A tool for automated scientific benchmarking


Keywords
benchmarking, bioinformatics, reproducibility, workflow-engine
License
Apache-2.0
Install
pip install omnibenchmark==0.3.0

Documentation

omnibenchmark

tests result Coverage Status License: Apache 2.0

Linter: Ruff

Omnibenchmark, a continuous benchmarking tool.

Install

Recent versions of omnibenchmark should be installable from pypi:

pip install omnibenchmark

Do note that if you plan to use conda as a software execution backend, you will want to use omnibenchmark from within a conda environment manager. At the time of this writing, we recommend miniforge. See the tutorial for more details.

Releases

See our tags.

User documentation

Live documentation is avilable for every published release and the main branch.

Documentation includes a CLI reference.

Configuration

Omnibenchmark uses a configuration file to store paths for Easybuild modules, dataset storage, and other settings. The configuration file is automatically created and managed by the system. See the Configuration documentation for details.

Developer notes

Check CONTRIBUTING.md.

Acknowledgements

Omnibenchmark incorporates great FOSS components, including but not limited to: snakemake, easybuild, apptainer, lmod and git. Thank you!

Pre-prints