code/compact_v1/validate_compact_dataset.py

#!/usr/bin/env python3
"""Sample-level validation for a GNNCP compact graph dataset.

This program never iterates the full legacy dataset.  When ``--legacy`` is
provided it opens the old monolithic .pt with ``torch.load(..., mmap=True)``
and touches only the requested sample tensors.
"""

from __future__ import annotations

import argparse
import json
import random
import resource
import sys
from pathlib import Path
from typing import Any, Dict, Iterable, List, Optional, Sequence

import torch

from compact_graph_dataset import CompactGraphDataset


CORE_FIELDS = (
    "x",
    "edge_index",
    "edge_attr",
    "pos",
    "is_protein",
    "y_true",
    "y_pred",
    "y_grt",
)
FLOAT_FIELDS = {
    "x",
    "edge_attr",
    "pos",
    "is_protein",
    "y_true",
    "y_pred",
    "y_grt",
}


def _rss_mib() -> float:
    value = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
    # Linux reports KiB; macOS reports bytes.
    if sys.platform == "darwin":
        return value / (1024.0 * 1024.0)
    return value / 1024.0


def _parse_indices(text: Optional[str], length: int) -> Optional[List[int]]:
    if text is None:
        return None
    values: List[int] = []
    for token in text.split(","):
        token = token.strip()
        if not token:
            continue
        if ":" in token:
            parts = token.split(":")
            if len(parts) not in (2, 3):
                raise ValueError(f"bad index range: {token!r}")
            start = int(parts[0]) if parts[0] else 0
            stop = int(parts[1]) if parts[1] else length
            step = int(parts[2]) if len(parts) == 3 and parts[2] else 1
            values.extend(range(start, stop, step))
        else:
            values.append(int(token))
    normalised = []
    for index in values:
        if index < 0:
            index += length
        if not 0 <= index < length:
            raise IndexError(f"sample index {index} outside [0,{length})")
        normalised.append(index)
    return list(dict.fromkeys(normalised))


def _choose_indices(length: int, count: int, seed: int) -> List[int]:
    if length <= 0:
        return []
    count = min(max(int(count), 1), length)
    selected = {0, length - 1}
    rng = random.Random(seed)
    while len(selected) < count:
        selected.add(rng.randrange(length))
    return sorted(selected)[:count]


def _tensor_stats(
    actual: torch.Tensor,
    expected: torch.Tensor,
    *,
    atol: float,
    rtol: float,
) -> Dict[str, Any]:
    result: Dict[str, Any] = {
        "actual_shape": list(actual.shape),
        "expected_shape": list(expected.shape),
        "actual_dtype": str(actual.dtype),
        "expected_dtype": str(expected.dtype),
    }
    if tuple(actual.shape) != tuple(expected.shape):
        result.update({"passed": False, "reason": "shape_mismatch"})
        return result
    if actual.dtype != expected.dtype:
        result["dtype_match"] = False
    else:
        result["dtype_match"] = True

    if actual.numel() == 0:
        result.update(
            {
                "passed": bool(result["dtype_match"]),
                "exact": True,
                "max_abs": 0.0,
                "mean_abs": 0.0,
            }
        )
        return result

    if actual.is_floating_point() or expected.is_floating_point():
        actual_f64 = actual.to(torch.float64)
        expected_f64 = expected.to(torch.float64)
        finite_match = torch.equal(torch.isfinite(actual_f64), torch.isfinite(expected_f64))
        diff = torch.abs(actual_f64 - expected_f64)
        finite_diff = diff[torch.isfinite(diff)]
        max_abs = float(finite_diff.max().item()) if finite_diff.numel() else float("inf")
        mean_abs = float(finite_diff.mean().item()) if finite_diff.numel() else float("inf")
        close = bool(
            torch.allclose(actual_f64, expected_f64, atol=atol, rtol=rtol, equal_nan=True)
        )
        result.update(
            {
                "passed": bool(close and result["dtype_match"] and finite_match),
                "exact": bool(torch.equal(actual, expected)),
                "finite_pattern_match": finite_match,
                "max_abs": max_abs,
                "mean_abs": mean_abs,
            }
        )
    else:
        exact = bool(torch.equal(actual, expected))
        result.update(
            {
                "passed": bool(exact and result["dtype_match"]),
                "exact": exact,
            }
        )
    return result


