Bump to v2.0.0 + require KNIME 4

sverhoeven · sverhoeven · commit 0cbfc53cc6e7 · 2019-07-03T08:34:57.000+02:00
Fixes #2
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,9 @@
 target/
+
+# Eclipse
 .project
 .settings
+
+# IDEA
+*.iml
+.idea
diff --git a/.travis.yml b/.travis.yml
@@ -1,4 +1,3 @@
-sudo: false
 language: java
 cache:
   directories:
@@ -8,7 +7,7 @@ cache:
 matrix:
  include:
  - os: linux
-   jdk: oraclejdk8
+   jdk: openjdk8
    script: xvfb-run mvn verify -B
    before_install:
     - if [ ! -e $HOME/conda/bin/activate ]; then
diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,4 @@
+{
+  "title": "KNIME Python node archetype",
+  "license": "Apache-2.0"
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,18 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ## [Unreleased]
 
+## [2.0.0] - 2019-07-03
+
+### Added
+
+* CITATION.cff and .zenodo.json files, for better citation support
+
+### Changed
+
+* Requires KNIME version 4 ([#2](https://github.com/3D-e-Chem/knime-python-node-archetype/issues/2))
+* Switched from KNIME SDK to Eclipse + target platform
+* Source jars for plugin have been replaced with source reference in MANIFEST.MF
+
 ## [1.4.0] - 2018-02-07
 
 Synced with [tycho-knime-node-archetype v1.5.0](https://github.com/3D-e-Chem/tycho-knime-node-archetype/releases/tag/v1.5.0).
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,15 @@
+# YAML 1.2
+# 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: KNIME node archetype
+doi: 10.5281/zenodo.3266165
+authors:
+- given-names: Stefan
+  family-names: Verhoeven
+  affiliation: Nederlands eScience Center
+  orcid: https://orcid.org/0000-0002-5821-2060
+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
diff --git a/README.md b/README.md
@@ -26,7 +26,7 @@ See https://github.com/3D-e-Chem/knime-python-wrapper for more information how t
 
 ## Requirements
 
-* Java >=1.8
+* Java ==8
 * Maven >=3.0
 
 The archetype is hosted on a [BinTray repository](https://dl.bintray.com/nlesc/knime-python-node-archetyp).
@@ -61,7 +61,7 @@ The following command will generate a skeleton project
 ```sh
 mvn archetype:generate -DarchetypeGroupId=nl.esciencecenter \
   -DarchetypeArtifactId=knime-python-node-archetype \
-  -DarchetypeVersion=1.4.0 \
+  -DarchetypeVersion=2.0.0 \
   -P pythonknimearchetype
 ```
 
@@ -96,26 +96,32 @@ 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
-3.1. Goto Window > Preferences > Maven > Archetypes
-3.2. Add a remove catalog with `https://github.com/3D-e-Chem/knime-python-node-archetype/raw/master/archetype-catalog.xml`
-4. Create a new project based on archetype
-4.1. Goto File > New > Project ... > Maven
-4.2. Select Maven Project & press Next button
-4.3. Use default location & press Next button
-4.4. Select Catalog you added in 3.2
-4.5. Select the archetype with artifact id `knime-python-node-archetype` & press Next button
-4.6. Fill in the form & press Finish button
+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 remote catalog with `https://github.com/3D-e-Chem/knime-python-node-archetype/raw/master/archetype-catalog.xml`
+
+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 step 4.2
+      5. Select the archetype with artifact id `tknime-python-node-archetype` & press Next button
+      6. Fill in the form & press Finish button
+
+Further instructions about generated project can be found in it's README.md file.
 
 ## New release
 
 1. Adjust version in pom.xml
-2. Update CHANGELOG.md & README.md & archetype-catalog.xml
+2. Update CHANGELOG.md & README.md & archetype-catalog.xml & CITATION.cff
 3. Commit & push
-4. Create GitHub release
-5. Correct License in the Zenodo entry and publish the entry
+4. Test archetype by running `mvn verify`
+5. Create GitHub release
 6. Deploy to Bintray, see Deploy chapter below
 
 ### Deploy
@@ -125,11 +131,13 @@ To deploy current version to Bintray.
 1. Add bintray API key to [~/.m2/settings.xml](https://maven.apache.org/settings.html)
 
 ```
-<server>
-    <id>bintray-nlesc-knime-python-node-archetype</id>
-    <username>************</username>
-    <password>********************************</password>
-</server>
+<servers>
+    <server>
+        <id>bintray-nlesc-knime-python-node-archetype</id>
+        <username>************</username>
+        <password>********************************</password>
+    </server>
+<servers>
 ```
 
