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INSTALL.md

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Compilation using Maven

It is the actual way how to compile this project, we are using building tool Maven. See brief info about Maven. There are basically three ways how to run then Maven - compile, test, install

  • compile - using command "mvn compile" compiles the source code
  • test - using command "mvn test" runs all internal tests and show the results
  • install - using command "mvn install" combines the compile + tests and also install the plugin into the ImageJ/Fiji instance. Check the location of you ImageJ/Fiji in the pom.xml file (variable imagej.app.directory).

Note: Download the ImageJ or Fiji as appropriate for your operation system (e.g Linux 64bit). Note2: the installation into plugin folder is done only it does not already exist so manual removing from plugin folder is needed

Description of the pom.xml file

some important/interesting facts:

  • the "artifactId" has to contain an underscore to be installed among plugins, otherwise it is installed into the jars/ folder
  • "SNAPSHOT" in version marks that the actual version is "in process"
  • the "imagej.app.directory" property specifies the location of ImageJ/Fiji instance for an installation
  • "dependencies" specifies the list of used libraries and their versions
  • "parent" defines the project parent - org.scijava - where some other stuff is declared, e.g. how to install the plugin, etc.

Local Maven Repos

We follow this article to provide dependencies from a project-local repository that are not available from any official Maven repositories. In particular, we provide a current version of the Java Library for Machine Learning. It was "deployed" using this command-line:

mvn deploy:deploy-file -Durl=file:$(pwd)/repo/ -Dfile=JML-2.8-JRE-1.6.jar -DgroupId=net.sourceforge -DartifactId=jml -Dpackaging=jar -Dversion=2.8-SNAPSHOT

The same command-line needs to be used to update the locally-deployed version to a new one.