ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software

TL;DR

ARTENOLIS is an automated, cross-platform continuous integration framework designed to ensure reproducibility and stability of open-source software that depends on licensed software, specifically tailored for the COBRA Toolbox and similar tools.

Contribution

It introduces a general-purpose CI infrastructure that manages licensed dependencies and tests code across multiple operating systems and software versions.

Findings

Ensures stability and integrity of licensed-dependent code

Supports multiple OS and software versions

Provides free access to the CI infrastructure

Abstract

Motivation: Automatically testing changes to code is an essential feature of continuous integration. For open-source code, without licensed dependencies, a variety of continuous integration services exist. The COnstraint-Based Reconstruction and Analysis (COBRA) Toolbox is a suite of open-source code for computational modelling with dependencies on licensed software. A novel automated framework of continuous integration in a semi-licensed environment is required for the development of the COBRA Toolbox and related tools of the COBRA community. Results: ARTENOLIS is a general-purpose infrastructure software application that implements continuous integration for open-source software with licensed dependencies. It uses a master-slave framework, tests code on multiple operating systems, and multiple versions of licensed software dependencies. ARTENOLIS ensures the stability, integrity, and cross-platform compatibility of code in the COBRA Toolbox and related tools. Availability and Implementation: The continuous integration server, core of the reproducibility and testing infrastructure, can be freely accessed under artenolis.lcsb.uni.lu. The continuous integration framework code is located in the /.ci directory and at the root of the repository freely available under github.com/opencobra/cobratoolbox.