payment_configuration.php

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<?php
use Magento\Config\Model\Config;
use Magento\Framework\App\Config\ScopeConfigInterface;
use Magento\Framework\Encryption\EncryptorInterface;
use Magento\Store\Model\ScopeInterface;
use Magento\TestFramework\Helper\Bootstrap;

$objectManager = Bootstrap::getObjectManager();

$encryptor = $objectManager->get(EncryptorInterface::class);

$processConfigData = function (Config $config, array $data) {
    foreach ($data as $key => $value) {
        $config->setDataByPath($key, $value);
        $config->save();
    }
};

// save payment configuration for the default scope
$configData = [
    'payment/braintree/merchant_id' => 'def_merchant_id',
    'payment/braintree/public_key' => $encryptor->encrypt('def_public_key'),
    'payment/braintree/private_key' => $encryptor->encrypt('def_private_key'),
];
$defConfig = $objectManager->create(Config::class);
$defConfig->setScope(ScopeConfigInterface::SCOPE_TYPE_DEFAULT);
$processConfigData($defConfig, $configData);

// save payment configuration per store
require __DIR__ . '/../../Store/_files/store.php';
$storeConfigData = [
    'payment/braintree/merchant_id' => 'store_merchant_id',
    'payment/braintree/public_key' => $encryptor->encrypt('store_public_key'),
];
$storeConfig = $objectManager->create(Config::class);
$storeConfig->setScope(ScopeInterface::SCOPE_STORES);
$storeConfig->setStore('test');
$processConfigData($storeConfig, $storeConfigData);

// save payment website config data
require __DIR__ . '/../../Store/_files/second_website_with_two_stores.php';
$websiteConfigData = [
    'payment/braintree/merchant_id' => 'website_merchant_id',
    'payment/braintree/private_key' => $encryptor->encrypt('website_private_key'),
];
$websiteConfig = $objectManager->create(Config::class);
$websiteConfig->setScope(ScopeInterface::SCOPE_WEBSITES);
$websiteConfig->setWebsite($websiteId);
$processConfigData($websiteConfig, $websiteConfigData);