From 82582e2ea8ce36f98195f206d3b8da00366ab613 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Wed, 22 Nov 2023 08:46:57 +0100 Subject: [PATCH 1/3] Support KNIME 5.1 --- .github/workflows/build.yml | 38 +++++---------- .mvn/extensions.xml | 8 ++++ CHANGELOG.md | 12 ++++- CITATION.cff | 1 - README.md | 16 +++---- plugin/META-INF/MANIFEST.MF | 8 ++-- plugin/pom.xml | 2 +- pom.xml | 34 ++++++++++---- .../KNIME Analytics Platform.launch | 2 +- ...NIME-AP-4.0.target => KNIME-AP-5.1.target} | 40 ++++++++-------- tests/META-INF/MANIFEST.MF | 8 ++-- tests/pom.xml | 47 +++++++++++++++++-- 12 files changed, 137 insertions(+), 79 deletions(-) create mode 100644 .mvn/extensions.xml rename targetplatform/{KNIME-AP-4.0.target => KNIME-AP-5.1.target} (50%) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 03b73d3..431f5b8 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -5,10 +5,10 @@ name: Java CI with Maven on: push: + branches: + - master pull_request: - types: - - "opened" - - "reopened" + types: [opened, synchronize, reopened] jobs: build: @@ -17,29 +17,17 @@ jobs: run: shell: bash -l {0} steps: - - uses: actions/checkout@v2 - - name: Set up JDK 1.8 - uses: actions/setup-java@v1 + - uses: actions/checkout@v3 with: - java-version: 1.8 - - name: Cache Maven packages - uses: actions/cache@v2 + fetch-depth: 0 + - name: Set up JDK 17 + uses: actions/setup-java@v3 with: - path: ~/.m2 - key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml', '**/MANIFEST.MF', 'targetplatform/*.target') }} - restore-keys: ${{ runner.os }}-m2 - - name: OS dependencies - run: sudo apt-get install xvfb - - name: Build with Maven - run: mvn -B package - - name: Run tests - run: xvfb-run mvn verify -B - - name: Set up JDK 11 for SonarCloud analysis - uses: actions/setup-java@v1 - with: - java-version: 11 - - name: SonarCloud analysis - run: mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN + java-version: 17 + distribution: 'temurin' + cache: maven + - name: Build and analyze env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + 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-kripodb 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 7239129..68e7ac4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,9 +6,15 @@ The file is formatted as described on http://keepachangelog.com/. ## Unreleased +## [3.0.1] - 2023-11-22 + +### Changed + +- Require KNIME 5.1 + ## [3.0.0] - 2021-02-12 -## Removed +### Removed - Python based nodes in favour of web service nodes ([#25](https://github.com/3D-e-Chem/knime-kripodb/issues/25)) @@ -171,7 +177,9 @@ Version >= 2.0.0 uses KripoDB Knime node which have there own dialog with combo - Python templates to use KripoDB package - Example workflow on Github repo. -[unreleased]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.5.0...HEAD +[unreleased]: https://github.com/3D-e-Chem/knime-kripodb/compare/v3.0.1...HEAD +[2.5.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v3.0.0...v3.0.1 +[2.5.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.5.0...v3.0.0 [2.5.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.4.2...v2.5.0 [2.4.2]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.3.1...v2.4.2 [2.4.1]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.3.0...v2.3.1 diff --git a/CITATION.cff b/CITATION.cff index 93e6353..5d61a47 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -9,6 +9,5 @@ authors: family-names: Verhoeven affiliation: Netherlands eScience Center orcid: https://orcid.org/0000-0002-5821-2060 -date-released: 2019-07-02 repository-code: https://github.com/3D-e-Chem/knime-kripodb license: GPL-3.0 diff --git a/README.md b/README.md index 3883911..1fa23e6 100644 --- a/README.md +++ b/README.md @@ -5,15 +5,15 @@ KRIPO stands for [Key Representation of Interaction in POckets](http://dx.doi.or [KNIME](http://www.knime.org) nodes for KripoDB (https://github.com/3D-e-Chem/kripodb). [![Java CI with Maven](https://github.com/3D-e-Chem/knime-kripodb/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/3D-e-Chem/knime-kripodb/actions?query=workflow%3A%22Java+CI+with+Maven%22) -[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb) -[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb) +[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-kripodb&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-kripodb) +[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-kripodb&metric=coverage)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-kripodb) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597262.svg)](https://doi.org/10.5281/zenodo.597262) # Installation Requirements: -- KNIME, https://www.knime.org, version 4.0 or higher +- KNIME, https://www.knime.org, version 5.1 or higher Optionally: @@ -24,7 +24,7 @@ Steps to get KripoDB nodes inside KNIME: 1. Goto Help > Install new software ... menu 2. Press add button -3. Fill text fields with `https://3d-e-chem.github.io/updates` +3. Fill text fields with `https://3d-e-chem.github.io/updates/5.1` 4. Select --all sites-- in work with pulldown 5. Open KNIME 3D-e-Chem Contributions folder 6. Select KripoDB @@ -45,11 +45,11 @@ Development requirements: 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.kripodb.