From daa94eed56f43fe40d6103a2a7622f612742d4f5 Mon Sep 17 00:00:00 2001
From: Pascal Birchler <pascalb@google.com>
Date: Tue, 31 Mar 2026 19:43:39 +0200
Subject: [PATCH 1/6] Add initial PHPStan config

---
 phpstan.neon.dist            | 14 ++++++++++++++
 src/Check/Option_Value.php   | 21 +++++++++++++--------
 src/Checks.php               |  7 ++++---
 tests/phpstan/scan-files.php |  6 ++++++
 4 files changed, 37 insertions(+), 11 deletions(-)
 create mode 100644 phpstan.neon.dist
 create mode 100644 tests/phpstan/scan-files.php

diff --git a/phpstan.neon.dist b/phpstan.neon.dist
new file mode 100644
index 0000000..565f7e3
--- /dev/null
+++ b/phpstan.neon.dist
@@ -0,0 +1,14 @@
+parameters:
+  level: 1
+  paths:
+    - src
+    - doctor-command.php
+  scanDirectories:
+    - vendor/wp-cli/wp-cli/php
+  scanFiles:
+    - vendor/php-stubs/wordpress-stubs/wordpress-stubs.php
+    - tests/phpstan/scan-files.php
+  treatPhpDocTypesAsCertain: false
+  ignoreErrors:
+    - '#Call to deprecated method setAccessible\(\) of class ReflectionProperty\.#'
+
diff --git a/src/Check/Option_Value.php b/src/Check/Option_Value.php
index 5122fe5..c8c269c 100644
--- a/src/Check/Option_Value.php
+++ b/src/Check/Option_Value.php
@@ -38,6 +38,12 @@ public function run() {
 			return;
 		}
 
+		if ( ! isset( $this->value ) && ! isset( $this->value_is_not ) ) {
+			$this->set_status( 'error' );
+			$this->set_message( 'You must use either "value" or "value_is_not".' );
+			return;
+		}
+
 		$actual_value = get_option( $this->option );
 
 		if ( isset( $this->value ) ) {
@@ -48,14 +54,13 @@ public function run() {
 				$status  = 'error';
 				$message = "Option '{$this->option}' is '{$actual_value}' but expected to be '{$this->value}'.";
 			}
-		} elseif ( isset( $this->value_is_not ) ) {
-			if ( $actual_value == $this->value_is_not ) { // phpcs:ignore Universal.Operators.StrictComparisons -- Keep existing behavior.
-				$status  = 'error';
-				$message = "Option '{$this->option}' is '{$actual_value}' and expected not to be.";
-			} else {
-				$status  = 'success';
-				$message = "Option '{$this->option}' is not '{$this->value_is_not}' as expected.";
-			}
+		} elseif ( $actual_value == $this->value_is_not ) { // phpcs:ignore Universal.Operators.StrictComparisons -- Keep existing behavior.
+			$status  = 'error';
+			$message = "Option '{$this->option}' is '{$actual_value}' and expected not to be.";
+
+		} else {
+			$status  = 'success';
+			$message = "Option '{$this->option}' is not '{$this->value_is_not}' as expected.";
 		}
 
 		$this->set_status( $status );
diff --git a/src/Checks.php b/src/Checks.php
index d13f9b7..fc1f64e 100644
--- a/src/Checks.php
+++ b/src/Checks.php
@@ -4,7 +4,8 @@
 
 use Mustangostang\Spyc;
 use WP_CLI;
-use WP_CLI\Utils;
+use WP_CLI\Path;
+
 
 class Checks {
 
@@ -78,7 +79,7 @@ public static function register_config( $file ) {
 	 * Register a check with the Doctor
 	 *
 	 * @param string $name Name for the check.
-	 * @param string $class Check class name.
+	 * @param string $check Check class name.
 	 */
 	public static function add_check( $name, $check ) {
 
