Fix CLI config handling: --config on convert/generate, and missing config files

docs/cli.md

@@ -99,6 +99,10 @@ You can also select SevenNet with the `--model-type` flag
 
 **Note:**
 - If `--config` is not specified, `config.json` in the current directory is loaded by default.
+  If that file does not exist either, GPUMA runs on its built-in defaults and logs a warning
+  naming the default model. A `--config` path that does not exist is an error.
+- Global flags (`--device`, `--model-type`, `--verbose`, `--quiet`) go before the subcommand,
+  e.g. `gpuma --device cuda:1 batch ...`.
 - Direct CLI flags are supported, but using a config file is preferred for all workflows.
 - Unless explicitly overridden, the electronic state defaults are always
   `charge = 0` and `multiplicity = 1`.

src/gpuma/cli.py

@@ -18,6 +18,7 @@
 
 import argparse
 import logging
+import os
 import sys
 import warnings
 
@@ -281,6 +282,12 @@ def setup_parser() -> argparse.ArgumentParser:
         required=True,
         help="Output XYZ file path",
     )
+    convert_parser.add_argument(
+        "--config",
+        "-c",
+        type=str,
+        help="Configuration file path (default: config.json if exists)",
+    )
 
     # Conformer generation (utility)
     generate_parser = subparsers.add_parser(
@@ -307,6 +314,12 @@ def setup_parser() -> argparse.ArgumentParser:
         required=True,
         help="Output multi-XYZ file path for conformer ensemble",
     )
+    generate_parser.add_argument(
+        "--config",
+        "-c",
+        type=str,
+        help="Configuration file path (default: config.json if exists)",
+    )
 
     # Configuration management
     config_parser = subparsers.add_parser(
@@ -565,6 +578,9 @@ def cmd_config(args, config: Config) -> None:
         save_config_to_file(config, args.create)
         logger.info("Configuration file created")
     elif args.validate:
+        if not os.path.exists(args.validate):
+            logger.error("Configuration file not found: %s", args.validate)
+            sys.exit(1)
         logger.info("Validating configuration file at %s", args.validate)
         _ = load_config_from_file(args.validate)
         logger.info("Configuration file is valid")
@@ -590,6 +606,20 @@ def _apply_model_type_override(config: Config, model_type) -> None:
         config.model.model_type = model_type
 
 
+def _resolve_config_path(args, parser: argparse.ArgumentParser) -> tuple[str, bool]:
+    """Return the config path to load and whether built-in defaults stand in for it.
+
+    An explicit ``--config`` that does not exist is a usage error, so a typo
+    cannot silently swap in the default model.
+    """
+    explicit = getattr(args, "config", None)
+    if explicit is not None:
+        if not os.path.exists(explicit):
+            parser.error(f"config file not found: {explicit}")
+        return explicit, False
+    return "config.json", not os.path.exists("config.json")
+
+
 def main(argv=None) -> int:
     """Entry point for the ``gpuma`` CLI.
 
@@ -608,8 +638,7 @@ def main(argv=None) -> int:
     parser = setup_parser()
     args = parser.parse_args(argv)
 
-    # Load configuration from file if specified, otherwise try default
-    cfg_path = getattr(args, "config", None) or "config.json"
+    cfg_path, using_defaults = _resolve_config_path(args, parser)
     config = load_config_from_file(cfg_path)
 
     # Apply verbosity, device, and model-type flags
@@ -625,6 +654,14 @@ def main(argv=None) -> int:
         parser.print_help()
         return 1
 
+    if using_defaults and args.command != "config":
+        logger.warning(
+            "No --config given and no config.json in the working directory; "
+            "using built-in defaults (model %s / %s).",
+            config.model.model_type,
+            config.model.model_name,
+        )
+
     if args.command in ("optimize", "smiles"):
         cmd_optimize(args, config)
     elif args.command == "ensemble":

tests/test_cli.py

@@ -323,3 +323,42 @@ def fake_ensemble(smiles, num_confs, multiplicity=None, seed=None, config=None):
     cli.cmd_generate(args, config)
 
     assert seen["multiplicity"] == 3
+
+
+# ---------------------------------------------------------------------------
+# Config handling: --config on every command, missing files
+# ---------------------------------------------------------------------------
+
+
+@pytest.mark.parametrize("command", [["convert"], ["generate", "--conformers", "2"]])
+def test_convert_and_generate_accept_config(command):
+    from gpuma.cli import setup_parser
+
+    args = setup_parser().parse_args([*command, "--smiles", "C", "-o", "x.xyz", "-c", "c.json"])
+
+    assert args.config == "c.json"
+
+
+def test_missing_explicit_config_is_a_usage_error(tmp_path):
+    with pytest.raises(SystemExit) as exc_info:
+        main(["optimize", "--smiles", "C", "-o", str(tmp_path / "x.xyz"), "-c", "nope.json"])
+    assert exc_info.value.code == 2
+
+
+def test_validate_rejects_a_missing_file(tmp_path):
+    with pytest.raises(SystemExit) as exc_info:
+        main(["config", "--validate", str(tmp_path / "nope.json")])
+    assert exc_info.value.code == 1
+
+
+def test_no_config_anywhere_reports_defaults(tmp_path, monkeypatch):
+    import argparse
+
+    from gpuma.cli import _resolve_config_path, setup_parser
+
+    monkeypatch.chdir(tmp_path)
+    path, using_defaults = _resolve_config_path(argparse.Namespace(config=None), setup_parser())
+    assert (path, using_defaults) == ("config.json", True)
+
+    (tmp_path / "config.json").write_text("{}")
+    assert _resolve_config_path(argparse.Namespace(config=None), setup_parser())[1] is False