HeshamFS/fair-simulation-packager
skills/data-management/fair-simulation-packager/SKILL.md
Create FAIR-minded reproducibility bundles for materials simulations by collecting input/output file inventories, hashes, units, engine versions, structure identifiers, provenance, and NOMAD/OPTIMADE/Materials Project friendly metadata. Use before publishing, sharing, archiving, or handing simulation results to another agent.
$ install --global
skillsauthnpx skillsauth add HeshamFS/materials-simulation-skills fair-simulation-packagerInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Last scanned: May 19, 2026, 5:30 AM144.5s5 files scanned
SKILL.md
- name:
- fair-simulation-packager
- description:
- >
- allowed-tools:
- Read, Bash, Write, Grep, Glob
- author:
- HeshamFS
- version:
- 1.0.0
- security_tier:
- high
- security_reviewed:
- true
- eval_cases:
- 3
- last_reviewed:
- 2026-05-18
FAIR Simulation Packager
Goal
Build a minimal reproducibility manifest for materials simulation results so another person or agent can understand what was run, with which inputs, and how outputs should be interpreted.
Requirements
- Python 3.10+
- No external dependencies
- Works on Linux, macOS, and Windows
Inputs to Gather
| Input | Description | Example |
|-------|-------------|---------|
| Project name | Human-readable bundle name | al-cu-diffusion-study |
| Engine | Simulation code | LAMMPS, VASP, MOOSE |
| Input files | Files needed to rerun | in.lammps,data.lmp |
| Output files | Files needed to verify results | log.lammps,traj.dump |
| Structure ID | Database or local identifier | mp-149 |
| Units | Field/unit mapping | energy=eV,length=angstrom |
Decision Guidance
- Always include input files, output files, code version, and units.
- Include hashes for every file that exists locally.
- Include structure identifiers when using Materials Project, NOMAD, OPTIMADE, CIF, POSCAR, or internal database records.
- Record missing files as warnings instead of silently dropping them.
Script Outputs
scripts/fair_packager.py emits:
manifestfile_inventorymissing_filesfair_checksrecommended_next_steps
Workflow
python3 skills/data-management/fair-simulation-packager/scripts/fair_packager.py \
--project-name al-cu-diffusion \
--engine LAMMPS \
--inputs in.lammps,data.lmp \
--outputs log.lammps,traj.dump \
--units energy=eV,length=angstrom,time=ps \
--structure-id local:alcu-cell-001 \
--json
Use --out manifest.json only when the user wants a manifest file written.
Error Handling
Missing files are reported in missing_files; invalid unit fields or unsafe paths stop with exit code 2.
Limitations
This skill creates a metadata manifest. It does not upload to NOMAD, Materials Project, or an OPTIMADE provider.
Security
- File paths are read only for metadata and SHA-256 hashing.
- The script rejects control characters and oversized files above 500 MB.
- Optional manifest writing is restricted to the requested output path.
- The skill uses
Bashonly to run the bundled script.
References
- See
references/fair_manifest.mdfor recommended manifest fields.
Version History
- 1.0.0: Initial FAIR simulation packaging skill.
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