re-adds back covered_only

src/Contracts/Configuration.php

@@ -30,6 +30,8 @@ public function min(float $minScore, ?bool $failOnZeroMutations = null): self;
 
     public function ignoreMinScoreOnZeroMutations(bool $ignore = true): self;
 
+    public function coveredOnly(bool $coveredOnly = true): self;
+
     public function parallel(bool $parallel = true): self;
 
     public function processes(?int $processes = null): self;

src/Options/CoveredOnlyOption.php

@@ -0,0 +1,28 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Pest\Mutate\Options;
+
+use Symfony\Component\Console\Input\InputOption;
+
+class CoveredOnlyOption
+{
+    final public const ARGUMENT = 'covered-only';
+
+    public static function remove(): bool
+    {
+        return true;
+    }
+
+    public static function match(string $argument): bool
+    {
+        return $argument === sprintf('--%s', self::ARGUMENT) ||
+            str_starts_with($argument, sprintf('--%s=', self::ARGUMENT));
+    }
+
+    public static function inputOption(): InputOption
+    {
+        return new InputOption(sprintf('--%s', self::ARGUMENT), null, InputOption::VALUE_OPTIONAL, '');
+    }
+}

src/Repositories/ConfigurationRepository.php

@@ -94,7 +94,7 @@ public function mergedConfiguration(): Configuration
         }
 
         return $this->mergedConfiguration = new Configuration(
-            coveredOnly: true,
+            coveredOnly: $config['covered_only'] ?? false,
             paths: $config['paths'] ?? $this->pathsFromPhpunitConfiguration(),
             pathsToIgnore: $config['paths_to_ignore'] ?? [],
             mutators: array_diff($config['mutators'] ?? DefaultSet::mutators(), $config['excluded_mutators'] ?? []),

src/Support/Configuration/AbstractConfiguration.php

@@ -16,6 +16,11 @@ abstract class AbstractConfiguration implements ConfigurationContract
      */
     private ?array $paths = null;
 
+    /**
+     * @var bool
+     */
+    private ?bool $coveredOnly = null;
+
     /**
      * @var string[]|null
      */
@@ -114,6 +119,13 @@ public function ignoreMinScoreOnZeroMutations(bool $ignore = true): self
         return $this;
     }
 
+    public function coveredOnly(bool $coveredOnly = true): self
+    {
+        $this->coveredOnly = $coveredOnly;
+
+        return $this;
+    }
+
     public function parallel(bool $parallel = true): self
     {
         $this->parallel = $parallel;
@@ -185,11 +197,12 @@ public function everything(): self
     }
 
     /**
-     * @return array{paths?: string[], paths_to_ignore?: string[], mutators?: class-string<Mutator>[], excluded_mutators?: class-string<Mutator>[], classes?: string[], parallel?: bool, processes?: int, profile?: bool, min_score?: float, ignore_min_score_on_zero_mutations?: bool, covered_only?: bool, stop_on_untested?: bool, stop_on_uncovered?: bool, mutation_id?: string, retry?: bool, everything?: bool}
+     * @return array{covered_only?: bool, paths?: string[], paths_to_ignore?: string[], mutators?: class-string<Mutator>[], excluded_mutators?: class-string<Mutator>[], classes?: string[], parallel?: bool, processes?: int, profile?: bool, min_score?: float, ignore_min_score_on_zero_mutations?: bool, covered_only?: bool, stop_on_untested?: bool, stop_on_uncovered?: bool, mutation_id?: string, retry?: bool, everything?: bool}
      */
     public function toArray(): array
     {
         return array_filter([
+            'covered_only' => $this->coveredOnly,
             'paths' => $this->paths,
             'paths_to_ignore' => $this->pathsToIgnore,
             'mutators' => $this->mutators !== null ? array_values(array_diff($this->mutators, $this->excludedMutators ?? [])) : null,

src/Support/Configuration/CliConfiguration.php

@@ -8,6 +8,7 @@
 use Pest\Mutate\Options\BailOption;
 use Pest\Mutate\Options\ClassOption;
 use Pest\Mutate\Options\ClearCacheOption;
+use Pest\Mutate\Options\CoveredOnlyOption;
 use Pest\Mutate\Options\EverythingOption;
 use Pest\Mutate\Options\ExceptOption;
 use Pest\Mutate\Options\IgnoreMinScoreOnZeroMutationsOption;
@@ -51,6 +52,7 @@ class CliConfiguration extends AbstractConfiguration
         NoCacheOption::class,
         ClearCacheOption::class,
         EverythingOption::class,
+        CoveredOnlyOption::class,
     ];
 
     /**
@@ -94,6 +96,10 @@ public function fromArguments(array $arguments): array
             $this->except(explode(',', (string) $input->getOption(ExceptOption::ARGUMENT))); // @phpstan-ignore-line
         }
 
+        if ($input->hasOption(CoveredOnlyOption::ARGUMENT)) {
+            $this->coveredOnly($input->getOption(CoveredOnlyOption::ARGUMENT) !== 'false');
+        }
+
         if ($input->hasOption(MinScoreOption::ARGUMENT)) {
             $this->min((float) $input->getOption(MinScoreOption::ARGUMENT)); // @phpstan-ignore-line
         }

tests/Features/Profiles/HandlesCliProfileConfigurationTest.php

@@ -39,6 +39,24 @@
         ->paths_to_ignore->toEqual(['src/path-1', 'src/path-2']);
 });
 
+it('enables covered only option if --covered-only argument is passed', function (): void {
+    $this->configuration->fromArguments(['--mutate='.ConfigurationRepository::FAKE]);
+    expect($this->configuration->toArray())
+        ->covered_only->toBeNull();
+
+    $this->configuration->fromArguments(['--covered-only']);
+    expect($this->configuration->toArray())
+        ->covered_only->toBeTrue();
+
+    $this->configuration->fromArguments(['--covered-only=true']);
+    expect($this->configuration->toArray())
+        ->covered_only->toBeTrue();
+
+    $this->configuration->fromArguments(['--covered-only=false']);
+    expect($this->configuration->toArray())
+        ->covered_only->toBeFalse();
+});
+
 it('sets the mutators if --mutators argument is passed', function (): void {
     $this->configuration->fromArguments(['--mutator=SetArithmetic']);
     expect($this->configuration->toArray())