From d73d05e5e0b428939880fcca16a9e267d8c70fbc Mon Sep 17 00:00:00 2001
From: Andre Wachsmuth <awa@xima.de>
Date: Tue, 9 Jan 2024 21:52:42 +0100
Subject: [PATCH 1/4] Fixes #1987, no empty files with biome when formatting
 ignored files

The issue happens only with the latest release 1.5.0.

* When the biome output is empty, the contents of the input file to format are used unchanged instead.
* When biome outputs warnings / errors to stderr, these are now logged. This includes warnings such as
  when biome ignores files. Otherwise people would be left wondering why certain files are not formatted.

I also added a test for this scenarion.

On another note, I mostly use Maven, so I always need to look up how to run tests via Gradle. I added
a short section to CONTRIBUTING.md that gives some example commands how to run tests for this project,
especially how to run only a single test.
---
 CHANGES.md                                    |  2 ++
 CONTRIBUTING.md                               | 20 +++++++++++++
 .../com/diffplug/spotless/rome/RomeStep.java  | 18 ++++++++++--
 plugin-gradle/README.md                       | 23 +++++++++++----
 .../gradle/spotless/BiomeIntegrationTest.java | 28 +++++++++++++++++++
 plugin-maven/README.md                        | 20 ++++++++++---
 .../spotless/maven/biome/BiomeMavenTest.java  | 16 +++++++++++
 .../main/resources/biome/json/package.json    |  3 ++
 .../resources/biome/json/packageAfter.json    |  3 ++
 .../resources/biome/json/packageBefore.json   |  3 ++
 .../diffplug/spotless/rome/RomeStepTest.java  | 13 +++++++++
 11 files changed, 138 insertions(+), 11 deletions(-)
 create mode 100644 testlib/src/main/resources/biome/json/package.json
 create mode 100644 testlib/src/main/resources/biome/json/packageAfter.json
 create mode 100644 testlib/src/main/resources/biome/json/packageBefore.json

diff --git a/CHANGES.md b/CHANGES.md
index dc040c9aa2..23f58ea9d1 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -12,6 +12,8 @@ We adhere to the [keepachangelog](https://keepachangelog.com/en/1.0.0/) format (
 ## [Unreleased]
 ### Added
 * New static method to `DiffMessageFormatter` which allows to retrieve diffs with their line numbers ([#1960](https://github.com/diffplug/spotless/issues/1960))
+### Fixed
+* Fix empty files with biome >= 1.5.0 when formatting files that are in the ignore list of the biome configuration file. (fixes [#1987](https://github.com/diffplug/spotless/issues/1987))
 ### Changes
 * Use palantir-java-format 2.39.0 on Java 21. ([#1948](https://github.com/diffplug/spotless/pull/1948))
 
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 287d835bca..6fb993f419 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -151,6 +151,26 @@ The gist of it is that you will have to:
 
 If you get something running, we'd love to host your plugin within this repo as a peer to `plugin-gradle` and `plugin-maven`.
 
+## Run tests
+
+To run all tests, simply do
+
+> gradlew test
+
+Since that takes some time, you might only want to run the tests
+concerning what you are working on:
+
+```shell
+# Run only from test from the "lib" project
+gradlew :testlib:test --tests com.diffplug.spotless.generic.IndentStepTest
+
+# Run only one test from the "plugin-maven" project
+gradlew :plugin-maven:test --tests com.diffplug.spotless.maven.pom.SortPomMavenTest
+
+# Run only one test from the "plugin-gradle" project
+gradlew :plugin-gradle:test --tests com.diffplug.gradle.spotless.FreshMarkExtensionTest
+```
+
 ## Integration testing
 
