partial_invoice.php

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<?php
declare(strict_types=1);

use Magento\Sales\Api\InvoiceRepositoryInterface;
use Magento\Sales\Api\TransactionRepositoryInterface;
use Magento\Sales\Model\Order;
use Magento\Sales\Model\Service\InvoiceService;
use Magento\TestFramework\ObjectManager;

require __DIR__ . '/order.php';

$objectManager = ObjectManager::getInstance();

$invoiceService = $objectManager->get(InvoiceService::class);
$invoice = $invoiceService->prepareInvoice($order);
$invoice->setIncrementId('100000002');
$invoice->register();

$items = $invoice->getAllItems();
$item = array_pop($items);
$item->setQty(1);
$invoice->setTotalQty(1);

$items = $order->getAllItems();
$item = array_pop($items);
$item->setQtyInvoiced(1);
$invoice->collectTotals();

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

$transactionRepository = $objectManager->get(TransactionRepositoryInterface::class);
$transaction = $transactionRepository->create();
$transaction->setTxnType('capture');
$transaction->setPaymentId($order->getPayment()->getEntityId());
$transaction->setOrderId($order->getEntityId());
$transactionRepository->save($transaction);