From eb4887aafb9c7ae5aefd3baf62cb162f9a597318 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Wed, 22 Nov 2023 11:30:52 +0100 Subject: [PATCH 1/4] Support KNIME 5.1 --- .github/workflows/build.yml | 57 +++++++++++++++++++ .mvn/extensions.xml | 8 +++ CHANGELOG.md | 6 ++ CITATION.cff | 2 - README.md | 23 ++++---- bin.linux/META-INF/MANIFEST.MF | 2 +- bin.macosx/META-INF/MANIFEST.MF | 2 +- bin.windows/META-INF/MANIFEST.MF | 2 +- bin.windows32/META-INF/MANIFEST.MF | 2 +- plugin/META-INF/MANIFEST.MF | 12 ++-- plugin/pom.xml | 2 +- .../configure/SingleStringCellFactory.java | 4 ++ pom.xml | 36 ++++++++---- ...NIME-AP-4.0.target => KNIME-AP-5.1.target} | 11 ++-- tests/META-INF/MANIFEST.MF | 10 ++-- tests/pom.xml | 38 +++++++++++-- 16 files changed, 166 insertions(+), 51 deletions(-) create mode 100644 .github/workflows/build.yml create mode 100644 .mvn/extensions.xml rename targetplatform/{KNIME-AP-4.0.target => KNIME-AP-5.1.target} (89%) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..6c06153 --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,57 @@ +# 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: Java CI with Maven + +on: + push: + branches: + - master + pull_request: + types: [opened, synchronize, reopened] + +jobs: + build: + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + java-version: 17 + distribution: 'temurin' + cache: maven + - name: Build and analyze + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any + SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} + run: xvfb-run mvn -B verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=3D-e-Chem_knime-plants + build-windows: + runs-on: windows-latest + steps: + - uses: actions/checkout@v3 + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + java-version: 17 + distribution: 'temurin' + cache: maven + - name: Build + run: mvn -B verify + build-macos: + runs-on: macos-latest + steps: + - uses: actions/checkout@v3 + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + java-version: 17 + distribution: 'temurin' + cache: maven + - name: Build + run: Xvfb :5009 & export DISPLAY=:5009 && mvn -B verify diff --git a/.mvn/extensions.xml b/.mvn/extensions.xml new file mode 100644 index 0000000..3fceb34 --- /dev/null +++ b/.mvn/extensions.xml @@ -0,0 +1,8 @@ + + + + org.eclipse.tycho + tycho-build + 2.7.5 + + diff --git a/CHANGELOG.md b/CHANGELOG.md index 361939b..61aa3db 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,12 @@ The file is formatted as described on http://keepachangelog.com/. ## [Unreleased] +## [0.3.6] 2023-11-22 + +### Changes + +- Requires KNIME 5.1 + ## [0.3.5] 2019-06-27 ### Changes diff --git a/CITATION.cff b/CITATION.cff index 7521079..54b1ead 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -24,8 +24,6 @@ authors: - given-names: Chris family-names: de Graaf affiliation: Vrije Universiteit Amsterdam -version: v0.3.5 -date-released: 2019-06-27 repository-code: https://github.com/3D-e-Chem/knime-plants license: Apache-2.0 references: diff --git a/README.md b/README.md index 39ef1b3..4987ff9 100644 --- a/README.md +++ b/README.md @@ -2,19 +2,18 @@ KNIME nodes to configure, run and analyze PLANTS protein-ligand docking -PLANTS homepage at http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants.html +PLANTS homepage at http://www.tcd.uni-konstanz.de/research/plants.php -[![Build Status Linux & OS X ](https://travis-ci.org/3D-e-Chem/knime-plants.