 ### Gradle - locally
diff --git a/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java b/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
index 5ba33d593d..92a0fdc689 100644
--- a/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
+++ b/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
@@ -427,9 +427,23 @@ private String format(ProcessRunner runner, String input, File file) throws IOEx
 			var stdin = input.getBytes(StandardCharsets.UTF_8);
 			var args = buildBiomeCommand(file);
 			if (logger.isDebugEnabled()) {
-				logger.debug("Running Biome comand to format code: '{}'", String.join(", ", args));
+				logger.debug("Running Biome command to format code: '{}'", String.join(", ", args));
+			}
+			var runnerResult = runner.exec(stdin, args);
+			var stdErr = runnerResult.stdErrUtf8();
+			if (stdErr != null && !stdErr.isEmpty()) {
+				logger.warn("Biome stderr ouptut for file '{}'\n{}", file, stdErr.trim());
+			}
+			var formatted = runnerResult.assertExitZero(StandardCharsets.UTF_8);
+			// When biome encounters an ignored file, it does not output any formatted code
+			// Ignored files come from (a) the biome.json configuration file and (b) from
+			// a list of hard-coded file names, such as package.json or tsconfig.json.
+			if (formatted == null || formatted.isEmpty()) {
+				return input;
+			}
+			else {
+				return formatted;
 			}
-			return runner.exec(stdin, args).assertExitZero(StandardCharsets.UTF_8);
 		}
 
 		/**
diff --git a/plugin-gradle/README.md b/plugin-gradle/README.md
index 7ad010567a..98416cdd05 100644
--- a/plugin-gradle/README.md
+++ b/plugin-gradle/README.md
@@ -1218,11 +1218,6 @@ spotless {
 }
 ```
 
-**Limitations:**
-
-- The auto-discovery of config files (up the file tree) will not work when using
-  Biome within spotless.
-
 To apply Biome to more kinds of files with a different configuration, just add
 more formats:
 
@@ -1243,6 +1238,24 @@ spotless {
 }
 ```
 
+**Limitations:**
+
+- The auto-discovery of config files (up the file tree) will not work when using
+  Biome within spotless.
+- The `ignore` option of the `biome.json` configuration file will not be applied.
+  Include and exclude patterns are configured in the spotless configuration in the
+  Gradle settings file instead.
+
+Note: Due to a limitation of biome, if the name of a file matches a pattern in
+the `ignore` option of the specified `biome.json` configuration file, it will not be
+formatted, even if included in the biome configuration section of the Gradle settings
+file.
+You could specify a different `biome.json` configuration file without an `ignore`
+pattern to circumvent this.
+
+Note 2: Biome is hard-coded to ignore certain special files, such as `package.json`
+or `tsconfig.json`. These files will never be formatted.
+
 ### Biome binary
 
 To format with Biome, spotless needs to find the Biome binary. By default,
diff --git a/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java b/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java
index a2665a3bf1..139d477bf0 100644
--- a/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java
+++ b/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java
@@ -340,4 +340,32 @@ void failureWhenNotParseable() throws Exception {
 		assertThat(spotlessApply.getOutput()).contains("Format with errors is disabled.");
 		assertThat(spotlessApply.getOutput()).contains("Step 'biome' found problem in 'biome_test.js'");
 	}
+
+	/**
+	 * Biome is hard-coded to ignore certain files, such as package.json. Since version 1.5.0,
+	 * the biome CLI does not output any formatted code anymore, whereas previously it printed
+	 * the input as-is. This tests checks that when the biome formatter outputs an empty string,
+	 * the contents of the file to format are used instead.
+	 *
+	 * @throws Exception When a test failure occurs.
+	 */
+	@Test
+	void preservesIgnoredFiles() throws Exception {
+		setFile("build.gradle").toLines(
+			"plugins {",
+			"    id 'com.diffplug.spotless'",
+			"}",
+			"repositories { mavenCentral() }",
+			"spotless {",
+			"    json {",
+			"        target '**/*.json'",
+			"        biome('1.5.0')",
+			"    }",
+			"}");
+		setFile("package.json").toResource("biome/json/packageBefore.json");
+
+		var spotlessApply = gradleRunner().withArguments("--stacktrace", "spotlessApply").build();
+		assertThat(spotlessApply.getOutput()).contains("BUILD SUCCESSFUL");
+		assertFile("package.json").sameAsResource("biome/json/packageAfter.json");
+	}
 }
diff --git a/plugin-maven/README.md b/plugin-maven/README.md
index f632d78ea7..593368c7ac 100644
--- a/plugin-maven/README.md
+++ b/plugin-maven/README.md
@@ -1300,10 +1300,6 @@ usually you will be creating a generic format.
 </configuration>
 ```
 
-**Limitations:**
-- The auto-discovery of config files (up the file tree) will not work when using
-  Biome within spotless.
-
 To apply Biome to more kinds of files with a different configuration, just add
 more formats:
 
@@ -1315,6 +1311,22 @@ more formats:
 </configuration>
 ```
 