@@ -125,7 +126,7 @@ public static function get_checks( $args = array() ) {
 	 * @param string $base Base path to prepend.
 	 */
 	private static function absolutize( $path, $base ) {
-		if ( ! empty( $path ) && ! Utils\is_path_absolute( $path ) ) {
+		if ( ! empty( $path ) && ! Path::is_absolute( $path ) ) {
 			$path = $base . DIRECTORY_SEPARATOR . $path;
 		}
 		return $path;
diff --git a/tests/phpstan/scan-files.php b/tests/phpstan/scan-files.php
new file mode 100644
index 0000000..81f3d91
--- /dev/null
+++ b/tests/phpstan/scan-files.php
@@ -0,0 +1,6 @@
+<?php
+// phpcs:ignoreFile
+
+namespace {
+	define( 'WPINC', 'wp-includes' );
+}

From 7217c5f47b531be13c02f23e7f0fffae1338a37c Mon Sep 17 00:00:00 2001
From: Pascal Birchler <pascalb@google.com>
Date: Wed, 1 Apr 2026 10:42:31 +0200
Subject: [PATCH 2/6] Level 2

---
 phpstan.neon.dist  | 2 +-
 src/Check/File.php | 7 +++++++
 src/Checks.php     | 3 ++-
 src/Command.php    | 1 +
 4 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/phpstan.neon.dist b/phpstan.neon.dist
index 565f7e3..de04797 100644
--- a/phpstan.neon.dist
+++ b/phpstan.neon.dist
@@ -1,5 +1,5 @@
 parameters:
-  level: 1
+  level: 2
   paths:
     - src
     - doctor-command.php
diff --git a/src/Check/File.php b/src/Check/File.php
index fc1b496..8d78f37 100644
--- a/src/Check/File.php
+++ b/src/Check/File.php
@@ -58,4 +58,11 @@ public function get_options() {
 			'path'            => $this->path,
 		);
 	}
+
+	/**
+	 * Check a specific file.
+	 *
+	 * @param \SplFileInfo $file File to check.
+	 */
+	abstract public function check_file( \SplFileInfo $file );
 }
diff --git a/src/Checks.php b/src/Checks.php
index fc1f64e..29d0a29 100644
--- a/src/Checks.php
+++ b/src/Checks.php
@@ -101,9 +101,10 @@ public static function add_check( $name, $check ) {
 	}
 
 	/**
-	 * Get checks registred with the Doctor.
+	 * Get checks registered with the Doctor.
 	 *
 	 * @param array $args Filter checks based on some attribute.
+	 * @return array<string, Check>
 	 */
 	public static function get_checks( $args = array() ) {
 		if ( ! empty( $args['name'] ) ) {
diff --git a/src/Command.php b/src/Command.php
index 2f6d6db..f2b1057 100644
--- a/src/Command.php
+++ b/src/Command.php
@@ -185,6 +185,7 @@ static function () use ( $file_checks, &$completed, &$progress ) {
 								if ( ! in_array( $file->getExtension(), $extension, true ) ) {
 									continue;
 								}
+								/** @var Check\File $check */
 								$check->check_file( $file );
 							}
 						}

From 47d180932029186559e4d1d39c73f4742f0ffbe3 Mon Sep 17 00:00:00 2001
From: Pascal Birchler <pascalb@google.com>
Date: Wed, 1 Apr 2026 14:54:02 +0200
Subject: [PATCH 3/6] Level 3

---
 phpstan.neon.dist                   | 2 +-
 src/Check/Autoload_Options_Size.php | 2 +-
 src/Check/File.php                  | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/phpstan.neon.dist b/phpstan.neon.dist
index de04797..dc67c05 100644
--- a/phpstan.neon.dist
+++ b/phpstan.neon.dist
@@ -1,5 +1,5 @@
 parameters:
-  level: 2
+  level: 3
   paths:
     - src
     - doctor-command.php
diff --git a/src/Check/Autoload_Options_Size.php b/src/Check/Autoload_Options_Size.php
index db2437d..f9c122f 100644
--- a/src/Check/Autoload_Options_Size.php
+++ b/src/Check/Autoload_Options_Size.php
@@ -43,6 +43,6 @@ public function run() {
 	private static function format_bytes( $size, $precision = 2 ) {
 		$base     = log( $size, 1024 );
 		$suffixes = array( '', 'kb', 'mb', 'g', 't' );
-		return round( pow( 1024, $base - floor( $base ) ), $precision ) . $suffixes[ floor( $base ) ];
+		return round( pow( 1024, $base - floor( $base ) ), $precision ) . $suffixes[ (int) floor( $base ) ];
 	}
 }
diff --git a/src/Check/File.php b/src/Check/File.php
index 8d78f37..2a25d99 100644
--- a/src/Check/File.php
+++ b/src/Check/File.php
@@ -12,7 +12,7 @@ abstract class File extends Check {
 	/**
 	 * File checks are run as their own group.
 	 */
-	protected $_when = false;
+	protected $_when = 'manual'; // Run manually via group
 
