Remove ignores made stale by --fix-ignored for a list of files too

e2e/fix-ignored-entries/fix-ignored-entries_test.sh

@@ -30,3 +30,24 @@ function test_fix_ignored_entries() {
 	assert_contains 'Untouched.php:?:Ignored error pattern #^Stale$#' "$OUTPUT"
 	assert_not_contains 'src/In' "$OUTPUT"
 }
+
+function test_fix_ignored_entries_in_list_of_files() {
+	composer install
+	rm -rf src tmp && cp -r original src && cp baseline-original.php baseline.php && cp baseline-original.neon baseline.neon
+	# a list of files is a partial analysis, like a git hook that passes the changed files,
+	# the ignores in the files the first round changed are still fixed in the second round
+	OUTPUT=$(../../bin/phpstan analyse --fix-ignored src/InComment.php src/InNeonBaseline.php src/InPhpBaseline.php src/Untouched.php src/functions.php 2>&1) && CODE=0 || CODE=$?
+	assert_same "0" "$CODE"
+	echo "$OUTPUT"
+	assert_contains 'Round 1: fixed 5 errors in 3 files' "$OUTPUT"
+	assert_contains 'Round 2: fixed 3 errors in 3 files' "$OUTPUT"
+	assert_contains '[OK] 8 errors fixed in 5 files' "$OUTPUT"
+	for file in InComment.php InNeonBaseline.php InPhpBaseline.php; do diff -u expected/$file src/$file; done
+	diff -u expected/baseline.php baseline.php
+	diff -u expected/baseline.neon baseline.neon
+	OUTPUT=$(../../bin/phpstan analyse --error-format raw 2>&1) && CODE=0 || CODE=$?
+	assert_same "1" "$CODE"
+	echo "$OUTPUT"
+	assert_contains 'Untouched.php:?:Ignored error pattern #^Stale$#' "$OUTPUT"
+	assert_not_contains 'src/In' "$OUTPUT"
+}

src/Analyser/Ignore/IgnoredErrorHelperResult.php

@@ -7,8 +7,10 @@
 use PHPStan\File\FileHelper;
 use PHPStan\ShouldNotHappenException;
 use function array_fill_keys;
+use function array_flip;
 use function array_key_exists;
 use function array_keys;
+use function array_map;
 use function count;
 use function is_array;
 use function is_string;
@@ -91,12 +93,14 @@ private static function filterIgnoreErrorsByIdentifier(array $ignoreErrors, ?str
 	/**
 	 * @param list<Error> $errors
 	 * @param string[] $analysedFiles
+	 * @param string[] $filesChangedByFix Files changed by the previous rounds of --fix, their unmatched ignores are reported even for a list of files.
 	 */
 	public function process(
 		array $errors,
 		bool $onlyFiles,
 		array $analysedFiles,
 		bool $hasInternalErrors,
+		array $filesChangedByFix = [],
 	): IgnoredErrorHelperProcessedResult
 	{
 		$unmatchedIgnoredErrors = $this->ignoreErrors;
@@ -355,6 +359,7 @@ public function process(
 		}
 
 		$analysedFilesKeys = array_fill_keys($analysedFiles, true);
+		$filesChangedByFixKeys = array_flip(array_map(fn (string $file): string => $this->fileHelper->normalizePath($file), $filesChangedByFix));
 
 		if (!$hasInternalErrors) {
 			foreach ($unmatchedIgnoredErrors as $i => $unmatchedIgnoredError) {
@@ -396,7 +401,10 @@ public function process(
 						continue;
 					}
 
-					if ($onlyFiles) {
+					// an earlier round of --fix can leave an ignore in a file it changed unmatched, like the one
+					// that matched an error fixed by --fix-ignored, so it is reported for a list of files too
+					// and the next round removes it
+					if ($onlyFiles && !array_key_exists($unmatchedIgnoredError['realPath'], $filesChangedByFixKeys)) {
 						continue;
 					}
 

src/Command/AnalyseApplication.php

@@ -53,6 +53,7 @@ public function __construct(
 	/**
 	 * @param string[] $files
 	 * @param mixed[]|null $projectConfigArray
+	 * @param string[] $filesChangedByFix
 	 * @throws InceptionNotSuccessfulException
 	 */
 	public function analyse(
@@ -67,6 +68,7 @@ public function analyse(
 		?string $tmpFile,
 		?string $insteadOfFile,
 		InputInterface $input,
+		array $filesChangedByFix = [],
 	): AnalysisResult
 	{
 		$isResultCacheUsed = false;
@@ -167,7 +169,7 @@ public function analyse(
 			$workerCount = $analyserResult->getWorkerCount();
 			$isResultCacheUsed = !$resultCache->isFullAnalysis();
 
-			$ignoredErrorHelperProcessedResult = $ignoredErrorHelperResult->process($errors, $onlyFiles, $files, $hasInternalErrors);
+			$ignoredErrorHelperProcessedResult = $ignoredErrorHelperResult->process($errors, $onlyFiles, $files, $hasInternalErrors, $filesChangedByFix);
 			$fileSpecificErrors = $ignoredErrorHelperProcessedResult->getNotIgnoredErrors();
 			$notFileSpecificErrors = $ignoredErrorHelperProcessedResult->getOtherIgnoreMessages();
 			foreach ($ignoredErrorHelperProcessedResult->getIgnoredErrors() as [$ignoredError]) {

src/Command/AnalyseCommand.php

@@ -397,6 +397,9 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 			$inceptionResult->getErrorOutput()->writeLineFormatted('Analysing files...');
 		}
 