+**Limitations:**
+- The auto-discovery of config files (up the file tree) will not work when using
+  Biome within spotless.
+- The `ignore` option of the `biome.json` configuration file will not be applied.
+  Include and exclude patterns are configured in the spotless configuration in the
+  Maven pom instead.
+
+Note: Due to a limitation of biome, if the name of a file matches a pattern in
+the `ignore` option of the specified `biome.json` configuration file, it will not be
+formatted, even if included in the biome configuration section of the Maven pom.
+You could specify a different `biome.json` configuration file without an `ignore`
+pattern to circumvent this.
+
+Note 2: Biome is hard-coded to ignore certain special files, such as `package.json`
+or `tsconfig.json`. These files will never be formatted.
+
 ### Biome binary
 
 To format with Biome, spotless needs to find the Biome binary. By default,
diff --git a/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java b/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java
index e015b934f5..ffbd73484f 100644
--- a/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java
+++ b/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java
@@ -199,4 +199,20 @@ void failureWhenNotParseable() throws Exception {
 		assertThat(result.stdOutUtf8()).contains("Unable to format file");
 		assertThat(result.stdOutUtf8()).contains("Step 'biome' found problem in 'biome_test.js'");
 	}
+
+	/**
+	 * Biome is hard-coded to ignore certain files, such as package.json. Since version 1.5.0,
+	 * the biome CLI does not output any formatted code anymore, whereas previously it printed
+	 * the input as-is. This tests checks that when the biome formatter outputs an empty string,
+	 * the contents of the file to format are used instead.
+	 *
+	 * @throws Exception When a test failure occurs.
+	 */
+	@Test
+	void preservesIgnoredFiles() throws Exception {
+		writePomWithJsonSteps("**/*.json", "<biome><version>1.5.0</version></biome>");
+		setFile("package.json").toResource("biome/json/packageBefore.json");
+		mavenRunner().withArguments("spotless:apply").runNoError();
+		assertFile("package.json").sameAsResource("biome/json/packageAfter.json");
+	}
 }
diff --git a/testlib/src/main/resources/biome/json/package.json b/testlib/src/main/resources/biome/json/package.json
new file mode 100644
index 0000000000..94e8f88de5
--- /dev/null
+++ b/testlib/src/main/resources/biome/json/package.json
@@ -0,0 +1,3 @@
+{
+"name": "test-package","version": "0.0.1"
+  }
\ No newline at end of file
diff --git a/testlib/src/main/resources/biome/json/packageAfter.json b/testlib/src/main/resources/biome/json/packageAfter.json
new file mode 100644
index 0000000000..94e8f88de5
--- /dev/null
+++ b/testlib/src/main/resources/biome/json/packageAfter.json
@@ -0,0 +1,3 @@
+{
+"name": "test-package","version": "0.0.1"
+  }
\ No newline at end of file
diff --git a/testlib/src/main/resources/biome/json/packageBefore.json b/testlib/src/main/resources/biome/json/packageBefore.json
new file mode 100644
index 0000000000..94e8f88de5
--- /dev/null
+++ b/testlib/src/main/resources/biome/json/packageBefore.json
@@ -0,0 +1,3 @@
+{
+"name": "test-package","version": "0.0.1"
+  }
\ No newline at end of file
diff --git a/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java b/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java
index f723a561c2..7ab4112bef 100644
--- a/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java
+++ b/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java
@@ -392,6 +392,19 @@ void testAutoDetectTsx() {
 				var stepHarness = StepHarnessWithFile.forStep(RomeStepTest.this, step);
 				stepHarness.testResource("biome/ts/fileBefore.tsx", "biome/ts/fileAfter.tsx");
 			}
+
+			/**
+			 * Biome is hard-coded to ignore certain files, such as package.json. Since version 1.5.0,
+			 * the biome CLI does not output any formatted code anymore, whereas previously it printed
+			 * the input as-is. This tests checks that when the biome formatter outputs an empty string,
+			 * the contents of the file to format are used instead.
+			 */
+			@Test
+			void preservesIgnoredFiles() {
+				var step = RomeStep.withExeDownload(BiomeFlavor.BIOME, "1.5.0", downloadDir.toString()).create();
+				var stepHarness = StepHarnessWithFile.forStep(RomeStepTest.this, step);
+				stepHarness.testResource("biome/json/package.json", "biome/json/packageAfter.json");
+			}
 		}
 
