omnibenchmark - v0.3.0

Refer to CHANGELOG.md for the details of the changes in this version.

- Python
Published by btraven00 7 months ago

omnibenchmark - v0.2.2

See CHANGELOG for features and bugfixes.

- Python
Published by btraven00 7 months ago

omnibenchmark - v0.2.1

What's Changed

• fix --continue-on-error (Closes: #126) by @btraven00 in https://github.com/omnibenchmark/omnibenchmark/pull/131

Full Changelog: https://github.com/omnibenchmark/omnibenchmark/compare/v0.2.0...v0.2.1

- Python
Published by btraven00 9 months ago

omnibenchmark - 0.2.0

See CHANGELOG for features and bugfixes.

- Python
Published by btraven00 9 months ago

omnibenchmark - v0.1.0

• fix: fixed race conditions at the module repository cloning step
• fix: pin test environment dependencies

- Python
Published by DanInci 10 months ago

omnibenchmark - v0.1.0-rc.3

Includes major features and fixes.

• cli: added dynamic versioning managed by poetry-dynamic-versioning , using a semvar style.
• cli: added ob --version which outputs the current version of the cli
• logging: added uniform logging + configuration and management across the whole codebase, no longer using click.echo, rather logger.log
• ci/cd: added a black pre-commit hook
• logging and workflow: for each rule execution, subprocess.stdout and subprocess.stderr, if not empty, are kept as logs next to the rule output(s)
• software: fixes path checks on ob software conda prepare -b [yaml]
• workflow: modifies rule generation to populate software (conda, envmodules, container) directives defensively to align with snakemake>8.25.2
• snakemake: pins snakemake==8.25.1

- Python
Published by imallona about 1 year ago

omnibenchmark - v0.1.0-rc.2

Major features and bugfixes. - example: added a realistic tests/data/Clustering.yaml defining a clustering benchmark - tests: replaced tests/data/Benchmark_001.yaml by tests/data/Clustering.yaml during benchmark execution testing (e.g. envmodules) - tests: added dummy envmodule (lua) files to ./tests/data/envs so envmodules are not only searched at and loaded from the easybuild modulepath - tests: fixed several aspects of envmodule validations so envmodules are tested by searching their availability and load-ability from the modulepath - remote storage: added filtering objects by version - workflow: updated the materialized Snakefile storage policy: switched to temporary file - workflow: added benchmark layout exporting to a graph or plot via mermaid - workflow: decoupled workflow rule setup software backends (e.g. adding conda, envmodules etc to rules) from execution (e.g. --use conda during the snmk syscall)

- Python
Published by imallona about 1 year ago

omnibenchmark - v0.1.0-rc.1

• Snakemake-based workflow dynamic generation
• Snakemake execution: benchmarks or modules
• Local and remote (s3) storage handling
• Easybuild, conda, apptainer software capabilities
• click CLI
• Not back-compatible with older omnibenchmark versions
• Renku-free

Notice older versions are not tagged but are openly available on https://pypi.org/project/omnibenchmark. Last version there is 0.0.48

- Python
Published by imallona over 1 year ago