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.kripodb.targetplatform/KNIME-AP-5.1.target` target definition. 6. A KNIME Analytics Platform instance can be started by right clicking on the `targetplatform/KNIME\ Analytics\ Platform.launch` file and selecting `Run As → KNIME Analytics Platform`. The KNIME instance will contain the target platform together with all extensions defined in the workspace. During import the Tycho Eclipse providers must be installed. diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index 00c1713..66731c3 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -3,11 +3,11 @@ Bundle-ManifestVersion: 2 Bundle-Name: 3D-e-Chem KNIME KripoDB nodes Bundle-SymbolicName: nl.esciencecenter.e3dchem.kripodb.plugin;singleton:=true Bundle-Version: 3.0.0.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Activator: nl.esciencecenter.e3dchem.kripodb.Activator -Require-Bundle: org.knime.core;bundle-version="[4.0.0,5.0.0)", - org.knime.base;bundle-version="[4.0.0,5.0.0)", - org.knime.chem.types;bundle-version="[4.0.0,5.0.0)", +Require-Bundle: org.knime.core;bundle-version="[4.0.0,6.0.0)", + org.knime.base;bundle-version="[4.0.0,6.0.0)", + org.knime.chem.types;bundle-version="[4.0.0,6.0.0)", org.rdkit.knime.types, nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)", nl.esciencecenter.e3dchem.knime.pharmacophore.plugin;bundle-version="[1.0.0,2.0.0)" diff --git a/plugin/pom.xml b/plugin/pom.xml index 7607aef..8e5a623 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -11,7 +11,7 @@ nl.esciencecenter.e3dchem.kripodb.plugin eclipse-plugin - ../tests/target/jacoco.exec + ../tests/target/report/jacoco.xml ../tests/target/surefire-reports src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/**/* diff --git a/pom.xml b/pom.xml index b98d405..d2917ec 100644 --- a/pom.xml +++ b/pom.xml @@ -26,8 +26,8 @@ - Travis CI - http://travis-ci.org/3D-e-Chem/knime-kripodb + GitHub actions + https://github.com/3D-e-Chem/knime-kripodb/actions @@ -43,15 +43,34 @@ - 1.4.0 - 1.4.0 + 2.7.5 + ${tycho.version} -Xmx512m + 0.8.10 + 17 + 3.10.1 UTF-8 UTF-8 scm:git:https://github.com/3D-e-Chem/knime-kripodb.git - KNIME-AP-4.0 + 5.1 + KNIME-AP-${knime.version} 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 @@ -119,11 +138,6 @@ - - org.eclipse.tycho.extras - tycho-pack200a-plugin - ${tycho.extras.version} - diff --git a/targetplatform/KNIME Analytics Platform.launch b/targetplatform/KNIME Analytics Platform.launch index 26777e0..6ff97de 100644 --- a/targetplatform/KNIME Analytics Platform.launch +++ b/targetplatform/KNIME Analytics Platform.launch @@ -15,7 +15,7 @@ - + diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-5.1.target similarity index 50% rename from targetplatform/KNIME-AP-4.0.target rename to targetplatform/KNIME-AP-5.1.target index 54c6699..3fcde71 100644 --- a/targetplatform/KNIME-AP-4.0.target +++ b/targetplatform/KNIME-AP-5.1.target @@ -1,7 +1,8 @@ - + + - - + + @@ -11,27 +12,26 @@ - + - - + - - - - - - - - - - - + + + + + + + + + + - - + + -server -Dsun.java2d.d3d=false -Dosgi.classloader.lock=classname @@ -46,4 +46,4 @@ -Dsun.net.client.defaultReadTimeout=0 -Dorg.eclipse.swt.internal.gtk.disablePrinting - \ No newline at end of file + diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index 4251e5d..3f886f7 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/tests/META-INF/MANIFEST.MF @@ -3,11 +3,11 @@ Bundle-ManifestVersion: 2 Bundle-Name: Tests Bundle-SymbolicName: nl.esciencecenter.e3dchem.kripodb.tests Bundle-Version: 3.0.0.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Require-Bundle: org.junit, - 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.