+		/** @var string[] $filesChangedByFix */
+		$filesChangedByFix = $input->getOption(self::OPTION_FIXED_IGNORED_IN);
+
 		try {
 			$analysisResult = $application->analyse(
 				$files,
@@ -410,6 +413,7 @@ protected function execute(InputInterface $input, OutputInterface $output): int
 				$inceptionResult->getEditorModeTmpFile(),
 				$inceptionResult->getEditorModeInsteadOfFile(),
 				$input,
+				$filesChangedByFix,
 			);
 		} catch (Throwable $t) {
 			if ($debug) {

tests/PHPStan/Analyser/AnalyserTest.php

@@ -657,6 +657,44 @@ public function testDoNotReportUnmatchedIgnoredErrorsFromPathWithCountIfPathWasN
 		$this->assertNoErrors($result);
 	}
 
+	/**
+	 * @return iterable<string, array{bool, list<string>, bool}>
+	 */
+	public static function dataReportUnmatchedIgnoredErrorFromPathInFileChangedByFix(): iterable
+	{
+		yield 'list of files' => [true, [], false];
+		yield 'list of files, file changed by an earlier fix round' => [true, [__DIR__ . '/data/empty/empty.php'], true];
+		yield 'list of files, file changed by an earlier fix round, path not normalized' => [true, [__DIR__ . '/data/empty/../empty/empty.php'], true];
+		yield 'list of files, another file changed by an earlier fix round' => [true, [__DIR__ . '/data/two-fails.php'], false];
+		yield 'full analysis' => [false, [], true];
+	}
+
+	/**
+	 * @param list<string> $filesChangedByFix
+	 */
+	#[DataProvider('dataReportUnmatchedIgnoredErrorFromPathInFileChangedByFix')]
+	public function testReportUnmatchedIgnoredErrorFromPathInFileChangedByFix(bool $onlyFiles, array $filesChangedByFix, bool $expectReported): void
+	{
+		$ignoreErrors = [
+			[
+				'message' => '#Fail\.#',
+				'path' => __DIR__ . '/data/empty/empty.php',
+			],
+		];
+		$result = $this->runAnalyser($ignoreErrors, true, __DIR__ . '/data/empty/empty.php', $onlyFiles, false, [], [], $filesChangedByFix);
+		if (!$expectReported) {
+			$this->assertNoErrors($result);
+			return;
+		}
+
+		$expectedPath = $this->getFileHelper()->normalizePath(__DIR__ . '/data/empty/empty.php');
+		$this->assertCount(1, $result);
+		$this->assertInstanceOf(Error::class, $result[0]);
+		$this->assertSame('Ignored error pattern #Fail\.# in path ' . $expectedPath . ' was not matched in reported errors.', $result[0]->getMessage());
+		$this->assertSame($expectedPath, $result[0]->getFilePath());
+		$this->assertSame('ignore.unmatched', $result[0]->getIdentifier());
+	}
+
 	public function testIgnoreNextLine(): void
 	{
 		$result = $this->runAnalyser([], false, [
@@ -851,6 +889,7 @@ public function testIgnoreErrorExplicitReportUnmatchedEnableMulti(): void
 	 * @param string|string[] $filePaths
 	 * @param list<Collector<Node, mixed>> $collectors
 	 * @param list<Rule<CollectedDataNode>> $collectedDataRules
+	 * @param list<string> $filesChangedByFix
 	 * @return string[]|Error[]
 	 */
 	private function runAnalyser(
@@ -861,6 +900,7 @@ private function runAnalyser(
 		bool $reportIgnoresWithoutComments = false,
 		array $collectors = [],
 		array $collectedDataRules = [],
+		array $filesChangedByFix = [],
 	): array
 	{
 		$analyser = $this->createAnalyser($reportIgnoresWithoutComments, $collectors);
@@ -901,7 +941,13 @@ private function runAnalyser(
 		);
 		$analyserResult = $finalizer->finalize($analyserResult, $onlyFiles, false)->getAnalyserResult();
 
-		$ignoredErrorHelperProcessedResult = $ignoredErrorHelperResult->process($analyserResult->getErrors(), $onlyFiles, $normalizedFilePaths, $analyserResult->hasReachedInternalErrorsCountLimit());
+		$ignoredErrorHelperProcessedResult = $ignoredErrorHelperResult->process(
+			$analyserResult->getErrors(),
+			$onlyFiles,
+			$normalizedFilePaths,
+			$analyserResult->hasReachedInternalErrorsCountLimit(),
+			$filesChangedByFix,
+		);
 		$errors = $ignoredErrorHelperProcessedResult->getNotIgnoredErrors();
 		$errors = array_merge($errors, $ignoredErrorHelperProcessedResult->getOtherIgnoreMessages());
 		if ($analyserResult->hasReachedInternalErrorsCountLimit()) {