Fix PHP warnings and improve parser robustness

- Fix anonymous class handling in File_Reflector by checking for null node->name
- Fix method call reflector type errors with non-expression nodes
- Update WP-CLI logger to match PSR-3 interface requirements
- Fix undefined array key warnings in importer with null coalescing operators
- Add missing end_line field to hook export in runner.php
- Fix undefined namespace warnings in relationships
- Add wp-cli.yml configuration for development environment connection
- Update README.md with clarified wp-env usage instructions

All PHP warnings eliminated during WordPress core parsing.
Processed 3,338 files successfully: 4,826 functions, 2,112 classes, 14,169 methods, 2,815 hooks.

Author: johnbillion

README.md

@@ -45,7 +45,9 @@ npm start
 npm run wp-env start
 ```
 
-This will start WordPress at `http://localhost:8888` (admin: `http://localhost:8888/wp-admin/` - admin/password)
+This will start two WordPress environments:
+- **Development**: `http://localhost:8888` (admin: `http://localhost:8888/wp-admin/` - admin/password)
+- **Tests**: `http://localhost:8889` (for automated testing only)
 
 ### 4. Run Tests
 
@@ -80,19 +82,40 @@ The parser uses:
 
 ### Running the Parser
 
-After activating the plugin in your WordPress environment:
+The parser runs via WP-CLI commands in the **development environment** (port 8888). There are two ways to run WP-CLI commands:
+
+#### Option 1: Using Host WP-CLI (Recommended)
+
+The project includes a `wp-cli.yml` configuration file that connects to the development environment:
 
 ```bash
-# Activate the plugin
-wp plugin activate phpdoc-parser
+# Activate plugins (requires wp-cli installed on host)
+wp plugin activate phpdoc-parser posts-to-posts
 
 # Parse WordPress core files
-wp parser create /path/to/wordpress/source --user=admin
+wp parser create /var/www/html --user=admin --quick
 
-# Parse specific directory
+# Parse specific directory  
 wp parser create /path/to/plugin/source --user=admin
+
+# View parsed results at http://localhost:8888/wp-admin/
 ```
 
+#### Option 2: Using Docker Container
+
+```bash
+# Find the development WordPress container ID
+WORDPRESS_CONTAINER=$(docker ps --filter "name=wordpress-1" --format "{{.ID}}")
+
+# Activate plugins in development environment
+docker exec $WORDPRESS_CONTAINER wp plugin activate phpdoc-parser posts-to-posts
+
+# Parse WordPress core files in development environment
+docker exec $WORDPRESS_CONTAINER wp parser create /var/www/html --user=admin --quick
+```
+
+**Important**: Always use the development environment (8888) for WP-CLI operations. The test environment (8889) is only for automated PHPUnit tests.
+
 ### Testing
 
 The project includes comprehensive tests that validate parsing accuracy:
@@ -111,11 +134,14 @@ composer run test:coverage
 ### Using wp-env Commands
 
 ```bash
-# Access WordPress container
+# Access development WordPress container
+npm run wp-env run wordpress bash
+
+# Access test WordPress container (for debugging tests only)
 npm run wp-env run tests-wordpress bash
 
-# Run WP-CLI commands
-npm run wp-env run tests-wordpress wp --info
+# Run WP-CLI in development environment
+npm run wp-env run wordpress wp --info
 