 2. Run `mvn deploy`
diff --git a/archetype-catalog.xml b/archetype-catalog.xml
@@ -6,7 +6,7 @@
     <archetype>
       <groupId>nl.esciencecenter</groupId>
       <artifactId>knime-python-node-archetype</artifactId>
-      <version>1.4.0</version>
+      <version>2.0.0</version>
       <description>knime.node.archetype</description>
       <repository>https://dl.bintray.com/nlesc/knime-python-node-archetype</repository>
     </archetype>
diff --git a/pom.xml b/pom.xml
@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>nl.esciencecenter</groupId>
     <artifactId>knime-python-node-archetype</artifactId>
-    <version>1.4.0</version>
+    <version>2.0.0</version>
     <name>Archetype - KNIME Python node</name>
     <packaging>maven-archetype</packaging>
     <licenses>
@@ -29,7 +29,7 @@
     </ciManagement>
 
 	<properties>
-		<archetype.version>3.0.0</archetype.version>
+		<archetype.version>3.0.1</archetype.version>
 	</properties>
 
     <build>
diff --git a/src/main/resources/META-INF/maven/archetype-metadata.xml b/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>3.5</defaultValue>
+        <defaultValue>4.0</defaultValue>
 		</requiredProperty>
 		<requiredProperty key="github_organization" />
 		<requiredProperty key="github_repository" />
@@ -27,6 +27,8 @@
 			<includes>
 				<include>README.md</include>
 				<include>.travis.yml</include>
+			        <include>.zenodo.json</include>
+			        <include>CITATION.cff</include>
 			</includes>
 		</fileSet>
 		<fileSet encoding="UTF-8">
@@ -129,5 +131,15 @@
 				</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>
+</archetype-descriptor>
diff --git a/src/main/resources/archetype-resources/.gitignore b/src/main/resources/archetype-resources/.gitignore
@@ -1,4 +1,5 @@
 *.class
+*.pyc
 
 # Mobile Tools for Java (J2ME)
 .mtj.tmp/
diff --git a/src/main/resources/archetype-resources/.travis.yml b/src/main/resources/archetype-resources/.travis.yml
@@ -4,13 +4,12 @@
 ${symbol_pound} To trigger a Travis-CI build for every GitHub push or Pull Request:
 ${symbol_pound} 1. Goto https://travis-ci.org/profile/${github_organization}
 ${symbol_pound} 2. Flip the switch for the `${github_repository}` repo
-sudo: false
 language: java
 matrix:
  fast_finish: true
  include:
  - os: linux
-   jdk: oraclejdk8
+   jdk: openjdk8
    script: xvfb-run mvn verify -B
    before_install:
     - if [ ! -e $HOME/conda/bin/activate ]; then
diff --git a/src/main/resources/archetype-resources/.zenodo.json b/src/main/resources/archetype-resources/.zenodo.json
@@ -0,0 +1,4 @@
+{
+    "title": "${node}",
+    "license": "Apache-2.0"
+}
diff --git a/src/main/resources/archetype-resources/CITATION.cff b/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}
diff --git a/src/main/resources/archetype-resources/README.md b/src/main/resources/archetype-resources/README.md
@@ -52,40 +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 + Python wrapper
-
-    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/${knime_version}
-      * http://download.eclipse.org/eclipse/updates/4.6
-      * http://download.eclipse.org/releases/neon
-      * https://3d-e-chem.github.io/updates (only required for 3D-e-Chem node)
-
-    3. Goto Help -> Check for updates
-    4. Install any updates found & restart
-    5. Goto Help > Install new software ...
-    6. Select --All Available sites-- in work with pulldown
-    7. Wait for list to be filled, `Pending...` should disappear
-    8. Select the following items:
-
-      * m2e - Maven integration for Eclipse (includes Incubating components)
-      * Test KNIME workflows from a Junit test
-      * Splash & node category for 3D-e-Chem KNIME nodes (only required for 3D-e-Chem node)
-      * Abstract Python wrapper KNIME node and helpers
+${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
 
@@ -94,7 +74,7 @@ Tests can be executed with `mvn verify`, they will be run in a separate KNIME en
 Test results will be written to `test/target/surefire-reports` directory.
 Code coverage reports (html+xml) can be found in the `tests/target/jacoco/report/` directory.
 
