Add logback as logging framework

.github/workflows/build.yml

@@ -0,0 +1,25 @@
+# This workflow will build a Java project with Maven
+
+name: Java CI with Maven
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Java
+        uses: actions/setup-java@v2
+        with:
+          java-version: '8'
+          distribution: 'zulu'
+          cache: 'maven'
+      - name: Build with Maven
+        run: mvn -B package --file pom.xml

.github/workflows/sonarcloud.yml

@@ -39,10 +39,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Java
+      - name: Set up JDK 11
         uses: actions/setup-java@v2
         with:
-          java-version: '8'
+          java-version: '11'
           distribution: 'zulu'
           cache: 'maven'
 

.gitignore

@@ -9,3 +9,4 @@ buildNumber.properties
 .mvn/timing.properties
 # https://github.com/takari/maven-wrapper#usage-without-binary-jar
 .mvn/wrapper/maven-wrapper.jar
+/logs/

pom.xml

@@ -60,6 +60,26 @@
             <artifactId>mastodon</artifactId>
             <version>${mastodon.version}</version>
         </dependency>
+
+        <!-- include simple logging facade for logging -->
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+
+        <!-- include logback-classic at test runtime -->
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <!-- include logback-core at test runtime -->
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-core</artifactId>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>sc.fiji</groupId>
             <artifactId>spim_data</artifactId>
@@ -126,7 +146,7 @@
             <url>https://maven.scijava.org/content/groups/public</url>
         </repository>
     </repositories>
-    
+
     <profiles>
         <profile>
             <id>coverage</id>

src/test/java/org/mastodon/mamut/deeplineage/StartImageJ.java

@@ -30,6 +30,10 @@
 
 import org.scijava.Context;
 import org.scijava.ui.UIService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.lang.invoke.MethodHandles;
 
 /**
  * Shows the ImageJ main window, with Mastodon installed.
@@ -38,8 +42,11 @@
  */
 public class StartImageJ
 {
+	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
+
 	public static void main( String... args )
 	{
+		logger.info( "Starting ImageJ..." );
 		Context context = new Context();
 		UIService uiService = context.service( UIService.class );
 		uiService.showUI();

src/test/resources/logback-test.xml

@@ -0,0 +1,125 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<configuration debug="false">
+
+    <property name="LOGS" value="./logs"/>
+
+    <appender name="stdout" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%highlight(%-5level) %d{yyyy-MM-dd HH:mm:ss.SSS} [%blue(%t)] \(%file:%line\) - %m%n
+            </pattern>
+        </encoder>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>INFO</level>
+        </filter>
+    </appender>
+    <appender name="stderr" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%highlight(%-5level) %d{yyyy-MM-dd HH:mm:ss.SSS} [%blue(%t)] \(%file:%line\) - %m%n
+            </pattern>
+        </encoder>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>WARN</level>
+        </filter>
+    </appender>
+    <appender name="file-trace" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/trace.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/trace.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>TRACE</level>
+        </filter>
+    </appender>
+    <appender name="file-debug" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/debug.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/debug.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>DEBUG</level>
+        </filter>
+    </appender>
+    <appender name="file-info" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/info.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/info.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>INFO</level>
+        </filter>
+    </appender>
+    <appender name="file-warn" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/warn.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/warn.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>WARN</level>
+        </filter>
+    </appender>
+    <appender name="file-error" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <File>${LOGS}/error.log</File>
+        <encoder>
+            <Pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %-5p [%c{1}:%M:%L] - %m%n</Pattern>
+        </encoder>
+        <rollingPolicy class="ch.qos.logback.core.rolling.SizeAndTimeBasedRollingPolicy">
+            <!-- rollover daily -->
+            <fileNamePattern>${LOGS}/error.%d{yyyy-MM-dd}.%i.log.zip</fileNamePattern>
+            <!-- each file should be at most 10MB, keep 60 days worth of history, but at most 1GB-->
+            <maxFileSize>20MB</maxFileSize>
+            <maxHistory>60</maxHistory>
+            <totalSizeCap>1GB</totalSizeCap>
+        </rollingPolicy>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>ERROR</level>
+        </filter>
+    </appender>
+
+    <!-- Set root log level to DEBUG -->
+    <root level="DEBUG">
+        <appender-ref ref="stdout"/>
+        <appender-ref ref="file-trace"/>
+        <appender-ref ref="file-debug"/>
+        <appender-ref ref="file-info"/>
+        <appender-ref ref="file-warn"/>
+        <appender-ref ref="file-error"/>
+    </root>
+
+    <!-- Example how to change log level for certain packages -->
+    <logger name="org.mastodon.mamut.util" level="DEBUG"/>
+
+
+</configuration>