Merge branch 'main' of https://github.com/HenriquesLab/SReD

HenriquesLab · Sep 12, 2024 · f474445 · f474445
2 parents 640da93 + 3ec4eeb
commit f474445
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diff --git a/Docs/Logo/logo.png b/Docs/Logo/logo.png
diff --git a/Docs/Logo/placeholder b/Docs/Logo/placeholder
@@ -0,0 +1 @@
+
diff --git a/README.md b/README.md
@@ -1,3 +1,5 @@
+<img src="https://github.com/HenriquesLab/SReD/blob/main/Docs/Logo/logo.png" align="right" width="300"/>
+
 # SReD: Structural Repetition Detector Plugin for ImageJ and Fiji
 
 SReD (Structural Repetition Detector) is an ImageJ and Fiji plugin for analyzing structural repetition in microscopy images. It introduces a novel approach utilising a custom sampling scheme and correlation metrics to compute Repetition Maps. These maps highlight and quantify the degree of structural repetition present within images, providing valuable insights for image analysis and structural studies.

diff --git a/pom.xml b/pom.xml
@@ -2,15 +2,15 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
-		<groupId>org.scijava</groupId>
-		<artifactId>pom-scijava</artifactId>
-		<version>38.0.1</version>
-		<relativePath />
-	</parent>
+        <groupId>org.scijava</groupId>
+        <artifactId>pom-scijava</artifactId>
+        <version>38.0.1</version>
+        <relativePath />
+    </parent>
 
     <groupId>groupId</groupId>
     <artifactId>SReD_</artifactId>
-    <version>1.0-SNAPSHOT</version>
+    <version>1.0</version>
 
     <name>SReD</name>
     <description>SReD (Structural Repetition Detector) is an ImageJ and Fiji plugin for analyzing structural repetition in microscopy images.</description>
@@ -77,23 +77,18 @@
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
         <imagej.app.directory>/Applications/Fiji.app</imagej.app.directory>
-		<license.licenseName>MIT</license.licenseName>
-		<license.copyrightOwners>SReD developers.</license.copyrightOwners>
+        <license.licenseName>MIT</license.licenseName>
+        <license.copyrightOwners>SReD developers.</license.copyrightOwners>
     </properties>
 
     <dependencies>
-		<dependency>
-			<groupId>net.imagej</groupId>
-			<artifactId>ij</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>net.imagej</groupId>
-			<artifactId>imagej-common</artifactId>
-		</dependency>
         <dependency>
-            <groupId>org.apache.maven.plugins</groupId>
-            <artifactId>maven-assembly-plugin</artifactId>
-            <version>3.6.0</version>
+            <groupId>net.imagej</groupId>
+            <artifactId>ij</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>net.imagej</groupId>
+            <artifactId>imagej-common</artifactId>
         </dependency>
         <dependency>
             <groupId>org.jogamp.jocl</groupId>
@@ -117,32 +112,32 @@
             <scope>test</scope>
         </dependency>
     </dependencies>
+
     <repositories>
-		<repository>
-			<id>scijava.public</id>
-			<url>https://maven.scijava.org/content/groups/public</url>
-		</repository>
-	</repositories>
+        <repository>
+            <id>scijava.public</id>
+            <url>https://maven.scijava.org/content/groups/public</url>
+        </repository>
+    </repositories>
+
     <build>
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-assembly-plugin</artifactId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.3.0</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
                         <goals>
-                            <goal>single</goal>
+                            <goal>shade</goal>
                         </goals>
+                        <configuration>
+                            <createDependencyReducedPom>false</createDependencyReducedPom>
+                        </configuration>
                     </execution>
                 </executions>
-                <configuration>
-                    <descriptorRefs>
-                        <descriptorRef>jar-with-dependencies</descriptorRef>
-                    </descriptorRefs>
-                </configuration>
             </plugin>
         </plugins>
     </build>
-
-</project>
+</project>