I have integration tests set up. The install-wp-tests.sh is taken from the wpcli scaffold plugin tests. I'm on VVV and I have wordpress-develop set up.

In my plugin I have phpunit.integration.xml.dist

<?xml version="1.0" encoding="UTF-8"?>
<phpunit
  backupGlobals="false"
  backupStaticAttributes="false"
  bootstrap="tests/bootstrap-integration.php"
  colors="true"
  convertErrorsToExceptions="true"
  convertNoticesToExceptions="true"
  convertWarningsToExceptions="true"
  printerClass="Codedungeon\PHPUnitPrettyResultPrinter\Printer"
  stopOnError="false"
  stopOnFailure="false"
  stopOnIncomplete="false"
  stopOnSkipped="false"
  syntaxCheck="false"
  verbose="true"
  >
  <testsuites>
    <testsuite name="integration">
      <directory prefix="test-" suffix=".php">./tests/integration/</directory>
    </testsuite>
  </testsuites>
  <filter>
    <whitelist>
      <directory>./</directory>
      <exclude>
        <directory>./node_modules</directory>
        <directory>./vendor</directory>
        <directory>./tests</directory>
      </exclude>
    </whitelist>
  </filter>
  <logging>
    <log type="coverage-html" target="tests/_reports/coverage-integration" charset="UTF-8" yui="true" highlight="true" lowUpperBound="35" highLowerBound="80" />
    <log type="coverage-clover" target="tests/_reports/logs/clover-integration.xml"/>
    <log type="coverage-php" target="tests/_reports/logs/coverage-integration.cov"/>
    <log type="junit" target="tests/_reports/logs/logfile-integration.xml"/>
  </logging>
</phpunit>

In my composer.json I have (currently not using some of the packages like wp_mock and brainMonkey)

{
  "require-dev": {
    "10up/wp_mock": "^0.3.0",
    "brain/monkey": "^2.2",
    "codedungeon/phpunit-result-printer": "^0.20.1",
    "dealerdirect/phpcodesniffer-composer-installer": "^0.5",
    "infinum/coding-standards-wp": "*",
    "php-mock/php-mock-mockery": "^1.3",
    "phpunit/phpunit": "^6.5",
    "roave/security-advisories": "dev-master"
  },
  "autoload": {
    "classmap": [
      "src/",
      "views/",
      "tests/"
    ]
  },
  "config": {
    "sort-packages": true,
    "optimize-autoloader": true,
    "process-timeout": 2000
  },
  "scripts"    : {
    "check-cs": "@php ./vendor/bin/phpcs --extensions=php --ignore=/vendor/",
    "fix-cs": "@php ./vendor/bin/phpcbf --extensions=php --ignore=/vendor/",
    "punit": "@php ./vendor/bin/phpunit -c phpunit.xml.dist --no-coverage --colors=always",
    "punit-cov": "@php ./vendor/bin/phpunit -c phpunit.xml.dist --colors=always",
    "pint": "@php ./vendor/bin/phpunit -c phpunit.integration.xml.dist --no-coverage --colors=always",
    "pint-cov": "@php ./vendor/bin/phpunit -c phpunit.integration.xml.dist --colors=always"
  }
}

My boostrap-integration.php file looks like this:

<?php
/**
 * PHPUnit bootstrap file
 *
 * Integration tests bootstrap file.
 *
 * @package Developer_Portal
 */

$_tests_dir = getenv( 'WP_TESTS_DIR' );

if ( ! $_tests_dir ) {
  $_tests_dir = rtrim( sys_get_temp_dir(), '/\\' ) . '/wordpress-tests-lib';
}

if ( ! file_exists( $_tests_dir . 'includes/functions.php' ) ) {
  echo "Could not find {$_tests_dir}includes/functions.php, have you run bin/install-wp-tests.sh ?" . PHP_EOL; // WPCS: XSS ok.
  exit( 1 );
}

// Give access to tests_add_filter() function.
require_once $_tests_dir . '/includes/functions.php';

/**
 * Manually load the plugin being tested.
 */
function _manually_load_plugin() {
  require dirname( __FILE__, 3 ) . '/advanced-custom-fields-pro/acf.php';
  require dirname( __FILE__, 2 ) . '/my-plugin.php';

  $plugins_to_activate = [
    'advanced-custom-fields-pro/acf.php',
    'my-plugin/my-plugin.php',
  ];

  update_option( 'active_plugins', $plugins_to_activate );
}

tests_add_filter( 'plugins_loaded', '_manually_load_plugin' );

// Start up the WP testing environment.
require $_tests_dir . '/includes/bootstrap.php';

Here I've replaced the default (which I've also tested with)

/**
 * Manually load the plugin being tested.
 */
function _manually_load_plugin() {
  require dirname( __FILE__, 3 ) . '/advanced-custom-fields-pro/acf.php';
  require dirname( __FILE__, 2 ) . '/my-plugin.php';
}

tests_add_filter( 'muplugins_loaded', '_manually_load_plugin' );

My test looks like this

<?php
/**
 * Class Admin Menu tests
 *
 * @package My_Plugin\Tests\Integration\Src\Admin_Menus
 */

use My_Plugin\Admin_Menus\Credentials;
use My_Plugin\Core\Service;

/**
 * Class that tests the admin menu.
 *
 * @runTestsInSeparateProcesses
 * @preserveGlobalState disabled
 */
class Credentials_Menu_Integration_Test extends WP_UnitTestCase {

  /**
   * Test suite setUp method
   */
  public function setUp() {
    parent::setUp();
    // This is needed to create a user. Internal implementation.
    $_REQUEST['_wpnonce_create-user'] = wp_create_nonce( 'create-user' );

    wp_set_current_user(
      self::factory()->user->create(
        [
          'role' => 'administrator',
        ]
      )
    );
  }

  /**
   * Test default template name
   */
  public function test_apigee_menu_render() {
    $cred_menu = new Credentials();
    $cred_menu->register();
    $cred_menu->process_admin_menu( [] );
    $cred_menu->render();

    $this->assertInstanceOf( 'My_Plugin\Core\Service', $cred_menu );
    $this->assertNotEmpty( menu_page_url( Credentials::MENU_SLUG ) );
  }

}

The code works when I look at the WordPress page. I can see the credentials menu and all, but this

$this->assertNotEmpty( menu_page_url( Credentials::MENU_SLUG ) );

fails.

It looks like in the tests the plugins are not active at all. The instance of test passes, the coverage shows that the public methods are passed during testing.

I just don't know what to think of this. The plugin files are required in the bootstrap, but it's like when I do integration tests the plugins are not actually loaded/activated in the test WordPress.

EDIT

The entire test suite is working. I just created tests that extended WP_Ajax_UnitTestCase and I successfully tested my AJAX callback methods...

I'm not sure I understand why the above happens still.