chore: fixes tests

diceplayer/config/dice_config.py

@@ -0,0 +1,27 @@
+from pydantic import BaseModel, Field
+
+from diceplayer.shared.utils.dataclass_protocol import Dataclass
+
+from dataclasses import dataclass, fields
+from typing import List, Literal
+
+
+class DiceConfig(BaseModel):
+    """
+    Data Transfer Object for the Dice configuration.
+    """
+
+    ljname: str = Field(..., description="Name of the Lennard-Jones potential file")
+    outname: str = Field(..., description="Name of the output file for the simulation results")
+    dens: float = Field(..., description="Density of the system")
+    nmol: List[int] = Field(..., description="List of the number of molecules for each component")
+    nstep: List[int] = Field(..., description="List of the number of steps for each component", min_length=2, max_length=3)
+
+    upbuf: int = Field(360, description="Buffer size for the potential energy calculations")
+    combrule: Literal["+", "*"] = Field("*", description="Combination rule for the Lennard-Jones potential")
+    isave: int = Field(1000, description="Frequency of saving the simulation results")
+    press: float = Field(1.0, description="Pressure of the system")
+    temp: float = Field(300.0, description="Temperature of the system")
+    progname: str = Field("dice", description="Name of the program to run the simulation")
+    randominit: str = Field("first", description="Method for initializing the random number generator")
+    seed: int | None = Field(None, description="Seed for the random number generator")

diceplayer/config/gaussian_config.py

@@ -0,0 +1,21 @@
+from typing import Literal
+
+from pydantic import BaseModel, Field
+
+from diceplayer.shared.utils.dataclass_protocol import Dataclass
+
+from dataclasses import dataclass, fields
+
+
+class GaussianConfig(BaseModel):
+    """
+    Data Transfer Object for the Gaussian configuration.
+    """
+
+    level: str = Field(..., description="Level of theory for the QM calculations")
+    qmprog: Literal["g03", "g09", "g16"] = Field("g16", description="QM program to use for the calculations")
+
+    chgmult: list[int] = Field(default_factory=lambda: [0, 1], description="List of charge and multiplicity for the QM calculations")
+    pop: str = Field("chelpg", description="Population analysis method for the QM calculations")
+    chg_tol: float = Field(0.01, description="Charge tolerance for the QM calculations")
+    keywords: str = Field(None, description="Additional keywords for the QM calculations")

diceplayer/config/player_config.py

@@ -1,5 +1,5 @@
-from diceplayer.shared.config.dice_config import DiceConfig
+from diceplayer.config.dice_config import DiceConfig
-from diceplayer.shared.config.gaussian_config import GaussianDTO
+from diceplayer.config.gaussian_config import GaussianConfig
 from diceplayer.shared.utils.dataclass_protocol import Dataclass
 
 from dataclasses import dataclass, fields
@@ -17,7 +17,7 @@ class PlayerConfig(Dataclass):
     ncores: int
 
     dice: DiceConfig
-    gaussian: GaussianDTO
+    gaussian: GaussianConfig
 
     mem: int = None
     switchcyc: int = 3
@@ -35,11 +35,11 @@ class PlayerConfig(Dataclass):
     def from_dict(cls, params: dict):
         if params["dice"] is None:
             raise ValueError("Error: 'dice' keyword not specified in config file.")
-        params["dice"] = DiceConfig.from_dict(params["dice"])
+        params["dice"] = DiceConfig.model_validate(params["dice"])
 
         if params["gaussian"] is None:
             raise ValueError("Error: 'gaussian' keyword not specified in config file.")
-        params["gaussian"] = GaussianDTO.from_dict(params["gaussian"])
+        params["gaussian"] = GaussianConfig.model_validate(params["gaussian"])
 
         params = {f.name: params[f.name] for f in fields(cls) if f.name in params}
 

diceplayer/player.py

@@ -1,7 +1,9 @@
+from pydantic import BaseModel
+
 from diceplayer import VERSION, logger
-from diceplayer.shared.config.dice_config import DiceConfig
+from diceplayer.config.dice_config import DiceConfig
-from diceplayer.shared.config.gaussian_config import GaussianDTO
+from diceplayer.config.gaussian_config import GaussianConfig
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.player_config import PlayerConfig
 from diceplayer.shared.environment.atom import Atom
 from diceplayer.shared.environment.molecule import Molecule
 from diceplayer.shared.environment.system import System
@@ -16,7 +18,6 @@ import yaml
 import os
 import pickle
 import sys
-from dataclasses import fields
 from pathlib import Path
 from typing import Tuple, Type
 
