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Commit acb6577c authored by Thomas MUSSET's avatar Thomas MUSSET
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target/
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### IntelliJ IDEA ###
.idea/
*.iws
*.iml
*.ipr
### Eclipse ###
.apt_generated
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.settings
.springBeans
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.vscode/
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README.md
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# Apache Commons IO
# Apache Commons Codec
<!-- badges: start -->
[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![Twitter](https://img.shields.io/twitter/follow/Icy_BioImaging?style=social)](https://twitter.com/Icy_BioImaging)
[![Image.sc forum](https://img.shields.io/badge/discourse-forum-brightgreen.svg?style=flat)](https://forum.image.sc/tag/icy)
<!-- badges: end -->
This is the repository for the source code of *Apache Commons IO*, a plugin for the [bioimage analysis software Icy](http://icy.bioimageanalysis.org/), 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 plugin 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.
## Getting started
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Plugin description
## Add your files
<!-- Short description of goals of package, with descriptive links to the documentation website -->
The Apache Commons IO Library.
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
Apache Commons IO (TM) is a library of utilities to assist with developing IO functionality.
```
cd existing_repo
git remote add origin https://gitlab.pasteur.fr/bia/icy/extensions/apache-commons-io.git
git branch -M main
git push -uf origin main
```
https://commons.apache.org/proper/commons-io/
## Integrate with your tools
Distributed on the Apache License, Version 2.0
A more detailed user documentation can be found on the Apache Commons Codec documentation page on the Icy website: http://icy.bioimageanalysis.org/plugin/apache-commons-io/
- [ ] [Set up project integrations](https://gitlab.pasteur.fr/bia/icy/extensions/apache-commons-io/-/settings/integrations)
## Collaborate with your team
## Installation instructions
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
For end-users, refer to the documentation on the Icy website on [how to install an Icy plugin](http://icy.bioimageanalysis.org/tutorial/how-to-install-an-icy-plugin/).
## Test and Deploy
For developers, see our [Contributing guidelines](https://gitlab.pasteur.fr/bia/icy/-/blob/master/CONTRIBUTING.md) and [Code of Conduct](https://gitlab.pasteur.fr/bia/icy/-/blob/master/CODE-OF-CONDUCT.md).
Use the built-in continuous integration in GitLab.
<!-- Here we should have some explanations on how to fork this repo (for an example see https://gitlab.pasteur.fr/bia/wellPlateReader). Add any info related to Maven etc. How the project is build (for an example see https://gitlab.pasteur.fr/bia/wellPlateReader). Any additional setup required (authentication tokens, etc). -->
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
## Main functions and usage
# Editing this README
<!-- list main functions, explain architecture, classname, give info on how to get started with the plugin. If applicable, how the package compares to other similar packages and/or how it relates to other packages -->
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
Classname: `plugins.tmusset.apache.ApacheCommonsIOPlugin`
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
Choose a self-explaining name for your project.
## Citation
## Description
Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
Please cite this plugins as follows:
## Badges
On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
## Visuals
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
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
## Installation
Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
## Usage
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
## Author(s)
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
Thomas Musset
## Additional information
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
## Authors and acknowledgment
Show your appreciation to those who have contributed to the project.
## License
For open source projects, say how it is licensed.
## Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<!-- Inherited Icy Parent POM -->
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
<version>2.1.7</version>
</parent>
<!-- Project Information -->
<artifactId>apache-commons-io</artifactId>
<version>1.0.0</version>
<packaging>jar</packaging>
<name>Apache Commons IO</name>
<description>
The Apache Commons IO Library.
Apache Commons IO is a library of utilities to assist with developing IO functionality.</description>
<url>https://icy.bioimageanalysis.org/plugin/apache-commons-io/</url>
<inceptionYear>2025</inceptionYear>
<organization>
<name>Institut Pasteur</name>
<url>https://pasteur.fr</url>
</organization>
<licenses>
<license>
<name>GNU GPLv3</name>
<url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<id>tmusset</id>
<name>Thomas Musset</name>
<url>https://research.pasteur.fr/fr/member/thomas-musset/</url>
<roles>
<role>founder</role>
<role>lead</role>
<role>architect</role>
<role>developer</role>
<role>debugger</role>
<role>tester</role>
<role>maintainer</role>
<role>support</role>
</roles>
</developer>
</developers>
<properties>
<artifact-to-extract>commons-io</artifact-to-extract>
</properties>
<!-- List of project's dependencies -->
<dependencies>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.18.0</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>icy</id>
<url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
</repository>
</repositories>
</project>
src/main/java/plugins/tmusset/apache/ApacheCommonsIOPlugin.java 0 → 100644
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/*
* Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Icy is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
package plugins.tmusset.apache;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginLibrary;
/**
* Icy wrapper for the Apache Commons IO library.
*
* @author Thomas Musset
*/
public class ApacheCommonsIOPlugin extends Plugin implements PluginLibrary {
//
}
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src/main/resources/plugins/tmusset/apache/io.png

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