Merge pull request #1 from Wouter1/master

move atk to maven and fix issues

Author: thomasabeel

.github/workflows/maven-test.yml

@@ -0,0 +1,30 @@
+# This workflow will build a package using Maven and then publish it to GitHub packages when a release is created
+# For more information see: https://github.com/actions/setup-java/blob/main/docs/advanced-usage.md#apache-maven-with-a-settings-path
+
+name: Maven Package
+
+on:
+  push:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up JDK 11
+      uses: actions/setup-java@v4
+      with:
+        java-version: '11'
+        distribution: 'temurin'
+        server-id: github # Value of the  distributionManagement/repository/id field of the pom.xml
+        settings-path: ${{ github.workspace }} # location for the settings.xml file
+
+    - name: Build with Maven
+      run: mvn clean test
+
+

.gitignore

@@ -15,4 +15,8 @@ build
 /test.txt.gz
 /tmp.txt
 /tmp2.txt
-/.url-cache
+/.url-cache
+/target/
+/.project
+/.settings/
+/export.pdf

.project

@@ -1,5 +1,4 @@
-atk
-===
+# atk
 
 Abeel ToolKit -- a set of quite useful java and scala classes, objects and traits.
 
@@ -8,13 +7,52 @@ Some classes may have more specific license than the complete package, please re
 
 Individual tools may have specific licenses to accommodate library and/or package licenses
 
+## Overview 
+The ATK library contains a large collection of small tools:
 
-Eclipse setup
-===
-Add scala library (2.12.3)
-Add Java runtime (1.11)
+* compbio: phylogenetic tree for storing evolutional history between species
+* io: file filters, GZIP tools, 
+* net: email tool, client http tools
+* util: MD5, ColorGradient, TimeInterval
+* bioinformatics: FASTA format, some DNA util classes
+* concurrency: DeamonThread
+* graphics: Image handling tools
+* gui: some panels and fields
+* jfreechart: wrapper for JFreeChart
+* util: alternatives for hashmap, alternative RNG
 
 
-Nightly builds
-===
-https://abeellab.org/jenkins/atk
+
+## Additional libraries
+This library also contains hard copies of other libraries, which are not available on an external artifactory:
+
+* edu.northwestern.at.utils which is a math toolbox
+
+* org.arabidopsis.ahocorasick which is a string searching automaton.
+
+
+# Maven Dependency
+You can use this from maven with the following dependency.
+
+```
+	    <dependency>
+		    <groupId>be.abeel</groupId>
+		    <artifactId>atk</artifactId>
+		    <version>1.2.1</version>
+		</dependency>
+```
+
+and with the following repository
+
+```
+	<repositories>
+		<repository>
+			<id>artifactory.ewi.tudelft.nl</id>
+			<url>https://artifactory.ewi.tudelft.nl/artifactory/libs-release</url>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+		</repository>
+	</repositories>
+```
+