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-plants) -[![Build status Windows ](https://ci.appveyor.com/api/projects/status/wnwuac96jd7v76ri?svg=true)](https://ci.appveyor.com/project/3D-e-Chem/knime-plants) -[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants) -[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants) +[![Java CI with Maven](https://github.com/3D-e-Chem/knime-plants/actions/workflows/build.yml/badge.svg)](https://github.com/3D-e-Chem/knime-plants/actions/workflows/build.yml) +[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-plants&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-plants) +[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-plants&metric=coverage)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-plants) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.997272.svg)](https://doi.org/10.5281/zenodo.997272) This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform build steps. # License -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). +Included in PLANTS nodes plugin is the PLANTS executable with academic license (http://www.tcd.uni-konstanz.de/research/plants.php). When installing the plugin you have to accept 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. @@ -24,13 +23,13 @@ The PLANTS KNIME nodes themselves have the Apache 2.0 license. Requirements: -* KNIME, https://www.knime.org, version 4.0 or higher +* KNIME, https://www.knime.org, version 5.1 or higher Steps to get the PLANTS KNIME node inside KNIME: 1. Goto Help > Install new software ... menu 2. Press add button -3. Fill text fields with the `https://3d-e-chem.github.io/updates` update site url. +3. Fill text fields with the `https://3d-e-chem.github.io/updates/5.1` update site url. 4. Select --all sites-- in `work with` pulldown 5. Select the node 6. Install software @@ -59,11 +58,11 @@ The update site can be used to perform a local installation. Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup: -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 +1. Install Java 17 +2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/installer) +3. Configure Java 17 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 (4.0) - nl.esciencecenter.e3dchem.knime.plants.targetplatform/KNIME-AP-4.0.target` target definition. +5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the `KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.plants.targetplatform/KNIME-AP-5.1.target` target definition. During import the Tycho Eclipse providers must be installed. diff --git a/bin.linux/META-INF/MANIFEST.MF b/bin.linux/META-INF/MANIFEST.MF index 8d4241a..f417d3b 100644 --- a/bin.linux/META-INF/MANIFEST.MF +++ b/bin.linux/META-INF/MANIFEST.MF @@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, Linux binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.linux;singleton:=true Bundle-Version: 0.3.5.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy Bundle-ClassPath: . diff --git a/bin.macosx/META-INF/MANIFEST.MF b/bin.macosx/META-INF/MANIFEST.MF index 7f69a65..c80e13c 100644 --- a/bin.macosx/META-INF/MANIFEST.MF +++ b/bin.macosx/META-INF/MANIFEST.MF @@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, MacOSX binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.macosx;singleton:=true Bundle-Version: 0.3.5.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy Bundle-ClassPath: . diff --git a/bin.windows/META-INF/MANIFEST.MF b/bin.windows/META-INF/MANIFEST.MF index 23ada35..ce1c266 100644 --- a/bin.windows/META-INF/MANIFEST.MF +++ b/bin.windows/META-INF/MANIFEST.MF @@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, Windows binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.windows;singleton:=true Bundle-Version: 0.3.5.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy Bundle-ClassPath: . diff --git a/bin.windows32/META-INF/MANIFEST.MF b/bin.windows32/META-INF/MANIFEST.MF index 95a71ff..5513c6b 100644 --- a/bin.windows32/META-INF/MANIFEST.MF +++ b/bin.windows32/META-INF/MANIFEST.MF @@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, Windows binaries 32bit Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.windows32;singleton:=true Bundle-Version: 0.3.5.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy Bundle-ClassPath: . diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index d905bca..12abc1e 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -3,15 +3,15 @@ Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.plugin;singleton:=true Bundle-Version: 0.3.5.