cleanup

Readme.md

@@ -227,6 +227,14 @@ artifact server. Therefore this only works within the PSI networks and if you
 have a certain maven configuration. An example Maven settings.xml that you can
 copy to `~/.m2/settings.xml` is located [here](settings.xml).
 
+## Dependencies
+The java HDF5 libary as well as the precompiled code we downloaded and copied from:
+https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page
+All the necessary jars where copied from there into the /lib directory.
+
+The files in the package hdf.objects in this repository were copied from the hdfviewer source code. We were not able to find a jar that contained them.
+ 
+
 # Acknowledgements
 This project was inspired by the ImageJ HDF Plugin of Matthias Schlachter Chair
 of Pattern Recognition and Image Processing, University of Freiburg, Germany (

src/main/assembly/assembly.xml

@@ -1,28 +0,0 @@
-<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
-  
-  <includeBaseDirectory>false</includeBaseDirectory>
-    <id>bin</id>
-    <!-- Generates a zip package containing the needed files -->
-    <formats>
-        <format>zip</format>
-    </formats>
-
-    <fileSets>
-        <fileSet>
-        	<directory>src/main/assembly/lib</directory>
-            <outputDirectory>lib</outputDirectory>
-            <includes>
-                <include>**/*</include>
-            </includes>
-        </fileSet>
-        <!-- adds fat-jar assembled earlier to the root directory of zip package -->
-        <fileSet>
-            <directory>target</directory>
-            <outputDirectory>plugins</outputDirectory>
-            <includes>
-                <include>HDF5_Viewer*.jar</include>
-            </includes>
-        </fileSet>
-    </fileSets>
-</assembly>

src/main/assembly/assembly_jar.xml

@@ -1,18 +0,0 @@
-<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0" 
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
-  <!-- TODO: a jarjar format would be better -->
-  <id>jar-with-dependencies</id>
-  <formats>
-    <format>jar</format>
-  </formats>
-  <includeBaseDirectory>false</includeBaseDirectory>
-  <dependencySets>
-    <dependencySet>
-      <outputDirectory>/</outputDirectory>
-      <useProjectArtifact>true</useProjectArtifact>
-      <unpack>true</unpack>
-      <scope>runtime</scope>
-    </dependencySet>
-  </dependencySets>
-</assembly>