from __future__ import annotations import gzip import hashlib import json from concurrent.futures import ThreadPoolExecutor from pathlib import Path import pytest from simulator.config import Config from simulator.dataset_state import SAMPLE_GENERATOR_SCHEMA_VERSION, generation_config_state from simulator import replacement as v1 from simulator import replacement_pool as pool GENERATION_PLAN_SHA = "9" * 64 def _canonical(value: object) -> str: return hashlib.sha256( json.dumps( value, ensure_ascii=False, allow_nan=False, sort_keys=True, separators=(",", ":"), ).encode("utf-8") ).hexdigest() def _write_json(path: Path, value: dict) -> None: path.parent.mkdir(parents=True, exist_ok=True) path.write_text(json.dumps(value), encoding="utf-8") def _file_record(path: Path) -> dict: return { "size_bytes": path.stat().st_size, "sha256": hashlib.sha256(path.read_bytes()).hexdigest(), } def _source_plan(root: Path, *, n_samples: int, seed: int) -> dict: config = Config( preset="full_v01", n_samples=n_samples, seed=seed, shard_size=2, compute_chunk_size=1, out_dir=str(root), workers=1, ) state = generation_config_state(config) layout = { "n_samples": n_samples, "shard_size": 2, "compute_chunk_size": 1, "n_shards": (n_samples + 1) // 2, "n_chunks": n_samples, "sample_id_rule": "sim_{global_sample_index:08d}", "seed_rule": "config.seed + global_sample_index * 7919", "partition_rule": "chunk_idx_mod_world_size", "array_schema_version": SAMPLE_GENERATOR_SCHEMA_VERSION, } plan = { "schema_version": 1, "kind": "dlcoalsim_generation_plan", "sample_generation_config": state, "layout": layout, "layout_sha256": _canonical(layout), "empirical_maps_sha256": hashlib.sha256(b"maps").hexdigest(), "empirical_ne_templates_sha256": hashlib.sha256(b"templates").hexdigest(), "runtime_environment_sha256": hashlib.sha256(b"runtime").hexdigest(), } plan["plan_sha256"] = _canonical(plan) _write_json(root / "samples" / "PLAN.json", plan) return plan def _source_fragment(root: Path, plan: dict, index: int) -> None: shard = index // 2 relative = f"samples/.fragments/fragment_{index:08d}.npz" npz = root / relative metadata = npz.with_suffix(".jsonl.gz") npz.parent.mkdir(parents=True, exist_ok=True) npz.write_bytes(f"source-npz-{index}".encode()) metadata.write_bytes(f"source-meta-{index}".encode()) receipt = { "schema_version": 1, "plan_sha256": plan["plan_sha256"], "result": { "chunk_idx": index, "shard_idx": shard, "start": index, "n_samples": 1, "fragment_path": relative, }, "files": { "npz": _file_record(npz), "metadata_jsonl_gz": _file_record(metadata), }, } receipt["receipt_sha256"] = _canonical(receipt) _write_json( root / "samples" / ".fragments" / f"fragment_{index:08d}.done.json", receipt, ) def _patch_generator( monkeypatch: pytest.MonkeyPatch, output: Path, runtime_sha256: str, ) -> list[list[str]]: calls: list[list[str]] = [] monkeypatch.setattr( v1, "_runtime_probe", lambda root, python: { "simulator_file": str(root / "simulator" / "__init__.py"), "runtime_environment_sha256": runtime_sha256, }, ) def fake_run( root, python, arguments, *, module=True, capture_output=True, ): calls.append(list(arguments)) if "--prepare-only" in arguments: _write_json(output / "samples" / "PLAN.json", {"test": True}) return type( "Completed", (), {"returncode": 0, "stdout": "", "stderr": ""}, )() monkeypatch.setattr(v1, "_run_generator_subprocess", fake_run) monkeypatch.setattr( v1, "_validate_replacement_generation_plan", lambda out, config, source: { "plan_sha256": GENERATION_PLAN_SHA, **dict(source), }, ) return calls def _prepare( tmp_path: Path, monkeypatch: pytest.MonkeyPatch, *, name: str = "case", n_samples: int = 5, completed: int = 2, candidate_count: int = 5, ) -> tuple[Path, Path, dict, list[list[str]]]: source = tmp_path / f"{name}-source" source_plan = _source_plan(source, n_samples=n_samples, seed=100) for index in range(completed): _source_fragment(source, source_plan, index) output = tmp_path / f"{name}-pool" calls = _patch_generator( monkeypatch, output, source_plan["runtime_environment_sha256"] ) generator_root = tmp_path / f"{name}-generator" (generator_root / "simulator").mkdir(parents=True) (generator_root / "simulator" / "__init__.py").write_text("") generator_python = tmp_path / f"{name}-python" generator_python.write_text("") plan = pool.prepare_pool( [source], target_total=n_samples, candidate_count=candidate_count, out_dir=output, generator_root=generator_root, generator_python=generator_python, ) return output, source, plan, calls def _candidate_fragment( output: Path, plan: dict, index: int, *, seed: int | None = None, ) -> None: expected = plan["candidates"][index] npz = output / expected["npz_path"] metadata = output / expected["metadata_path"] receipt_path = output / expected["receipt_path"] npz.parent.mkdir(parents=True, exist_ok=True) npz.write_bytes(f"candidate-npz-{index}".encode()) with gzip.open(metadata, "wt", encoding="utf-8") as handle: handle.write( json.dumps( { "sample_id": expected["expected_sample_id"], "sample_index": index, "seed": expected["seed"] if seed is None else seed, # These fields must never participate in pool selection. "target": [999], "n_variants": 999, "demography_type": "ignored", } ) + "\n" ) receipt = { "schema_version": 1, "plan_sha256": plan["generation_plan_sha256"], "result": { "chunk_idx": index, "shard_idx": expected["shard_index"], "start": index, "n_samples": 1, "fragment_path": expected["npz_path"], }, "files": { "npz": _file_record(npz), "metadata_jsonl_gz": _file_record(metadata), }, } receipt["receipt_sha256"] = _canonical(receipt) _write_json(receipt_path, receipt) def test_k3_c5_freezes_out_of_order_prefix_and_late_is_immutable( tmp_path: Path, monkeypatch: pytest.MonkeyPatch ) -> None: output, _, plan, _ = _prepare(tmp_path, monkeypatch) assert plan["required_k"] == 3 assert plan["candidate_count"] == 5 assert plan["candidate_config"]["n_samples"] == 5 assert plan["candidate_config"]["compute_chunk_size"] == 1 assert plan["candidate_config"]["workers"] == 1 assert plan["candidate_groups"]["primary"]["candidate_indices"] == [0, 1, 2] assert plan["candidate_groups"]["standby"]["candidate_indices"] == [3, 4] for index in (4, 1, 3): _candidate_fragment(output, plan, index) result = pool.register_candidate(output, index) assert result["selection_frozen"] is True selection_path = output / pool.SELECTION_NAME before = selection_path.read_bytes() selection = json.loads(before) assert selection["selected_candidate_indices"] == [4, 1, 3] assert selection["registration_cutoff_ordinal"] == 3 assert [item["registration_ordinal"] for item in selection["selected_candidates"]] == [ 1, 2, 3, ] assert selection["runtime_censoring"]["applied"] is True assert ( selection["selection_rule"]["target_variant_demography_fields_read"] is False ) for item in selection["selected_candidates"]: for key in ("receipt", "npz", "metadata_jsonl_gz"): source_record = item["source_artifacts"][key] sealed_record = item["sealed_artifacts"][key] assert sealed_record["size_bytes"] == source_record["size_bytes"] assert sealed_record["sha256"] == source_record["sha256"] assert (output / sealed_record["path"]).samefile( output / source_record["path"] ) _candidate_fragment(output, plan, 0) assert pool.register_candidate(output, 0)["status"] == "selection_frozen" assert pool.register_candidate(output, 4)["status"] == "already_selected" assert selection_path.read_bytes() == before assert pool.pool_status(output)["selected_candidate_indices"] == [4, 1, 3] def test_concurrent_registration_has_one_unique_k_prefix( tmp_path: Path, monkeypatch: pytest.MonkeyPatch ) -> None: output, _, plan, _ = _prepare(tmp_path, monkeypatch, name="concurrent") for index in range(5): _candidate_fragment(output, plan, index) with ThreadPoolExecutor(max_workers=5) as executor: results = list( executor.map(lambda index: pool.register_candidate(output, index), range(5)) ) assert