Add pre-processing config file option

mace/tools/arg_parser.py

@@ -21,7 +21,7 @@ def build_default_arg_parser() -> argparse.ArgumentParser:
             "--config",
             type=str,
             is_config_file=True,
-            help="config file to agregate options",
+            help="config file to aggregate options",
         )
     except ImportError:
         parser = argparse.ArgumentParser(
@@ -714,9 +714,24 @@ def build_default_arg_parser() -> argparse.ArgumentParser:
 
 
 def build_preprocess_arg_parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-    )
+    try:
+        import configargparse
+
+        parser = configargparse.ArgumentParser(
+            config_file_parser_class=configargparse.YAMLConfigFileParser,
+            formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        )
+        parser.add(
+            "--config",
+            type=str,
+            is_config_file=True,
+            help="config file to aggregate options",
+        )
+    except ImportError:
+        parser = argparse.ArgumentParser(
+            formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        )
+
     parser.add_argument(
         "--train_file",
         help="Training set h5 file",

tests/test_preprocess.py

@@ -6,6 +6,7 @@
 import ase.io
 import numpy as np
 import pytest
+import yaml
 from ase.atoms import Atoms
 
 pytest_mace_dir = Path(__file__).parent.parent
@@ -164,3 +165,42 @@ def test_preprocess_data(tmp_path, sample_configs):
     np.testing.assert_allclose(original_forces, h5_forces, rtol=1e-5, atol=1e-8)
 
     print("All checks passed successfully!")
+
+
+def test_preprocess_config(tmp_path, sample_configs):
+    ase.io.write(tmp_path / "sample.xyz", sample_configs)
+
+    preprocess_params = {
+        "train_file": str(tmp_path / "sample.xyz"),
+        "r_max": 5.0,
+        "config_type_weights": "{'Default':1.0}",
+        "num_process": 2,
+        "valid_fraction": 0.1,
+        "h5_prefix": str(tmp_path / "preprocessed_"),
+        "compute_statistics": None,
+        "seed": 42,
+        "energy_key": "REF_energy",
+        "forces_key": "REF_forces",
+        "stress_key": "REF_stress",
+    }
+    filename = tmp_path / "config.yaml"
+    with open(filename, "w", encoding="utf-8") as file:
+        yaml.dump(preprocess_params, file)
+
+    run_env = os.environ.copy()
+    sys.path.insert(0, str(Path(__file__).parent.parent))
+    run_env["PYTHONPATH"] = ":".join(sys.path)
+    print("DEBUG subprocess PYTHONPATH", run_env["PYTHONPATH"])
+
+    cmd = (
+        sys.executable
+        + " "
+        + str(preprocess_data)
+        + " "
+        + "--config"
+        + " "
+        + str(filename)
+    )
+
+    p = subprocess.run(cmd.split(), env=run_env, check=True)
+    assert p.returncode == 0