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fair-simulation-packager

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person作者: TashanworldhubOpenAPI
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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 --json prints an envelope with two top-level keys:

  • inputs: the parsed CLI arguments echoed back (note: inputs.inputs is the raw comma-separated string passed via --inputs, not the per-file records).
  • results: contains a single key manifest.

results.manifest contains these fields:

  • project_name, engine, engine_version, structure_id, units
  • file_inventory with inputs and outputs, each a list of per-file records (path, exists, and when the file exists, size_bytes and sha256)
  • missing_files: paths that do not exist on disk
  • provenance (working_directory, manifest_schema)
  • fair_checks: has_inputs, has_outputs, has_units, has_engine_version, and has_hashes_for_existing_files (true/false, or null when no files exist so the check is not applicable)
  • recommended_next_steps

Parse fields at results.manifest.<field>. When --out PATH is given, only the bare manifest object (not the inputs/results envelope) is written to PATH.

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 (exit code 0). Invalid input stops with exit code 2: malformed unit entries, fields containing control characters, fields longer than 4096 characters, more than 1000 input or output entries, or a file larger than 500 MB. Note that ordinary file paths — including absolute paths and paths containing .. — are accepted and inventoried; the tool reads file contents only to compute metadata and SHA-256 hashes.

Limitations

This skill creates a metadata manifest. It does not upload to NOMAD, Materials Project, or an OPTIMADE provider.

Verification checklist

  • [ ] Confirmed fair_checks.has_hashes_for_existing_files is true (not null or false); a null means no listed file existed on disk, so re-run from the directory where the files actually live before trusting the manifest.
  • [ ] Reviewed missing_files and confirmed it is empty, or recorded an explicit reason for each entry — every missing path means an input/output was named but not hashed, so the bundle is not reproducible as-is.
  • [ ] Spot-checked at least one sha256 in results.manifest.file_inventory against an independent sha256sum/Get-FileHash of the same file to confirm the recorded digest matches the bytes on disk.
  • [ ] Confirmed engine_version is a real version string and not the default "unknown"; pass --engine-version so the bundle records the exact code build.
  • [ ] Verified units is non-empty and every reported quantity (energy, length, time, etc.) has an entry, so downstream consumers do not have to guess the unit system.
  • [ ] Confirmed structure_id is populated when a Materials Project / NOMAD / OPTIMADE / CIF / POSCAR structure was used, so the structure identity is recoverable.
  • [ ] When --out PATH was used, opened PATH and confirmed it holds the bare manifest object (not the inputs/results envelope) and that no unintended path outside the working directory was written.

Common pitfalls & rationalizations

| Tempting shortcut | Why it's wrong / what to do | |-------------------|-----------------------------| | "It exited 0, so the bundle is complete." | Exit 0 only means no validation error; missing files are reported in missing_files with exit 0. Inspect missing_files and fair_checks before trusting completeness. | | "has_hashes_for_existing_files is null, close enough to true." | null means no listed file existed on disk — nothing was hashed. Re-run from the correct directory so the files are found and actually digested. | | "Skip --engine-version, the engine name is enough." | The script defaults engine_version to "unknown", which silently breaks reproducibility. Always pass the concrete build/version. | | "Parsing inputs.inputs from the JSON gives me the per-file records." | inputs.inputs is the raw comma-separated CLI string echoed back, not the records. Read per-file data from results.manifest.file_inventory.inputs/outputs. | | "The manifest captures the structure, so the run is fully reproducible." | This skill only inventories files, hashes, units, and IDs. It does not record code commit, container digest, or parser versions — follow recommended_next_steps and add those yourself. | | "Absolute paths or .. will be rejected, so the inventory is sandboxed." | Paths are not sandboxed — absolute and .. paths are inventoried as given, and --out can write outside the working directory. Verify the paths you pass are the intended ones. |

Security

Input Validation

  • --project-name and --engine are required and must be non-empty after stripping whitespace; an empty value stops with exit code 2.
  • --project-name, --engine, --structure-id (when given), and every file path are checked for control characters (ord < 32) and a 4096-character maximum length; either condition stops with exit code 2.
  • --inputs and --outputs are split on commas and capped at 1000 entries each; more entries stop with exit code 2.
  • --units entries must be key=value; both the key and the value must match the allowlist ^[A-Za-z0-9_.:/@+-]+$. A missing = or a non-matching key/value stops with exit code 2.
  • There are no numeric inputs, so no finite/positive numeric checks are performed.

File Access

  • The script reads each existing input/output file in 1 MB chunks to compute its size_bytes and SHA-256 hash; files that do not exist are recorded but not read.
  • A file larger than 500 MB stops with exit code 2 before it is hashed.
  • The script writes no files unless --out PATH is given, in which case it writes exactly one file (the bare manifest JSON) to that path; otherwise all output goes to stdout.
  • Paths are not sandboxed: absolute paths and paths containing .. are accepted for both the inventoried files and --out. If --out points outside the working directory, the file is written there as requested.

Tool Restrictions

  • Bash is used to run the bundled scripts/fair_packager.py.
  • Read, Write, Grep, and Glob are declared so the skill can inspect the working directory and read or write manifest/metadata files when guiding the user; they are not invoked by the script itself, which performs all of its own file I/O directly.

Safety Measures

  • No eval, exec, os.system, or subprocess calls; the script does not shell out and parses arguments with argparse.
  • Output is emitted as JSON via json.dumps (or a short plain-text summary without --json).
  • DoS caps bound resource use: 500 MB per file, 1000 entries per input/output list, and 4096 characters per field.

References

  • See references/fair_manifest.md for recommended manifest fields.

Version History

  • 1.2.0: Made eval cases discriminating by pinning the script's exact --json output (per-file sha256/size_bytes, units, structure_id, engine_version, missing_files, and the tri-state has_hashes_for_existing_files) against committed evals/files/ fixtures.
  • 1.1.0: Documented the real --json envelope shape; made has_hashes_for_existing_files tri-state (null when no files exist); added entry-count (1000) and field-length (4096) caps; corrected the Error Handling and Security wording to describe actual path behavior.
  • 1.0.0: Initial FAIR simulation packaging skill.