Datasets:
Formats:
parquet
Size:
100K - 1M
Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
License:
| from __future__ import annotations | |
| import sys | |
| import pytest | |
| from simulator import cli | |
| from simulator.config import Config | |
| from simulator.dataset_state import DatasetConfigMismatchError | |
| from simulator.empirical_maps import EmpiricalMapStore | |
| from simulator.shards import ( | |
| DatasetGenerationIncompleteError, | |
| DatasetGenerationLockedError, | |
| dataset_output_lock, | |
| ) | |
| def test_cli_reports_completed_dataset_mismatch_without_traceback( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| cfg = Config(out_dir=str(tmp_path), recomb_map="", mut_map="") | |
| monkeypatch.setattr(cli, "parse_args", lambda: cfg) | |
| monkeypatch.setattr(cli, "load_empirical_maps", lambda _cfg: EmpiricalMapStore()) | |
| def reject_reuse(_cfg, _empirical, **_kwargs): | |
| raise DatasetConfigMismatchError("configuration changed; rerun with --force") | |
| monkeypatch.setattr(cli, "generate_dataset", reject_reuse) | |
| with pytest.raises(SystemExit, match=r"^\[error\].*--force$"): | |
| cli.main() | |
| def test_cli_rejects_enabled_empirical_source_when_maps_are_unavailable( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| cfg = Config( | |
| out_dir=str(tmp_path), | |
| recomb_map="", | |
| mut_map="", | |
| p_clean_constant=0.0, | |
| p_random_global=0.0, | |
| p_custom_hetero=0.0, | |
| p_empirical_slice=1.0, | |
| p_stdpopsim_anchor=0.0, | |
| ) | |
| monkeypatch.setattr(cli, "parse_args", lambda: cfg) | |
| monkeypatch.setattr(cli, "load_empirical_maps", lambda _cfg: EmpiricalMapStore()) | |
| with pytest.raises( | |
| SystemExit, | |
| match="refusing to disable the requested empirical source", | |
| ): | |
| cli.main() | |
| def test_unknown_preset_is_an_argparse_error_without_traceback( | |
| monkeypatch: pytest.MonkeyPatch, | |
| capsys: pytest.CaptureFixture[str], | |
| ) -> None: | |
| monkeypatch.setattr(sys, "argv", ["dlcoalsim", "--preset", "unknown"]) | |
| with pytest.raises(SystemExit) as exc_info: | |
| cli.parse_args() | |
| assert exc_info.value.code == 2 | |
| stderr = capsys.readouterr().err | |
| assert "Unknown preset" in stderr | |
| assert "Traceback" not in stderr | |
| def test_unusable_output_path_has_a_clean_cli_error( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| parent_file = tmp_path / "not-a-directory" | |
| parent_file.write_text("occupied", encoding="utf-8") | |
| cfg = Config( | |
| out_dir=str(parent_file / "dataset"), | |
| recomb_map="", | |
| mut_map="", | |
| ) | |
| monkeypatch.setattr(cli, "parse_args", lambda: cfg) | |
| with pytest.raises(SystemExit, match=r"^\[error\] filesystem operation failed"): | |
| cli.main() | |
| def test_parse_args_records_distributed_generation_options( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| monkeypatch.setattr( | |
| sys, | |
| "argv", | |
| [ | |
| "dlcoalsim", | |
| "--generate-only", | |
| "--rank", | |
| "2", | |
| "--world-size", | |
| "5", | |
| "--out-dir", | |
| str(tmp_path), | |
| ], | |
| ) | |
| cfg = cli.parse_args() | |
| assert cfg._generation_mode == "generate" | |
| assert cfg._distributed_rank == 2 | |
| assert cfg._distributed_world_size == 5 | |
