Merge pull request #14 from 3D-e-Chem/knime-43

Reintroduce kripo and sygma nodes
3D-e-Chem · Feb 12, 2021 · 0727ec5 · 0727ec5
2 parents 6fab8ba + 9a8345d
commit 0727ec5
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,29 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Package
+
+on:
+  push:
+  pull_request:
+    types:
+      - "opened"
+      - "reopened"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 1.8
+      uses: actions/setup-java@v1
+      with:
+        java-version: 1.8
+    - name: Cache Maven packages
+      uses: actions/cache@v2
+      with:
+        path: ~/.m2
+        key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml', '**/MANIFEST.MF', 'targetplatform/*.target') }}
+        restore-keys: ${{ runner.os }}-m2
+    - name: Build with Maven
+      run: mvn -B package --file pom.xml
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 KNIME feature for all 3D-e-Chem nodes.
 
-[![Build Status](https://travis-ci.org/3D-e-Chem/knime-node-collection.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-node-collection)
+[![Java CI with Maven](https://github.com/3D-e-Chem/knime-node-collection./workflows/Package/badge.svg)](https://github.com/3D-e-Chem/knime-node-collection./actions?query=workflow%3A%22Package%22)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1168906.svg)](https://doi.org/10.5281/zenodo.1168906)
 
 The 3D-e-chem project of the Netherlands eScience Center, VU Medicinal Chemistry, CMBI Radboud University made a set of KNIME nodes listed at https://www.knime.com/3d-e-chem-nodes-for-knime, this repository combines all the nodes into a single feature which can be installed from the
@@ -12,7 +12,7 @@ This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform bui
 
 Requirements:
 
-* KNIME, https://www.knime.org, version 4.0 or higher
+- KNIME, https://www.knime.org, version 4.3 or higher
 
 Steps to get the 3D-e-Chem nodes inside KNIME:
 
@@ -36,15 +36,15 @@ When using this update site in KNIME, it will list a single feature for all 3D-e
 
 Cons of using this repo:
 
-* New nodes need to be tracked in the feature/feature.xml file
-* Each update of a node requires a new release of this repo aswell
-* License is for all nodes together instead of separate license for each node
-* Maintenance overhead of 2 update sites (1. only one 3D-e-Chem nodes feature, 2. set of 3D-e-Chem node features)
+- New nodes need to be tracked in the feature/feature.xml file
+- Each update of a node requires a new release of this repo aswell
+- License is for all nodes together instead of separate license for each node
+- Maintenance overhead of 2 update sites (1. only one 3D-e-Chem nodes feature, 2. set of 3D-e-Chem node features)
 
 Pros of using this repo:
 
-* Single checkbox to install all 3D-e-Chem nodes
-* Integrated into KNIME Community Contributions update site under `KNIME Community nodes - Cheminformatics` folder. Users do not need to configure an extra update site.
+- Single checkbox to install all 3D-e-Chem nodes
+- Integrated into KNIME Community Contributions update site under `KNIME Community nodes - Cheminformatics` folder. Users do not need to configure an extra update site.
 
 So to have the latest version of each node you should use `https://3d-e-chem.github.io/updates`, but for stable releases use `https://3d-e-chem.github.io/knime-node-collection`.
 
@@ -82,34 +82,34 @@ During import the Tycho Eclipse providers must be installed.
 
 1. Make sure the local clone of this repo is up to date using
 
-    ```
-    git pull
-    ```
+   ```
+   git pull
+   ```
 
 2. Make sure all included plugins are up to date on https://3d-e-chem.github.io/updates or https://github.com/3D-e-Chem/3D-e-Chem.github.io/tree/master/updates
 3. Learn current version by looking in `./pom.xml` file for the `<version>x.y.z-SNAPSHOT</version>` tag.
 4. Increase version. Increase minor version when KNIME node has been added or removed. Increase patch version when KNIME node has been updated. Use following command to update multiple xml files with the new version.
 
-    ```
-    mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<new version>-SNAPSHOT
-    ```
+   ```
+   mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<new version>-SNAPSHOT
+   ```
 
