From c2d040c0c0bf196199e07151db6815ed54bb4e44 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 27 Jun 2019 11:26:04 +0200 Subject: [PATCH 1/5] Added CITATION.cff --- CITATION.cff | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..3eb6615 --- /dev/null +++ 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 nodes and example workflows for software made by Silicos-it, ie. align-it, shape-it +doi: 10.5281/zenodo.1043818 +authors: +- given-names: Stefan + family-names: Verhoeven + affiliation: Netherlands eScience Center + orcid: https://orcid.org/0000-0002-5821-2060 +version: 1.1.2 +date-released: 2017-11-08 +repository-code: https://github.com/3D-e-Chem/knime-silicos-it +license: Apache-2.0 From 6062109998800a3612392215372eb6d798cf3767 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 27 Jun 2019 11:27:50 +0200 Subject: [PATCH 2/5] Added .zenodo.json --- .zenodo.json | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .zenodo.json diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..96e7eb7 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,4 @@ +{ + "title": "KNIME Silicos-it nodes", + "license": "Apache-2.0" +} From 9b3e5ab665b815a28954a98872f097e013671d3b Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 27 Jun 2019 11:52:38 +0200 Subject: [PATCH 3/5] KNIME 4 compatible + target platform Refs #8 --- .travis.yml | 3 +- CHANGELOG.md | 6 ++++ README.md | 29 ++++++------------ plugin/META-INF/MANIFEST.MF | 10 +++---- plugin/pom.xml | 1 + pom.xml | 37 ++++++++++------------- targetplatform/KNIME-AP-4.0.target | 48 ++++++++++++++++++++++++++++++ targetplatform/pom.xml | 26 ++++++++++++++++ tests/META-INF/MANIFEST.MF | 6 ++-- 9 files changed, 114 insertions(+), 52 deletions(-) create mode 100644 targetplatform/KNIME-AP-4.0.target create mode 100644 targetplatform/pom.xml diff --git a/.travis.yml b/.travis.yml index 4e36b45..7c7d246 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,12 +1,11 @@ # To trigger a Travis-CI build for every GitHub push or Pull Request: # 1. Goto https://travis-ci.org/profile/3D-e-Chem # 2. Flip the switch for the `knime-silicos-it` repo -sudo: false language: java matrix: include: - os: linux - jdk: oraclejdk8 + jdk: openjdk8 addons: apt: packages: diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f73cd8..1cf541e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,12 @@ The file is formatted as described on http://keepachangelog.com/. ## [Unreleased] +## [1.1.3] - 2019-06-27 + +### Changes + +- Requires KNIME 4.0 [#8](https://github.com/3D-e-Chem/knime-silicos-it/issues/8) + ## [1.1.2] - 2017-11-08 ### Fixed diff --git a/README.md b/README.md index e1fea26..788f9f3 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,8 @@ KNIME nodes and example workflows for software made by [Silicos-it](http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/index.html) like shape-it to align molecules based on shape and align-it to align molecules based on their pharmacophore. [![Build Status Linux & OSX](https://travis-ci.org/3D-e-Chem/knime-silicos-it.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-silicos-it) -[![SonarQube Gate](https://sonarqube.com/api/badges/gate?key=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit)](https://sonarqube.com/dashboard?id=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit) -[![SonarQube Coverage](https://sonarqube.com/api/badges/measure?key=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit&metric=coverage)](https://sonarqube.com/component_measures/domain/Coverage?id=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit) +[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit) +[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597793.svg)](https://doi.org/10.5281/zenodo.597793) This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform build steps. @@ -13,7 +13,7 @@ This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform bui Requirements: -* KNIME, https://www.knime.org, version 3.3 or higher +* KNIME, https://www.knime.org, version 4.0 or higher Steps to get the Silicos-it KNIME node inside KNIME: @@ -52,24 +52,13 @@ See `./.travis.yml` file how to trigger a Travis-CI build for every push or pull # Development -Steps to get development environment setup: +Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup: -1. Download KNIME SDK from https://www.knime.org/downloads/overview -2. Install/Extract/start KNIME SDK -3. Start SDK -4. Install m2e (Maven integration for Eclipse) + Test workflows in JUnit + Chem base + Python - - 1. Goto Help > Install new software ... - 2. Make sure Update site http://update.knime.org/analytics-platform/3.3 