fix: resolve PHPCS errors and PHPUnit test failures for CI

Move declare(strict_types=1) after file-level docblock in all 12 class
files to satisfy WordPress Coding Standards docblock placement rule.
Fix multi-line function call formatting in class-psa-admin.php. Align
array double arrows and equals signs. Fix escaped backticks in
AIGeneratorTest heredoc that broke markdown fence stripping tests.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

includes/class-psa-admin.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Admin settings page for Peptide Search AI.
  *
@@ -12,6 +11,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-cost-tracker.php
  * @see     includes/class-psa-post-type.php
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;
@@ -74,21 +74,21 @@ class PSA_Admin {
 		$api_key_value = '';
 
 		if ( ! empty( $api_key_input ) && '••••••••' !== $api_key_input ) {
-			$sanitized = sanitize_text_field( $api_key_input );
-			$encrypted = PSA_Encryption::encrypt( $sanitized );
+			$sanitized     = sanitize_text_field( $api_key_input );
+			$encrypted     = PSA_Encryption::encrypt( $sanitized );
 			$api_key_value = ( false !== $encrypted ) ? $encrypted : '';
 		} else {
-			$existing = self::get_setting( 'api_key', '' );
+			$existing      = self::get_setting( 'api_key', '' );
 			$api_key_value = $existing;
 		}
 
 		return array(
-			'api_key'          => $api_key_value,
-			'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' ),
-			'use_pubchem'      => ! empty( $input['use_pubchem'] ) ? '1' : '0',
-			'monthly_budget'   => max( 0, floatval( $input['monthly_budget'] ?? PSA_Config::DEFAULT_MONTHLY_BUDGET ) ),
+			'api_key'            => $api_key_value,
+			'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' ),
+			'use_pubchem'        => ! empty( $input['use_pubchem'] ) ? '1' : '0',
+			'monthly_budget'     => max( 0, floatval( $input['monthly_budget'] ?? PSA_Config::DEFAULT_MONTHLY_BUDGET ) ),
 		);
 	}
 
@@ -106,20 +106,28 @@ class PSA_Admin {
 
 		if ( 'migrate_categories' === $action && wp_verify_nonce( $nonce, 'psa_migrate_categories' ) ) {
 			self::run_category_migration();
-			add_action( 'admin_notices', function () {
-				echo '<div class="notice notice-success is-dismissible"><p>' . esc_html__( 'Category migration completed.', 'peptide-search-ai' ) . '</p></div>';
-			} );
+			add_action(
+				'admin_notices',
+				function () {
+					echo '<div class="notice notice-success is-dismissible"><p>' . esc_html__( 'Category migration completed.', 'peptide-search-ai' ) . '</p></div>';
+				}
+			);
 		}
 
 		if ( 'reenrich' === $action && wp_verify_nonce( $nonce, 'psa_reenrich' ) ) {
 			$queued = self::queue_reenrichment();
-			add_action( 'admin_notices', function () use ( $queued ) {
-				echo '<div class="notice notice-success is-dismissible"><p>' . esc_html( sprintf(
-					/* translators: %d = number of peptides queued */
-					__( '%d peptides queued for re-enrichment.', 'peptide-search-ai' ),
-					$queued
-				) ) . '</p></div>';
-			} );
+			add_action(
+				'admin_notices',
+				function () use ( $queued ) {
+					echo '<div class="notice notice-success is-dismissible"><p>' . esc_html(
+						sprintf(
+							/* translators: %d = number of peptides queued */
+							__( '%d peptides queued for re-enrichment.', 'peptide-search-ai' ),
+							$queued
+						)
+					) . '</p></div>';
+				}
+			);
 		}
 	}
 