 	/**
 	 * File extension to check.
@@ -49,7 +49,7 @@ abstract class File extends Check {
 	/**
 	 * Get the options for this check
 	 *
-	 * @return string
+	 * @return array<string, bool|string>
 	 */
 	public function get_options() {
 		return array(

From 3a2737fb9859765f56c6823b4ba09a5679a388b6 Mon Sep 17 00:00:00 2001
From: Pascal Birchler <pascalb@google.com>
Date: Wed, 1 Apr 2026 17:51:04 +0200
Subject: [PATCH 4/6] Level 4

---
 phpstan.neon.dist                 | 2 +-
 src/Check/Constant_Definition.php | 6 +++---
 src/Check/File_Contents.php       | 4 ++--
 src/Check/File_Type.php           | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/phpstan.neon.dist b/phpstan.neon.dist
index dc67c05..a4b9f4a 100644
--- a/phpstan.neon.dist
+++ b/phpstan.neon.dist
@@ -1,5 +1,5 @@
 parameters:
-  level: 3
+  level: 4
   paths:
     - src
     - doctor-command.php
diff --git a/src/Check/Constant_Definition.php b/src/Check/Constant_Definition.php
index 765a6b8..a3f03e7 100644
--- a/src/Check/Constant_Definition.php
+++ b/src/Check/Constant_Definition.php
@@ -26,9 +26,9 @@ class Constant_Definition extends Check {
 	/**
 	 * Whether or not the constant is expected to be a falsy value.
 	 *
-	 * @var bool
+	 * @var bool|null
 	 */
-	protected $falsy;
+	protected $falsy = null;
 
 	/**
 	 * Expected value of the constant.
@@ -99,7 +99,7 @@ public function run() {
 			return;
 		}
 
-		if ( $this->defined && ! isset( $this->value ) ) {
+		if ( ! isset( $this->value ) ) {
 			$this->set_status( 'success' );
 			$this->set_message( "Constant '{$this->constant}' is defined." );
 			return;
diff --git a/src/Check/File_Contents.php b/src/Check/File_Contents.php
index 4927c08..baa569b 100644
--- a/src/Check/File_Contents.php
+++ b/src/Check/File_Contents.php
@@ -12,9 +12,9 @@ class File_Contents extends File {
 	/**
 	 * Regex pattern to check against each file’s contents.
 	 *
-	 * @var string
+	 * @var string|null
 	 */
-	protected $regex;
+	protected $regex = null;
 
 	/**
 	 * Assert existence or absence of the regex pattern.
diff --git a/src/Check/File_Type.php b/src/Check/File_Type.php
index 1a161f1..d9e2a33 100644
--- a/src/Check/File_Type.php
+++ b/src/Check/File_Type.php
@@ -12,9 +12,9 @@ class File_Type extends File {
 	/**
 	 * Assert the file type is or isn't a symlink.
 	 *
-	 * @var bool
+	 * @var bool|null
 	 */
-	protected $symlink;
+	protected $symlink = null;
 
 	public function run() {
 

From 5bff4a9bbc8aa3de3d6e29724e63652c362d61e0 Mon Sep 17 00:00:00 2001
From: Pascal Birchler <pascalb@google.com>
Date: Thu, 2 Apr 2026 09:50:22 +0200
Subject: [PATCH 5/6] Level 5