 5. Commit changes
-6. Update `docs/` directory with new update site using
+6. Update `docs/4.3/` directory with new update site using
 
-    ```
-    mvn install
-    ```
+   ```
+   mvn install
+   ```
 
 7. Stage new files, commit and push changes.
 
-    ```
-    git add docs/
-    git commit -a
-    git push
-    ```
+   ```
+   git add docs/
+   git commit -a
+   git push
+   ```
 
 8. For major or minor release
 
-  * add message to https://www.knime.com/forum/3d-e-chem-nodes
-  * create a GitHub release and DOI entry
+- add message to https://www.knime.com/forum/3d-e-chem-nodes
+- create a GitHub release and DOI entry
diff --git a/docs/4.3/artifacts.jar b/docs/4.3/artifacts.jar
diff --git a/docs/4.3/content.jar b/docs/4.3/content.jar
diff --git a/docs/4.3/features/nl.esciencecenter.e3dchem.collection.feature_1.6.0.v202102121219.jar b/docs/4.3/features/nl.esciencecenter.e3dchem.collection.feature_1.6.0.v202102121219.jar
diff --git a/docs/4.3/plugins/nl.esciencecenter.e3dchem.kripodb.plugin_3.0.0.v202102121204.jar b/docs/4.3/plugins/nl.esciencecenter.e3dchem.kripodb.plugin_3.0.0.v202102121204.jar
diff --git a/docs/4.3/plugins/nl.esciencecenter.e3dchem.python.plugin_2.0.4.v202101141233.jar b/docs/4.3/plugins/nl.esciencecenter.e3dchem.python.plugin_2.0.4.v202101141233.jar
diff --git a/docs/4.3/plugins/nl.esciencecenter.e3dchem.sygma.plugin_2.0.0.v202102121148.jar b/docs/4.3/plugins/nl.esciencecenter.e3dchem.sygma.plugin_2.0.0.v202102121148.jar
diff --git a/feature/feature.xml b/feature/feature.xml
@@ -1,22 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<feature
-      id="nl.esciencecenter.e3dchem.collection.feature"
-      label="3D-e-Chem KNIME nodes"
-      version="1.5.0.qualifier"
-      provider-name="Netherlands eScience Center &amp; Division of Medicinal Chemistry - VU University Amsterdam &amp; CMBI Radboud University"
-      plugin="nl.esciencecenter.e3dchem.plugin"
-      os="linux,macosx,win32"
-      arch="x86_64,x86">
-
-   <description url="https://3d-e-chem.github.io">
+<feature id="nl.esciencecenter.e3dchem.collection.feature" label="3D-e-Chem KNIME nodes" version="1.6.0.qualifier" provider-name="Netherlands eScience Center &amp; Division of Medicinal Chemistry - VU University Amsterdam &amp; CMBI Radboud University" plugin="nl.esciencecenter.e3dchem.plugin" os="linux,macosx,win32" arch="x86_64,x86">
+
+  <description url="https://3d-e-chem.github.io">
       Collection of 3D-e-Chem KNIME nodes. Nodes build for 3D-e-Chem project (https://3d-e-chem.github.io/).
-   </description>
+  </description>
 
-   <copyright url="https://3d-e-chem.github.io">
+  <copyright url="https://3d-e-chem.github.io">
       Copyright Netherlands eScience Center &amp; Division of Medicinal Chemistry - VU University Amsterdam &amp; CMBI Radboud University 2017
-   </copyright>
+  </copyright>
 
