artenolis

Automated Reproducibility and Testing Environment for Licensed Software

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Automated Reproducibility and
Testing Environment for Licensed Software

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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. However, a novel automated framework of continuous integration is required for the development of computational biology tools in a semi-licensed environment.

ARTENOLIS is a general-purpose and flexible 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. Although ARTENOLIS may used with any software, we illustrate in detail the developments for the most widely used software of the COnstraint-Based Reconstruction and Analysis (COBRA) community, namely the COBRA Toolbox <https://opencobra.github.io/cobratoolbox>_, which is a suite of open-source code for computational modelling with dependencies on licensed software. As it is dependent on the licensed software MATLAB (The Mathworks, Inc.), ARTENOLIS is required to ensure stability, integrity, and cross-platform compatibility.

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The full documentation is available here <https://opencobra.github.io/artenolis>_.

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