Tom/eDNA_Stream_E01_custom_models
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Added --out optional flag for build subcommand to make usage in snakemake cleaner

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Tom Kasper
2026-09-29 08:55:00 +01:00
parent 88e98effad
commit 96ae5d78ba
1 changed files with 10 additions and 2 deletions
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src/custom_models/cli.py
+10 -2
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@@ -260,7 +260,7 @@ def _cmd_build(args: argparse.Namespace) -> int:
Args: Args:
args: Parsed arguments (arch, budget, stride, d-embed, args: Parsed arguments (arch, budget, stride, d-embed,
budget-tol, n-heads, n-classes, seed). budget-tol, n-heads, n-classes, seed, out).
Returns: Returns:
Exit code 0 on success. Exit code 0 on success.
@@ -292,7 +292,14 @@ def _cmd_build(args: argparse.Namespace) -> int:
"n_classes": args.n_classes, "n_classes": args.n_classes,
"count_params": count_params(probe), "count_params": count_params(probe),
} }
print(json.dumps(payload, indent=2, sort_keys=True)) text = json.dumps(payload, indent=2, sort_keys=True)
if args.out:
out = Path(args.out)
out.parent.mkdir(parents=True, exist_ok=True)
out.write_text(text + "\n", encoding="utf-8")
print(f"wrote {out}")
else:
print(text)
return 0 return 0
@@ -480,6 +487,7 @@ def build_parser() -> argparse.ArgumentParser:
_add_model_args(p_build, required=True) _add_model_args(p_build, required=True)
p_build.add_argument("--n-classes", type=int, default=11) p_build.add_argument("--n-classes", type=int, default=11)
p_build.add_argument("--seed", type=int, default=0) p_build.add_argument("--seed", type=int, default=0)
p_build.add_argument("--out", default=None, help="Write the JSON payload to PATH instead of stdout")
p_build.set_defaults(func=_cmd_build) p_build.set_defaults(func=_cmd_build)
p_store = sub.add_parser("store", help="build a signal store (pod5+labels or synthetic)") p_store = sub.add_parser("store", help="build a signal store (pod5+labels or synthetic)")