all(result["status"] in {"registered", "selection_frozen"} for result in results) selection = json.loads((output / pool.SELECTION_NAME).read_text()) selected = selection["selected_candidate_indices"] assert len(selected) == 3 assert len(set(selected)) == 3 assert sorted( item["registration_ordinal"] for item in selection["selected_candidates"] ) == [1, 2, 3] registry_before = (output / pool.REGISTRY_NAME).read_bytes() pool.register_candidate(output, selected[0]) assert (output / pool.REGISTRY_NAME).read_bytes() == registry_before @pytest.mark.parametrize("failure", ["receipt", "payload", "seed"]) def test_bad_receipt_hash_or_seed_fails_before_registration( tmp_path: Path, monkeypatch: pytest.MonkeyPatch, failure: str, ) -> None: output, _, plan, _ = _prepare( tmp_path, monkeypatch, name=f"bad-{failure}" ) _candidate_fragment(output, plan, 0) expected = plan["candidates"][0] if failure == "receipt": receipt_path = output / expected["receipt_path"] receipt = json.loads(receipt_path.read_text()) receipt["result"]["start"] = 1 _write_json(receipt_path, receipt) elif failure == "payload": (output / expected["npz_path"]).write_bytes(b"tampered") else: _candidate_fragment(output, plan, 0, seed=expected["seed"] + 1) with pytest.raises(pool.ReplacementPoolError): pool.register_candidate(output, 0) assert not (output / pool.SELECTION_NAME).exists() assert pool.pool_status(output)["registered_count"] == 0 def test_less_than_k_does_not_publish_and_missing_candidate_does_not_block( tmp_path: Path, monkeypatch: pytest.MonkeyPatch ) -> None: output, _, plan, _ = _prepare(tmp_path, monkeypatch, name="missing") for index in (1, 2): _candidate_fragment(output, plan, index) pool.register_candidate(output, index) status = pool.pool_status(output) assert status["registered_count"] == 2 assert status["remaining_to_freeze"] == 1 assert not (output / pool.SELECTION_NAME).exists() # Candidate zero never produces a receipt. Candidate three is enough to # freeze the exact K=3 prefix without waiting for it. _candidate_fragment(output, plan, 3) pool.register_candidate(output, 3) assert pool.pool_status(output)["selected_candidate_indices"] == [1, 2, 3] assert not (output / plan["candidates"][0]["receipt_path"]).exists() def test_selected_payload_tamper_is_detected_through_sealed_hardlink( tmp_path: Path, monkeypatch: pytest.MonkeyPatch ) -> None: output, _, plan, _ = _prepare(tmp_path, monkeypatch, name="tamper") for index in (0, 1, 2): _candidate_fragment(output, plan, index) pool.register_candidate(output, index) (output / plan["candidates"][1]["npz_path"]).write_bytes(b"changed") with pytest.raises(pool.ReplacementPoolError, match="sealed artifact"): pool.pool_status(output) def test_generate_requires_one_rank_per_candidate( tmp_path: Path, monkeypatch: pytest.MonkeyPatch ) -> None: output, _, plan, calls = _prepare(tmp_path, monkeypatch, name="generate") with pytest.raises(pool.ReplacementPoolError, match="world_size"): pool.generate_candidate(output, rank=0, world_size=4) result = pool.generate_candidate(output, rank=4, world_size=5) assert result["candidate_index"] == 4 assert result["seed"] == plan["candidates"][4]["seed"] assert calls[-1][-5:] == [ "--generate-only", "--rank", "4", "--world-size", "5", ] def test_k_zero_is_an_empty_frozen_noop( tmp_path: Path, monkeypatch: pytest.MonkeyPatch ) -> None: output, _, plan, calls = _prepare( tmp_path, monkeypatch, name="zero", n_samples=2, completed=2, candidate_count=0, ) assert plan["required_k"] == 0 assert plan["candidate_config"] is None assert not any("--prepare-only" in call for call in calls) selection = json.loads((output / pool.SELECTION_NAME).read_text()) assert selection["selected_candidates"] == [] assert selection["runtime_censoring"]["applied"] is False assert pool.generate_candidate(output) == { "no_op": True, "required_k": 0, "candidate_count": 0, } status = pool.pool_status(output) assert status["status"] == "complete" assert status["no_op"] is True