---
 phpstan.neon.dist | 2 +-
 src/Checks.php    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/phpstan.neon.dist b/phpstan.neon.dist
index a4b9f4a..b32b47f 100644
--- a/phpstan.neon.dist
+++ b/phpstan.neon.dist
@@ -1,5 +1,5 @@
 parameters:
-  level: 4
+  level: 5
   paths:
     - src
     - doctor-command.php
diff --git a/src/Checks.php b/src/Checks.php
index 29d0a29..16131b1 100644
--- a/src/Checks.php
+++ b/src/Checks.php
@@ -78,8 +78,8 @@ public static function register_config( $file ) {
 	/**
 	 * Register a check with the Doctor
 	 *
-	 * @param string $name Name for the check.
-	 * @param string $check Check class name.
+	 * @param string        $name  Name for the check.
+	 * @param object|string $check Check class name or instance.
 	 */
 	public static function add_check( $name, $check ) {
 

From 37dffc69e60791e50fc12a746b3885bf0428754b Mon Sep 17 00:00:00 2001
From: Pascal Birchler <pascalb@google.com>
Date: Thu, 2 Apr 2026 11:27:11 +0200
Subject: [PATCH 6/6] Level 6

---
 phpstan.neon.dist                       |  2 +-
 src/Check.php                           | 11 ++++++++++-
 src/Check/Autoload_Options_Size.php     |  8 ++++++++
 src/Check/Cache_Flush.php               |  3 +++
 src/Check/Constant_Definition.php       | 17 ++++++++++++++---
 src/Check/Core_Verify_Checksums.php     |  6 ++++++
 src/Check/Cron.php                      |  6 ++++++
 src/Check/Cron_Count.php                |  3 +++
 src/Check/Cron_Duplicates.php           |  3 +++
 src/Check/File.php                      |  3 ++-
 src/Check/File_Contents.php             |  4 ++++
 src/Check/File_Type.php                 |  8 +++++---
 src/Check/Network_Required_Plugins.php  | 14 +++++++++-----
 src/Check/Network_Site_Count.php        |  6 ++++++
 src/Check/Network_Site_Option_Value.php |  3 +++
 src/Check/Option_Value.php              |  3 +++
 src/Check/PHP_In_Upload.php             |  5 ++++-
 src/Check/Plugin.php                    |  6 ++++++
 src/Check/Plugin_Active_Count.php       |  3 +++
 src/Check/Plugin_Deactivated.php        |  3 +++
 src/Check/Plugin_Status.php             |  6 ++++++
 src/Check/Plugin_Update.php             |  3 +++
 src/Check/Theme_Update.php              |  3 +++
 src/Checks.php                          | 22 +++++++++++++++++++---
 src/Command.php                         | 12 ++++++++++++
 25 files changed, 145 insertions(+), 18 deletions(-)

diff --git a/phpstan.neon.dist b/phpstan.neon.dist
index b32b47f..87732c3 100644
--- a/phpstan.neon.dist
+++ b/phpstan.neon.dist
@@ -1,5 +1,5 @@
 parameters:
-  level: 5
+  level: 6
   paths:
     - src
     - doctor-command.php
diff --git a/src/Check.php b/src/Check.php
index c0fc4e2..c86b31b 100644
--- a/src/Check.php
+++ b/src/Check.php
@@ -31,6 +31,8 @@ abstract class Check {
 
 	/**
 	 * Initialize the check.
+	 *
+	 * @param array<string, mixed> $options
 	 */
 	public function __construct( $options = array() ) {
 
@@ -48,6 +50,8 @@ public function __construct( $options = array() ) {
 
 	/**
 	 * Get when the check is expected to run.
+	 *
+	 * @return string
 	 */
 	public function get_when() {
 		return $this->_when;
@@ -57,6 +61,7 @@ public function get_when() {
 	 * Set when the check is expected to run.
 	 *
 	 * @param string $when
+	 * @return void
 	 */
 	public function set_when( $when ) {
 		$this->_when = $when;
@@ -66,6 +71,7 @@ public function set_when( $when ) {
 	 * Set the status of the check.
 	 *
 	 * @param string $status
+	 * @return void
 	 */
 	protected function set_status( $status ) {
 		$this->_status = $status;
@@ -75,6 +81,7 @@ protected function set_status( $status ) {
 	 * Set the message of the check.
 	 *
 	 * @param string $message
+	 * @return void
 	 */
 	protected function set_message( $message ) {
 		$this->_message = $message;
@@ -85,13 +92,15 @@ protected function set_message( $message ) {
 	 *
 	 * Because each check checks for something different, this method must be
 	 * subclassed. Method is expected to set $status_code and $status_message.
+	 *
+	 * @return void
 	 */
 	abstract public function run();
 