-   <license url="http://www.gnu.org/licenses/gpl-3.0.txt">
+  <license url="http://www.gnu.org/licenses/gpl-3.0.txt">
       Included in PLANTS nodes plugin is the PLANTS executable with academic license (http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants.html).
 By accepting this license agreement, you agree to use the included PLANTS executable only for academic usage.
 To use these nodes in a commercial manner you need to acquire a valid license yourself and configure the PLANTS node to use the commercial executable.
@@ -698,137 +691,49 @@ may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
 &lt;http://www.gnu.org/philosophy/why-not-lgpl.html&gt;.
-   </license>
-
-   <url>
-      <update label="Update site" url="https://3d-e-chem.github.io/updates"/>
-      <discovery label="Discovery site" url="https://3d-e-chem.github.io"/>
-   </url>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.pharmacophore.plugin"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.gpcrdb"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.modifiedtanimoto"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.sstea.plugin"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.molviewer.plugin"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.vu_compmedchem.klifs"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.silicosit.plugin"
-         os="linux,macosx"
-         arch="x86_64"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.plants.plugin"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.plugin"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.molviewer.server"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.plants.bin.linux"
-         os="linux"
-         arch="x86_64"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         fragment="true"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.plants.bin.macosx"
-         os="macosx"
-         arch="x86_64"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         fragment="true"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.plants.bin.windows"
-         os="win32"
-         arch="x86_64"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         fragment="true"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.plants.bin.windows32"
-         os="win32"
-         arch="x86"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         fragment="true"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.silicosit.bin.linux"
-         os="linux"
-         arch="x86_64"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         fragment="true"/>
-
-   <plugin
-         id="nl.esciencecenter.e3dchem.knime.silicosit.bin.macosx"
-         os="macosx"
-         arch="x86_64"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         fragment="true"/>
+  </license>
+
+  <url>
+    <update label="Update site" url="https://3d-e-chem.github.io/updates"/>
+    <discovery label="Discovery site" url="https://3d-e-chem.github.io"/>
+  </url>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.pharmacophore.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.gpcrdb" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.modifiedtanimoto" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.sstea.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.kripodb.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.sygma.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.molviewer.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.vu_compmedchem.klifs" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.silicosit.plugin" os="linux,macosx" arch="x86_64" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.plants.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.python.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.plugin" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.molviewer.server" download-size="0" install-size="0" version="0.0.0" unpack="false"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.plants.bin.linux" os="linux" arch="x86_64" download-size="0" install-size="0" version="0.0.0" fragment="true"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.plants.bin.macosx" os="macosx" arch="x86_64" download-size="0" install-size="0" version="0.0.0" fragment="true"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.plants.bin.windows" os="win32" arch="x86_64" download-size="0" install-size="0" version="0.0.0" fragment="true"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.plants.bin.windows32" os="win32" arch="x86" download-size="0" install-size="0" version="0.0.0" fragment="true"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.silicosit.bin.linux" os="linux" arch="x86_64" download-size="0" install-size="0" version="0.0.0" fragment="true"/>
+
+  <plugin id="nl.esciencecenter.e3dchem.knime.silicosit.bin.macosx" os="macosx" arch="x86_64" download-size="0" install-size="0" version="0.0.0" fragment="true"/>
 
 </feature>
diff --git a/feature/pom.xml b/feature/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.collection</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.collection</artifactId>
-		<version>1.5.0-SNAPSHOT</version>
+		<version>1.6.0-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.collection.feature</artifactId>

diff --git a/p2/category.xml b/p2/category.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-	<feature url="features/nl.esciencecenter.e3dchem.collection.feature-1.5.0.qualifier.jar"
-		id="nl.esciencecenter.e3dchem.collection.feature" version="1.5.0.qualifier">
+	<feature url="features/nl.esciencecenter.e3dchem.collection.feature-1.6.0.qualifier.jar"
+		id="nl.esciencecenter.e3dchem.collection.feature" version="1.6.0.qualifier">
 		<category name="org.knime.community.build.config/category.xml.cheminf" />
 	</feature>
 	<category-def name="org.knime.community.build.config/category.xml.cheminf" label="KNIME Community Contributions - Cheminformatics">

diff --git a/p2/pom.xml b/p2/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<artifactId>nl.esciencecenter.e3dchem.collection</artifactId>
 		<groupId>nl.esciencecenter.e3dchem.collection</groupId>
-		<version>1.5.0-SNAPSHOT</version>
+		<version>1.6.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.collection.p2</artifactId>
 	<packaging>eclipse-repository</packaging>

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>nl.esciencecenter.e3dchem.collection</groupId>
 	<artifactId>nl.esciencecenter.e3dchem.collection</artifactId>
-	<version>1.5.0-SNAPSHOT</version>
+	<version>1.6.0-SNAPSHOT</version>
 	<packaging>pom</packaging>
 
 	<scm>