def _invariants(graph: Any, cutoff: float, atol: float) -> Dict[str, Any]:
    checks: Dict[str, bool] = {}
    n = int(graph.num_nodes)
    checks["x_Nx82"] = tuple(graph.x.shape) == (n, 82)
    checks["edge_index_2xE"] = graph.edge_index.ndim == 2 and graph.edge_index.shape[0] == 2
    edge_count = int(graph.edge_index.shape[1]) if checks["edge_index_2xE"] else -1
    checks["edge_attr_Ex4"] = tuple(graph.edge_attr.shape) == (edge_count, 4)
    checks["pos_Nx3"] = tuple(graph.pos.shape) == (n, 3)
    checks["is_protein_Nx1"] = tuple(graph.is_protein.shape) == (n, 1)
    checks["y_true_Nx1"] = tuple(graph.y_true.shape) == (n, 1)
    checks["y_pred_Nx3"] = tuple(graph.y_pred.shape) == (n, 3)
    checks["y_grt_Nx3"] = tuple(graph.y_grt.shape) == (n, 3)
    checks["x_float32"] = graph.x.dtype == torch.float32
    checks["edge_index_int64"] = graph.edge_index.dtype == torch.int64
    checks["edge_attr_float32"] = graph.edge_attr.dtype == torch.float32
    checks["coordinates_float32"] = (
        graph.pos.dtype == graph.y_pred.dtype == graph.y_grt.dtype == torch.float32
    )
    checks["pos_equals_y_pred"] = bool(torch.equal(graph.pos, graph.y_pred))

    if edge_count >= 0 and graph.edge_index.numel():
        src, dst = graph.edge_index
        checks["edge_bounds"] = bool(
            (src.min() >= 0)
            and (dst.min() >= 0)
            and (src.max() < n)
            and (dst.max() < n)
        )
        checks["no_self_edges"] = bool(torch.all(src != dst).item())
        key = src * n + dst
        checks["legacy_edge_order"] = bool(torch.all(key[1:] > key[:-1]).item())
        reversed_key = dst * n + src
        checks["edges_are_bidirectional"] = bool(
            torch.equal(torch.sort(key).values, torch.sort(reversed_key).values)
        )
        distance = torch.sqrt(
            torch.sum(
                (
                    graph.pos[src].to(torch.float64)
                    - graph.pos[dst].to(torch.float64)
                )
                ** 2,
                dim=1,
            )
        )
        checks["edges_within_cutoff"] = bool(
            torch.all(distance <= cutoff + atol).item()
        )
        checks["edge_attr_distance"] = bool(
            torch.allclose(
                graph.edge_attr[:, 0].to(torch.float64),
                distance / cutoff,
                atol=atol,
                rtol=0.0,
            )
        )
        is_protein = graph.is_protein[:, 0]
        checks["edge_attr_endpoint_types"] = bool(
            torch.equal(graph.edge_attr[:, 2], is_protein[src])
            and torch.equal(graph.edge_attr[:, 3], is_protein[dst])
        )
    else:
        checks["edge_bounds"] = True
        checks["no_self_edges"] = True
        checks["legacy_edge_order"] = True
        checks["edges_are_bidirectional"] = True
        checks["edges_within_cutoff"] = True
        checks["edge_attr_distance"] = True
        checks["edge_attr_endpoint_types"] = True

    protein = graph.is_protein[:, 0] > 0.5
    checks["protein_first"] = bool(
        not protein.numel()
        or not bool((~protein).any().item())
        or not bool(protein[torch.nonzero(~protein, as_tuple=False)[0, 0] :].any().item())
    )
    checks["protein_y_true_zero"] = bool(
        torch.all(graph.y_true[protein] == 0).item()
    )
    ligand_error = torch.sqrt(
        torch.sum((graph.y_pred[~protein] - graph.y_grt[~protein]) ** 2, dim=1)
    )
    checks["ligand_y_true_matches_coordinates"] = bool(
        torch.allclose(
            graph.y_true[~protein, 0],
            ligand_error,
            atol=atol,
            rtol=0.0,
        )
    )
    return {"passed": all(checks.values()), "checks": checks}


def _load_legacy(path: Path, allow_eager: bool) -> Sequence[Any]:
    try:
        return torch.load(
            path,
            map_location="cpu",
            mmap=True,
            weights_only=False,
        )
    except (TypeError, RuntimeError, ValueError) as exc:
        if not allow_eager:
            raise RuntimeError(
                f"could not mmap legacy dataset {path}: {exc}. "
                "Refusing an eager multi-GB load; pass --allow-eager-legacy "
                "only inside a suitably sized Slurm job."
            ) from exc
        return torch.load(path, map_location="cpu", weights_only=False)


