KNIME nodes and example workflows for software made by Silicos-it like shape-it to align molecules based on shape and align-it to align molecules based on their pharmacophore. Nodes can only be run on either Linux or OSX. The Silicos-it Windows binaries do not exist so the Silicos-it KNIME nodes are not available for WIndows aswell.
This project uses Eclipse Tycho to perform build steps.
Requirements:
Steps to get the Silicos-it KNIME node inside KNIME:
https://3d-e-chem.github.io/updates/5.1
work with
pulldownThe examples/
folder contains example KNIME workflows.
mvn verify
An Eclipse update site will be made in p2/target/repository
directory.
The update site can be used to perform a local installation.
Configuration files to run Continuous Integration builds on GitHub actions are present in .github/workflows
.
Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.silicosit.targetplatform/KNIME-AP-5.1.target
target definition.During import the Tycho Eclipse providers must be installed.
This plugin uses metanodes as it's public nodes. They are created in the following way:
examples/
directory.name
and customDescription
field inside examples/**/workflow.knime
is filled.plugin/src/knime/
directory.plugin/plugin.xml
as PersistedMetaNode in the org.knime.workbench.repository.metanode
extension.Tests for the node are in tests/src
directory.
Tests can be executed with mvn verify
, they will be run in a separate KNIME environment.
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.
There are no tests for the meta nodes as they are copied from the plugin to a workflow each time, which would make the test test itself.
Unit tests written in Junit4 format can be put in tests/src/java
.
See https://github.com/3D-e-Chem/knime-testflow#3-add-test-workflow
Running mvn commands can take a long time as Tycho fetches indices of all p2 update sites.
This can be skipped by running maven offline using mvn -o
.
mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT
command.mvn package
, will create update site in p2/target/repository
mvn verify
mvn install -Dtarget.update.site=<path to update site>