WordPress Plugin: Loops through all users on your site, spread out throughout the day for efficiency. Provides a hook to do any sort of maintenance on those users. Does not actually modify any users, this just an API of sorts.

aa-process-all-users-once-daily.php

<?php
/*
Plugin Name: RS Process Users Daily
Description: Provides an API action for developers which iterates all users once per day, based on cofigurable settings.  Usage: <code class="code">add_action( 'aa_process_all_users_daily/user', 'example_process_user' );</code>
Author: Radley Sustaire
Version: 1.1.0
*/

/*
// EXAMPLE
// Add an action that will process a single user. Will be called numerous times throughout the day until all users have been processed.
function example_process_user( WP_User $user ) {
	$checked_count = (int) get_user_meta( $user->ID, 'checked_count', true );
	$checked_count += 1;

	update_user_meta( $user->ID, 'checked_count', $checked_count );
}
add_action( 'aa_process_all_users_daily/user', 'example_process_user' );

// When all users are done for one iteration
add_action( 'aa_process_all_users_daily/iteration_complete', 'something' );

// When an entire batch is completed
add_action( 'aa_process_all_users_daily/restart_batch', 'something' );
*/

class AA_Process_All_Users_Daily {
	
	// Interval settings
	// The more frequent these schedules, the fewer users need to be queried at a time.
	public $schedule = array(
		'interval' => 5 * MINUTE_IN_SECONDS,
		'key' => '5min',
		'label' => '5 Minutes',
	);
	
	public function __construct() {
		
		// Start and stop cron schedule when plugin is enabled or disabled
		register_activation_hook( __FILE__, array( $this, 'start_cron' ) );
		register_deactivation_hook( __FILE__, array( $this, 'clear_cron' ) );
		
		// Add a 5 minute cron schedule
		add_filter( 'cron_schedules', array( $this, 'add_custom_schedule' ) );
		
		// Run the process on normal cron schedule
		add_action( 'aa_process_all_users_daily/schedule', array( $this, 'process_users' ) );
		
		// Run manually with: ?process_all_users_daily=1
		// Start over with:   ?process_all_users_daily=1&start_over=1
		if ( !empty($_GET['process_all_users_daily']) ) {
			add_action( 'init', array( $this, 'process_manually' ) );
		}
		
	}
	
	/**
	 * Returns total number of users from the wp_users table
	 *
	 * @return int
	 */
	public function get_total_users() {
		global $wpdb;
		
		$sql = "SELECT COUNT(*) FROM {$wpdb->users};";
		
		return (int) $wpdb->get_var( $sql );
	}
	
	
	/**
	 * Save details from the last batch process in the options, and optionally send an email.
	 *
	 * @param $debug
	 */
	public function maybe_stash_last_batch( $debug ) {
		// Get the previous process
		$last_process = get_option( 'aapaud-batch-settings' );
		if ( empty($last_process) ) return;
		
		$started = $last_process['start_time'];
		$ended = time();
		$user_index = (int) get_option( 'aapaud-user-index' );
		
		$last_batch = array(
			'started' => $started,
			'ended' => $ended,
			'time_diff' => $started ? human_time_diff( $started, $ended ) : "N/A first run",
			'users_processed' => $user_index,
		);
		
		// save the details of the last batch
		update_option( 'aapaud-last-batch', $last_batch, false );
	}
	
	/**
	 * Setup the process to start from the beginning. If a previous batch was in progress, save some information from that batch for review and debugging.
	 *
	 * @param $debug
	 */
	public function restart_process( $debug ) {
		
		// Check if we should start a new batch now (option may be 0 first run, that's ok)
		$next_batch_time = (int) get_option( 'aapaud-next-batch-time' );
		
		if ( $next_batch_time > time() ) {
			// Do not restart the process now, wait until next batch time has been reached.
			if ( $debug ) {
				echo 'Batch complete, will start next day\'s batch in '. human_time_diff( $next_batch_time, time() )  .'.<br><br>Last batch:<br>';
				echo '<pre>';
				var_dump(get_option('aapaud-last-batch'));
				echo '</pre>';
				exit;
			}
			return;
		}
		
		// Store details from the last batch before we reset all the settings.
		$this->maybe_stash_last_batch( $debug );
		
		// Clear previous settings
		delete_option( 'aapaud-batch-settings' );
		
		// Let plugins know a new batch is starting now
		do_action( 'aa_process_all_users_daily/restart_batch' );
		
		// Get the total number of users at this time.
		$total_users = $this->get_total_users();
		
		// How many queries will occur per day? Based on schedule interval (in seconds). Final values might look like:
		// 5min = 288
		// hourly = 24
		// twicedaily = 2
		// daily = 1
		$queries_per_day = ceil(DAY_IN_SECONDS / $this->schedule['interval']);
		
		// How many users should we get per query?
		$users_per_query = ceil( $total_users / $queries_per_day );
		
		// Save the settings, these will be used until the end of the entire batch.
		$settings = array(
			'total_users' => $total_users,
			'users_per_query' => $users_per_query,
			'start_time' => time(),
		);
		
		update_option( 'aapaud-batch-settings', $settings, false );
		