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Activator: nl.esciencecenter.e3dchem.knime.plants.Activator Bundle-Vendor: Netherlands eScience Center Require-Bundle: org.eclipse.core.runtime, - org.knime.workbench.core;bundle-version="[4.0.0,5.0.0)", - org.knime.workbench.repository;bundle-version="[4.0.0,5.0.0)", - org.knime.base;bundle-version="[4.0.0,5.0.0)", - org.knime.core;bundle-version="[4.0.0,5.0.0)", - org.knime.chem.types;bundle-version="[4.0.0,5.0.0)", + org.knime.workbench.core;bundle-version="[4.0.0,6.0.0)", + org.knime.workbench.repository;bundle-version="[4.0.0,6.0.0)", + org.knime.base;bundle-version="[4.0.0,6.0.0)", + org.knime.core;bundle-version="[4.0.0,6.0.0)", + org.knime.chem.types;bundle-version="[4.0.0,6.0.0)", com.vernalis.knime;bundle-version="[1.20.3,2.0.0)", nl.esciencecenter.e3dchem.plugin, org.eclipse.jface diff --git a/plugin/pom.xml b/plugin/pom.xml index 9a9629a..ef24b20 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -9,7 +9,7 @@ nl.esciencecenter.e3dchem.knime.plants.plugin eclipse-plugin - ../tests/target/jacoco.exec + ../tests/target/jacoco/report/jacoco.xml ../tests/target/surefire-reports diff --git a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java index 7909aae..221c873 100644 --- a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java +++ b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java @@ -19,4 +19,8 @@ public DataCell getCell(DataRow row) { return new StringCell(content); } + @Override + public DataCell[] getCells(final DataRow row, final long rowIndex) { + return new DataCell[] { getCell(row, rowIndex) }; + } } diff --git a/pom.xml b/pom.xml index 34b6d3f..5ecb198 100644 --- a/pom.xml +++ b/pom.xml @@ -18,8 +18,8 @@ https://github.com/3D-e-Chem/knime-plants/issues - Travis CI - http://travis-ci.org/3D-e-Chem/knime-plants + GitHub actions + https://github.com/3D-e-Chem/knime-plants/issues @@ -27,15 +27,34 @@ - 1.4.0 - 1.4.0 + 2.7.5 + ${tycho.version} -Xmx512m + 0.8.10 + 17 + 3.10.1 UTF-8 UTF-8 - KNIME-AP-4.0 + 5.1 + KNIME-AP-${knime.version} scm:git:https://github.com/3D-e-Chem/knime-plants.git https://sonarcloud.io 3d-e-chem + + --add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED + --add-opens=java.base/sun.security.ssl=ALL-UNNAMED + --add-opens=java.base/sun.security.util=ALL-UNNAMED + --add-opens=java.base/java.lang=ALL-UNNAMED + --add-opens=java.base/java.lang.invoke=ALL-UNNAMED + --add-opens=java.base/java.net=ALL-UNNAMED + --add-opens=java.base/java.nio=ALL-UNNAMED + --add-opens=java.base/java.nio.channels=ALL-UNNAMED + --add-opens=java.base/java.util=ALL-UNNAMED + --add-opens=java.base/sun.nio.ch=ALL-UNNAMED + --add-opens=java.base/sun.nio=ALL-UNNAMED + --add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED + --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED + -Dmisc.io.testing=true @@ -103,11 +122,6 @@ - - org.eclipse.tycho.extras - tycho-pack200a-plugin - ${tycho.extras.version} - @@ -149,6 +163,6 @@ bin.macosx bin.windows bin.windows32 - targetplatform + targetplatform diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-5.1.target similarity index 89% rename from targetplatform/KNIME-AP-4.0.target rename to targetplatform/KNIME-AP-5.1.target index b6aa027..9b45459 100644 --- a/targetplatform/KNIME-AP-4.0.target +++ b/targetplatform/KNIME-AP-5.1.target @@ -1,7 +1,6 @@ - @@ -11,16 +10,16 @@ - + - + - + @@ -29,10 +28,10 @@ - + - + -server -Dsun.java2d.d3d=false diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index 9bbb883..712206d 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/tests/META-INF/MANIFEST.MF @@ -3,12 +3,12 @@ Bundle-ManifestVersion: 2 Bundle-Name: Tests Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.tests Bundle-Version: 0.3.5.