and https://3d-e-chem.github.io/updates are in the pull down list otherwise add them - 3. Select --all sites-- in work with pulldown - 4. Select m2e (Maven integration for Eclipse) - 5. Select `Test Knime workflows from a Junit test` - 6. Select `Splash & node category for 3D-e-Chem KNIME nodes` - 7. Select `KNIME Base Chemistry Types & Nodes` - 8. Select `KNIME Python Integration` - 9. Install software & restart - -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 (4.0) - nl.esciencecenter.e3dchem.knime.silicosit.targetplatform/KNIME-AP-4.0.target` target definition. During import the Tycho Eclipse providers must be installed. diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index 993a17a..eb8dfa1 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -6,11 +6,11 @@ Bundle-Version: 1.1.2.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Bundle-Vendor: Netherlands eScience Center Require-Bundle: org.eclipse.core.runtime, - org.knime.workbench.core;bundle-version="[3.3.0,4.0.0)", - org.knime.workbench.repository;bundle-version="[3.3.0,4.0.0)", - org.knime.base;bundle-version="[3.3.0,4.0.0)", - org.knime.chem.base;bundle-version="[3.3.0,4.0.0)", - org.knime.python.nodes;bundle-version="[3.3.0,4.0.0)", + 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.chem.base;bundle-version="[4.0.0,5.0.0)", + org.knime.python.nodes;bundle-version="[4.0.0,5.0.0)", nl.esciencecenter.e3dchem.plugin, nl.esciencecenter.e3dchem.knime.pharmacophore.plugin;bundle-version="[1.0.0,2.0.0)" Bundle-ActivationPolicy: lazy diff --git a/plugin/pom.xml b/plugin/pom.xml index 4d7e9a5..ca2f31a 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -10,5 +10,6 @@ eclipse-plugin ../tests/target/jacoco.exec + ../tests/target/surefire-reports diff --git a/pom.xml b/pom.xml index a097ec0..0f17581 100644 --- a/pom.xml +++ b/pom.xml @@ -26,34 +26,16 @@ - 3.3 - http://update.knime.org/analytics-platform/${knime.version}/ - 1.0.0 - 1.0.0 + 1.4.0 + 1.4.0 -Xmx512m UTF-8 UTF-8 + KNIME-AP-4.0 scm:git:https://github.com/3D-e-Chem/knime-silicos-it.git - https://sonarqube.com + https://sonarcloud.io 3d-e-chem - - - knime - p2 - ${knime.update.site} - - - 3d-e-chem - p2 - https://3d-e-chem.github.io/updates - - - swtbot - p2 - http://download.eclipse.org/technology/swtbot/releases/latest/ - - @@ -82,6 +64,14 @@ x86_64 + + + nl.esciencecenter.e3dchem.knime.silicosit + nl.esciencecenter.e3dchem.knime.silicosit.targetplatform + ${project.version} + ${target.file} + + @@ -132,6 +122,8 @@ true 'v'yyyyMMddHHmm + + @@ -144,5 +136,6 @@ tests bin.linux bin.macosx + targetplatform diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-4.0.target new file mode 100644 index 0000000..f36e5db --- /dev/null +++ b/targetplatform/KNIME-AP-4.0.target @@ -0,0 +1,48 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-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 + + \ No newline at end of file diff --git a/targetplatform/pom.xml b/targetplatform/pom.xml new file mode 100644 index 0000000..858b1ec --- /dev/null +++ b/targetplatform/pom.xml @@ -0,0 +1,26 @@ + + + + 4.0.0 + + nl.esciencecenter.e3dchem.knime.silicosit.targetplatform + pom + + + nl.esciencecenter.e3dchem.knime.silicosit + nl.esciencecenter.e3dchem.knime.silicosit + 1.1.2-SNAPSHOT + + + diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index 003f5c9..20d2bb7 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/tests/META-INF/MANIFEST.MF @@ -5,9 +5,9 @@ Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.tests Bundle-Version: 1.1.2.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Require-Bundle: org.junit;bundle-version="4.12.0", - org.knime.core;bundle-version="[3.3.0,4.0.0)", - org.knime.base;bundle-version="[3.3.0,4.0.0)", - org.knime.testing;bundle-version="[3.3.0,4.0.0)", + 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.eclipse.ui;bundle-version="3.108.0", org.eclipse.swtbot.eclipse.finder;bundle-version="2.6.0", org.eclipse.swtbot.junit4_x;bundle-version="2.6.0", From 9d584d2267f893701a0cf6d353fb6be4e9fbc48c Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 27 Jun 2019 11:57:16 +0200 Subject: [PATCH 4/5] Bump to 1.1.3 --- README.md | 5 ++--- bin.linux/META-INF/MANIFEST.MF | 2 +- bin.linux/pom.xml | 2 +- bin.macosx/META-INF/MANIFEST.MF | 2 +- bin.macosx/pom.xml | 2 +- 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 +- 15 files changed, 16 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 788f9f3..eac4e54 100644 --- a/README.md +++ b/README.md @@ -64,7 +64,7 @@ During import the Tycho Eclipse providers must be installed. ## Meta nodes -This plugin uses metanodes as it's public nodes. The are created in the following way: +This plugin uses metanodes as it's public nodes. They are created in the following way: 1. The meta nodes are first created and tested inside the example workflows in the `examples/` directory. 