Merge pull request #20 from 3D-e-Chem/knime4

Requires KNIME version 4

CHANGELOG.md

@@ -5,6 +5,18 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ## [Unreleased]
 
+## [2.0.0] - 2019-07-02
+
+### Added
+
+* CITATION.cff and .zenodo.json files, for better citation support
+
+### Changed
+
+* Requires KNIME version 4 ([#19](https://github.com/3D-e-Chem/tycho-knime-node-archetype/issues/19))
+* Switched from KNIME SDK to Eclipse + target platform ([#18](https://github.com/3D-e-Chem/tycho-knime-node-archetype/issues/18))
+* Source jars for plugin have been replaced with source reference in MANIFEST.MF
+
 ## [1.7.0] - 2018-03-23
 
 ### Changed

CITATION.cff

@@ -9,7 +9,7 @@ authors:
   family-names: Verhoeven
   affiliation: Nederlands eScience Center
   orcid: https://orcid.org/0000-0002-5821-2060
-version: 1.7.0
-date-released: 2018-03-23
+version: 2.0.0
+date-released: 2019-07-02
 repository-code: https://github.com/3D-e-Chem/tycho-knime-node-archetype
 license: Apache-2.0

README.md

@@ -20,7 +20,7 @@ The [Maven archetype](https://maven.apache.org/guides/introduction/introduction-
 
 ## Requirements
 
-* Java >=1.8
+* Java ==8
 * Maven >=3.0
 
 The archetype is hosted on a [BinTray repository](https://dl.bintray.com/nlesc/tycho-knime-node-archetype).
@@ -53,7 +53,7 @@ The following command will generate a skeleton project
 ```sh
 mvn archetype:generate -DarchetypeGroupId=nl.esciencecenter \
 -DarchetypeArtifactId=tycho-knime-node-archetype \
--DarchetypeVersion=1.7.0 -P knimearchetype
+-DarchetypeVersion=2.0.0 -P knimearchetype
 ```
 
 The command will ask the following questions:
@@ -87,19 +87,20 @@ Further instructions about generated project can be found in it's README.md file
 
 ## Generate from inside KNIME SDK
 
-1. Start up the KNIME SDK
-2. Install the `m2e - Maven Integration for Eclipse` software, (you might need to add the add the Eclipse software site which is `http://download.eclipse.org/releases/neon` for the version 3.5.1 of the KNIME SDK)
-3. Register the archetype catalog which contains this archetype
+1. Install Java 8
+2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/release/2018-12/r/eclipse-ide-rcp-and-rap-developers)
+3. Configure Java 8 inside Eclipse Window > Preferences > Java > Installed JREs
+4. Register the archetype catalog which contains this archetype
 
       1. Goto Window > Preferences > Maven > Archetypes
-      2. Add a remove catalog with `https://github.com/3D-e-Chem/tycho-knime-node-archetype/raw/master/archetype-catalog.xml`
+      2. Add a remote catalog with `https://github.com/3D-e-Chem/tycho-knime-node-archetype/raw/master/archetype-catalog.xml`
 
-4. Create a new project based on archetype
+5. Create a new project based on archetype
 
       1. Goto File > New > Project ... > Maven
       2. Select Maven Project & press Next button
       3. Use default location & press Next button
-      4. Select Catalog you added in 3.2
+      4. Select Catalog you added in step 4.2
       5. Select the archetype with artifact id `tycho-knime-node-archetype` & press Next button
       6. Fill in the form & press Finish button
 

archetype-catalog.xml

@@ -6,7 +6,7 @@
     <archetype>
       <groupId>nl.esciencecenter</groupId>
       <artifactId>tycho-knime-node-archetype</artifactId>
-      <version>1.7.0</version>
+      <version>2.0.0</version>
       <description>Archetype for a KNIME node.</description>
       <repository>https://dl.bintray.com/nlesc/tycho-knime-node-archetype</repository>
     </archetype>