 		@Nested

From b82e75bbba14371bed58efd59e79107c7e900a0d Mon Sep 17 00:00:00 2001
From: Andre Wachsmuth <awa@xima.de>
Date: Tue, 9 Jan 2024 22:01:31 +0100
Subject: [PATCH 2/4] Update changelog

---
 CHANGES.md               | 2 +-
 plugin-gradle/CHANGES.md | 2 ++
 plugin-maven/CHANGES.md  | 2 ++
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index 23f58ea9d1..cd641ef75f 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -13,7 +13,7 @@ We adhere to the [keepachangelog](https://keepachangelog.com/en/1.0.0/) format (
 ### Added
 * New static method to `DiffMessageFormatter` which allows to retrieve diffs with their line numbers ([#1960](https://github.com/diffplug/spotless/issues/1960))
 ### Fixed
-* Fix empty files with biome >= 1.5.0 when formatting files that are in the ignore list of the biome configuration file. (fixes [#1987](https://github.com/diffplug/spotless/issues/1987))
+* Fix empty files with biome >= 1.5.0 when formatting files that are in the ignore list of the biome configuration file. ([#1989](https://github.com/diffplug/spotless/pull/1989) fixes [#1987](https://github.com/diffplug/spotless/issues/1987))
 ### Changes
 * Use palantir-java-format 2.39.0 on Java 21. ([#1948](https://github.com/diffplug/spotless/pull/1948))
 
diff --git a/plugin-gradle/CHANGES.md b/plugin-gradle/CHANGES.md
index d888f4863f..20c9a6029c 100644
--- a/plugin-gradle/CHANGES.md
+++ b/plugin-gradle/CHANGES.md
@@ -3,6 +3,8 @@
 We adhere to the [keepachangelog](https://keepachangelog.com/en/1.0.0/) format (starting after version `3.27.0`).
 
 ## [Unreleased]
+### Fixed
+* Fix empty files with biome >= 1.5.0 when formatting files that are in the ignore list of the biome configuration file. ([#1989](https://github.com/diffplug/spotless/pull/1989) fixes [#1987](https://github.com/diffplug/spotless/issues/1987))
 ### Changes
 * Use palantir-java-format 2.39.0 on Java 21. ([#1948](https://github.com/diffplug/spotless/pull/1948))
 
diff --git a/plugin-maven/CHANGES.md b/plugin-maven/CHANGES.md
index 55f451ad4e..cea32ce89e 100644
--- a/plugin-maven/CHANGES.md
+++ b/plugin-maven/CHANGES.md
@@ -5,6 +5,8 @@ We adhere to the [keepachangelog](https://keepachangelog.com/en/1.0.0/) format (
 ## [Unreleased]
 ### Added
 * M2E support: Emit file specific errors during incremental build. ([#1960](https://github.com/diffplug/spotless/issues/1960))
+### Fixed
+* Fix empty files with biome >= 1.5.0 when formatting files that are in the ignore list of the biome configuration file. ([#1989](https://github.com/diffplug/spotless/pull/1989) fixes [#1987](https://github.com/diffplug/spotless/issues/1987))
 ### Changes
 * Use palantir-java-format 2.39.0 on Java 21. ([#1948](https://github.com/diffplug/spotless/pull/1948))
 

From c431a705ab0745459d1be9f64e24722335c0f99a Mon Sep 17 00:00:00 2001
From: Andre Wachsmuth <awa@xima.de>
Date: Tue, 9 Jan 2024 22:04:04 +0100
Subject: [PATCH 3/4] Format code

