Github actions scientific ci starter
Skill ma-compbio-lab/SkillFoundry/skills/reproducible-workflows/github-actions-scientific-ci-starter
A framework for discovering, compiling, and validating reusable skills for scientific agents.
npx -y skills add ma-compbio-lab/SkillFoundry --skill github-actions-scientific-ci-starterAssembled from the repository path, not quoted from the project. Check it against their README if it does not work.
SKILL.md
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GitHub Actions Scientific CI Starter
Use this skill to generate a repository-aware GitHub Actions workflow that runs validation, site generation, tests, and a small smoke subset for this project.
What This Skill Does
- renders a ready-to-commit workflow YAML file
- targets the repository's
make validate,make build-site, andmake testentry points - optionally includes a list of smoke targets for faster CI confidence checks
When To Use It
- when you need a starter for
ci-for-scientific-pipelines - when you want a canonical Actions workflow around the current
Makefile - when you need a reproducible template before adding heavier matrix or cache logic
Run
python3 skills/reproducible-workflows/github-actions-scientific-ci-starter/scripts/render_github_actions_scientific_ci.py --workflow-out scratch/github-actions/sciskill_ci.yml --summary-out scratch/github-actions/sciskill_ci_summary.json --smoke-target smoke-zarr --smoke-target smoke-openmm-md --smoke-target smoke-optuna
Notes
- The generated workflow is intentionally conservative and single-job.
- Extend it only after the base validation path is stable in your own CI environment.