@@ -108,14 +109,16 @@ class Player:
         geoms_file_path.touch()
 
     def print_keywords(self) -> None:
-        def log_keywords(config: Dataclass, dto: Type[Dataclass]):
+        def log_keywords(config: BaseModel):
-            for key in sorted(list(map(lambda f: f.name, fields(dto)))):
+            for key, value in sorted(config.model_dump().items()):
-                if getattr(config, key) is not None:
+                if value is None:
-                    if isinstance(getattr(config, key), list):
+                    continue
-                        string = " ".join(str(x) for x in getattr(config, key))
+                if isinstance(value, list):
+                    string = " ".join(str(x) for x in value)
                     logger.info(f"{key} = [ {string} ]")
                 else:
-                        logger.info(f"{key} = {getattr(config, key)}")
+                    logger.info(f"{key} = {value}")
+
 
         logger.info(
             f"##########################################################################################\n"
@@ -138,7 +141,7 @@ class Player:
             "------------------------------------------------------------------------------------------\n"
         )
 
-        log_keywords(self.config.dice, DiceConfig)
+        log_keywords(self.config.dice)
 
         logger.info(
             "------------------------------------------------------------------------------------------\n"
@@ -146,7 +149,7 @@ class Player:
             "------------------------------------------------------------------------------------------\n"
         )
 
-        log_keywords(self.config.gaussian, GaussianDTO)
+        log_keywords(self.config.gaussian)
 
         logger.info("\n")
 

diceplayer/shared/config/dice_config.py

@@ -1,51 +0,0 @@
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-
-from dataclasses import dataclass, fields
-from typing import List
-
-
-@dataclass
-class DiceConfig(Dataclass):
-    """
-    Data Transfer Object for the Dice configuration.
-    """
-
-    ljname: str
-    outname: str
-    dens: float
-    nmol: List[int]
-    nstep: List[int]
-
-    upbuf = 360
-    combrule = "*"
-    isave: int = 1000
-    press: float = 1.0
-    temp: float = 300.0
-    progname: str = "dice"
-    randominit: str = "first"
-
-    def __post_init__(self):
-        if not isinstance(self.ljname, str):
-            raise ValueError("Error: 'ljname' keyword not specified in config file")
-
-        if not isinstance(self.outname, str):
-            raise ValueError("Error: 'outname' keyword not specified in config file")
-
-        if not isinstance(self.dens, float):
-            raise ValueError("Error: 'dens' keyword not specified in config file")
-
-        if not isinstance(self.nmol, list):
-            raise ValueError(
-                "Error: 'nmol' keyword not defined appropriately in config file"
-            )
-
-        if not isinstance(self.nstep, list) or len(self.nstep) not in (2, 3):
-            raise ValueError(
-                "Error: 'nstep' keyword not defined appropriately in config file"
-            )
-
-    @classmethod
-    def from_dict(cls, params: dict):
-        params = {f.name: params[f.name] for f in fields(cls) if f.name in params}
-
-        return cls(**params)

diceplayer/shared/config/gaussian_config.py

@@ -1,30 +0,0 @@
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-
-from dataclasses import dataclass, fields
-
-
-@dataclass
-class GaussianDTO(Dataclass):
-    """
-    Data Transfer Object for the Gaussian configuration.
-    """
-
-    level: str
-    qmprog: str
-
-    chgmult = [0, 1]
-    pop: str = "chelpg"
-    chg_tol: float = 0.01
-    keywords: str = None
-
-    def __post_init__(self):
-        if self.qmprog not in ("g03", "g09", "g16"):
-            raise ValueError("Error: invalid qmprog value.")
-        if self.level is None:
-            raise ValueError("Error: 'level' keyword not specified in config file.")
-
-    @classmethod
-    def from_dict(cls, params: dict):
-        params = {f.name: params[f.name] for f in fields(cls) if f.name in params}
-
-        return cls(**params)

diceplayer/shared/interface/__interface.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.player_config import PlayerConfig
 from diceplayer.shared.environment.system import System
 
 from abc import ABC, abstractmethod

diceplayer/shared/interface/dice_interface.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.player_config import PlayerConfig
 from diceplayer.shared.environment.system import System
 from diceplayer.shared.interface import Interface
 

diceplayer/shared/interface/gaussian_interface.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.player_config import PlayerConfig
 from diceplayer.shared.environment.atom import Atom
 from diceplayer.shared.environment.molecule import Molecule
 from diceplayer.shared.environment.system import System

poetry.lock

@@ -1,5 +1,17 @@
 # This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand.
 
