Datasets:
Formats:
parquet
Size:
100K - 1M
Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
License:
| from __future__ import annotations | |
| import dataclasses | |
| import numpy as np | |
| from simulator.config import Config | |
| from simulator.empirical_maps import EmpiricalMapStore, PiecewiseRateMap | |
| from simulator.sample import _close_worker_shared_maps, _get_worker_empirical, init_worker | |
| from simulator.shared_maps import ( | |
| attach_shared_empirical_map_store, | |
| create_shared_empirical_map_store, | |
| release_shared_memory, | |
| ) | |
| def _tiny_store() -> EmpiricalMapStore: | |
| rate_map = PiecewiseRateMap( | |
| chrom="chr1", | |
| position=np.array([0.0, 10.0, 25.0], dtype=np.float64), | |
| rate=np.array([1.0e-8, 2.0e-8], dtype=np.float64), | |
| scaling_method="identity", | |
| source_format="bed_intervals", | |
| ) | |
| return EmpiricalMapStore( | |
| rec_maps={"chr1": rate_map}, | |
| mut_maps={"chr1": rate_map}, | |
| metadata={"fixture": {"name": "tiny"}}, | |
| ) | |
| def test_shared_store_attaches_read_only_views() -> None: | |
| source = _tiny_store() | |
| assert source.is_available(10) | |
| spec, owner_handles = create_shared_empirical_map_store(source) | |
| assert len(owner_handles) == 1 | |
| assert spec.memory_name == owner_handles[0].name | |
| attached = None | |
| attached_handles = [] | |
| try: | |
| attached, attached_handles = attach_shared_empirical_map_store(spec) | |
| np.testing.assert_array_equal(attached.rec_maps["chr1"].position, [0.0, 10.0, 25.0]) | |
| np.testing.assert_array_equal(attached.mut_maps["chr1"].rate, [1.0e-8, 2.0e-8]) | |
| assert not attached.rec_maps["chr1"].position.flags.writeable | |
| assert not attached.mut_maps["chr1"].rate.flags.writeable | |
| assert attached.metadata == {"fixture": {"name": "tiny"}} | |
| assert attached.common_chroms(10) == ["chr1"] | |
| assert attached._common_span_cache == source._common_span_cache | |
| assert attached._usable_chrom_cache == source._usable_chrom_cache | |
| finally: | |
| attached = None | |
| release_shared_memory(attached_handles) | |
| release_shared_memory(owner_handles, unlink=True) | |
| def test_worker_uses_shared_store_without_reloading_files() -> None: | |
| cfg = Config( | |
| recomb_map="this-file-must-not-be-read.bed", | |
| mut_map="this-file-must-not-be-read.bed", | |
| ) | |
| spec, owner_handles = create_shared_empirical_map_store(_tiny_store()) | |
| try: | |
| init_worker(dataclasses.asdict(cfg), empirical_shared_spec=spec) | |
| attached = _get_worker_empirical(cfg) | |
| assert attached.is_available(10) | |
| assert attached.metadata["fixture"]["name"] == "tiny" | |
| finally: | |
| _close_worker_shared_maps() | |
| release_shared_memory(owner_handles, unlink=True) | |