Datasets:
Formats:
parquet
Size:
100K - 1M
Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
License:
File size: 15,897 Bytes
ee5b44c | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 | from __future__ import annotations
import dataclasses
import hashlib
import json
from pathlib import Path
import pytest
from simulator import replacement
from simulator.config import Config
from simulator.dataset_state import SAMPLE_GENERATOR_SCHEMA_VERSION, generation_config_state
def _canonical(value: object) -> str:
return hashlib.sha256(
json.dumps(
value,
sort_keys=True,
separators=(",", ":"),
allow_nan=False,
).encode()
).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: int, seed: int, marker: str = "same") -> dict:
cfg = Config(
preset="full_v01",
n_samples=n,
seed=seed,
shard_size=2,
compute_chunk_size=1,
out_dir=str(root),
workers=4,
)
state = generation_config_state(cfg)
layout = {
"n_samples": n,
"shard_size": 2,
"compute_chunk_size": 1,
"n_shards": (n + 1) // 2,
"n_chunks": n,
"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(f"map-{marker}".encode()).hexdigest(),
"empirical_ne_templates_sha256": hashlib.sha256(
f"template-{marker}".encode()
).hexdigest(),
"runtime_environment_sha256": hashlib.sha256(
f"runtime-{marker}".encode()
).hexdigest(),
}
plan["plan_sha256"] = _canonical(plan)
_write_json(root / "samples" / "PLAN.json", plan)
return plan
def _receipt(
root: Path,
plan: dict,
*,
kind: str,
index: int,
shard: int,
start: int,
count: int,
) -> None:
if kind == "final":
relative = f"samples/shard_{shard:05d}.npz"
receipt_path = root / "samples" / ".receipts" / f"shard_{shard:05d}.done.json"
result = {
"shard_idx": shard,
"start": start,
"n_samples": count,
"shard_path": relative,
}
else:
relative = f"samples/.fragments/fragment_{index:08d}.npz"
receipt_path = (
root
/ "samples"
/ ".fragments"
/ f"fragment_{index:08d}.done.json"
)
result = {
"chunk_idx": index,
"shard_idx": shard,
"start": start,
"n_samples": count,
"fragment_path": relative,
}
npz = root / relative
metadata = npz.with_suffix(".jsonl.gz")
npz.parent.mkdir(parents=True, exist_ok=True)
npz.write_bytes(f"npz-{kind}-{index}".encode())
metadata.write_bytes(f"meta-{kind}-{index}".encode())
receipt = {
"schema_version": 1,
"plan_sha256": plan["plan_sha256"],
"result": result,
"files": {
"npz": _file_record(npz),
"metadata_jsonl_gz": _file_record(metadata),
},
}
receipt["receipt_sha256"] = _canonical(receipt)
_write_json(receipt_path, receipt)
def _sources(tmp_path: Path) -> tuple[Path, Path, dict, dict]:
left = tmp_path / "left"
right = tmp_path / "right"
left_plan = _source_plan(left, n=4, seed=100)
right_plan = _source_plan(
right, n=3, seed=100 + 4 * replacement.SEED_STRIDE
)
return left, right, left_plan, right_plan
def test_scan_prefers_final_receipt_and_never_double_counts(tmp_path: Path) -> None:
left, _, plan, _ = _sources(tmp_path)
_receipt(left, plan, kind="final", index=0, shard=0, start=0, count=2)
_receipt(left, plan, kind="fragment", index=0, shard=0, start=0, count=1)
_receipt(left, plan, kind="fragment", index=1, shard=0, start=1, count=1)
_receipt(left, plan, kind="fragment", index=2, shard=1, start=2, count=1)
snapshot = replacement._scan_source(left)
assert snapshot["completed_samples"] == 3
assert snapshot["selected_final_receipts"] == 1
assert snapshot["selected_fragment_receipts"] == 1
assert snapshot["ignored_fragments_covered_by_final"] == 2
assert [(row["kind"], row["start"]) for row in snapshot["selected_receipts"]] == [
("final", 0),
("fragment", 2),
]
def test_audit_rejects_config_hash_and_seed_overlap(tmp_path: Path) -> None:
left, right, left_plan, right_plan = _sources(tmp_path)
_receipt(left, left_plan, kind="fragment", index=0, shard=0, start=0, count=1)
_receipt(right, right_plan, kind="fragment", index=0, shard=0, start=0, count=1)
assert len(replacement._audit_sources([left, right])) == 2
changed = json.loads((right / "samples" / "PLAN.json").read_text())
changed["empirical_maps_sha256"] = "0" * 64
changed.pop("plan_sha256")
changed["plan_sha256"] = _canonical(changed)
_write_json(right / "samples" / "PLAN.json", changed)
_receipt(
right,
changed,
kind="fragment",
index=0,
shard=0,
start=0,
count=1,
)
