugin queries PubChem\'s free API to validate molecular weight, formula, and other properties.', 'peptide-search-ai' ); ?></p>
+		<?php
+	}
 
-    // -------------------------------------------------------------------------
-    // Settings page
-    // -------------------------------------------------------------------------
+	// -------------------------------------------------------------------------
+	// Settings page
+	// -------------------------------------------------------------------------
 
-    public static function render_settings_page() {
-        ?>
-        <div class="wrap">
-            <h1><?php esc_html_e( 'Peptide Search AI Settings', 'peptide-search-ai' ); ?></h1>
+	public static function render_settings_page() {
+		?>
+		<div class="wrap">
+			<h1><?php esc_html_e( 'Peptide Search AI Settings', 'peptide-search-ai' ); ?></h1>
 
-            <form method="post" action="options.php">
-                <?php
-                settings_fields( 'psa_settings_group' );
-                do_settings_sections( 'peptide-search-ai' );
-                submit_button();
-                ?>
-            </form>
+			<form method="post" action="options.php">
+				<?php
+				settings_fields( 'psa_settings_group' );
+				do_settings_sections( 'peptide-search-ai' );
+				submit_button();
+				?>
+			</form>
 
-            <hr />
-            <h2><?php esc_html_e( 'How It Works', 'peptide-search-ai' ); ?></h2>
-            <ol style="max-width:600px; line-height:1.8;">
-                <li><?php esc_html_e( 'Add the shortcode [peptide_search] to any page.', 'peptide-search-ai' ); ?></li>
-                <li><?php esc_html_e( 'Visitors search for a peptide name.', 'peptide-search-ai' ); ?></li>
-                <li><?php esc_html_e( 'If found, results appear instantly.', 'peptide-search-ai' ); ?></li>
-                <li><?php esc_html_e( 'If not found, the system automatically validates the name, creates a placeholder, and generates content in the background.', 'peptide-search-ai' ); ?></li>
-                <li><?php esc_html_e( 'The visitor sees a "being added" message and can check back later.', 'peptide-search-ai' ); ?></li>
-            </ol>
+			<hr />
+			<h2><?php esc_html_e( 'How It Works', 'peptide-search-ai' ); ?></h2>
+			<ol style="max-width:600px; line-height:1.8;">
+				<li><?php esc_html_e( 'Add the shortcode [peptide_search] to any page.', 'peptide-search-ai' ); ?></li>
+				<li><?php esc_html_e( 'Visitors search for a peptide name.', 'peptide-search-ai' ); ?></li>
+				<li><?php esc_html_e( 'If found, results appear instantly.', 'peptide-search-ai' ); ?></li>
+				<li><?php esc_html_e( 'If not found, the system automatically validates the name, creates a placeholder, and generates content in the background.', 'peptide-search-ai' ); ?></li>
+				<li><?php esc_html_e( 'The visitor sees a "being added" message and can check back later.', 'peptide-search-ai' ); ?></li>
+			</ol>
 
-            <hr />
-            <h2><?php esc_html_e( 'Shortcode', 'peptide-search-ai' ); ?></h2>
-            <p><code>[peptide_search]</code></p>
-            <p><?php esc_html_e( 'Customize placeholder:', 'peptide-search-ai' ); ?> <code>[peptide_search placeholder="Search peptides..."]</code></p>
+			<hr />
+			<h2><?php esc_html_e( 'Shortcode', 'peptide-search-ai' ); ?></h2>
+			<p><code>[peptide_search]</code></p>
+			<p><?php esc_html_e( 'Customize placeholder:', 'peptide-search-ai' ); ?> <code>[peptide_search placeholder="Search peptides..."]</code></p>
 
-            <hr />
-            <h2><?php esc_html_e( 'REST API', 'peptide-search-ai' ); ?></h2>
-            <p><code>GET /wp-json/peptides/v1/search?q=BPC-157</code></p>
-            <p class="description"><?php esc_html_e( 'The REST endpoint returns published peptides only — it does not trigger auto-generation.', 'peptide-search-ai' ); ?></p>
-        </div>
-        <?php
-    }
+			<hr />
+			<h2><?php esc_html_e( 'REST API', 'peptide-search-ai' ); ?></h2>
+			<p><code>GET /wp-json/peptides/v1/search?q=BPC-157</code></p>
+			<p class="description"><?php esc_html_e( 'The REST endpoint returns published peptides only — it does not trigger auto-generation.', 'peptide-search-ai' ); ?></p>
+		</div>
+		<?php
+	}
 
-    /**
-     * Helper to get a single setting with a default.
-     *
-     * @param string $key     Setting key.
-     * @param mixed  $default Default value.
-     * @return mixed
-     */
-    private static function get_setting( $key, $default = '' ) {
-        $options = get_option( 'psa_settings', array() );
-        return $options[ $key ] ?? $default;
-    }
+	/**
+	 * Helper to get a single setting with a default.
+	 *
+	 * @param string $key     Setting key.
+	 * @param mixed  $default Default value.
+	 * @return mixed
+	 */
+	private static function get_setting( $key, $default = '' ) {
+		$options = get_option( 'psa_settings', array() );
+		return $options[ $key ] ?? $default;
+	}
 }
diff --git a/includes/class-psa-config.php b/includes/class-psa-config.php
index 119fe2d..f361f95 100644
--- a/includes/class-psa-config.php
+++ b/includes/class-psa-config.php
@@ -21,19 +21,18 @@ class PSA_Config {
 	const AJAX_RATE_LIMIT = 10;
 
 	// Generation timing
-	const PENDING_TIMEOUT = 300; // seconds (5 minutes)
+	const PENDING_TIMEOUT        = 300; // seconds (5 minutes)
 	const MAX_GENERATION_RETRIES = 3;
 
 	// AI token limits
-	const VALIDATION_MAX_TOKENS = 300;
-	const GENERATION_MAX_TOKENS = 4096;
+	const VALIDATION_MAX_TOKENS  = 300;
+	const GENERATION_MAX_TOKENS  = 4096;
 
 	// Cache TTL
-	const VALIDATION_CACHE_TTL = null; // Set to DAY_IN_SECONDS at runtime
-	const PUBCHEM_CACHE_TTL = null; // Set to 7 * DAY_IN_SECONDS at runtime
+	const VALIDATION_CACHE_TTL   = null; // Set to DAY_IN_SECONDS at runtime
+	const PUBCHEM_CACHE_TTL      = null; // Set to 7 * DAY_IN_SECONDS at runtime
 
 	// API retry settings
-	const API_RETRY_MAX = 3;
-	const API_RETRY_BASE_DELAY = 5; // seconds
-
+	const API_RETRY_MAX          = 3;
+	const API_RETRY_BASE_DELAY   = 5; // seconds
 }