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>nl.esciencecenter</groupId>
 	<artifactId>tycho-knime-node-archetype</artifactId>
-	<version>1.7.0</version>
+	<version>2.0.0</version>
 	<name>Archetype - Knime node</name>
 	<packaging>maven-archetype</packaging>
 	<licenses>

src/main/resources/META-INF/maven/archetype-metadata.xml

@@ -4,13 +4,13 @@
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
     <requiredProperties>
       <requiredProperty key="tycho_version">
-        <defaultValue>1.1.0</defaultValue>
+        <defaultValue>1.4.0</defaultValue>
       </requiredProperty>
       <requiredProperty key="java_version">
         <defaultValue>1.8</defaultValue>
       </requiredProperty>
       <requiredProperty key="knime_version">
-        <defaultValue>3.3</defaultValue>
+        <defaultValue>4.0</defaultValue>
       </requiredProperty>
       <requiredProperty key="github_organization"/>
       <requiredProperty key="github_repository"/>
@@ -24,6 +24,8 @@
       <includes>
         <include>README.md</include>
         <include>.travis.yml</include>
+        <include>.zenodo.json</include>
+        <include>CITATION.cff</include>
       </includes>
     </fileSet>
     <fileSet encoding="UTF-8">
@@ -120,5 +122,15 @@
         </fileSet>
       </fileSets>
     </module>
+    <module id="${rootArtifactId}.targetplatform" dir="targetplatform" name="${rootArtifactId}.targetplatform">
+      <fileSets>
+        <fileSet filtered="true" encoding="UTF-8">
+          <directory></directory>
+          <includes>
+            <include>KNIME-AP-4.0.target</include>
+          </includes>
+        </fileSet>
+      </fileSets>
+    </module>
   </modules>
 </archetype-descriptor>

src/main/resources/archetype-resources/.zenodo.json

@@ -0,0 +1,4 @@
+{
+    "title": "${node}",
+    "license": "Apache-2.0"
+}

src/main/resources/archetype-resources/CITATION.cff

@@ -0,0 +1,17 @@
+#set( $symbol_pound = '#' )
+#set( $symbol_dollar = '$' )
+#set( $symbol_escape = '\' )
+${symbol_pound} YAML 1.2
+${symbol_pound} Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+cff-version: 1.0.3
+message: If you use this software, please cite it as below.
+title: ${node}
+authors: []
+${symbol_pound}${symbol_pound} Uncomment and replace `<changeme>` with actual author names
+${symbol_pound}- given-names: <changeme>
+${symbol_pound}  family-names: <changeme>
+${symbol_pound}  affiliation: <changeme>
+${symbol_pound}  orcid: https://orcid.org/<changeme>
+repository-code: https://github.com/${github_organization}/${github_repository}
+license: Apache-2.0
+version: ${version}

src/main/resources/archetype-resources/README.md

@@ -52,39 +52,20 @@ Also see `./.travis.yml` file how to perform a [SonarCloud](https://sonarcloud.i
 
 See `./appveyor.yml` file how to run on https://www.appveyor.com .
 
-${symbol_pound} Development
-
-Steps to get development environment setup:
-
-1. Download KNIME SDK from https://www.knime.org/downloads/overview
-2. Install/extract KNIME SDK
-3. Start KNIME SDK
-4. Install m2e (Maven integration for Eclipse) + Test workflows in JUnit
-
-    1. Goto Window -> Preferences -> Install/Update -> Available Software Sites
-    2. Make sure the following Software Sites (or a version of them) are present otherwise add them:
+To cite the KNIME node, a [DOI](https://en.wikipedia.org/wiki/Digital_object_identifier) can be generated when a GitHub release is made. To enable, the GitHub repository must be connected on https://zenodo.org/account/settings/github/ . The connection must be made before creating a GitHub release.
+To [cite the software](https://research-software.org/citation/developers/) a human and computer readable file called `CITATION.cff` is included.
 
-      * http://update.knime.org/analytics-platform/${knime_version}
-      * http://download.eclipse.org/eclipse/updates/4.6
-      * http://download.eclipse.org/releases/neon
-      * https://3d-e-chem.github.io/updates (only required for 3D-e-Chem node)
-
-    3. Goto Help -> Check for updates
-    4. Install any updates found & restart
-    5. Goto Help > Install new software ...
-    6. Select --All Available sites-- in work with pulldown
-    7. Wait for list to be filled, `Pending...` should disappear
-    8. Select the following items:
-
-      * m2e - Maven integration for Eclipse (includes Incubating components)
-      * Test KNIME workflows from a Junit test
-      * Splash & node category for 3D-e-Chem KNIME nodes (only required for 3D-e-Chem node)
+${symbol_pound} Development
 
-    9. Install software & restart
+Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
 
-5. Import this repo as an Existing Maven project
+1. Install Java 8
+2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/release/2018-12/r/eclipse-ide-rcp-and-rap-developers)
+3. Configure Java 8 inside Eclipse Window > Preferences > Java > Installed JREs
+4. Import this repo as an Existing Maven project
+5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the `KNIME Analytics Platform (${knime_version}) - ${artifactId}.targetplatform/KNIME-AP-${knime_version}.target` target definition.
 