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)", nl.esciencecenter.e3dchem.knime.testing.plugin;bundle-version="[1.0.2,2.0.0)", nl.esciencecenter.e3dchem.kripodb.plugin Bundle-Vendor: Netherlands eScience Center diff --git a/tests/pom.xml b/tests/pom.xml index 1da1140..4f55bef 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -16,7 +16,7 @@ org.jacoco jacoco-maven-plugin - 0.7.8 + ${jacoco.version} @@ -38,7 +38,7 @@ org.jacoco org.jacoco.ant - 0.7.8 + ${jacoco.version} ant-contrib @@ -106,11 +106,52 @@ tycho-surefire-plugin ${tycho.version} - ${tycho.testArgLine} ${tycho.test.jvmArgs} + ${tycho.testArgLine} + ${tycho.test.jvmArgs} + ${knime.ini.testArgs} 1 alphabetical + + org.eclipse.tycho + target-platform-configuration + ${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 + + + + + + From 29c8264d73977437e53466af64869c970a5fab66 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Mon, 16 Sep 2024 09:17:26 +0200 Subject: [PATCH 2/3] Depend on newer rdkit --- plugin/META-INF/MANIFEST.MF | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index 1ed7e25..82a6ce7 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -8,7 +8,7 @@ Bundle-Activator: nl.esciencecenter.e3dchem.kripodb.Activator Require-Bundle: org.knime.core;bundle-version="[4.0.0,6.0.0)", org.knime.base;bundle-version="[4.0.0,6.0.0)", org.knime.chem.types;bundle-version="[4.0.0,6.0.0)", - org.rdkit.knime.types;bundle-version="[4.6.1,5.0.0)", + org.rdkit.knime.types;bundle-version="[5.1.0,6.0.0)", nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)", nl.esciencecenter.e3dchem.knime.pharmacophore.plugin;bundle-version="[1.0.0,2.0.0)" Bundle-Vendor: Netherlands eScience Center From 21fd0da458a89d7a0dde0e1c7edae83f80fcefab Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Mon, 16 Sep 2024 09:22:23 +0200 Subject: [PATCH 3/3] Bump to 3.0.2 --- CHANGELOG.md | 4 ++++ feature/feature.xml | 2 +- feature/pom.xml | 2 +- p2/category.xml | 2 +- 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 +- 11 files changed, 14 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 68e7ac4..d644299 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,10 @@ The file is formatted as described on http://keepachangelog.com/. ## Unreleased +## [3.0.2] - 2024--9-16 + +- Require rdkit >5.1.0 + ## [3.0.1] - 2023-11-22 ### Changed diff --git a/feature/feature.xml b/feature/feature.xml index 3bc44d7..7297b65 100644 --- a/feature/feature.xml +++ b/feature/feature.xml @@ -2,7 +2,7 @@ diff --git a/feature/pom.xml b/feature/pom.xml index 1c2c61b..ae1ae02 100644 --- a/feature/pom.xml +++ b/feature/pom.xml @@ -6,7 +6,7 @@ nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 3.0.1-SNAPSHOT + 3.0.2-SNAPSHOT nl.esciencecenter.e3dchem.kripodb.feature diff --git a/p2/category.xml b/p2/category.xml index 143c74c..c5c21dd 100644 --- a/p2/category.xml +++ b/p2/category.xml @@ -1,6 +1,6 @@ - + diff --git a/p2/pom.xml b/p2/pom.xml index 4ba7a5f..e86f469 100644 --- a/p2/pom.xml +++ b/p2/pom.xml @@ -3,7 +3,7 @@ nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 3.0.1-SNAPSHOT + 3.0.2-SNAPSHOT nl.esciencecenter.e3dchem.kripodb.p2 eclipse-repository diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index 82a6ce7..06456cd 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: 3D-e-Chem KNIME KripoDB nodes Bundle-SymbolicName: nl.esciencecenter.e3dchem.kripodb.plugin;singleton:=true -Bundle-Version: 3.0.1.qualifier +Bundle-Version: 3.0.2.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-Activator: nl.esciencecenter.e3dchem.kripodb.Activator Require-Bundle: org.knime.core;bundle-version="[4.0.0,6.0.0)", diff --git a/plugin/pom.xml b/plugin/pom.xml index 5239944..7564d0b 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -6,7 +6,7 @@ nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 3.0.1-SNAPSHOT + 3.0.2-SNAPSHOT nl.esciencecenter.e3dchem.kripodb.plugin eclipse-plugin diff --git a/pom.xml b/pom.xml index bdfa8d9..d0bd758 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ 4.0.0 nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 3.0.1-SNAPSHOT + 3.0.2-SNAPSHOT pom diff --git a/targetplatform/pom.xml b/targetplatform/pom.xml index d9243d1..9f6b6bf 100644 --- a/targetplatform/pom.xml +++ b/targetplatform/pom.xml @@ -20,7 +20,7 @@ Contributors: nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 3.0.1-SNAPSHOT + 3.0.2-SNAPSHOT diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index 2030dfa..5859e39 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.kripodb.tests -Bundle-Version: 3.0.1.qualifier +Bundle-Version: 3.0.2.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-17 Require-Bundle: org.junit, org.knime.core;bundle-version="[4.0.0,6.0.0)", diff --git a/tests/pom.xml b/tests/pom.xml index ccecb38..ebc72bf 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -5,7 +5,7 @@ nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 3.0.1-SNAPSHOT + 3.0.2-SNAPSHOT nl.esciencecenter.e3dchem.kripodb.tests