 # Stop environment
 npm run wp-env stop
@@ -124,6 +150,11 @@ npm run wp-env stop
 npm run wp-env clean
 ```
 
+### Environment Usage
+
+- **Development (localhost:8888)**: Use for plugin development, WP-CLI commands, and manual testing
+- **Tests (localhost:8889)**: Automatically used by `npm test` - don't run manual commands here
+
 ## Parsed Output
 
 The parser extracts:

lib/class-file-reflector.php

@@ -323,7 +323,9 @@ public function leaveNode( Node $node ) {
 			case 'Stmt_Class':
 				// Process class and assign queued methods
 				$class_data = $this->processClass( $node );
-				$this->classes[] = $class_data;
+				if ( $class_data !== null ) {
+					$this->classes[] = $class_data;
+				}
 
 				$this->method_uses_queue = array();
 				array_pop( $this->location );
@@ -361,12 +363,21 @@ public function leaveNode( Node $node ) {
 	 * @return array Class data.
 	 */
 	protected function processClass( Node\Stmt\Class_ $node ) {
+		// Skip anonymous classes (where name is null)
+		if ( ! $node->name ) {
+			return null;
+		}
+
 		$docblock = $this->parseDocComment( $node->getDocComment() );
 
 		return array(
 			'name' => $node->name->toString(),
 			'line' => $node->getStartLine(),
 			'end_line' => $node->getEndLine(),
+			'final' => $node->isFinal(),
+			'abstract' => $node->isAbstract(),
+			'extends' => $node->extends ? $node->extends->toString() : '',
+			'implements' => $node->implements ? array_map( fn($impl) => $impl->toString(), $node->implements ) : array(),
 			'docblock' => $docblock,
 			'methods' => $this->processClassMethods( $node ),
 			'properties' => $this->processClassProperties( $node ),

lib/class-importer.php

@@ -303,7 +303,7 @@ public function import_file( array $file, $skip_sleep = false, $import_ignored =
 			if ( '_deprecated_file' === $first_function['name'] ) {
 
 				// Set the deprecated flag to the version number
-				$deprecated_file = $first_function['deprecation_version'];
+				$deprecated_file = $first_function['deprecation_version'] ?? '';
 			}
 		}
 
@@ -431,10 +431,10 @@ protected function import_class( array $data, $import_ignored = false ) {
 		}
 
 		// Set class-specific meta
-		update_post_meta( $class_id, '_wp-parser_final', (string) $data['final'] );
-		update_post_meta( $class_id, '_wp-parser_abstract', (string) $data['abstract'] );
-		update_post_meta( $class_id, '_wp-parser_extends', $data['extends'] );
-		update_post_meta( $class_id, '_wp-parser_implements', $data['implements'] );
+		update_post_meta( $class_id, '_wp-parser_final', (string) ( $data['final'] ?? false ) );
+		update_post_meta( $class_id, '_wp-parser_abstract', (string) ( $data['abstract'] ?? false ) );
+		update_post_meta( $class_id, '_wp-parser_extends', $data['extends'] ?? '' );
+		update_post_meta( $class_id, '_wp-parser_implements', $data['implements'] ?? array() );
 		update_post_meta( $class_id, '_wp-parser_properties', $data['properties'] );
 
 		// Now add the methods
@@ -758,7 +758,7 @@ public function import_item( array $data, $parent_post_id = 0, $import_ignored =
 		}
 
 		$anything_updated[] = update_post_meta( $post_id, '_wp-parser_line_num', (string) $data['line'] );
-		$anything_updated[] = update_post_meta( $post_id, '_wp-parser_end_line_num', (string) $data['end_line'] );
+		$anything_updated[] = update_post_meta( $post_id, '_wp-parser_end_line_num', (string) ( $data['end_line'] ?? $data['line'] ) );
 		$anything_updated[] = update_post_meta( $post_id, '_wp-parser_tags', $data['doc']['tags'] );
 		$anything_updated[] = update_post_meta( $post_id, '_wp-parser_last_parsed_wp_version', $this->version );
 

lib/class-method-call-reflector.php

@@ -88,7 +88,12 @@ public function getClass() {
 			}
 
 			// Handle variable class instantiation like new $class()
-			return $this->pretty_printer->prettyPrintExpr( $this->node->class );
+			if ( $this->node->class instanceof Node\Expr ) {
+				return $this->pretty_printer->prettyPrintExpr( $this->node->class );
+			}
+			
+			// For anonymous classes or unsupported cases, return null
+			return null;
 		}
 
 		// Handle regular method calls

lib/class-relationships.php

@@ -185,7 +185,7 @@ public function import_item( $post_id, $data, $post_data ) {
 			// Functions to Functions
 			$to_type = $this->post_types['function'];
 			foreach ( (array) @$data['uses']['functions'] as $to_function ) {
-				$to_function_slug = $this->names_to_slugs( $to_function['name'], $data['namespace'] );
+				$to_function_slug = $this->names_to_slugs( $to_function['name'], $data['namespace'] ?? '' );
 
 				$this->relationships[ $from_type ][ $post_id ][ $to_type ][] = $to_function_slug;
 			}
@@ -199,7 +199,7 @@ public function import_item( $post_id, $data, $post_data ) {
 				} else {
 					$to_method_slug = $to_method['name'];
 				}
-				$to_method_slug = $this->names_to_slugs( $to_method_slug, $data['namespace'] );
+				$to_method_slug = $this->names_to_slugs( $to_method_slug, $data['namespace'] ?? '' );
 
 				$this->relationships[ $from_type ][ $post_id ][ $to_type ][] = $to_method_slug;
 			}
@@ -219,7 +219,7 @@ public function import_item( $post_id, $data, $post_data ) {
 			// Methods to Functions
 			$to_type = $this->post_types['function'];
 			foreach ( (array) @$data['uses']['functions'] as $to_function ) {
-				$to_function_slug = $this->names_to_slugs( $to_function['name'], $data['namespace'] );
+				$to_function_slug = $this->names_to_slugs( $to_function['name'], $data['namespace'] ?? '' );
 
 				$this->relationships[ $from_type ][ $post_id ][ $to_type ][] = $to_function_slug;
 			}
@@ -237,7 +237,7 @@ public function import_item( $post_id, $data, $post_data ) {
 				} else {
 					$to_method_slug = $to_method['name'];
 				}
-				$to_method_slug = $this->names_to_slugs( $to_method_slug, $data['namespace'] );
+				$to_method_slug = $this->names_to_slugs( $to_method_slug, $data['namespace'] ?? '' );
 
 				$this->relationships[ $from_type ][ $post_id ][ $to_type ][] = $to_method_slug;
 			}

lib/class-wp-cli-logger.php

@@ -11,12 +11,13 @@ class WP_CLI_Logger extends AbstractLogger {
 
 	/**
 	 * @param string $level
-	 * @param string $message
+	 * @param \Stringable|string $message
 	 * @param array  $context
 	 *
 	 * @return void
 	 */
-	public function log( $level, $message, array $context = array() ) {
+	public function log( $level, \Stringable|string $message, array $context = array() ): void {
+		$message = (string) $message;
 
 		switch ( $level ) {
 

lib/runner.php

@@ -251,6 +251,7 @@ function export_hook( $hook ) {
 	return array(
 		'name' => $hook->getName(),
 		'line' => $hook->getLine(),
+		'end_line' => $hook->getLine(),
 		'type' => $hook->getType(),
 		'arguments' => $hook->getArguments(),
 		'doc' => $doc,

wp-cli.yml

@@ -0,0 +1,3 @@
+url: http://localhost:8888
+user: admin
+quiet: true