with pytest.raises(replacement.ReplacementPlanError, match="empirical_maps"):
replacement._audit_sources([left, right])
overlapping = tmp_path / "overlap"
overlap_plan = _source_plan(
overlapping, n=2, seed=100 + replacement.SEED_STRIDE
)
_receipt(
overlapping,
overlap_plan,
kind="fragment",
index=0,
shard=0,
start=0,
count=1,
)
with pytest.raises(replacement.ReplacementPlanError, match="seed sequences overlap"):
replacement._audit_sources([left, overlapping])
def test_corrupt_receipt_or_missing_artifact_fails_closed(tmp_path: Path) -> None:
left, _, plan, _ = _sources(tmp_path)
_receipt(left, plan, kind="fragment", index=0, shard=0, start=0, count=1)
receipt_path = (
left / "samples" / ".fragments" / "fragment_00000000.done.json"
)
receipt = json.loads(receipt_path.read_text())
receipt["result"]["start"] = 1
_write_json(receipt_path, receipt)
with pytest.raises(replacement.ReplacementPlanError, match="fingerprint"):
replacement._scan_source(left)
_receipt(left, plan, kind="fragment", index=0, shard=0, start=0, count=1)
(left / "samples" / ".fragments" / "fragment_00000000.npz").unlink()
with pytest.raises(replacement.ReplacementPlanError, match="missing"):
replacement._scan_source(left)
def test_prepare_freezes_deficit_tail_and_immutable_runtime(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
left, right, left_plan, right_plan = _sources(tmp_path)
for index in range(3):
_receipt(
left,
left_plan,
kind="fragment",
index=index,
shard=index // 2,
start=index,
count=1,
)
for index in range(2):
_receipt(
right,
right_plan,
kind="fragment",
index=index,
shard=index // 2,
start=index,
count=1,
)
runtime = left_plan["runtime_environment_sha256"]
monkeypatch.setattr(
replacement,
"_runtime_probe",
lambda root, python: {
"simulator_file": str(root / "simulator" / "__init__.py"),
"runtime_environment_sha256": runtime,
},
)
prepared_config: dict | None = None
def fake_run(root, python, arguments, *, module=True):
nonlocal prepared_config
assert module
assert arguments[-1] == "--prepare-only"
values = {}
iterator = iter(arguments[:-1])
for token in iterator:
if token.startswith("--") and token not in {
"--include-truth",
"--enable-stdpopsim",
"--mut-map-scale-to-baseline",
"--no-mut-map-scale-to-baseline",
"--no-compression",
}:
values[token] = next(iterator)
prepared_config = values
return type("Completed", (), {"stdout": "", "stderr": ""})()
monkeypatch.setattr(replacement, "_run_generator_subprocess", fake_run)
expected_generation_plan = {
"plan_sha256": "9" * 64,
"empirical_maps_sha256": left_plan["empirical_maps_sha256"],
"empirical_ne_templates_sha256": left_plan[
"empirical_ne_templates_sha256"
],
"runtime_environment_sha256": runtime,
}
monkeypatch.setattr(
replacement,
"_validate_replacement_generation_plan",
lambda out, config, source: expected_generation_plan,
)
generator_root = tmp_path / "deploy"
generator_root.mkdir()
generator_python = tmp_path / "python"
generator_python.write_text("")
output = tmp_path / "replacement"
plan = replacement.prepare_replacement(
[left, right],
target_total=7,
out_dir=output,
generator_root=generator_root,
generator_python=generator_python,
workers=8,
)
assert plan["completed_source_samples"] == 5
assert plan["deficit_samples"] == 2
assert plan["tail_seed"] == 100 + 7 * replacement.SEED_STRIDE
assert plan["replacement_config"]["n_samples"] == 2
assert plan["replacement_config"]["seed"] == plan["tail_seed"]
assert plan["replacement_config"]["compute_chunk_size"] == 1
assert plan["replacement_config"]["workers"] == 8
assert prepared_config["--n-samples"] == "2"
assert prepared_config["--seed"] == str(plan["tail_seed"])
assert (output / replacement.PLAN_NAME).is_file()
def test_zero_deficit_is_a_safe_noop(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
left = tmp_path / "left"
source_plan = _source_plan(left, n=2, seed=10)
_receipt(left, source_plan, kind="final", index=0, shard=0, start=0, count=2)
runtime = source_plan["runtime_environment_sha256"]
monkeypatch.setattr(
replacement,
"_runtime_probe",
lambda root, python: {
"simulator_file": str(root / "simulator" / "__init__.py"),
"runtime_environment_sha256": runtime,
},
)
monkeypatch.setattr(
replacement,
"_run_generator_subprocess",