 	/**
 	 * Get results of the check.
 	 *
-	 * @return array
+	 * @return array<string, string>
 	 */
 	public function get_results() {
 		return array(
diff --git a/src/Check/Autoload_Options_Size.php b/src/Check/Autoload_Options_Size.php
index f9c122f..8752410 100644
--- a/src/Check/Autoload_Options_Size.php
+++ b/src/Check/Autoload_Options_Size.php
@@ -17,6 +17,9 @@ class Autoload_Options_Size extends Check {
 	 */
 	protected $threshold_kb = 900;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		ob_start();
 		WP_CLI::run_command(
@@ -40,6 +43,11 @@ public function run() {
 		}
 	}
 
+	/**
+	 * @param int|float $size Size in bytes.
+	 * @param int       $precision Precision.
+	 * @return string
+	 */
 	private static function format_bytes( $size, $precision = 2 ) {
 		$base     = log( $size, 1024 );
 		$suffixes = array( '', 'kb', 'mb', 'g', 't' );
diff --git a/src/Check/Cache_Flush.php b/src/Check/Cache_Flush.php
index 3f82d9f..27d868d 100644
--- a/src/Check/Cache_Flush.php
+++ b/src/Check/Cache_Flush.php
@@ -11,6 +11,9 @@
  */
 class Cache_Flush extends File_Contents {
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 
 		// Path to wp-content directory.
diff --git a/src/Check/Constant_Definition.php b/src/Check/Constant_Definition.php
index a3f03e7..89618dc 100644
--- a/src/Check/Constant_Definition.php
+++ b/src/Check/Constant_Definition.php
@@ -39,6 +39,8 @@ class Constant_Definition extends Check {
 
 	/**
 	 * Initialize the constant check
+	 *
+	 * @param array<string, mixed> $options
 	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
@@ -47,6 +49,9 @@ public function __construct( $options = array() ) {
 		}
 	}
 
+		/**
+	 * @return void
+	 */
 	public function run() {
 
 		if ( isset( $this->falsy ) ) {
@@ -118,12 +123,18 @@ public function run() {
 		}
 	}
 
+	/**
+	 * @param mixed $value
+	 * @return string
+	 */
 	private static function human_value( $value ) {
 		if ( true === $value ) {
-			$value = 'true';
+			return 'true';
 		} elseif ( false === $value ) {
-			$value = 'false';
+			return 'false';
+		} elseif ( is_null( $value ) ) {
+			return 'null';
 		}
-		return $value;
+		return (string) $value;
 	}
 }
diff --git a/src/Check/Core_Verify_Checksums.php b/src/Check/Core_Verify_Checksums.php
index 3b7abdf..300dc50 100644
--- a/src/Check/Core_Verify_Checksums.php
+++ b/src/Check/Core_Verify_Checksums.php
@@ -10,11 +10,17 @@
  */
 class Core_Verify_Checksums extends Check {
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
 		$this->set_when( 'before_wp_load' );
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$return_code = WP_CLI::runcommand(
 			'core verify-checksums',
diff --git a/src/Check/Cron.php b/src/Check/Cron.php
index 3b4e1de..8e09109 100644
--- a/src/Check/Cron.php
+++ b/src/Check/Cron.php
@@ -7,8 +7,14 @@
 
 abstract class Cron extends Check {
 
+	/**
+	 * @var array<mixed>|null
+	 */
 	protected static $crons;
 