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Require-Bundle: org.junit;bundle-version="4.12.0", - org.knime.core;bundle-version="[4.0.0,5.0.0)", - org.knime.base;bundle-version="[4.0.0,5.0.0)", - org.knime.testing;bundle-version="[4.0.0,5.0.0)", - org.knime.jsnippets;bundle-version="[4.0.0,5.0.0)", + org.knime.core;bundle-version="[4.0.0,6.0.0)", + org.knime.base;bundle-version="[4.0.0,6.0.0)", + org.knime.testing;bundle-version="[4.0.0,6.0.0)", + org.knime.jsnippets;bundle-version="[4.0.0,6.0.0)", org.eclipse.ui;bundle-version="[3.0.0,4.0.0)", org.eclipse.swtbot.junit4_x, org.eclipse.swtbot.eclipse.finder, diff --git a/tests/pom.xml b/tests/pom.xml index bc57201..d67ead7 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -17,7 +17,7 @@ org.jacoco jacoco-maven-plugin - 0.8.0 + ${jacoco.version} @@ -41,7 +41,7 @@ org.jacoco org.jacoco.ant - 0.8.0 + ${jacoco.version} ant-contrib @@ -109,7 +109,9 @@ tycho-surefire-plugin ${tycho.version} - ${tycho.testArgLine} ${tycho.test.jvmArgs} + ${tycho.testArgLine} + ${tycho.test.jvmArgs} + ${knime.ini.testArgs} true false @@ -120,15 +122,43 @@ ${tycho.version} + + + eclipse-feature + org.knime.features.clfixes + 0.0.0 + + + eclipse-feature + org.knime.features.workbench + 0.0.0 + + + eclipse-feature + org.knime.features.core + 0.0.0 + + + eclipse-feature + org.knime.features.testing.application + 0.0.0 + + + eclipse-feature + org.knime.features.base + 0.0.0 + eclipse-feature nl.esciencecenter.e3dchem.knime.plants.feature 0.0.0 - + + From b1308c78c1df5858fad8022e93ed79ac7fccd614 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Wed, 22 Nov 2023 12:33:09 +0100 Subject: [PATCH 2/4] Split binaries into own feature --- bin.feature/build.properties | 1 + bin.feature/feature.xml | 260 ++++++++++++++++++ bin.feature/pom.xml | 13 + feature/feature.xml | 43 +-- p2/category.xml | 3 + plugin/META-INF/MANIFEST.MF | 1 - .../configure/SingleStringCellFactory.java | 7 +- pom.xml | 1 + tests/pom.xml | 2 +- 9 files changed, 290 insertions(+), 41 deletions(-) create mode 100644 bin.feature/build.properties create mode 100644 bin.feature/feature.xml create mode 100644 bin.feature/pom.xml diff --git a/bin.feature/build.properties b/bin.feature/build.properties new file mode 100644 index 0000000..64f93a9 --- /dev/null +++ b/bin.feature/build.properties @@ -0,0 +1 @@ +bin.includes = feature.xml diff --git a/bin.feature/feature.xml b/bin.feature/feature.xml new file mode 100644 index 0000000..9f65cea --- /dev/null +++ b/bin.feature/feature.xml @@ -0,0 +1,260 @@ + + + + + KNIME nodes to configure, run and analyze PLANTS protein-ligand docking + + + + Copyright Netherlands eScience Center 2015 + + + + 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. + +Apache License +Version 2.0, January 2004 +http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright (c) 2012, 2013 The Nodeclipse Authors. All rights reserved. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + + + + + + + + + + diff --git a/bin.feature/pom.xml b/bin.feature/pom.xml new file mode 100644 index 0000000..9076147 --- /dev/null +++ b/bin.feature/pom.xml @@ -0,0 +1,13 @@ + + + 4.0.0 + + + nl.esciencecenter.e3dchem.knime.plants + nl.esciencecenter.e3dchem.knime.plants + 0.3.5-SNAPSHOT + + + nl.esciencecenter.e3dchem.knime.plants.bin.feature + eclipse-feature + diff --git a/feature/feature.xml b/feature/feature.xml index 2261bd9..d064d6e 100644 --- a/feature/feature.xml +++ b/feature/feature.xml @@ -3,9 +3,7 @@ id="nl.esciencecenter.e3dchem.knime.plants.feature" label="KNIME PLANTS extension" version="0.3.5.qualifier" - provider-name="Netherlands eScience Center" - os="linux,macosx,win32" - arch="x86,x86_64"> + provider-name="Netherlands eScience Center"> KNIME nodes to configure, run and analyze PLANTS protein-ligand docking @@ -228,6 +226,10 @@ http://www.apache.org/licenses/ + + - - - - - - - diff --git a/p2/category.xml b/p2/category.xml index 299ddf9..dbe19c7 100644 --- a/p2/category.xml +++ b/p2/category.xml @@ -1,5 +1,8 @@ + + + diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index 12abc1e..028d6d5 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -21,4 +21,3 @@ Bundle-ClassPath: ., Export-Package: nl.esciencecenter.e3dchem.knime.plants, nl.esciencecenter.e3dchem.knime.plants.configure, nl.esciencecenter.e3dchem.knime.plants.run -Eclipse-PlatformFilter: (| (& (osgi.arch=x86) (osgi.os=win32)) (& (osgi.arch=x86_64) (| (osgi.os=macosx) (osgi.os=linux) (osgi.os=win32)))) diff --git a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java index 221c873..1c26ab3 100644 --- a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java +++ b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/plants/configure/SingleStringCellFactory.java @@ -19,8 +19,13 @@ public DataCell getCell(DataRow row) { return new StringCell(content); } + @Override + public DataCell[] getCells(final DataRow row) { + return new DataCell[] { getCell(row) }; + } + @Override public DataCell[] getCells(final DataRow row, final long rowIndex) { - return new DataCell[] { getCell(row, rowIndex) }; + return new DataCell[] { getCell(row) }; } } diff --git a/pom.xml b/pom.xml index 5ecb198..e238e84 100644 --- a/pom.xml +++ b/pom.xml @@ -163,6 +163,7 @@ bin.macosx bin.windows bin.windows32 + bin.feature targetplatform diff --git a/tests/pom.xml b/tests/pom.xml index d67ead7..06b34e4 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -152,7 +152,7 @@ eclipse-feature - nl.esciencecenter.e3dchem.knime.plants.feature + nl.esciencecenter.e3dchem.knime.plants.bin.feature 0.0.0 From dc006f00fd5d9d3f4f28ce5a0571a8dd9354969c Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Wed, 22 Nov 2023 13:05:00 +0100 Subject: [PATCH 3/4] Dont run test suite on non-linux, just build and test PLANTS executable --- .github/workflows/build.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 6c06153..a4584c4 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -42,7 +42,9 @@ jobs: distribution: 'temurin' cache: maven - name: Build - run: mvn -B verify + run: mvn -B package + - name: Test executable + run: bin.windows/src/main/resources/bin/PLANTS build-macos: runs-on: macos-latest steps: @@ -54,4 +56,6 @@ jobs: distribution: 'temurin' cache: maven - name: Build - run: Xvfb :5009 & export DISPLAY=:5009 && mvn -B verify + run: mvn package + - name: Test executable + run: bin.macosx/src/main/resources/bin/PLANTS From 50a69a66b78acf259e75fa879c6d386328b8dd5d Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Wed, 22 Nov 2023 13:07:06 +0100 Subject: [PATCH 4/4] Bump to 0.3.6 --- bin.feature/feature.xml | 2 +- bin.feature/pom.xml | 2 +- bin.linux/META-INF/MANIFEST.MF | 2 +- bin.linux/pom.xml | 2 +- bin.macosx/META-INF/MANIFEST.MF | 2 +- bin.macosx/pom.xml | 2 +- bin.windows/META-INF/MANIFEST.MF | 2 +- bin.windows/pom.xml | 2 +- bin.windows32/META-INF/MANIFEST.MF | 2 +- bin.windows32/pom.xml | 2 +- feature/feature.xml | 2 +- feature/pom.xml | 2 +- p2/category.xml | 4 ++-- p2/pom.xml | 2 +- plugin/META-INF/MANIFEST.MF | 2 +- plugin/pom.xml | 2 +- pom.xml | 2 +- targetplatform/pom.xml | 2 +- tests/META-INF/MANIFEST.MF | 2 +- tests/pom.xml | 2 +- 20 files changed, 21 insertions(+), 21 deletions(-) diff --git a/bin.feature/feature.xml b/bin.feature/feature.xml index 9f65cea..2751c6d 100644 --- a/bin.feature/feature.xml +++ b/bin.feature/feature.xml @@ -2,7 +2,7 @@ diff --git a/bin.feature/pom.xml b/bin.feature/pom.xml index 9076147..1197531 100644 --- a/bin.feature/pom.xml +++ b/bin.feature/pom.xml @@ -5,7 +5,7 @@ nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants.bin.feature diff --git a/bin.linux/META-INF/MANIFEST.MF b/bin.linux/META-INF/MANIFEST.MF index f417d3b..b2de56e 100644 --- a/bin.linux/META-INF/MANIFEST.MF +++ b/bin.linux/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, Linux binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.linux;singleton:=true -Bundle-Version: 0.3.5.qualifier +Bundle-Version: 0.3.6.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy diff --git a/bin.linux/pom.xml b/bin.linux/pom.xml index 823e2d8..5317d01 100644 --- a/bin.linux/pom.xml +++ b/bin.linux/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants.bin.linux diff --git a/bin.macosx/META-INF/MANIFEST.MF b/bin.macosx/META-INF/MANIFEST.MF index c80e13c..2fd91b2 100644 --- a/bin.macosx/META-INF/MANIFEST.MF +++ b/bin.macosx/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, MacOSX binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.macosx;singleton:=true -Bundle-Version: 0.3.5.qualifier +Bundle-Version: 0.3.6.