repare 0.1.4__py3-none-any.whl

repare/__init__.py

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+from .pedigree import Pedigree
+from .pedigree_reconstructor import PedigreeReconstructor
+
+__all__ = ["Pedigree", "PedigreeReconstructor"]

repare/main.py

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+import argparse
+import logging
+from datetime import datetime
+from pathlib import Path
+
+from tqdm.contrib.logging import logging_redirect_tqdm
+
+from repare.pedigree_reconstructor import PedigreeReconstructor
+
+
+def parse_arguments():
+    base_parser = argparse.ArgumentParser(add_help=False)
+    base_parser.add_argument(
+        "--print-allowed-constraints",
+        action="store_true",
+        help="Print the list of allowed constraint strings and exit.",
+    )
+
+    # Handle the informational flag before enforcing required arguments
+    base_args, remaining_args = base_parser.parse_known_args()
+    if base_args.print_allowed_constraints:
+        for constraint in sorted(PedigreeReconstructor.get_allowed_constraints()):
+            print(constraint)
+        base_parser.exit()
+
+    parser = argparse.ArgumentParser(
+        parents=[base_parser],
+        description="Reconstruct (ancient) pedigrees from pairwise kinship relations.",
+    )
+    parser.add_argument("-n", "--nodes", type=str, required=True, help="Path to the nodes CSV file.")
+    parser.add_argument("-r", "--relations", type=str, required=True, help="Path to the relations CSV file.")
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=str,
+        default=datetime.now().strftime("repare_output_%Y%m%d_%H%M%S"),
+        help=(
+            "Directory to save the output files. Defaults to repare_output_<YYYYMMDD_HHMMSS> in the current directory."
+        ),
+    )
+    parser.add_argument(
+        "-m",
+        "--max_candidate_pedigrees",
+        type=int,
+        default=1000,
+        help="Number of pedigrees to keep after each iteration. Defaults to 1000.",
+    )
+    parser.add_argument(
+        "-e",
+        "--epsilon",
+        type=float,
+        default=0.2,
+        help="Parameter for adapted epsilon-greedy sampling at the end of each algorithm iteration. Defaults to 0.2.",
+    )
+    parser.add_argument("-s", "--seed", type=int, default=42, help="Random seed for reproducibility. Defaults to 42.")
+    parser.add_argument("-d", "--do_not_plot", action="store_false", help="Do not plot reconstructed pedigree(s).")
+    parser.add_argument(
+        "-w", "--write_alternates", action="store_true", help="Write outputs of alternate pedigrees to disk."
+    )
+    parser.add_argument("-v", "--verbose", action="store_true", help="Enable verbose output (INFO-level logging).")
+    return parser.parse_args(remaining_args)
+
+
+def main():
+    args = parse_arguments()
+    logging_level = logging.INFO if args.verbose else logging.WARNING
+    logging.basicConfig(level=logging_level, format="%(levelname)s - %(message)s")
+
+    output_dir = Path(args.output)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    with logging_redirect_tqdm():
+        print("Beginning pedigree reconstruction...")
+        pedigree_reconstructor = PedigreeReconstructor(
+            relations_path=args.relations,
+            nodes_path=args.nodes,
+            outputs_dir=output_dir,
+            max_candidate_pedigrees=args.max_candidate_pedigrees,
+            epsilon=args.epsilon,
+            plot=args.do_not_plot,
+            write_alternate_pedigrees=args.write_alternates,
+            random_seed=args.seed,
+        )
+        pedigree_reconstructor.find_best_pedigree()
+    print(f"Finished pedigree reconstruction. Outputs written to {output_dir.resolve()}.")
+
+
+if __name__ == "__main__":
+    main()