| def test_auto_mode_uses_slurm_rank_partition( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| cfg = Config(out_dir=str(tmp_path), recomb_map="", mut_map="") | |
| monkeypatch.setattr(cli, "parse_args", lambda: cfg) | |
| monkeypatch.setattr(cli, "load_empirical_maps", lambda _cfg: EmpiricalMapStore()) | |
| monkeypatch.setenv("SLURM_PROCID", "2") | |
| monkeypatch.setenv("SLURM_NTASKS", "4") | |
| calls: list[tuple[int, int]] = [] | |
| def generate_partition(_cfg, _empirical, *, rank, world_size): | |
| calls.append((rank, world_size)) | |
| return {"generated_chunks": 3, "reused_chunks": 1} | |
| monkeypatch.setattr(cli, "generate_dataset_partition", generate_partition) | |
| monkeypatch.setattr( | |
| cli, | |
| "generate_dataset", | |
| lambda *_args, **_kwargs: pytest.fail("single-node generator was called"), | |
| ) | |
| cli.main() | |
| assert calls == [(2, 4)] | |
| def test_prepare_only_loads_maps_and_allows_force( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| cfg = Config( | |
| out_dir=str(tmp_path), | |
| recomb_map="", | |
| mut_map="", | |
| force=True, | |
| ) | |
| cfg._generation_mode = "prepare" | |
| cfg._distributed_rank = None | |
| cfg._distributed_world_size = None | |
| empirical = EmpiricalMapStore() | |
| calls: list[tuple[Config, EmpiricalMapStore]] = [] | |
| monkeypatch.setattr(cli, "parse_args", lambda: cfg) | |
| monkeypatch.setattr(cli, "load_empirical_maps", lambda _cfg: empirical) | |
| monkeypatch.setattr( | |
| cli, | |
| "prepare_dataset", | |
| lambda called_cfg, called_empirical: calls.append( | |
| (called_cfg, called_empirical) | |
| ), | |
| ) | |
| cli.main() | |
| assert calls == [(cfg, empirical)] | |
| def test_finalize_only_skips_map_loading_and_writes_dataset_files( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| cfg = Config(out_dir=str(tmp_path), recomb_map="", mut_map="") | |
| cfg._generation_mode = "finalize" | |
| cfg._distributed_rank = None | |
| cfg._distributed_world_size = None | |
| manifest = {"n_samples": cfg.n_samples} | |
| writes: list[tuple[Config, dict]] = [] | |
| monkeypatch.setattr(cli, "parse_args", lambda: cfg) | |
| monkeypatch.setattr( | |
| cli, | |
| "load_empirical_maps", | |
| lambda _cfg: pytest.fail("finalization loaded empirical maps"), | |
| ) | |
| monkeypatch.setattr( | |
| cli, | |
| "finalize_dataset", | |
| lambda _cfg, **_kwargs: manifest, | |
| ) | |
| def record_write(called_cfg, called_manifest): | |
| with pytest.raises(DatasetGenerationLockedError): | |
| with dataset_output_lock(tmp_path): | |
| pass | |
| writes.append((called_cfg, called_manifest)) | |
| monkeypatch.setattr(cli, "write_dataset_files", record_write) | |
| cli.main() | |
| assert writes == [(cfg, manifest)] | |
| def test_finalize_only_reports_incomplete_generation_cleanly( | |
| monkeypatch: pytest.MonkeyPatch, | |
| tmp_path, | |
| ) -> None: | |
| cfg = Config(out_dir=str(tmp_path), recomb_map="", mut_map="") | |
| cfg._generation_mode = "finalize" | |
| cfg._distributed_rank = None | |
| cfg._distributed_world_size = None | |
| monkeypatch.setattr(cli, "parse_args", lambda: cfg) | |
| def reject_finalize(_cfg, **_kwargs): | |
| raise DatasetGenerationIncompleteError("2 chunks are still missing") | |
| monkeypatch.setattr(cli, "finalize_dataset", reject_finalize) | |
| with pytest.raises(SystemExit, match=r"^\[error\] 2 chunks are still missing$"): | |
| cli.main() | |