Convert yaml configuration hyphens to underscores (#113)

Co-authored-by: ElliottKasoar <ElliottKasoar@users.noreply.github.com>

README.md

@@ -173,7 +173,7 @@ properties:
   - "energy"
 out: "NaCl-results.xyz"
 arch: mace_mp
-calc_kwargs:
+calc-kwargs:
   model: medium
 ```
 
@@ -187,10 +187,6 @@ This will run a singlepoint energy calculation on `KCl.cif` using the [MACE-MP](
 > [!NOTE]
 > `properties` must be passed as a Yaml list, as above, not as a string.
 
-> [!WARNING]
-> Options in the Yaml file must use `_` instead of `-`.
-> For example, `calc_kwargs` should be used in the configuration file for the `--calc-kwargs` option.
-
 > [!WARNING]
 > If an option in the configuration file does not match any variable names, an error will **not** be raised.
 > Please check the summary file to ensure the configuration has been read correctly.

janus_core/cli.py

@@ -4,18 +4,19 @@
 import datetime
 import logging
 from pathlib import Path
-from typing import Annotated, Optional, Union, get_args
+from typing import Annotated, Any, Optional, Union, get_args
 
 from ase import Atoms
 import typer
-from typer_config import use_yaml_config
+from typer_config import conf_callback_factory, use_config, yaml_loader
 import yaml
 
 from janus_core import __version__
 from janus_core.geom_opt import optimize
 from janus_core.janus_types import ASEReadArgs, Ensembles
 from janus_core.md import NPH, NPT, NVE, NVT, NVT_NH
 from janus_core.single_point import SinglePoint
+from janus_core.utils import dict_paths_to_strs, dict_remove_hyphens
 
 app = typer.Typer(name="janus", no_args_is_help=True)
 
@@ -101,21 +102,29 @@ def _parse_typer_dicts(typer_dicts: list[TyperDict]) -> list[dict]:
     return typer_dicts
 
 
-def _dict_paths_to_strs(dictionary: dict) -> None:
+def yaml_converter_loader(config_file: str) -> dict[str, Any]:
     """
-    Recursively iterate over dictionary, converting Path values to strings.
+    Load yaml configuration and replace hyphens with underscores.
 
     Parameters
     ----------
-    dictionary : dict
-        Dictionary to be converted.
+    config_file : str
+        Yaml configuration file to read.
+
+    Returns
+    -------
+    dict[str, Any]
+        Dictionary with loaded configuration.
     """
-    for key, value in dictionary.items():
-        if isinstance(value, dict):
-            _dict_paths_to_strs(value)
-        elif isinstance(value, Path):
-            dictionary[key] = str(value)
+    if not config_file:
+        return {}
+
+    config = yaml_loader(config_file)
+    # Replace all "-"" with "_" in conf
+    return dict_remove_hyphens(config)
+
 
+yaml_converter_callback = conf_callback_factory(yaml_converter_loader)
 
 # Shared type aliases
 StructPath = Annotated[Path, typer.Option(help="Path of structure to simulate.")]
@@ -190,7 +199,7 @@ def print_version(
 
 
 @app.command(help="Perform single point calculations and save to file.")
-@use_yaml_config()
+@use_config(yaml_converter_callback)
 def singlepoint(
     # pylint: disable=too-many-locals
     # numpydoc ignore=PR02
@@ -308,7 +317,7 @@ def singlepoint(
     }
 
     # Convert all paths to strings in inputs nested dictionary
-    _dict_paths_to_strs(inputs)
+    dict_paths_to_strs(inputs)
 
     # Save summary information before singlepoint calculation begins
     save_info = {
@@ -335,7 +344,7 @@ def singlepoint(
 @app.command(
     help="Perform geometry optimization and save optimized structure to file.",
 )
-@use_yaml_config()
+@use_config(yaml_converter_callback)
 def geomopt(
     # pylint: disable=too-many-arguments,too-many-locals
     # numpydoc ignore=PR02
@@ -509,7 +518,7 @@ def geomopt(
     }
 
     # Convert all paths to strings in inputs nested dictionary
-    _dict_paths_to_strs(inputs)
+    dict_paths_to_strs(inputs)
 
     # Save summary information before optimization begins
     save_info = {
@@ -536,7 +545,7 @@ def geomopt(
 @app.command(
     help="Run molecular dynamics simulation, and save trajectory and statistics.",
 )
-@use_yaml_config()
+@use_config(yaml_converter_callback)
 def md(
     # pylint: disable=too-many-arguments,too-many-locals,invalid-name
     # numpydoc ignore=PR02
@@ -895,7 +904,7 @@ def md(
     }
 
     # Convert all paths to strings in inputs nested dictionary
-    _dict_paths_to_strs(inputs)
+    dict_paths_to_strs(inputs)
 
     # Save summary information before simulation begins
     save_info = {

janus_core/md.py

@@ -350,7 +350,7 @@ def _reset_velocities(self) -> None:
 
     def _optimize_structure(self) -> None:
         """Perform geometry optimization."""
-        if self.dyn.nsteps < self.equil_steps:
