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# Icy Parent POM
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This is the repository for the Maven configuration of *pom-icy, Icy's Parent POM*, a Maven file for [bioimage analysis software Icy](http://icy.bioimageanalysis.org/) and its plugins, which was developed by members or former members of the [Biological Image Analysis unit at Institut Pasteur](https://research.pasteur.fr/en/team/bioimage-analysis/). This project is licensed under GPL3 license.
Icy is developed and maintained by [Biological Image Analysis unit at Institut Pasteur](https://research.pasteur.fr/en/team/bioimage-analysis/). The [source code of Icy](https://gitlab.pasteur.fr/bia/icy) is also licensed under a GPL3 license.
## Description
To know more about how POM file in Maven projects works, you can check those resources:
- [Introduction to Maven](https://icy.bioimageanalysis.org/developer/introduction-to-maven/), an Icy article
- [Introduction to the POM](https://maven.apache.org/guides/introduction/introduction-to-the-pom.html#project-inheritance), Apache Maven Project
- [Maven - Parent and Child POM](https://howtodoinjava.com/maven/maven-parent-child-pom-example/), HowToDoInJava
- [Maven by Example, 6.2. The Simple Parent Project](https://books.sonatype.com/mvnex-book/reference/multimodule-sect-simple-parent.html), 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:
```xml
<parent>
<artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
</parent>
```
There is three profiles to facilitate project management:
- `core`: Dedicated to Icy core parts development (kernel and its dependencies).
Runs by default `clean` and `package`* goals.
- `plugin`: Dedicated to Icy plugin development (including default dependencies and rules).
Runs by default `clean` and `package`* goals.
- `library`: Dedicated to plugin library which need dependencies extraction, in which case you need to define artifact(s) to extract through the _artifact-to-extract_ property.
You should almost always use this profile along the _plugin_ profile.
* The `package` phase generate three JARs: one to executable for Icy, a source JAR and a JavaDoc JAR.
To deploy the project/artefact to the Icy's Nexus repositories just use the `deploy` goal instead. Note that Nexus development repositories (for _SNAPSHOT_ versions) are accessible only in Pasteur offices or through the private VPN.
You want to upload on our public repositories and you do not have an account ? Send a mail to [Icy Team,](mailto:icy.team@pasteur.fr) and we will grant you access.
Are you a Pasteur employee ? A connection through PasteurID is coming soon !
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To use a profile, you can:
- Run the command in your terminal: `mvn -P<profile-name>`, and to use multiple profiles, `mvn -P<profile-name-1>,<profile-name-2`
- In your IDE:
- In [IntelliJ](https://www.jetbrains.com/help/idea/work-with-maven-profiles.html#declare_maven_profiles)
- In [Eclipse](https://www.czetsuyatech.com/2011/11/maven-activate-maven-profile-on-eclipse.html)
- Overriding the profile activation in your project to have it by default:
```xml
<profiles>
<profile>
<id>same-id-as-the-one-to-override</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
</profile>
</profiles>
```
After, you can just run `mvn` or in your IDE without any configuration, and it will do everything for you!
-> 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 plugins, we have listed some most used plugins as dependency to others plugins and set its version.
To know them, check the `<properties>` block in the `pom.xml`.
To call them, you need to add the `<dependency>` block as follows:
```xml
<dependency>
<groupId>org.bioimagenalaysis.icy</groupId>
<artifactId>name-of-plugin</artifactId>
</dependency>
```
## 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](https://www.nature.com/articles/nmeth.2075), 9, pp. 690-696
http://icy.bioimageanalysis.org
## Authors
Amandine TOURNAY