-The tests can be run against a different KNIME version using `mvn verify -Dknime.version=3.5` where `3.5` is the major.minor version of KNIME.
+The tests can be run against a different KNIME version using `mvn verify -Dtarget.file=KNIME-AP-4.1` where `4.1` is the major.minor version of KNIME and `KNIME-AP-4.1` is a target platform definition file called `targetplatform/KNIME-AP-4.1.target`.
 
 ${symbol_pound}${symbol_pound}${symbol_pound} Unit tests
 
@@ -104,6 +84,8 @@ ${symbol_pound}${symbol_pound}${symbol_pound} Workflow tests
 
 See https://github.com/3D-e-Chem/knime-testflow${symbol_pound}3-add-test-workflow
 
+The tests expect a `python3` executable in PATH with numpy, pandas and protobuf packages installed.
+
 ${symbol_pound}${symbol_pound} Speed up builds
 
 Running mvn commands can take a long time as Tycho fetches indices of all p2 update sites.
@@ -124,3 +106,4 @@ ${symbol_pound} New release
   1. Correct authors
   2. Correct license
 9. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
+10. Update `CITATION.cff` file with new DOI, version, release date
diff --git a/src/main/resources/archetype-resources/p2/category.xml b/src/main/resources/archetype-resources/p2/category.xml
@@ -7,17 +7,10 @@
    <feature id="${parentArtifactId}.feature" version="${qversion}">
       <category name="nl.esciencecenter.3D-e-Chem"/>
    </feature>
-   <feature id="${parentArtifactId}.feature.source" version="${qversion}">
-      <category name="nl.esciencecenter.3D-e-Chem.sources"/>
-   </feature>
    <category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">
       <description>
-         3D-e-Chem: Collection KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem project
-      </description>
-   </category-def>
-   <category-def name="nl.esciencecenter.3D-e-Chem.sources" label="KNIME 3D-e-Chem Contributions Sources">
-      <description>
-         3D-e-Chem Sources: Sources of KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem project
+			3D-e-Chem: Collection KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem
+			project
       </description>
    </category-def>
 </site>
diff --git a/src/main/resources/archetype-resources/plugin/META-INF/MANIFEST.MF b/src/main/resources/archetype-resources/plugin/META-INF/MANIFEST.MF
@@ -11,10 +11,10 @@ Bundle-RequiredExecutionEnvironment: JavaSE-$java_version
 Bundle-Activator: ${package}.Activator
 Bundle-Vendor: ${vendor}
 Require-Bundle: org.eclipse.core.runtime,
- org.knime.workbench.core,
- org.knime.workbench.repository,
- org.knime.base,
- nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.1,3.0.0)",
+ org.knime.workbench.core;bundle-version="[${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)",
+ nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.3,3.0.0)",
  nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-ActivationPolicy: lazy
 Bundle-ClassPath: .
diff --git a/src/main/resources/archetype-resources/pom.xml b/src/main/resources/archetype-resources/pom.xml
diff --git a/src/main/resources/archetype-resources/targetplatform/KNIME-AP-4.0.target b/src/main/resources/archetype-resources/targetplatform/KNIME-AP-4.0.target
diff --git a/src/main/resources/archetype-resources/targetplatform/pom.xml b/src/main/resources/archetype-resources/targetplatform/pom.xml
diff --git a/src/main/resources/archetype-resources/tests/META-INF/MANIFEST.MF b/src/main/resources/archetype-resources/tests/META-INF/MANIFEST.MF
diff --git a/src/main/resources/archetype-resources/tests/pom.xml b/src/main/resources/archetype-resources/tests/pom.xml
diff --git a/src/main/resources/archetype-resources/tests/src/java/__node__WorkflowTest.java b/src/main/resources/archetype-resources/tests/src/java/__node__WorkflowTest.java
diff --git a/src/test/resources/projects/basic/archetype.properties b/src/test/resources/projects/basic/archetype.properties

-Original file line number
+Diff line change
@@ @@ -0,0 +1,4 @@ @@
 +{
 +  "title": "KNIME Python node archetype",
 +  "license": "Apache-2.0"
 +}
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`*.class`
	`2`	`+*.pyc`
`2`	`3`
`3`	`4`	`# Mobile Tools for Java (J2ME)`
`4`	`5`	`.mtj.tmp/`