add schema validation to user input

PyVOTCA/schemas.py

@@ -0,0 +1,48 @@
+
+"""Module with the schemas to validate the user input."""
+
+from multiprocessing import cpu_count
+from numbers import Integral
+from typing import Any, Dict
+
+import yaml
+from schema import Optional, Or, Schema, SchemaError
+
+__all__ = ["validate_input"]
+
+
+input_schema = Schema({
+    # Path to the molecule in xyz format
+    "molecule": str,
+
+    # Number of Threads to run the application
+    Optional("threads", default=cpu_count()): Integral,
+
+    # Functional
+    Optional("functional", default="PBE"): str,
+
+    # Basisset
+    Optional("basis", default=None): Or(str, None),
+
+    # AuxBasisset
+    Optional("auxbasis", default=None): Or(str, None),
+
+    # GW
+    Optional("gw", default=None): Or(str, None),
+
+    # BSE
+    Optional("bse", default=None): Or(str, None),
+})
+
+
+def validate_input(file_input: str) -> Dict[str, Any]:
+    """Check the input validation against an schema."""
+    with open(file_input, 'r') as handler:
+        dict_input = yaml.load(handler.read(), Loader=yaml.FullLoader)
+    try:
+        inp = input_schema.validate(dict_input)
+        return inp
+    except SchemaError as err:
+        msg = f"There was an error in the input yaml provided:\n{err}"
+        print(msg)
+        raise

PyVOTCA/xtp_gradient.py

@@ -6,6 +6,7 @@
 import sys
 
 from .numerical_gradient import NumericalGradient
+from .schemas import validate_input
 
 
 def exists(input_file: str) -> Path:
@@ -35,22 +36,24 @@ def xtp_gradient(args: argparse.Namespace):
 def parse_user_arguments() -> argparse.Namespace:
     """Read the user arguments."""
     parser = argparse.ArgumentParser("xtp_gradient")
-    parser.add_argument("-n", "--name", help="Molecule name")
-    parser.add_argument("-t", "--threads", help="Number of threads")
+    parser.add_argument(
+        "-i", "--input", help="Input file in YAML format", type=exists)
 
     # Read the arguments
     args = parser.parse_args()
 
-    if args.name is None:
+    if args.input is None:
         parser.print_help()
         sys.exit()
 
-    return args
+    return args.input
 
 
 def main():
-    args = parse_user_arguments()
-    xtp_gradient(args)
+    inp = parse_user_arguments()
+    args = validate_input(inp)
+    print(args)
+    # xtp_gradient(args)
 
 
 if __name__ == "__main__":

setup.py

@@ -38,8 +38,7 @@
             'xtp_gradient=PyVOTCA.xtp_gradient:main',
         ]
     },
-
-    install_requires=["h5py", "matplotlib", "numpy", "scipy"],
+    install_requires=["h5py", "matplotlib", "numpy", "pyyaml", "schema", "scipy"],
     extras_require={
         'test': ['coverage', 'mypy', 'pycodestyle', 'pytest>=3.9',
                  'pytest-asyncio', 'pytest-cov', 'pytest-mock'],

tests/files/example.yml

@@ -0,0 +1,2 @@
+molecule: test/files/ethylene.xyz
+