GitHub Action to run an omnibenchmark

Runs an omnibenchmark using GitHub actions.

Usage

Example usage

name: Testing ob via gh actions
on:
  push:
  workflow_dispatch:

jobs:
  build:
    name: Run ob                                     ## the name of the run
    runs-on: ubuntu-latest                           ## using the latest ubuntu(docker) GH runner
    steps:
      - name: Checkout                               ## to checkout the tested repo
        uses: actions/checkout@v4

      - name: Use action                             ## to run the benchmark specified within... 
        uses: omnibenchmark/run_omnibenchmark@main
        with:
          yaml: tests/Clustering_conda.yaml          ##  this yaml
          backend: conda                             ## using `conda` as software management strategy

Input variables

yaml

An omnibenchmark YAML. Required without default.

backend

The software backend to use. Either conda or apptainer. Defaults to conda.

cores

How many concurrent benchmarking tasks to run. Defaults to 1 (numeric).

omnibenchmark_branch

Which github.com/omnibenchmark/omnibenchmark branch to use. Defaults to main.

conda_handler

When using conda as a backend, the conda capabilities wrapper. Either micromamba or miniforge. Defaults to micromamba.

Notes

Own runners

You might want to register your own runners and not use the

    runs-on: ubuntu-latest

directive but rather

    runs-on: self-hosted

to compute elsewhere, and not GitHub's runners.

Disclaimer of warranty

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

Our workflow reuses actions from third party providers as well. Thank you!

Hence, and particularly when running this action on self-hosted runners: THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.