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chore: fixes tests

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This commit is contained in:
Vitor Hideyoshi
2026-02-26 06:23:30 -03:00
parent f56d6b6b36
commit e5c6282c86
18 changed files with 284 additions and 127 deletions
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0
diceplayer/shared/config/__init__.py → diceplayer/config/__init__.py
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27
diceplayer/config/dice_config.py Normal file
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@@ -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")

21
diceplayer/config/gaussian_config.py Normal file
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@@ -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")

10
diceplayer/shared/config/player_config.py → diceplayer/config/player_config.py
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@@ -1,5 +1,5 @@
from diceplayer.shared.config.dice_config import DiceConfig
from diceplayer.shared.config.gaussian_config import GaussianDTO
from diceplayer.config.dice_config import DiceConfig
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}

27
diceplayer/player.py
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@@ -1,7 +1,9 @@
from pydantic import BaseModel
from diceplayer import VERSION, logger
from diceplayer.shared.config.dice_config import DiceConfig
from diceplayer.shared.config.gaussian_config import GaussianDTO
from diceplayer.shared.config.player_config import PlayerConfig
from diceplayer.config.dice_config import DiceConfig
from diceplayer.config.gaussian_config import GaussianConfig
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]):
for key in sorted(list(map(lambda f: f.name, fields(dto)))):
if getattr(config, key) is not None:
if isinstance(getattr(config, key), list):
string = " ".join(str(x) for x in getattr(config, key))
def log_keywords(config: BaseModel):
for key, value in sorted(config.model_dump().items()):
if value is None:
continue
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")

51
diceplayer/shared/config/dice_config.py
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@@ -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)

30
diceplayer/shared/config/gaussian_config.py
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@@ -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)

2
diceplayer/shared/interface/__interface.py
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@@ -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

2
diceplayer/shared/interface/dice_interface.py
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@@ -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

2
diceplayer/shared/interface/gaussian_interface.py
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@@ -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

197
poetry.lock generated
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@@ -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"]
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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"
description = "Backported and Experimental Type Hints for Python 3.8+"
version = "4.15.0"
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-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
{file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
{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"

1
pyproject.toml
View File

@@ -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]

4
tests/shared/config/test_dice_dto.py
View File

@@ -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",

14
tests/shared/config/test_gaussian_dto.py
View File

@@ -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__":

12
tests/shared/config/test_player_dto.py
View File

@@ -1,6 +1,6 @@
from diceplayer.shared.config.dice_config import DiceConfig
from diceplayer.shared.config.gaussian_config import GaussianDTO
from diceplayer.shared.config.player_config import PlayerConfig
from diceplayer.config.dice_config import DiceConfig
from diceplayer.config.gaussian_config import GaussianConfig
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__":

2
tests/shared/interface/test_dice_interface.py
View File

@@ -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

2
tests/shared/interface/test_gaussian_interface.py
View File

@@ -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

3
tests/test_player.py
View File

@@ -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",