+        if self.dyn.nsteps == 0 or self.dyn.nsteps < self.equil_steps:
             if self.logger:
                 self.minimize_kwargs["log_kwargs"] = {
                     "filename": self.log_kwargs["filename"],
@@ -502,7 +502,7 @@ def run(self) -> None:
 
         else:
             if self.minimize:
-                optimize(self.struct, **self.minimize_kwargs)
+                self._optimize_structure()
             if self.rescale_velocities:
                 self._reset_velocities()
 

janus_core/utils.py

@@ -1,5 +1,6 @@
 """Utility functions for janus_core."""
 
+from pathlib import Path
 from typing import Optional
 
 
@@ -20,3 +21,39 @@ def none_to_dict(dictionaries: list[Optional[dict]]) -> list[dict]:
     for i, dictionary in enumerate(dictionaries):
         dictionaries[i] = dictionary if dictionary else {}
     return dictionaries
+
+
+def dict_paths_to_strs(dictionary: dict) -> None:
+    """
+    Recursively iterate over dictionary, converting Path values to strings.
+
+    Parameters
+    ----------
+    dictionary : dict
+        Dictionary to be converted.
+    """
+    for key, value in dictionary.items():
+        if isinstance(value, dict):
+            dict_paths_to_strs(value)
+        elif isinstance(value, Path):
+            dictionary[key] = str(value)
+
+
+def dict_remove_hyphens(dictionary: dict) -> dict:
+    """
+    Recursively iterate over dictionary, replacing hyphens with underscores in keys.
+
+    Parameters
+    ----------
+    dictionary : dict
+        Dictionary to be converted.
+
+    Returns
+    -------
+    dict
+        Dictionary with hyphens in keys replaced with underscores.
+    """
+    for key, value in dictionary.items():
+        if isinstance(value, dict):
+            dictionary[key] = dict_remove_hyphens(value)
+    return {k.replace("-", "_"): v for k, v in dictionary.items()}

tests/data/geomopt_config.yml

@@ -1,4 +1,4 @@
-struct_path: "NaCl.cif"
-out_file: "NaCl-results.xyz"
-opt_kwargs:
+struct: "NaCl.cif"
+out: "NaCl-results.xyz"
+opt-kwargs:
   alpha: 100

tests/data/md_config.yml

@@ -1,2 +1,5 @@
 ensemble: "nvt"
 temp: 200
+minimize-kwargs:
+  filter-kwargs:
+    hydrostatic-strain: True

tests/data/singlepoint_config.yml

@@ -1,8 +1,8 @@
-struct_path: "NaCl.cif"
+struct: "NaCl.cif"
 properties:
   - "energy"
-out_file: "NaCl-results.xyz"
-calc_kwargs:
+out: "NaCl-results.xyz"
+calc-kwargs:
   model: "small"
-read_kwargs:
+read-kwargs:
   index: ":"

tests/test_md_cli.py

@@ -260,6 +260,7 @@ def test_config(tmp_path):
             file_prefix,
             "--steps",
             2,
+            "--minimize",
             "--log",
             log_path,
             "--summary",
@@ -278,6 +279,14 @@ def test_config(tmp_path):
     assert md_summary["inputs"]["temp"] == 200
     # Check explicit option overwrites config
     assert md_summary["inputs"]["ensemble"] == "nve"
+    # Check nested dictionary
+    assert (
+        md_summary["inputs"]["minimize_kwargs"]["filter_kwargs"]["hydrostatic_strain"]
+        is True
+    )
+
+    # Check hydrostatic strain passed correctly
+    assert_log_contains(log_path, includes=["hydrostatic_strain: True"])
 
 
 def test_heating(tmp_path):

tests/test_utils.py

@@ -0,0 +1,48 @@
+"""Test utility functions."""
+
+from pathlib import Path
+
+from janus_core.utils import dict_paths_to_strs, dict_remove_hyphens
+
+
+def test_dict_paths_to_strs():
+    """Test Paths are converted to strings."""
+    dictionary = {
+        "key1": Path("/example/path"),
+        "key2": {
+            "key3": Path("another/example"),
+            "key4": "example",
+        },
+    }
+
+    # Check Paths are present
+    assert isinstance(dictionary["key1"], Path)
+    assert isinstance(dictionary["key2"]["key3"], Path)
+    assert not isinstance(dictionary["key1"], str)
+
+    dict_paths_to_strs(dictionary)
+
+    # Check Paths are now strings
+    assert isinstance(dictionary["key1"], str)
+    assert isinstance(dictionary["key2"]["key3"], str)
+
+
+def test_dict_remove_hyphens():
+    """Test hyphens are replaced with underscores."""
+    dictionary = {
+        "key-1": "value_1",
+        "key-2": {
+            "key-3": "value-3",
+            "key-4": 4,
+            "key_5": 5.0,
+            "key6": {"key-7": "value7"},
+        },
+    }
+    dictionary = dict_remove_hyphens(dictionary)
+
+    # Check hyphens are now strings
+    assert dictionary["key_1"] == "value_1"
+    assert dictionary["key_2"]["key_3"] == "value-3"
+    assert dictionary["key_2"]["key_4"] == 4
+    assert dictionary["key_2"]["key_5"] == 5.0
+    assert dictionary["key_2"]["key6"]["key_7"] == "value7"