"""Loader for the frozen stdpopsim single-population trajectories. These eighteen models, across eight species, are the held-out evaluation set. They exist so that generalisation can be measured against histories that were published by other people for other reasons, rather than against our own prior re-drawn -- which measures nothing. phlash validates the same way, on twelve stdpopsim models across eight species. The trajectories are frozen into ``data/templates/stdpopsim_single_pop`` by ``scripts/build_stdpopsim_single_pop.py`` rather than imported at runtime; the reasons are in that script's docstring. """ from __future__ import annotations import csv from dataclasses import dataclass from functools import lru_cache from pathlib import Path import numpy as np from .assets import asset_path from .config import NE_LOG10_BOUNDS, Config DEFAULT_STDPOPSIM_TEMPLATE_PATH = "data/templates/stdpopsim_single_pop/trajectories.csv" # Models held out of the draw because another recipe produces them. Empty at # present: Zigzag_1S14 had a recipe of its own for a while and was excluded here # so that exactly one code path produced it; that recipe is gone and the model # is back in the catalogue. The hand-written published event table stays in # ``demography.py`` as the independent source this freeze is checked against. CATALOGUE_EXCLUSIONS: frozenset[str] = frozenset() @dataclass(frozen=True) class StdpopsimTemplate: species: str model_id: str population: str generation_time_years: float breaks: tuple[float, ...] values: tuple[float, ...] growth_rates: tuple[float, ...] ne_rescale: float @property def key(self) -> str: return "%s/%s" % (self.species, self.model_id) def _fit_to_bounds(values: tuple[float, ...]) -> float: """Return the single factor that slides a trajectory into the Ne band. Two of the eighteen models -- *Anopheles gambiae* and the Indian *M. m. castaneus* -- carry effective sizes above a million, and one Holstein model dips below a hundred. Clipping them would flatten exactly the features they are held out to test, so the whole trajectory is multiplied by one constant instead: Ne is only identifiable jointly with the mutation rate, and a uniform factor leaves the shape -- which is what generalisation is being measured on -- bit-for-bit intact. The factor is recorded so the published model can always be recovered. """ low, high = 10.0 ** NE_LOG10_BOUNDS[0], 10.0 ** NE_LOG10_BOUNDS[1] smallest, largest = min(values), max(values) if largest / smallest > high / low: raise ValueError("trajectory spans more than the declared Ne band") if largest > high: return high / largest if smallest < low: return low / smallest return 1.0 @lru_cache(maxsize=4) def _load(path: str) -> tuple[StdpopsimTemplate, ...]: source = asset_path(path) if not source.exists(): return () grouped: dict[tuple[str, str], list[dict[str, str]]] = {} with source.open(newline="") as stream: for row in csv.DictReader(stream): grouped.setdefault((row["species"], row["model_id"]), []).append(row) out: list[StdpopsimTemplate] = [] for (species, model_id), rows in sorted(grouped.items()): rows.sort(key=lambda item: int(item["epoch_index"])) starts = [float(item["start_generations_ago"]) for item in rows] sizes = tuple(float(item["size"]) for item in rows) rates = tuple(float(item["growth_rate_per_generation"]) for item in rows) rescale = _fit_to_bounds(sizes) out.append( StdpopsimTemplate( species=species, model_id=model_id, population=rows[0]["population"], generation_time_years=float(rows[0]["generation_time_years"]), breaks=tuple(starts[1:]), values=tuple(size * rescale for size in sizes), growth_rates=rates, ne_rescale=float(rescale), ) ) return tuple(out) def load_stdpopsim_templates(cfg: Config) -> tuple[StdpopsimTemplate, ...]: return _load(str(getattr(cfg, "stdpopsim_template_path", DEFAULT_STDPOPSIM_TEMPLATE_PATH))) def stdpopsim_templates_available(cfg: Config) -> bool: return len(drawable_stdpopsim_templates(cfg)) > 0 def drawable_stdpopsim_templates(cfg: Config) -> tuple[StdpopsimTemplate, ...]: """The catalogue minus the models that have a recipe of their own.""" return tuple( template for template in load_stdpopsim_templates(cfg) if template.model_id not in CATALOGUE_EXCLUSIONS ) def choose_stdpopsim_template( rng: np.random.Generator, cfg: Config ) -> StdpopsimTemplate | None: templates = drawable_stdpopsim_templates(cfg) if not templates: return None return templates[int(rng.integers(0, len(templates)))]