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783ad76 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 | #!/usr/bin/env python3
"""Validate the standardized OneScience MatPL dataset package."""
from __future__ import annotations
import argparse
import hashlib
import sys
from pathlib import Path
import numpy as np
EXPECTED_TOP_LEVEL = ["AuAg", "Cu", "HfO2", "LiSiC"]
def sha256_file(path: Path) -> str:
digest = hashlib.sha256()
with path.open("rb") as handle:
for chunk in iter(lambda: handle.read(1024 * 1024), b""):
digest.update(chunk)
return digest.hexdigest()
def require_file(path: Path) -> None:
if not path.is_file():
raise FileNotFoundError(f"missing file: {path}")
def require_dir(path: Path) -> None:
if not path.is_dir():
raise FileNotFoundError(f"missing directory: {path}")
def check_movement(path: Path) -> None:
require_file(path)
with path.open(encoding="utf-8", errors="replace") as handle:
text = handle.read(4096)
if not text.strip():
raise ValueError(f"empty MOVEMENT file: {path}")
if "Iteration" not in text and "atoms" not in text.lower() and "lattice" not in text.lower():
raise ValueError(f"unexpected MOVEMENT header: {path}")
def check_xyz(path: Path) -> None:
require_file(path)
with path.open(encoding="utf-8", errors="replace") as handle:
first = handle.readline().strip()
second = handle.readline()
atoms = int(first)
if atoms <= 0:
raise ValueError(f"invalid xyz atom count in {path}")
if not second:
raise ValueError(f"missing xyz comment line in {path}")
def check_npy(path: Path) -> None:
require_file(path)
arr = np.load(path, allow_pickle=False)
if arr.size == 0:
raise ValueError(f"empty npy array: {path}")
def read_checksum_manifest(path: Path) -> list[tuple[str, str]]:
require_file(path)
entries: list[tuple[str, str]] = []
with path.open(encoding="utf-8") as handle:
for line_no, raw in enumerate(handle, start=1):
line = raw.strip()
if not line:
continue
parts = line.split(None, 1)
if len(parts) != 2:
raise ValueError(f"invalid checksum line {line_no}: {raw!r}")
entries.append((parts[0], parts[1]))
return entries
def validate_checksums(package_root: Path, manifest_path: Path) -> int:
entries = read_checksum_manifest(manifest_path)
for expected_hash, rel_path in entries:
target = package_root / rel_path
require_file(target)
if sha256_file(target) != expected_hash:
raise ValueError(f"checksum mismatch: {rel_path}")
return len(entries)
def main() -> int:
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--dataset-root", default="data/MatPL")
parser.add_argument("--checksum-manifest", default="metadata/sha256_manifest.txt")
parser.add_argument("--skip-checksum", action="store_true")
args = parser.parse_args()
package_root = Path.cwd()
dataset_root = Path(args.dataset_root)
for name in EXPECTED_TOP_LEVEL:
require_dir(dataset_root / name)
check_movement(dataset_root / "Cu/pwdata/0_300_MOVEMENT")
check_movement(dataset_root / "Cu/pwdata/1_500_MOVEMENT")
check_movement(dataset_root / "Cu/pwdata/valid_movement")
check_xyz(dataset_root / "AuAg/AuAg-5762.xyz")
npy_files = sorted(dataset_root.glob("**/*.npy"))
if len(npy_files) < 100:
raise ValueError(f"too few npy files: {len(npy_files)}")
for sample in npy_files[:8]:
check_npy(sample)
checksum_count = 0
if not args.skip_checksum:
checksum_count = validate_checksums(package_root, Path(args.checksum_manifest))
print("MatPL dataset validation passed")
print(f"top-level systems: {', '.join(EXPECTED_TOP_LEVEL)}")
print(f"npy files: {len(npy_files)}")
print(f"checksum entries verified: {checksum_count}")
return 0
if __name__ == "__main__":
try:
raise SystemExit(main())
except Exception as exc:
print(f"MatPL dataset validation failed: {exc}", file=sys.stderr)
raise SystemExit(1)
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