		// reset user index
		update_option( 'aapaud-user-index', 0, false );
		
		// Save when the next batch is allowed to start (so we do not process too often)
		update_option( 'aapaud-next-batch-time', strtotime('+24 hours'), false );
		
		if ( $debug ) {
			echo 'Batch complete. Ready to start a new batch, refresh the page to continue.<br><br>Last batch:<br>';
			echo '<pre>';
			var_dump(get_option('aapaud-last-batch'));
			echo '</pre>';
			exit;
		}
	}
	
	/**
	 * Check expiration date for a set of users.
	 *
	 * @param bool $debug
	 */
	public function process_users( $debug = false ) {
		// pluggable.php is required for get_user_count to work during cron
		if ( !function_exists('wp_get_current_user')) {
			include_once(ABSPATH . "wp-includes/pluggable.php");
		}
		
		// Get settings that we previously calculated
		$settings = get_option( 'aapaud-batch-settings' );
		
		if ( empty($settings['start_time']) ) {
			// First run, or settings got reset
			$this->restart_process( $debug );
			return;
		}else{
			// Allow admins to manually restart a batch
			if ( !empty($_GET['start_over']) && current_user_can('administrator') ) {
				$this->restart_process( $debug );
				return;
			}
		}
		
		// Total users (at start of batch)
		$total_users = $settings['total_users'];
		
		// How many users to get per query
		$users_per_query = $settings['users_per_query'];
		
		// Get the user index -- our progress in the batch. An index of 15 means that we start with the 16th user, and get $users_per_query more
		$user_index = (int) get_option( 'aapaud-user-index' );
		if ( !$user_index ) $user_index = 0;
		
		// start over if the user index exceeds the total number of users
		if ( $user_index > $total_users ) {
			$this->restart_process( $debug );
			return;
		}
		
		// Get users
		$args = array(
			// how many
			'number' => $users_per_query,
			
			// starting at
			'offset' => $user_index,
			
			// order by id. this means new users don't cause repeats
			'orderby' => 'ID',
			'order' => 'ASC',
		);
		
		$users = new WP_User_Query( $args );
		
		// if no users were returned, restart and skip the rest of this query
		if ( empty($users->get_results()) ) {
			$this->restart_process( $debug );
			return;
		}
		
		// loop through found users
		foreach( $users->get_results() as $user ) {
			
			/**
			 * Hook into this action to process a single user. Will be called multiple times in one PHP session.
			 *
			 * @hook "aa_process_all_users_daily/user"
			 * @param WP_User $user
			 * @param int     $user_index
			 * @param array   $settings
			 */
			do_action( 'aa_process_all_users_daily/user', $user, $user_index, $settings );
			
			// increase the user index
			$user_index++;
		}
		
		// When complete
		do_action( 'aa_process_all_users_daily/iteration_complete', $user_index, $settings );
		
		// save the user index so we can continue from where we left off next cron event
		update_option( 'aapaud-user-index', $user_index, false );
		
		// echo debugging stuff
		if ( $debug ) {
			ob_start();
			echo '<pre>';
			
			echo '$total_users: ', $total_users, '<br>';
			echo '$users_per_query: ', $users_per_query, '<br>';
			echo '$user_index: ', $user_index, '<br>';
			echo '% progress: ', round(100 * ($user_index / $total_users), 2), '%<br>';
			
			echo '$args: <br>';
			var_dump($args);
			
			echo '$users this query: ', count($users->get_results()), '<br>';
			
			echo '$users: <br>';
			
			foreach( $users->get_results() as $u ) {
				if ( !$u instanceof  WP_User ) continue;
				echo "\t", $u->get('display_name'), ' (#', $u->get('ID'), ')<br>';
			}
			
			echo 'this batch duration: <br>';
			var_dump( human_time_diff( $settings['start_time'], time() ) );
			
			echo 'last batch: <br>';
			var_dump( get_option('aapaud-last-batch') );
			
			echo '</pre>';
			exit;
		}
	}
	
	// Allow to run manually in the browser with debug info
	// Run manually with: ?process_all_users_daily=1
	// Start over with:   ?process_all_users_daily=1&start_over=1
	public function process_manually() {
		if ( current_user_can('administrator') ) {
			$this->process_users( true ); // true = debug mode
		}else{
			echo 'You must be an administrator to process all users manually.';
			exit;
		}
	}
	
	// Schedule a wp_cron event
	public function start_cron() {
		if ( !wp_next_scheduled ( 'aa_process_all_users_daily/schedule' ) ) {
			wp_schedule_event(time(), $this->schedule['key'], 'aa_process_all_users_daily/schedule');
		}
	}
	
	// Clear the scheduled event
	public function clear_cron() {
		wp_clear_scheduled_hook( 'aa_process_all_users_daily/schedule' );
	}
	
	// Add a custom cron event schedule
	public function add_custom_schedule( $schedules ) {
		$schedules[ $this->schedule['key'] ] = array(
			'interval' => $this->schedule['interval'],
			'display' => __( $this->schedule['label'] )
		);
		
		return $schedules;
	}
	
}

global $AA_Process_All_Users_Daily;

$AA_Process_All_Users_Daily = new AA_Process_All_Users_Daily();