+	/**
+	 * @return array<mixed>
+	 */
 	protected static function get_crons() {
 
 		if ( isset( self::$crons ) ) {
diff --git a/src/Check/Cron_Count.php b/src/Check/Cron_Count.php
index 31cdde9..f9494c6 100644
--- a/src/Check/Cron_Count.php
+++ b/src/Check/Cron_Count.php
@@ -14,6 +14,9 @@ class Cron_Count extends Cron {
 	 */
 	protected $threshold_count = 50;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$crons = self::get_crons();
 		if ( count( $crons ) >= $this->threshold_count ) {
diff --git a/src/Check/Cron_Duplicates.php b/src/Check/Cron_Duplicates.php
index b21eef5..0fec8e1 100644
--- a/src/Check/Cron_Duplicates.php
+++ b/src/Check/Cron_Duplicates.php
@@ -14,6 +14,9 @@ class Cron_Duplicates extends Cron {
 	 */
 	protected $threshold_count = 10;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$crons             = self::get_crons();
 		$job_counts        = array();
diff --git a/src/Check/File.php b/src/Check/File.php
index 2a25d99..2d9b95d 100644
--- a/src/Check/File.php
+++ b/src/Check/File.php
@@ -42,7 +42,7 @@ abstract class File extends Check {
 	/**
 	 * Any files matching the check.
 	 *
-	 * @var array
+	 * @var array<string|\SplFileInfo>
 	 */
 	protected $_matches = array();
 
@@ -63,6 +63,7 @@ public function get_options() {
 	 * Check a specific file.
 	 *
 	 * @param \SplFileInfo $file File to check.
+	 * @return void
 	 */
 	abstract public function check_file( \SplFileInfo $file );
 }
diff --git a/src/Check/File_Contents.php b/src/Check/File_Contents.php
index baa569b..20475c7 100644
--- a/src/Check/File_Contents.php
+++ b/src/Check/File_Contents.php
@@ -56,6 +56,10 @@ public function run() {
 		}
 	}
 
+	/**
+	 * @param SplFileInfo $file
+	 * @return void
+	 */
 	public function check_file( SplFileInfo $file ) {
 		if ( $file->isDir() || ! isset( $this->regex ) ) {
 			return;
diff --git a/src/Check/File_Type.php b/src/Check/File_Type.php
index d9e2a33..445c3d5 100644
--- a/src/Check/File_Type.php
+++ b/src/Check/File_Type.php
@@ -2,8 +2,6 @@
 
 namespace WP_CLI\Doctor\Check;
 
-use SplFileInfo;
-
 /**
  * Checks files on the filesystem to be of a certain type.
  */
@@ -32,7 +30,11 @@ public function run() {
 		}
 	}
 
-	public function check_file( SplFileInfo $file ) {
+	/**
+	 * @param \SplFileInfo $file
+	 * @return void
+	 */
+	public function check_file( \SplFileInfo $file ) {
 		if ( isset( $this->symlink ) ) {
 			if ( 'link' === $file->getType() && false === $this->symlink ) {
 				$this->_matches[] = $file;
diff --git a/src/Check/Network_Required_Plugins.php b/src/Check/Network_Required_Plugins.php
index 970bb90..a510bda 100644
--- a/src/Check/Network_Required_Plugins.php
+++ b/src/Check/Network_Required_Plugins.php
@@ -13,10 +13,13 @@ class Network_Required_Plugins extends Check {
 	/**
 	 * List of required plugin slugs.
 	 *
-	 * @var array
+	 * @var array<string>
 	 */
 	protected $plugins = array();
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
 
@@ -32,6 +35,9 @@ public function __construct( $options = array() ) {
 		}
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		if ( ! is_multisite() ) {
 			$this->set_status( 'success' );
@@ -80,10 +86,8 @@ public function run() {
 	}
 
 	/**
-	 * Resolve a plugin slug or file to an installed plugin file path.
-	 *
-	 * @param string $plugin_slug Requested plugin slug/file.
-	 * @param array  $installed_plugins Installed plugins keyed by plugin file.
+	 * @param string               $plugin_slug Requested plugin slug/file.
+	 * @param array<string, mixed> $installed_plugins Installed plugins keyed by plugin file.
 	 * @return string|null
 	 */
 	private function get_plugin_file( $plugin_slug, $installed_plugins ) {
diff --git a/src/Check/Network_Site_Count.php b/src/Check/Network_Site_Count.php
index f2359ef..721c498 100644
--- a/src/Check/Network_Site_Count.php
+++ b/src/Check/Network_Site_Count.php
@@ -24,6 +24,9 @@ class Network_Site_Count extends Check {
 	 */
 	protected $maximum = 500;
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
 