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+files = [
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
 [[package]]
 name = "argparse"
 version = "1.4.0"
@@ -407,6 +419,162 @@ nodeenv = ">=0.11.1"
 pyyaml = ">=5.1"
 virtualenv = ">=20.10.0"
 
+[[package]]
+name = "pydantic"
+version = "2.12.5"
+description = "Data validation using Python type hints"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "pydantic-2.12.5-py3-none-any.whl", hash = "sha256:e561593fccf61e8a20fc46dfc2dfe075b8be7d0188df33f221ad1f0139180f9d"},
+    {file = "pydantic-2.12.5.tar.gz", hash = "sha256:4d351024c75c0f085a9febbb665ce8c0c6ec5d30e903bdb6394b7ede26aebb49"},
+]
+
+[package.dependencies]
+annotated-types = ">=0.6.0"
+pydantic-core = "2.41.5"
+typing-extensions = ">=4.14.1"
+typing-inspection = ">=0.4.2"
+
+[package.extras]
+email = ["email-validator (>=2.0.0)"]
+timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
+
+[[package]]
+name = "pydantic-core"
+version = "2.41.5"
+description = "Core functionality for Pydantic validation and serialization"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
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+]
+
+[package.dependencies]
+typing-extensions = ">=4.14.1"
+
 [[package]]
 name = "pyyaml"
 version = "6.0.1"
@@ -583,16 +751,31 @@ files = [
 
 [[package]]
 name = "typing-extensions"
-version = "4.12.2"
+version = "4.15.0"
-description = "Backported and Experimental Type Hints for Python 3.8+"
+description = "Backported and Experimental Type Hints for Python 3.9+"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
-    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
-    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
+    {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
 ]
-markers = {main = "python_version == \"3.9\"", dev = "python_version < \"3.11\""}
+markers = {dev = "python_version < \"3.11\""}
+
+[[package]]
+name = "typing-inspection"
+version = "0.4.2"
+description = "Runtime typing introspection tools"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "typing_inspection-0.4.2-py3-none-any.whl", hash = "sha256:4ed1cacbdc298c220f1bd249ed5287caa16f34d44ef4e9c3d0cbad5b521545e7"},
+    {file = "typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464"},
+]
+
+[package.dependencies]
+typing-extensions = ">=4.12.0"
 
 [[package]]
 name = "virtualenv"
@@ -618,4 +801,4 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.9"
-content-hash = "f1adb46e996bb9ce175110b2924da21fb8d5b7e2818dc981fca266ea95d51d3d"
+content-hash = "4a1819a86e32881c06191270ef503ebe87ef4ff519052fd8f0852510e31668e1"

pyproject.toml

@@ -23,6 +23,7 @@ argparse = "^1.4.0"
 setproctitle = "^1.3.2"
 pyyaml = "^6.0"
 nptyping = "^2.5.0"
+pydantic = "^2.12.5"
 
 
 [tool.poetry.group.dev.dependencies]

tests/shared/config/test_dice_dto.py

@@ -1,4 +1,4 @@
-from diceplayer.shared.config.dice_config import DiceConfig
+from diceplayer.config.dice_config import DiceConfig
 
 import unittest
 
@@ -83,7 +83,7 @@ class TestDiceDto(unittest.TestCase):
             )
 
     def test_from_dict(self):
-        dice_dto = DiceConfig.from_dict(
+        dice_dto = DiceConfig.model_validate(
             {
                 "ljname": "test",
                 "outname": "test",

tests/shared/config/test_gaussian_dto.py

@@ -1,21 +1,21 @@
-from diceplayer.shared.config.gaussian_config import GaussianDTO
+from diceplayer.config.gaussian_config import GaussianConfig
 
 import unittest
 
 
 class TestGaussianDTO(unittest.TestCase):
     def test_class_instantiation(self):
-        gaussian_dto = GaussianDTO(
+        gaussian_dto = GaussianConfig(
             level="test",
             qmprog="g16",
             keywords="test",
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianDTO)
+        self.assertIsInstance(gaussian_dto, GaussianConfig)
 
     def test_is_valid_qmprog(self):
         with self.assertRaises(ValueError):
-            gaussian_dto = GaussianDTO(
+            gaussian_dto = GaussianConfig(
                 level="test",
                 qmprog="test",
                 keywords="test",
@@ -23,14 +23,14 @@ class TestGaussianDTO(unittest.TestCase):
 
