from __future__ import annotations import argparse import dataclasses import sys from pathlib import Path from .config import Config, apply_preset, validate_config from .dataset_files import write_dataset_files from .dataset_state import DatasetConfigMismatchError from .empirical_maps import load_empirical_maps from .shards import ( DatasetGenerationIncompleteError, DatasetGenerationLockedError, DatasetSourceUnavailableError, UnsafeOutputDirectoryError, dataset_output_lock, finalize_dataset, generate_dataset, generate_dataset_partition, prepare_dataset, reuse_completed_dataset_if_compatible, ) from .slurm import SlurmEnvironmentError, distributed_context def parse_args() -> Config: base = apply_preset(Config()) parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) bool_fields = {"force", "compression", "include_truth", "enable_stdpopsim", "mut_map_scale_to_baseline"} choice_fields = {"recomb_map_unit", "mut_map_unit"} for f in dataclasses.fields(Config): if f.name in bool_fields or f.name in choice_fields: continue default = getattr(base, f.name) parser.add_argument("--" + f.name.replace("_", "-"), dest=f.name, type=type(default), default=None) parser.add_argument("--n", dest="n_samples", type=int, default=None, help="alias for --n-samples") parser.add_argument("--recomb-map-unit", choices=["per_bp", "cM_per_Mb"], default=None) parser.add_argument("--mut-map-unit", choices=["per_bp", "relative", "roulette_raw"], default=None) parser.add_argument("--force", action="store_true", help="overwrite an existing simulator output directory") parser.add_argument("--include-truth", action="store_true", help="store true maps for analysis; not model inputs") parser.add_argument("--enable-stdpopsim", action="store_true", help="include optional stdpopsim anchors") parser.add_argument( "--mut-map-scale-to-baseline", dest="mut_map_scale_to_baseline", action="store_true", help="normalize relative or raw mutation maps to baseline_mu after unit conversion", ) parser.add_argument( "--no-mut-map-scale-to-baseline", dest="mut_map_scale_to_baseline", action="store_false", help="preserve the absolute scale implied by --mut-map-unit", ) parser.add_argument("--no-compression", dest="compression", action="store_false", help="write uncompressed npz shards") parser.set_defaults(compression=None) parser.set_defaults(mut_map_scale_to_baseline=None) generation_mode = parser.add_mutually_exclusive_group() generation_mode.add_argument( "--prepare-only", dest="_generation_mode", action="store_const", const="prepare", help="create or validate the resumable generation plan, then exit", ) generation_mode.add_argument( "--generate-only", dest="_generation_mode", action="store_const", const="generate", help="generate only this rank's deterministic partition, then exit", ) generation_mode.add_argument( "--finalize-only", dest="_generation_mode", action="store_const", const="finalize", help="merge all committed fragments and publish the completed dataset", ) parser.add_argument( "--rank", dest="_distributed_rank", type=int, metavar="RANK", default=None, help="explicit zero-based generation rank (normally inferred from SLURM_PROCID)", ) parser.add_argument( "--world-size", dest="_distributed_world_size", type=int, metavar="N", default=None, help="explicit number of generation ranks (normally inferred from SLURM_NTASKS)", ) parser.set_defaults(_generation_mode="auto") ns = parser.parse_args() preset = ns.preset if ns.preset is not None else "mini" try: cfg = apply_preset(Config(preset=preset)) except ValueError as exc: parser.error(str(exc)) for f in dataclasses.fields(Config): val = getattr(ns, f.name, None) if val is not None: setattr(cfg, f.name, val) if cfg.enable_stdpopsim and cfg.p_stdpopsim_anchor == 0.0: cfg.p_stdpopsim_anchor = 0.10 cfg.p_custom_hetero = max(0.0, cfg.p_custom_hetero - 0.10) try: validate_config(cfg) except ValueError as exc: parser.error(str(exc)) cfg._generation_mode = ns._generation_mode cfg._distributed_rank = ns._distributed_rank cfg._distributed_world_size = ns._distributed_world_size return cfg def _load_maps(cfg: Config): try: return load_empirical_maps(cfg) except (OSError, ValueError) as exc: raise SystemExit(f"[error] failed to load empirical maps: {exc}") from None def _write_completed_dataset(cfg: Config, sample_manifest: dict) -> None: write_dataset_files(cfg, sample_manifest) print("[done] dataset written to", cfg.out_dir) print(" manifest:", Path(cfg.out_dir) / "manifest.json") print(" loader: ", Path(cfg.out_dir) / "scripts" / "loader.py") def main() -> None: cfg = parse_args() mode = getattr(cfg, "_generation_mode", "auto") explicit_rank = getattr(cfg, "_distributed_rank", None) explicit_world_size = getattr(cfg, "_distributed_world_size", None) print("=" * 80) print(f"DLCoalSim generator: {cfg.dataset_name}") print(f"out_dir={cfg.out_dir}") print( f"preset={cfg.preset} seq_len={cfg.seq_len:,} H={cfg.n_haplotypes} " f"target_T={cfg.time_bins} history_tol={cfg.demography_resolution_log10}" ) print("=" * 80) sys.stdout.flush() try: if mode in {"prepare", "finalize"}: if explicit_rank is not None or explicit_world_size is not None: raise ValueError( "--rank/--world-size apply only to generation, not " "--prepare-only or --finalize-only" ) if mode == "prepare": prepare_dataset(cfg, _load_maps(cfg)) print("[prepared] resumable generation plan:", Path(cfg.out_dir) / "samples" / "PLAN.json") return with dataset_output_lock(cfg.out_dir, blocking=True): sample_manifest = finalize_dataset( cfg, _lock_already_held=True, ) _write_completed_dataset(cfg, sample_manifest) return context = distributed_context( rank=explicit_rank, world_size=explicit_world_size, ) if mode == "generate" or context.distributed: rank_result = generate_dataset_partition( cfg, _load_maps(cfg), rank=context.rank, world_size=context.world_size, ) print( f"[rank done] rank={context.rank}/{context.world_size} " f"generated_chunks={rank_result.get('generated_chunks', 0)} " f"reused_chunks={rank_result.get('reused_chunks', 0)}" ) return with dataset_output_lock(cfg.out_dir): sample_manifest = reuse_completed_dataset_if_compatible( cfg, _lock_already_held=True, ) if sample_manifest is None: sample_manifest = generate_dataset( cfg, _load_maps(cfg), _lock_already_held=True, ) _write_completed_dataset(cfg, sample_manifest) except ( DatasetConfigMismatchError, DatasetGenerationIncompleteError, DatasetGenerationLockedError, DatasetSourceUnavailableError, SlurmEnvironmentError, UnsafeOutputDirectoryError, ValueError, ) as exc: raise SystemExit(f"[error] {exc}") from None except OSError as exc: raise SystemExit(f"[error] filesystem operation failed: {exc}") from None