-During import the Tycho Eclipse providers must be installed, Eclipse will ask for your permission.
+During import the Tycho Eclipse providers must be installed.
 
 ${symbol_pound}${symbol_pound} Tests
 
@@ -123,3 +104,4 @@ ${symbol_pound} New release
   1. Correct authors
   2. Correct license
 9. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
+10. Update `CITATION.cff` file with new DOI, version, release date

src/main/resources/archetype-resources/p2/category.xml

@@ -8,33 +8,17 @@
 	<feature id="${parentArtifactId}.feature" version="${qversion}">
 		<category name="nl.esciencecenter.3D-e-Chem" />
 	</feature>
-	<feature id="${parentArtifactId}.feature.source" version="${qversion}">
-		<category name="nl.esciencecenter.3D-e-Chem.sources" />
-	</feature>
 	<category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">
 		<description>
 			3D-e-Chem: Collection KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem
 			project
 		</description>
 	</category-def>
-	<category-def name="nl.esciencecenter.3D-e-Chem.sources"
-				  label="KNIME 3D-e-Chem Contributions Sources">
-		<description>
-			3D-e-Chem Sources: Sources of KNIME nodes &amp; Extensions for the NLeSC
-			3d-e-Chem project
-		</description>
-	</category-def>
 #else
 	<feature id="${parentArtifactId}.feature" version="${qversion}">
 		<category name="${vendor}" />
 	</feature>
-	<feature id="${parentArtifactId}.feature.source" version="${qversion}">
-		<category name="${vendor} Sources" />
-	</feature>
 	<category-def name="${vendor}" label="KNIME ${vendor} Contributions">
 	</category-def>
-	<category-def name="${vendor} Sources"
-				  label="KNIME ${vendor} Contributions Sources">
-	</category-def>
 #end
 </site>

src/main/resources/archetype-resources/plugin/META-INF/MANIFEST.MF

@@ -11,9 +11,9 @@ Bundle-RequiredExecutionEnvironment: JavaSE-$java_version
 Bundle-Activator: ${package}.Activator
 Bundle-Vendor: ${vendor}
 Require-Bundle: org.eclipse.core.runtime,
- org.knime.workbench.core;bundle-version="[${knime_version}.0,4.0.0)",
- org.knime.workbench.repository;bundle-version="[${knime_version}.0,4.0.0)",
- org.knime.base;bundle-version="[${knime_version}.0,4.0.0)"
+ org.knime.workbench.core;bundle-version="[${knime_version}.0,5.0.0)",
+ org.knime.workbench.repository;bundle-version="[${knime_version}.0,5.0.0)",
+ org.knime.base;bundle-version="[${knime_version}.0,5.0.0)"
 #if( $branded == "Y")
  ,nl.esciencecenter.e3dchem.plugin
 #end