@@ -34,6 +37,9 @@ public function __construct( $options = array() ) {
 		}
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		if ( ! is_multisite() ) {
 			$this->set_status( 'success' );
diff --git a/src/Check/Network_Site_Option_Value.php b/src/Check/Network_Site_Option_Value.php
index 3b750b7..9a3780f 100644
--- a/src/Check/Network_Site_Option_Value.php
+++ b/src/Check/Network_Site_Option_Value.php
@@ -30,6 +30,9 @@ class Network_Site_Option_Value extends Check {
 	 */
 	protected $value_is_not;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		if ( ! is_multisite() ) {
 			$this->set_status( 'success' );
diff --git a/src/Check/Option_Value.php b/src/Check/Option_Value.php
index c8c269c..ef61396 100644
--- a/src/Check/Option_Value.php
+++ b/src/Check/Option_Value.php
@@ -30,6 +30,9 @@ class Option_Value extends Check {
 	 */
 	protected $value_is_not;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 
 		if ( isset( $this->value ) && isset( $this->value_is_not ) ) {
diff --git a/src/Check/PHP_In_Upload.php b/src/Check/PHP_In_Upload.php
index ae257d5..a011dd1 100644
--- a/src/Check/PHP_In_Upload.php
+++ b/src/Check/PHP_In_Upload.php
@@ -14,10 +14,13 @@ class PHP_In_Upload extends Check {
 	/**
 	 * Array containing list of files found in the uploads folder
 	 *
-	 * @var array
+	 * @var array<\SplFileInfo>
 	 */
 	protected $php_files_array = array();
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 
 		// Path to the uploads folder.
diff --git a/src/Check/Plugin.php b/src/Check/Plugin.php
index b759be9..a191d62 100644
--- a/src/Check/Plugin.php
+++ b/src/Check/Plugin.php
@@ -7,8 +7,14 @@
 
 abstract class Plugin extends Check {
 
+	/**
+	 * @var array<mixed>|null
+	 */
 	protected static $plugins;
 
+	/**
+	 * @return array<mixed>
+	 */
 	protected static function get_plugins() {
 
 		if ( isset( self::$plugins ) ) {
diff --git a/src/Check/Plugin_Active_Count.php b/src/Check/Plugin_Active_Count.php
index ea0e7c5..a26b7e5 100644
--- a/src/Check/Plugin_Active_Count.php
+++ b/src/Check/Plugin_Active_Count.php
@@ -14,6 +14,9 @@ class Plugin_Active_Count extends Plugin {
 	 */
 	protected $threshold_count = 80;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$active = 0;
 		foreach ( self::get_plugins() as $plugin ) {
diff --git a/src/Check/Plugin_Deactivated.php b/src/Check/Plugin_Deactivated.php
index b63c95d..2b82649 100644
--- a/src/Check/Plugin_Deactivated.php
+++ b/src/Check/Plugin_Deactivated.php
@@ -14,6 +14,9 @@ class Plugin_Deactivated extends Plugin {
 	 */
 	protected $threshold_percentage = 40;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$plugins = self::get_plugins();
 
diff --git a/src/Check/Plugin_Status.php b/src/Check/Plugin_Status.php
index 20e5fe0..1ac9756 100644
--- a/src/Check/Plugin_Status.php
+++ b/src/Check/Plugin_Status.php
@@ -27,6 +27,9 @@ class Plugin_Status extends Plugin {
 	 */
 	protected $status;
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		$valid_statuses = array( 'uninstalled', 'installed', 'active' );
 		if ( ! in_array( $options['status'], $valid_statuses, true ) ) {
@@ -35,6 +38,9 @@ public function __construct( $options = array() ) {
 		parent::__construct( $options );
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$plugins = self::get_plugins();
 
