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Caveats

Mutations must occur when CodeCoverage has already started

It may happen that a mutation that fails a test isn’t reported as covered.
This can occur when the code-coverage profiler hasn’t started before the mutations occurs.
Take for example:

class SourceClassTest extends \PHPUnit\Framework\TestCase
{
 /**
 * @dataProvider instancesProvider
 */
 public function testAlwaysTrueFromFactoryMethod(SourceClass $class): void
{
 self::assertTrue($class->getValue());
 }

 public function instancesProvider(): array
{
 return [
 [SourceClass::factoryMethod()],
 ];
 }
}

class SourceClass
{
 private bool $value;

 private function __construct(bool $value)
{
 $this->value = $value;
 }

 public static function factoryMethod(): self
{
 return new self(true);
 }

 public function getValue(): bool
{
 return $this->value;
 }
}

If the TrueValue Boolean Substitution mutator is active, you
would expect the mutation to be correctly covered. But in the provided example the mutation
occurs in the @dataProvider which runs before the code-coverage driver gets started.

Be sure to check your mutated code runs inside the test in this case, so a workaround can be the following:

class SourceClassTest extends \PHPUnit\Framework\TestCase
{
 /**
 * @dataProvider instanceFactoriesProvider
 */
 public function testAlwaysTrueFromFactoryMethod(callable $classFactory): void
{
 $class = $classFactory();
 self::assertTrue($class->getValue());
 }

 public function instanceFactoriesProvider(): array
{
 return [
 [static function() {
 return SourceClass::factoryMethod();
 }],
 ];
 }
}

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Caveats

Mutations must occur when CodeCoverage has already started