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omnibenchmark

The omnibenchmark CLI

https://github.com/omnibenchmark/omnibenchmark

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: arxiv.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.7%) to scientific vocabulary

Keywords

benchmarking bioinformatics reproducibility workflow-engine
Last synced: 6 months ago · JSON representation ·

Repository

The omnibenchmark CLI

Basic Info
  • Host: GitHub
  • Owner: omnibenchmark
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage: https://omnibenchmark.org
  • Size: 2.53 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 3
  • Open Issues: 30
  • Releases: 8
Topics
benchmarking bioinformatics reproducibility workflow-engine
Created about 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

omnibenchmark

CI Pipeline PyPI codecov 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

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: omnibenchmark
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: 'Izaskun '
    family-names: Mallona
    orcid: 'https://orcid.org/0000-0002-2853-7526'
  - given-names: Almut
    family-names: Lütge
    orcid: 'https://orcid.org/0000-0003-1104-727X'
  - given-names: Ben
    family-names: Carrillo
    orcid: 'https://orcid.org/0009-0003-5704-4151'
  - given-names: 'Daniel '
    family-names: Incicau
    orcid: 'https://orcid.org/0009-0001-1748-6145'
  - given-names: Reto
    family-names: Gerber
    orcid: 'https://orcid.org/0000-0001-5414-8906'
  - given-names: 'Anthony '
    family-names: Sonrel
    orcid: 'https://orcid.org/0000-0002-2414-715X'
  - given-names: Charlotte
    family-names: Soneson
    orcid: 'https://orcid.org/0000-0003-3833-2169'
  - orcid: 'https://orcid.org/0000-0002-3048-5518'
    given-names: Mark
    name-particle: D
    family-names: Robinson
identifiers:
  - type: url
    value: 'https://arxiv.org/abs/2409.17038'
  - type: doi
    value: 10.48550/arXiv.2409.17038
repository-code: 'https://github.com/omnibenchmark/omnibenchmark/'
url: 'https://docs.omnibenchmark.org'
abstract: >-
  Benchmarking in bioinformatics is a process of designing,
  running and disseminating rigorous performance evaluations
  of methods (software). Benchmarking systems facilitate the
  benchmarking process by providing an entrypoint to store,
  coordinate and execute concrete benchmarks.

  We describe an alpha version of a new benchmarking system,
  Omnibenchmark, to facilitate benchmark formalization and
  execution in solo and community efforts. Omnibenchmark
  provides a benchmark definition syntax (in a configuration
  YAML file), a dynamic workflow generation based on
  Snakemake, S3-compatible storage handling, and
  reproducible software environments using EasyBuild, lmod,
  Apptainer or conda. Tutorials and installation
  instructions are available from this https URL. 
keywords:
  - benchmarking
  - reproducible
  - software
  - bioinformatics
  - continuous
  - community-driven
  - methods
  - metrics
  - Snakemake
  - conda
  - envmodules
  - Apptainer
  - workflow
license: Apache
commit: 9a71537
version: 0.2.1

GitHub Events

Total
  • Create event: 74
  • Commit comment event: 3
  • Release event: 7
  • Issues event: 76
  • Watch event: 4
  • Delete event: 66
  • Member event: 2
  • Issue comment event: 246
  • Push event: 446
  • Pull request review comment event: 175
  • Pull request event: 129
  • Pull request review event: 220
Last Year
  • Create event: 74
  • Commit comment event: 3
  • Release event: 7
  • Issues event: 76
  • Watch event: 4
  • Delete event: 66
  • Member event: 2
  • Issue comment event: 246
  • Push event: 446
  • Pull request review comment event: 175
  • Pull request event: 129
  • Pull request review event: 220

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 51
  • Total pull requests: 75
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 12 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 0.9
  • Average comments per pull request: 1.91
  • Merged pull requests: 41
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 51
  • Pull requests: 71
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 12 days
  • Issue authors: 6
  • Pull request authors: 5
  • Average comments per issue: 0.9
  • Average comments per pull request: 1.89
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • btraven00 (39)
  • imallona (7)
  • retogerber (2)
  • DanInci (1)
  • bio-traven (1)
  • junokreisler (1)
Pull Request Authors
  • btraven00 (29)
  • imallona (24)
  • DanInci (20)
  • retogerber (5)
  • bio-traven (1)
Top Labels
Issue Labels
bug (8) testing (7) documentation (5) enhancement (2) in-progress (1) environments (1) ready for review (1)
Pull Request Labels
documentation (5) enhancement (3) ready for review (2) bug (1) testing (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 202 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 1
  • Total versions: 55
  • Total maintainers: 4
pypi.org: omnibenchmark

A tool for automated scientific benchmarking

  • Versions: 55
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Downloads: 202 Last month
Rankings
Dependent packages count: 3.1%
Downloads: 14.1%
Average: 18.0%
Forks count: 19.1%
Dependent repos count: 21.7%
Stargazers count: 31.9%
Maintainers (4)
almutlue btraven dincicau imallona
Last synced: 6 months ago