lambda *args, **kwargs: pytest.fail("zero deficit invoked generator"),
)
generator_root = tmp_path / "deploy"
generator_root.mkdir()
generator_python = tmp_path / "python"
generator_python.write_text("")
output = tmp_path / "replacement"
plan = replacement.prepare_replacement(
[left],
target_total=2,
out_dir=output,
generator_root=generator_root,
generator_python=generator_python,
)
assert plan["deficit_samples"] == 0
assert plan["replacement_config"] is None
assert replacement.generate_replacement(output) == {
"no_op": True,
"deficit_samples": 0,
}
assert replacement.finalize_replacement(output) == {
"no_op": True,
"deficit_samples": 0,
}
assert not (output / "samples").exists()
assert not (output / replacement.DONE_NAME).exists()
def test_prepare_rejects_wrong_generator_runtime(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
left = tmp_path / "left"
source_plan = _source_plan(left, n=2, seed=10)
_receipt(left, source_plan, kind="fragment", index=0, shard=0, start=0, count=1)
monkeypatch.setattr(
replacement,
"_runtime_probe",
lambda root, python: {
"simulator_file": str(root / "simulator" / "__init__.py"),
"runtime_environment_sha256": "0" * 64,
},
)
root = tmp_path / "deploy"
root.mkdir()
python = tmp_path / "python"
python.write_text("")
with pytest.raises(replacement.ReplacementPlanError, match="runtime hash differs"):
replacement.prepare_replacement(
[left],
target_total=2,
out_dir=tmp_path / "replacement",
generator_root=root,
generator_python=python,
)
def test_prepare_rejects_noncontiguous_or_wrong_planned_coverage(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
left = tmp_path / "left"
right = tmp_path / "right"
left_plan = _source_plan(left, n=2, seed=10)
right_plan = _source_plan(
right, n=2, seed=10 + 3 * replacement.SEED_STRIDE
)
_receipt(left, left_plan, kind="fragment", index=0, shard=0, start=0, count=1)
_receipt(right, right_plan, kind="fragment", index=0, shard=0, start=0, count=1)
monkeypatch.setattr(
replacement,
"_runtime_probe",
lambda root, python: pytest.fail("coverage audit must precede runtime probe"),
)
root = tmp_path / "deploy"
root.mkdir()
python = tmp_path / "python"
python.write_text("")
with pytest.raises(replacement.ReplacementPlanError, match="strictly contiguous"):
replacement.prepare_replacement(
[left, right],
target_total=4,
out_dir=tmp_path / "replacement",
generator_root=root,
generator_python=python,
)
with pytest.raises(replacement.ReplacementPlanError, match="cover 2 planned"):
replacement.prepare_replacement(
[left],
target_total=3,
out_dir=tmp_path / "other",
generator_root=root,
generator_python=python,
)
def test_config_argv_roundtrips_boolean_intent() -> None:
cfg = dataclasses.asdict(Config())
cfg["force"] = False
cfg["include_truth"] = True
cfg["enable_stdpopsim"] = False
cfg["mut_map_scale_to_baseline"] = False
cfg["compression"] = False
argv = replacement._config_argv(cfg)
assert "--force" not in argv
assert "--include-truth" in argv
assert "--enable-stdpopsim" not in argv
assert "--no-mut-map-scale-to-baseline" in argv
assert "--no-compression" in argv
def test_generate_streams_subprocess_output(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
output = tmp_path / "replacement"
cfg = dataclasses.asdict(Config(n_samples=1, out_dir=str(output)))
plan = {
"schema_version": replacement.SCHEMA_VERSION,
"kind": "dlcoalsim_tail_replacement",
"out_dir": str(output.resolve()),
"target_total": 1,
"completed_source_samples": 0,
"deficit_samples": 1,
"tail_seed": 99,
"seed_stride": replacement.SEED_STRIDE,
"source_snapshot_sha256": "0" * 64,
"sources": [],
"source_provenance": {},
"immutable_generator": {
"root": str(tmp_path),
"python": str(tmp_path / "python"),
},
"replacement_config": cfg,
"generation_plan_sha256": "1" * 64,
}
plan["replacement_plan_sha256"] = _canonical(plan)
_write_json(output / replacement.PLAN_NAME, plan)
calls = []
def fake_run(root, python, arguments, *, module=True, capture_output=True):
calls.append((module, capture_output))
return type("Completed", (), {"returncode": 0})()
monkeypatch.setattr(replacement, "_run_generator_subprocess", fake_run)
result = replacement.generate_replacement(output, rank=0, world_size=1)
assert result["returncode"] == 0
assert calls == [(True, False)]
|