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy diff --git a/bin.macosx/pom.xml b/bin.macosx/pom.xml index 8c75241..8b6ef99 100644 --- a/bin.macosx/pom.xml +++ b/bin.macosx/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants.bin.macosx diff --git a/bin.windows/META-INF/MANIFEST.MF b/bin.windows/META-INF/MANIFEST.MF index ce1c266..68ef5a6 100644 --- a/bin.windows/META-INF/MANIFEST.MF +++ b/bin.windows/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, Windows binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.windows;singleton:=true -Bundle-Version: 0.3.5.qualifier +Bundle-Version: 0.3.6.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy diff --git a/bin.windows/pom.xml b/bin.windows/pom.xml index f461d91..33a2f30 100644 --- a/bin.windows/pom.xml +++ b/bin.windows/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants.bin.windows diff --git a/bin.windows32/META-INF/MANIFEST.MF b/bin.windows32/META-INF/MANIFEST.MF index 5513c6b..b374fd4 100644 --- a/bin.windows32/META-INF/MANIFEST.MF +++ b/bin.windows32/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS, Windows binaries 32bit Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.windows32;singleton:=true -Bundle-Version: 0.3.5.qualifier +Bundle-Version: 0.3.6.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy diff --git a/bin.windows32/pom.xml b/bin.windows32/pom.xml index a3654bd..f23628c 100644 --- a/bin.windows32/pom.xml +++ b/bin.windows32/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants.bin.windows32 diff --git a/feature/feature.xml b/feature/feature.xml index d064d6e..c4c2181 100644 --- a/feature/feature.xml +++ b/feature/feature.xml @@ -2,7 +2,7 @@ diff --git a/feature/pom.xml b/feature/pom.xml index 89ea3b4..57cfd63 100644 --- a/feature/pom.xml +++ b/feature/pom.xml @@ -5,7 +5,7 @@ nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants.feature diff --git a/p2/category.xml b/p2/category.xml index dbe19c7..0637752 100644 --- a/p2/category.xml +++ b/p2/category.xml @@ -1,9 +1,9 @@ - + - + diff --git a/p2/pom.xml b/p2/pom.xml index 589ff7f..86b5d02 100644 --- a/p2/pom.xml +++ b/p2/pom.xml @@ -4,7 +4,7 @@ nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants.p2 eclipse-repository diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index 028d6d5..67375ef 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: KNIME nodes for PLANTS Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.plugin;singleton:=true -Bundle-Version: 0.3.5.qualifier +Bundle-Version: 0.3.6.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Activator: nl.esciencecenter.e3dchem.knime.plants.Activator Bundle-Vendor: Netherlands eScience Center diff --git a/plugin/pom.xml b/plugin/pom.xml index ef24b20..865dfce 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -4,7 +4,7 @@ nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants.plugin eclipse-plugin diff --git a/pom.xml b/pom.xml index e238e84..011bf4b 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT pom diff --git a/targetplatform/pom.xml b/targetplatform/pom.xml index e47db46..562e636 100644 --- a/targetplatform/pom.xml +++ b/targetplatform/pom.xml @@ -20,7 +20,7 @@ Contributors: nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index 712206d..8c34047 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/tests/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: Tests Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.tests -Bundle-Version: 0.3.5.qualifier +Bundle-Version: 0.3.6.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Require-Bundle: org.junit;bundle-version="4.12.0", org.knime.core;bundle-version="[4.0.0,6.0.0)", diff --git a/tests/pom.xml b/tests/pom.xml index 06b34e4..be5d601 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -6,7 +6,7 @@ nl.esciencecenter.e3dchem.knime.plants nl.esciencecenter.e3dchem.knime.plants - 0.3.5-SNAPSHOT + 0.3.6-SNAPSHOT nl.esciencecenter.e3dchem.knime.plants.tests