Icy Parent POM

This is the repository for the Maven configuration of pom-icy, Icy's Parent POM, a Maven file for bioimage analysis software Icy and its plugins, which was developed by members or former members of the Biological Image Analysis unit at Institut Pasteur. This project is licensed under an LGPLv3 license.
Icy is developed and maintained by Biological Image Analysis unit at Institut Pasteur. The source code of Icy is also licensed under an LGPLv3 license.

Description

To know more about how a POM file in Maven projects works, you can check those resources:

• Introduction to Maven, an Icy article
• Introduction to the POM, Apache Maven Project
• Maven – Parent and Child POM, HowToDoInJava
• Maven by Example, 6.2. The Simple Parent Project, Sonatype Nexus

This project centralizes the Maven configuration for Icy as well as its plugins in one file. It will be inherited to the other projects with the parent block:

<parent>
    <groupId>org.bioimageanalysis.icy</groupId>
    <artifactId>pom-icy</artifactId>
    <version>3.0.0-a.6</version>
</parent>

Maven profiles are completely automated, so you shouldn't do anything to activate or deactivate profiles. You need to run the command just below to execute the default maven goals (clean and install)

mvn

If you want to execute specific goals, add them (each separated with a space character) after the previous command like that:

mvn clean package

• The clean phase will remove all the files generated by the previous build.
• The package phase generate three JARs: one to executable for Icy, a source JAR and a Javadoc JAR.
• The install phase will compile and install the project in your local Maven repository and in your Icy's extensions folder.

TODO: explain how to use the deploy phase.

To see which profiles are activated, run the command mvn help:active-profiles in your terminal.

Dependency list

To keep a cohesion between Icy and all extensions, we have listed all the extensions provided by Institut Pasteur/BIA. Some third parties can also be added to the list.

To know them, check the <properties> block in the pom.xml.

To call them, you need to add the <dependency> block as follows:

<dependencies>
    <dependency>
        <groupId>org.bioimagenalaysis.icy</groupId>
        <artifactId>name-of-extension</artifactId>
    </dependency>
</dependencies>

Usually you do not need to specify the version number, as it is already set in the pom-icy.

Installation

To install the POM in your local Maven repository, follow the instructions below:

1. clone the repository:

   git clone https://gitlab.pasteur.fr/bia/icy/pom-icy.git

2. go to the directory:

   cd pom-icy

3. run the Maven command:

   mvn

Citation

Please also cite the Icy software and mention the version of Icy you used (bottom right corner of the GUI or first lines of the Output tab):
de Chaumont, F. et al. (2012) Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, 9, pp. 690–696
https://icy.bioimageanalysis.org

Authors

• Amandine Tournay
• Thomas Musset