src/main/resources/archetype-resources/pom.xml

@@ -28,29 +28,17 @@
 		<maven>3.0</maven>
 	</prerequisites>
 	<properties>
-		<knime.version>${knime_version}</knime.version>
-		<knime.update.site>http://update.knime.org/analytics-platform/${symbol_dollar}{knime.version}/</knime.update.site>
 		<tycho.version>${tycho_version}</tycho.version>
 		<tycho.extras.version>${tycho_version}</tycho.extras.version>
 		<tycho.test.jvmArgs>-Xmx512m</tycho.test.jvmArgs>
+		<tycho.scmUrl>scm:git:https://github.com/${github_organization}/${github_repository}.git</tycho.scmUrl>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<tycho.scmUrl>scm:git:https://github.com/${github_organization}/${github_repository}.git</tycho.scmUrl>
 		<sonar.host.url>https://sonarcloud.io</sonar.host.url>
 		<sonar.organization>${github_organization.toLowerCase()}</sonar.organization>
+		<target.file>KNIME-AP-4.0</target.file>
 	</properties>
-	<repositories>
-		<repository>
-			<id>knime</id>
-			<layout>p2</layout>
-			<url>${symbol_dollar}{knime.update.site}</url>
-		</repository>
-		<repository>
-			<id>3d-e-chem</id>
-			<layout>p2</layout>
-			<url>https://3d-e-chem.github.io/updates</url>
-		</repository>
-	</repositories>
 	<build>
 		<plugins>
 			<plugin>
@@ -94,6 +82,14 @@
 							<arch>x86_64</arch>
 						</environment>
 					</environments>
+					 <target>
+						<artifact>
+							<groupId>${groupId}</groupId>
+							<artifactId>${artifactId}.targetplatform</artifactId>
+							<version>${symbol_dollar}{project.version}</version>
+							<classifier>${symbol_dollar}{target.file}</classifier>
+						</artifact>
+					</target>
 				</configuration>
 			</plugin>
 			<plugin>
@@ -114,10 +110,15 @@
 					</execution>
 				</executions>
 			</plugin>
+			<plugin>
+				<groupId>org.eclipse.tycho.extras</groupId>
+				<artifactId>tycho-pack200a-plugin</artifactId>
+				<version>${symbol_dollar}{tycho.extras.version}</version>
+			</plugin>
 			<plugin>
 				<groupId>org.eclipse.tycho.extras</groupId>
 				<artifactId>tycho-source-feature-plugin</artifactId>
-				<version>${tycho.extras.version}</version>
+				<version>${symbol_dollar}{tycho.extras.version}</version>
 				<executions>
 					<execution>
 						<id>source-feature</id>
@@ -131,7 +132,7 @@
 			<plugin>
 				<groupId>org.eclipse.tycho</groupId>
 				<artifactId>tycho-p2-plugin</artifactId>
-				<version>${tycho.version}</version>
+				<version>${symbol_dollar}{tycho.version}</version>
 				<executions>
 					<execution>
 						<id>attach-p2-metadata</id>
@@ -142,11 +143,6 @@
 					</execution>
 				</executions>
 			</plugin>
-			<plugin>
-				<groupId>org.eclipse.tycho.extras</groupId>
-				<artifactId>tycho-pack200a-plugin</artifactId>
-				<version>${tycho.extras.version}</version>
-			</plugin>
 		</plugins>
 		<pluginManagement>
 			<plugins>
@@ -163,7 +159,7 @@
 						<dependency>
 							<groupId>org.eclipse.tycho.extras</groupId>
 							<artifactId>tycho-sourceref-jgit</artifactId>
-							<version>${tycho.extras.version}</version>
+							<version>${symbol_dollar}{tycho.extras.version}</version>
 						</dependency>
 					</dependencies>
 					<configuration>

src/main/resources/archetype-resources/targetplatform/KNIME-AP-4.0.target

@@ -0,0 +1,44 @@
+#set( $symbol_pound = '#' )
+#set( $symbol_dollar = '$' )
+#set( $symbol_escape = '\' )
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><?pde version="3.8"?><target name="KNIME Analytics Platform (4.0)" sequenceNumber="1512743962">
+<locations>
+	<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
+<unit id="com.knime.features.explorer.serverspace.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.base.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.dbdrivers.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ensembles.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ext.itemset.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ext.jep.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ext.poi.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.js.quickforms.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.json.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.personalproductivity.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.testingapplication.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.xml.feature.group" version="0.0.0"/>
+<unit id="org.knime.targetPlatform.feature.group" version="0.0.0"/>
+<repository location="https://update.knime.org/analytics-platform/${knime_version}/"/>
+</location>
+	<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
+		<unit id="nl.esciencecenter.e3dchem.knime.testing.plugin" version="0.0.0"/>
+		<unit id="nl.esciencecenter.e3dchem.plugin" version="0.0.0"/>
+		<repository location="https://3d-e-chem.github.io/updates"/>
+	</location>
+</locations>
+<targetJRE path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-${java_version}"/>
+<launcherArgs>
+<vmArgs>-server
+-Dsun.java2d.d3d=false
+-Dosgi.classloader.lock=classname
+-XX:+UnlockDiagnosticVMOptions
+-XX:+UnsyncloadClass 
+-XX:+UseG1GC
+-ea
+-Dorg.eclipse.swt.internal.gtk.cairoGraphics=false
+-Dorg.eclipse.swt.internal.gtk.useCairo=false
+-Dorg.eclipse.swt.browser.IEVersion=10001
+-Dsun.awt.noerasebackground=true
+-Dsun.net.client.defaultReadTimeout=0
+-Dorg.eclipse.swt.internal.gtk.disablePrinting</vmArgs>
+</launcherArgs>
+</target>