def validate(args: argparse.Namespace) -> Dict[str, Any]:
    dataset = CompactGraphDataset(
        args.compact,
        max_cached_shards=args.max_cached_shards,
        strict=True,
    )
    indices = _parse_indices(args.indices, len(dataset))
    if indices is None:
        indices = _choose_indices(len(dataset), args.num_samples, args.seed)

    report: Dict[str, Any] = {
        "compact": str(Path(args.compact).resolve()),
        "num_graphs": len(dataset),
        "indices": indices,
        "atol": args.atol,
        "rtol": args.rtol,
        "rss_mib_before_samples": _rss_mib(),
        "samples": [],
    }

    legacy: Optional[Sequence[Any]] = None
    if args.legacy is not None:
        legacy = _load_legacy(Path(args.legacy), args.allow_eager_legacy)
        report["legacy"] = str(Path(args.legacy).resolve())
        report["legacy_num_graphs"] = len(legacy)
        if len(legacy) != len(dataset):
            report["length_match"] = False
        else:
            report["length_match"] = True

    all_passed = report.get("length_match", True)
    for index in indices:
        graph = dataset[index]
        sample_report: Dict[str, Any] = {
            "index": index,
            "metadata": dataset.metadata(index),
            "invariants": _invariants(graph, dataset.cutoff, args.atol),
        }
        sample_passed = bool(sample_report["invariants"]["passed"])

        if legacy is not None and index < len(legacy):
            reference = legacy[index]
            parity: Dict[str, Any] = {}
            for field in CORE_FIELDS:
                if not hasattr(reference, field):
                    parity[field] = {
                        "passed": False,
                        "reason": "missing_in_legacy_graph",
                    }
                    continue
                actual = getattr(graph, field)
                expected = getattr(reference, field)
                if not torch.is_tensor(actual) or not torch.is_tensor(expected):
                    parity[field] = {
                        "passed": False,
                        "reason": "field_is_not_tensor",
                    }
                    continue
                parity[field] = _tensor_stats(
                    actual,
                    expected,
                    atol=args.atol if field in FLOAT_FIELDS else 0.0,
                    rtol=args.rtol if field in FLOAT_FIELDS else 0.0,
                )
            sample_report["parity"] = parity
            sample_passed = sample_passed and all(
                bool(result["passed"]) for result in parity.values()
            )

        sample_report["passed"] = sample_passed
        all_passed = all_passed and sample_passed
        report["samples"].append(sample_report)

    report["rss_mib_after_samples"] = _rss_mib()
    report["passed"] = bool(all_passed)
    return report


def build_parser() -> argparse.ArgumentParser:
    parser = argparse.ArgumentParser(
        description="Validate compact GNNCP graphs and optionally compare with legacy tensors."
    )
    parser.add_argument(
        "--compact",
        required=True,
        help="Compact dataset directory or manifest.json",
    )
    parser.add_argument(
        "--legacy",
        help="Legacy list[torch_geometric.data.Data] .pt for mmap parity checks",
    )
    parser.add_argument(
        "--num-samples",
        type=int,
        default=8,
        help="Number of deterministic samples when --indices is omitted (default: 8)",
    )
    parser.add_argument(
        "--indices",
        help="Comma-separated indices/ranges, e.g. '0,10,20:24,-1'",
    )
    parser.add_argument("--seed", type=int, default=0)
    parser.add_argument(
        "--atol",
        type=float,
        default=1e-6,
        help="Absolute tolerance for reconstructed floating tensors",
    )
    parser.add_argument("--rtol", type=float, default=1e-6)
    parser.add_argument("--max-cached-shards", type=int, default=2)
    parser.add_argument(
        "--allow-eager-legacy",
        action="store_true",
        help="Allow fallback to an eager legacy torch.load if mmap is unavailable",
    )
    parser.add_argument(
        "--report",
        help="Optional JSON report path (written atomically by the caller/job filesystem)",
    )
    return parser


def main() -> int:
    args = build_parser().parse_args()
    report = validate(args)
    rendered = json.dumps(report, ensure_ascii=False, indent=2, sort_keys=True)
    print(rendered)
    if args.report:
        output = Path(args.report)
        output.parent.mkdir(parents=True, exist_ok=True)
        output.write_text(rendered + "\n", encoding="utf-8")
    return 0 if report["passed"] else 1


if __name__ == "__main__":
    raise SystemExit(main())