diff --git a/src/Check/Plugin_Update.php b/src/Check/Plugin_Update.php
index c37a277..b354f55 100644
--- a/src/Check/Plugin_Update.php
+++ b/src/Check/Plugin_Update.php
@@ -7,6 +7,9 @@
  */
 class Plugin_Update extends Plugin {
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$plugins      = self::get_plugins();
 		$update_count = 0;
diff --git a/src/Check/Theme_Update.php b/src/Check/Theme_Update.php
index dd3a679..6bc8c7f 100644
--- a/src/Check/Theme_Update.php
+++ b/src/Check/Theme_Update.php
@@ -10,6 +10,9 @@
  */
 class Theme_Update extends Check {
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		ob_start();
 		WP_CLI::run_command( array( 'theme', 'list' ), array( 'format' => 'json' ) );
diff --git a/src/Checks.php b/src/Checks.php
index 16131b1..e61b628 100644
--- a/src/Checks.php
+++ b/src/Checks.php
@@ -9,11 +9,24 @@
 
 class Checks {
 
+	/**
+	 * @var Checks|null
+	 */
 	private static $instance;
 
-	private $checks         = array();
+	/**
+	 * @var array<string, \WP_CLI\Doctor\Check>
+	 */
+	private $checks = array();
+
+	/**
+	 * @var array<string, array<string>>
+	 */
 	private $skipped_checks = array();
 
+	/**
+	 * @return Checks
+	 */
 	public static function get_instance() {
 		if ( ! isset( self::$instance ) ) {
 			self::$instance = new Checks();
@@ -25,6 +38,7 @@ public static function get_instance() {
 	 * Register checks from a config file
 	 *
 	 * @param string $file
+	 * @return void
 	 */
 	public static function register_config( $file ) {
 		if ( ! is_file( $file ) ) {
@@ -80,6 +94,7 @@ public static function register_config( $file ) {
 	 *
 	 * @param string        $name  Name for the check.
 	 * @param object|string $check Check class name or instance.
+	 * @return void
 	 */
 	public static function add_check( $name, $check ) {
 
@@ -103,8 +118,8 @@ public static function add_check( $name, $check ) {
 	/**
 	 * Get checks registered with the Doctor.
 	 *
-	 * @param array $args Filter checks based on some attribute.
-	 * @return array<string, Check>
+	 * @param array<string, mixed> $args Filter checks based on some attribute.
+	 * @return array<string, \WP_CLI\Doctor\Check>
 	 */
 	public static function get_checks( $args = array() ) {
 		if ( ! empty( $args['name'] ) ) {
@@ -125,6 +140,7 @@ public static function get_checks( $args = array() ) {
 	 *
 	 * @param string $path Path to file.
 	 * @param string $base Base path to prepend.
+	 * @return string
 	 */
 	private static function absolutize( $path, $base ) {
 		if ( ! empty( $path ) && ! Path::is_absolute( $path ) ) {
diff --git a/src/Command.php b/src/Command.php
index f2b1057..077a10a 100644
--- a/src/Command.php
+++ b/src/Command.php
@@ -108,6 +108,10 @@ class Command {
 	 *     +--------------------+--------+--------------------------------------------+
 	 *
 	 * @when before_wp_load
+	 *
+	 * @param array<string>        $args       Names of one or more checks to run.
+	 * @param array<string, mixed> $assoc_args Command options.
+	 * @return void
 	 */
 	public function check( $args, $assoc_args ) {
 
@@ -333,6 +337,10 @@ function ( $check ) {
 	 *
 	 * @when before_wp_load
 	 * @subcommand list
+	 *
+	 * @param array<string>        $args       Command arguments.
+	 * @param array<string, mixed> $assoc_args Command options.
+	 * @return void
 	 */
 	public function list_( $args, $assoc_args ) {
 
@@ -379,6 +387,8 @@ public function list_( $args, $assoc_args ) {
 
 	/**
 	 * Runs through the entirety of the WP bootstrap process
+	 *
+	 * @return void
 	 */
 	private function load_wordpress_with_template() {
 		global $wp_query;
@@ -446,6 +456,8 @@ private static function remove_decorations( $comment ) {
 
 	/**
 	 * Get the path to the default config file
+	 *
+	 * @return string
 	 */
 	private static function get_default_config() {
 		return dirname( __DIR__ ) . '/doctor.yml';