     def test_is_valid_level(self):
         with self.assertRaises(ValueError):
-            gaussian_dto = GaussianDTO(
+            gaussian_dto = GaussianConfig(
                 level=None,
                 qmprog="g16",
                 keywords="test",
             )
 
     def test_from_dict(self):
-        gaussian_dto = GaussianDTO.from_dict(
+        gaussian_dto = GaussianConfig.model_validate(
             {
                 "level": "test",
                 "qmprog": "g16",
@@ -38,7 +38,7 @@ class TestGaussianDTO(unittest.TestCase):
             }
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianDTO)
+        self.assertIsInstance(gaussian_dto, GaussianConfig)
 
 
 if __name__ == "__main__":

tests/shared/config/test_player_dto.py

@@ -1,6 +1,6 @@
-from diceplayer.shared.config.dice_config import DiceConfig
+from diceplayer.config.dice_config import DiceConfig
-from diceplayer.shared.config.gaussian_config import GaussianDTO
+from diceplayer.config.gaussian_config import GaussianConfig
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.player_config import PlayerConfig
 
 import unittest
 
@@ -36,7 +36,7 @@ class TestPlayerDTO(unittest.TestCase):
             nmol=[1],
             nstep=[1, 1],
         )
-        self.gaussian_dto = GaussianDTO(
+        self.gaussian_dto = GaussianConfig(
             level="test",
             qmprog="g16",
             keywords="test",
@@ -55,7 +55,7 @@ class TestPlayerDTO(unittest.TestCase):
 
         self.assertIsInstance(player_dto, PlayerConfig)
         self.assertIsInstance(player_dto.dice, DiceConfig)
-        self.assertIsInstance(player_dto.gaussian, GaussianDTO)
+        self.assertIsInstance(player_dto.gaussian, GaussianConfig)
 
     def test_min_altsteps(self):
         player_dto = PlayerConfig(
@@ -76,7 +76,7 @@ class TestPlayerDTO(unittest.TestCase):
 
         self.assertIsInstance(player_dto, PlayerConfig)
         self.assertIsInstance(player_dto.dice, DiceConfig)
-        self.assertIsInstance(player_dto.gaussian, GaussianDTO)
+        self.assertIsInstance(player_dto.gaussian, GaussianConfig)
 
 
 if __name__ == "__main__":

tests/shared/interface/test_dice_interface.py

@@ -1,5 +1,5 @@
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.player_config import PlayerConfig
 from diceplayer.shared.environment.atom import Atom
 from diceplayer.shared.environment.molecule import Molecule
 from diceplayer.shared.environment.system import System

tests/shared/interface/test_gaussian_interface.py

@@ -1,5 +1,5 @@
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.player_config import PlayerConfig
 from diceplayer.shared.environment.system import System
 from diceplayer.shared.interface.gaussian_interface import GaussianInterface
 from tests.mocks.mock_inputs import get_config_example

tests/test_player.py

@@ -71,6 +71,7 @@ class TestPlayer(unittest.TestCase):
             "INFO:diceplayer:Environment variables:",
             "INFO:diceplayer:OMP_STACKSIZE = Not set\n",
             "INFO:diceplayer:------------------------------------------------------------------------------------------\n                         DICE variables being used in this run:\n------------------------------------------------------------------------------------------\n",
+            "INFO:diceplayer:combrule = *",
             "INFO:diceplayer:dens = 0.75",
             "INFO:diceplayer:isave = 1000",
             "INFO:diceplayer:ljname = phb.ljc",
@@ -81,8 +82,10 @@ class TestPlayer(unittest.TestCase):
             "INFO:diceplayer:progname = ~/.local/bin/dice",
             "INFO:diceplayer:randominit = first",
             "INFO:diceplayer:temp = 300.0",
+            "INFO:diceplayer:upbuf = 360",
             "INFO:diceplayer:------------------------------------------------------------------------------------------\n                         GAUSSIAN variables being used in this run:\n------------------------------------------------------------------------------------------\n",
             "INFO:diceplayer:chg_tol = 0.01",
+            "INFO:diceplayer:chgmult = [ 0 1 ]",
             "INFO:diceplayer:keywords = freq",
             "INFO:diceplayer:level = MP2/aug-cc-pVDZ",
             "INFO:diceplayer:pop = chelpg",