2. The `name` and `customDescription` field inside `examples/**/workflow.knime` is filled. @@ -109,6 +109,5 @@ This can be skipped by running maven offline using `mvn -o`. 7. Create a GitHub release 8. Update Zenodo entry 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 CITIATION.cff with new DOI diff --git a/bin.linux/META-INF/MANIFEST.MF b/bin.linux/META-INF/MANIFEST.MF index 25807cf..38c62e0 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 Silicos-it software, Linux binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.bin.linux;singleton:=true -Bundle-Version: 1.1.2.qualifier +Bundle-Version: 1.1.3.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy diff --git a/bin.linux/pom.xml b/bin.linux/pom.xml index 0640794..ab63156 100644 --- a/bin.linux/pom.xml +++ b/bin.linux/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit.bin.linux diff --git a/bin.macosx/META-INF/MANIFEST.MF b/bin.macosx/META-INF/MANIFEST.MF index fd8afcc..6661929 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 Silicos-it software, Mac OSX binaries Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.bin.macosx;singleton:=true -Bundle-Version: 1.1.2.qualifier +Bundle-Version: 1.1.3.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Bundle-Vendor: Netherlands eScience Center Bundle-ActivationPolicy: lazy diff --git a/bin.macosx/pom.xml b/bin.macosx/pom.xml index 62c5daa..aee866d 100644 --- a/bin.macosx/pom.xml +++ b/bin.macosx/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit.bin.macosx diff --git a/feature/feature.xml b/feature/feature.xml index b6bbcfd..a71036b 100644 --- a/feature/feature.xml +++ b/feature/feature.xml @@ -2,7 +2,7 @@ diff --git a/feature/pom.xml b/feature/pom.xml index 7dace9c..ed1bbcc 100644 --- a/feature/pom.xml +++ b/feature/pom.xml @@ -5,7 +5,7 @@ nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT nl.esciencecenter.e3dchem.knime.silicosit.feature diff --git a/p2/category.xml b/p2/category.xml index 298566a..e5d71b4 100644 --- a/p2/category.xml +++ b/p2/category.xml @@ -1,6 +1,6 @@ - + diff --git a/p2/pom.xml b/p2/pom.xml index 13fce5a..efd7d3d 100644 --- a/p2/pom.xml +++ b/p2/pom.xml @@ -4,7 +4,7 @@ nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT nl.esciencecenter.e3dchem.knime.silicosit.p2 eclipse-repository diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index eb8dfa1..2ffc5ae 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 Silicos-it software Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.plugin;singleton:=true -Bundle-Version: 1.1.2.qualifier +Bundle-Version: 1.1.3.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Bundle-Vendor: Netherlands eScience Center Require-Bundle: org.eclipse.core.runtime, diff --git a/plugin/pom.xml b/plugin/pom.xml index ca2f31a..903039f 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -4,7 +4,7 @@ nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT nl.esciencecenter.e3dchem.knime.silicosit.plugin eclipse-plugin diff --git a/pom.xml b/pom.xml index 0f17581..ef41247 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT pom diff --git a/targetplatform/pom.xml b/targetplatform/pom.xml index 858b1ec..fed3cea 100644 --- a/targetplatform/pom.xml +++ b/targetplatform/pom.xml @@ -20,7 +20,7 @@ Contributors: nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index 20d2bb7..60f5a8a 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.silicosit.tests -Bundle-Version: 1.1.2.qualifier +Bundle-Version: 1.1.3.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Require-Bundle: org.junit;bundle-version="4.12.0", org.knime.core;bundle-version="[4.0.0,5.0.0)", diff --git a/tests/pom.xml b/tests/pom.xml index ca64d17..970ce89 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -6,7 +6,7 @@ nl.esciencecenter.e3dchem.knime.silicosit nl.esciencecenter.e3dchem.knime.silicosit - 1.1.2-SNAPSHOT + 1.1.3-SNAPSHOT nl.esciencecenter.e3dchem.knime.silicosit.tests From 2cf29af068d2c204197b0eb45d38c8bc67b11fcf Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 27 Jun 2019 12:15:31 +0200 Subject: [PATCH 5/5] Added pharmacophore plugin to target platform --- targetplatform/KNIME-AP-4.0.target | 1 + 1 file changed, 1 insertion(+) diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-4.0.target index f36e5db..58b2207 100644 --- a/targetplatform/KNIME-AP-4.0.target +++ b/targetplatform/KNIME-AP-4.0.target @@ -21,6 +21,7 @@ +