includes/class-psa-ai-generator.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Handles AI content generation for new peptide entries.
  *
@@ -13,6 +12,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-pubchem.php
  * @see     includes/class-psa-post-type.php
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-config.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Configuration constants for Peptide Search AI.
  *
@@ -9,6 +8,7 @@ declare( strict_types=1 );
  *
  * @package PeptideSearchAI
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-cost-tracker.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Tracks API usage costs and enforces monthly budget limits.
  *
@@ -10,6 +9,7 @@ declare( strict_types=1 );
  *
  * @package PeptideSearchAI
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-directory.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Browsable peptide directory — REST endpoint, shortcode, and data formatting.
  *
@@ -12,6 +11,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-search.php      — existing search shortcode (separate from directory)
  * @see     assets/js/psa-directory.js          — frontend grid, filter, modal logic
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-encryption.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Handles encryption/decryption of sensitive data at rest.
  *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-admin.php
  * @see     includes/class-psa-ai-generator.php
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-kb-builder.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Echo Knowledge Base article builder for generated peptide content.
  *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
  * @package PeptideSearchAI
  * @see     includes/class-psa-ai-generator.php
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-openrouter.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * OpenRouter API communication layer.
  *
@@ -12,6 +11,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-ai-generator.php
  * @see     includes/class-psa-cost-tracker.php
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;
@@ -90,15 +90,15 @@ class PSA_OpenRouter {
 			array(
 				'timeout' => 120,
 				'headers' => array(
-					'Content-Type'    => 'application/json',
-					'Authorization'   => 'Bearer ' . $api_key,
-					'HTTP-Referer'    => $site_url,
-					'X-Title'         => $site_name,
+					'Content-Type'   => 'application/json',
+					'Authorization'  => 'Bearer ' . $api_key,
+					'HTTP-Referer'   => $site_url,
+					'X-Title'        => $site_name,
 				),
 				'body' => wp_json_encode(
 					array(
-						'model'       => $model,
-						'messages'    => array(
+						'model'           => $model,
+						'messages'        => array(
 							array(
 								'role'    => 'system',
 								'content' => 'You are a scientific database assistant. Return only valid JSON.',
@@ -108,8 +108,8 @@ class PSA_OpenRouter {
 								'content' => $prompt,
 							),
 						),
-						'max_tokens'  => $max_tokens,
-						'temperature' => 0.3,
+						'max_tokens'      => $max_tokens,
+						'temperature'     => 0.3,
 					)
 				),
 			)
@@ -152,13 +152,13 @@ class PSA_OpenRouter {
 
 		PSA_Cost_Tracker::log_api_call(
 			array(
-				'provider'       => 'openrouter',
-				'model'          => $model,
-				'prompt_tokens'  => $prompt_tokens,
-				'completion_tokens' => $completion_tokens,
-				'request_type'   => $request_type,
-				'peptide_name'   => $peptide_name,
-				'success'        => true,
+				'provider'            => 'openrouter',
+				'model'               => $model,
+				'prompt_tokens'       => $prompt_tokens,
+				'completion_tokens'   => $completion_tokens,
+				'request_type'        => $request_type,
+				'peptide_name'        => $peptide_name,
+				'success'             => true,
 			)
 		);
 

includes/class-psa-post-type.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Registers the Peptide custom post type, taxonomy, and meta fields.
  *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-ai-generator.php  — auto-assigns category term after generation
  * @see     includes/class-psa-directory.php     — reads taxonomy for directory filtering
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-pubchem.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * PubChem PUG REST API integration for molecular data enrichment.
  *
@@ -10,6 +9,7 @@ declare( strict_types=1 );
  * @package PeptideSearchAI
  * @see     includes/class-psa-ai-generator.php
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-search.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Handles AJAX search, the [peptide_search] shortcode, and the REST API endpoint.
  *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-ai-generator.php
  * @see     includes/class-psa-config.php
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;

includes/class-psa-template.php

@@ -1,5 +1,4 @@
 <?php
-declare( strict_types=1 );
 /**
  * Custom template rendering for single peptide pages.
  *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
  * @see     includes/class-psa-post-type.php
  * @see     includes/class-psa-directory.php  — detail modal uses the same data via REST
  */
+declare( strict_types=1 );
 
 if ( ! defined( 'ABSPATH' ) ) {
 	exit;