---
 .../com/diffplug/spotless/rome/RomeStep.java  |  5 ++---
 .../gradle/spotless/BiomeIntegrationTest.java | 22 +++++++++----------
 .../spotless/maven/biome/BiomeMavenTest.java  |  2 +-
 .../diffplug/spotless/rome/RomeStepTest.java  |  2 +-
 4 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java b/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
index 92a0fdc689..0d0cca65a0 100644
--- a/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
+++ b/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2016-2023 DiffPlug
+ * Copyright 2016-2024 DiffPlug
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -440,8 +440,7 @@ private String format(ProcessRunner runner, String input, File file) throws IOEx
 			// a list of hard-coded file names, such as package.json or tsconfig.json.
 			if (formatted == null || formatted.isEmpty()) {
 				return input;
-			}
-			else {
+			} else {
 				return formatted;
 			}
 		}
diff --git a/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java b/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java
index 139d477bf0..db4ca4b027 100644
--- a/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java
+++ b/plugin-gradle/src/test/java/com/diffplug/gradle/spotless/BiomeIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2023 DiffPlug
+ * Copyright 2023-2024 DiffPlug
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -352,16 +352,16 @@ void failureWhenNotParseable() throws Exception {
 	@Test
 	void preservesIgnoredFiles() throws Exception {
 		setFile("build.gradle").toLines(
-			"plugins {",
-			"    id 'com.diffplug.spotless'",
-			"}",
-			"repositories { mavenCentral() }",
-			"spotless {",
-			"    json {",
-			"        target '**/*.json'",
-			"        biome('1.5.0')",
-			"    }",
-			"}");
+				"plugins {",
+				"    id 'com.diffplug.spotless'",
+				"}",
+				"repositories { mavenCentral() }",
+				"spotless {",
+				"    json {",
+				"        target '**/*.json'",
+				"        biome('1.5.0')",
+				"    }",
+				"}");
 		setFile("package.json").toResource("biome/json/packageBefore.json");
 
 		var spotlessApply = gradleRunner().withArguments("--stacktrace", "spotlessApply").build();
diff --git a/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java b/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java
index ffbd73484f..ff763c3cf8 100644
--- a/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java
+++ b/plugin-maven/src/test/java/com/diffplug/spotless/maven/biome/BiomeMavenTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2023 DiffPlug
+ * Copyright 2023-2024 DiffPlug
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
diff --git a/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java b/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java
index 7ab4112bef..8ab92e90e0 100644
--- a/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java
+++ b/testlib/src/test/java/com/diffplug/spotless/rome/RomeStepTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2023 DiffPlug
+ * Copyright 2023-2024 DiffPlug
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

From ac505ea898e9f7bd9213cbc5464a80745599e273 Mon Sep 17 00:00:00 2001
From: Andre Wachsmuth <awa@xima.de>
Date: Tue, 9 Jan 2024 22:14:02 +0100
Subject: [PATCH 4/4] Remove null check

---
 lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java b/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
index 0d0cca65a0..de5b3e80ee 100644
--- a/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
+++ b/lib/src/main/java/com/diffplug/spotless/rome/RomeStep.java
@@ -431,14 +431,14 @@ private String format(ProcessRunner runner, String input, File file) throws IOEx
 			}
 			var runnerResult = runner.exec(stdin, args);
 			var stdErr = runnerResult.stdErrUtf8();
-			if (stdErr != null && !stdErr.isEmpty()) {
+			if (!stdErr.isEmpty()) {
 				logger.warn("Biome stderr ouptut for file '{}'\n{}", file, stdErr.trim());
 			}
 			var formatted = runnerResult.assertExitZero(StandardCharsets.UTF_8);
 			// When biome encounters an ignored file, it does not output any formatted code
 			// Ignored files come from (a) the biome.json configuration file and (b) from
 			// a list of hard-coded file names, such as package.json or tsconfig.json.
-			if (formatted == null || formatted.isEmpty()) {
+			if (formatted.isEmpty()) {
 				return input;
 			} else {
 				return formatted;