invoice_with_bundle.php

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<?php
declare(strict_types=1);

use Magento\Sales\Api\InvoiceItemRepositoryInterface;
use Magento\Sales\Api\InvoiceRepositoryInterface;
use Magento\Sales\Model\Order\Invoice\ItemFactory;
use Magento\Sales\Model\Service\InvoiceService;
use Magento\TestFramework\ObjectManager;

require 'order_with_bundle_and_invoiced.php';
$objectManager = ObjectManager::getInstance();

$invoiceService = $objectManager->get(InvoiceService::class);
$invoice = $invoiceService->prepareInvoice($order);
$invoice->setIncrementId('100000001');
$invoice->register();

$invoiceRepository = $objectManager->get(InvoiceRepositoryInterface::class);
$invoice = $invoiceRepository->save($invoice);

$itemFactory = $objectManager->get(ItemFactory::class);
$itemRepository = $objectManager->get(InvoiceItemRepositoryInterface::class);

foreach ($order->getAllItems() as $item) {
    $invoiceItem = $itemFactory->create(['data' => $item->getData()]);
    $invoiceItem->setId(null)
        ->setInvoice($invoice)
        ->setOrderItem($item)
        ->setQty($item->getQtyInvoiced());
    $itemRepository->save($invoiceItem);
}