pythonQEPest 2.0.0a4__tar.gz → 2.0.0a5__tar.gz

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonQEPest
-Version: 2.0.0a4
+Version: 2.0.0a5
 Summary: Java QEPest but written in Python
 License-File: LICENSE
 Author: Lina
@@ -16,6 +16,7 @@ Requires-Dist: pydantic (==2.12.5)
 Requires-Dist: pyperclip (>=1.11.0,<2.0.0) ; extra == "gui"
 Requires-Dist: python-dotenv (>=1.2.1,<2.0.0)
 Requires-Dist: rdkit (>=2024.3.1,<2026.0.0) ; extra == "rdkit"
+Requires-Dist: ruff (>=0.15.13,<0.16.0)
 Description-Content-Type: text/markdown
 
 # pythonQEPest

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pyproject.toml

@@ -1,11 +1,11 @@
 [project]
 name = "pythonQEPest"
-version = "2.0.0a4"
+version = "2.0.0a5"
 description = "Java QEPest but written in Python"
 readme = "README.md"
 requires-python = ">=3.12,<3.15"
 authors = [{ name = "Lina", email = "knocker767@gmail.com" }]
-dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0"]
+dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0", "ruff (>=0.15.13,<0.16.0)"]
 
 [project.optional-dependencies]
 gui = ["pyperclip>=1.11.0,<2.0.0"]
@@ -22,10 +22,10 @@ packages = [{ include = "pythonQEPest" }]
 
 [dependency-groups]
 dev = [
-    "pytest (>=9.0.0)",
-    "pre-commit (>=4.3.0,<5.0.0)",
+    "pytest (>=9.0.3)",
+    "pre-commit (>=4.6.0,<5.0.0)",
     "pyinstaller (>=6.18.0,<7.0.0)",
-    "poethepoet[poetry_plugin] (>=0.39.0)",
+    "poethepoet[poetry_plugin] (>=0.46.0)",
     "pytest-cov (>=7.0.0,<8.0.0)",
     "twine (>=6.2.0,<7.0.0)",
 ]
@@ -34,11 +34,17 @@ dev = [
 requires = ["poetry-core>=1.0.0", "setuptools>=40.8.0"]
 build-backend = "poetry.core.masonry.api"
 
-[tool.flake8]
-max-line-length = 88
-extend-ignore = ["E203", "W503"]
+[tool.ruff]
+line-length = 88
 exclude = [".venv", ".git", "__pycache__", "build", "dist"]
 
+[tool.ruff.lint]
+select = ["E", "F", "W", "B", "C4", "UP"]
+ignore = ["E203"]
+
+[tool.ruff.format]
+quote-style = "double"
+
 [tool.poe.tasks]
 test = "pytest"
 build-simple = "pyinstaller --onefile pythonQEPest/main.py"

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/cli/cli.py

@@ -4,7 +4,7 @@ import argparse
 import logging
 from importlib.metadata import PackageNotFoundError, version
 from pathlib import Path
-from typing import Sequence
+from collections.abc import Sequence
 
 from pythonQEPest.dto import QEPestFile
 from pythonQEPest.services.QEPestFileService import QEPestFileService

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/config/qepest_config.py

@@ -1,12 +1,10 @@
-from typing import Optional
-
 from pydantic import BaseModel
 
 from pythonQEPest.dto.pest_type.PestTypeConfig import PestTypeConfig
 
 
 class QEPestConfig(BaseModel):
-    name: Optional[str] = "HerbInsectFung"
+    name: str | None = "HerbInsectFung"
     pest_types: list[PestTypeConfig]
 
     def get_pest_names(self) -> list[str]:

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/core/qepest.py

@@ -1,6 +1,5 @@
 import logging
 import math
-from typing import Optional
 
 from pythonQEPest.config import ConfigProvider
 from pythonQEPest.core.qepest_meta import QEPestMeta
@@ -20,7 +19,7 @@ logger = logging.getLogger(__name__)
 
 
 class QEPest(QEPestMeta):
-    def __init__(self, provider: Optional[ConfigProvider] = None, *args, **kwargs):
+    def __init__(self, provider: ConfigProvider | None = None, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
         self.config: QEPestConfig
@@ -33,7 +32,7 @@ class QEPest(QEPestMeta):
 
         logger.debug("QEPest initialization successful")
 
-    def initialise_config(self, provider: Optional[ConfigProvider] = None):
+    def initialise_config(self, provider: ConfigProvider | None = None):
         logger.debug("Config initialisation")
         if provider is None:
             logger.debug("Config is empty. Loading default one.")
@@ -65,7 +64,7 @@ class QEPest(QEPestMeta):
 
         if len(names) == 0:
             raise ValueError(
-                "No pest types configured. " "Please provide a valid configuration."
+                "No pest types configured. Please provide a valid configuration."
             )
 
         qe_values = dict.fromkeys(names, 0.0)

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/dto/QEPestFile.py

@@ -1,5 +1,4 @@
 from enum import Enum
-from typing import Optional
 
 from pydantic import BaseModel, model_validator
 
@@ -10,10 +9,10 @@ class QEPestFormat(Enum):
 
 
 class QEPestFile(BaseModel):
-    input_file: Optional[str] = None
-    output_file: Optional[str] = None
-    format: Optional[QEPestFormat] = QEPestFormat.TXT
-    smiles: Optional[bool] = False
+    input_file: str | None = None
+    output_file: str | None = None
+    format: QEPestFormat | None = QEPestFormat.TXT
+    smiles: bool | None = False
 
     model_config = {"arbitrary_types_allowed": True}
 

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/dto/QEPestInput.py

@@ -1,5 +1,4 @@
 import logging
-from typing import Union
 
 from pydantic import BaseModel
 
@@ -19,7 +18,7 @@ class QEPestInput(BaseModel):
     aromatic_rings: int = 0
 
     @classmethod
-    def from_array(cls, data: Union[list, tuple, set]):
+    def from_array(cls, data: list | tuple | set):
         if len(data) != 7:
             raise ValueError(f"Expected 7 elements, got {len(data)}")
         return cls(

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/dto/QEPestOutput.py

@@ -1,12 +1,10 @@
-from typing import Optional
-
 from pydantic import BaseModel
 from pythonQEPest.dto.QEPestData import QEPestData
 
 
 class QEPestOutput(BaseModel):
     data: QEPestData
-    name: Optional[str] = ""
+    name: str | None = ""
 
     def to_array(self) -> list:
         values = list(self.data.root.values())

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/dto/coefficients/QEPestCoefficientList.py

@@ -1,13 +1,11 @@
-from typing import Optional, List
-
 from pydantic import BaseModel
 
 from pythonQEPest.dto.coefficients import QEPestCoefficient
 
 
 class QEPestCoefficientList(BaseModel):
-    name: Optional[str]
-    named_coefficients: List[QEPestCoefficient]
+    name: str | None
+    named_coefficients: list[QEPestCoefficient]
 
     # TODO: Done all the cases and make some sort of docs here, pls
     def __init__(self, *args, **kwargs):

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/dto/normalisation/Normaliser.py

@@ -1,14 +1,11 @@
-from typing import Union
-
-
 class Normaliser:
-    def __init__(self, arr: Union[tuple, list]):
+    def __init__(self, arr: tuple | list):
         # if len(arr) != 6:
         #     raise ValueError(f"Array must be exact length of 6. Given: {len(arr)}")
 
         self.arr = arr
 
-    def norm(self, d: Union[int, float], descr: int) -> float:
+    def norm(self, d: int | float, descr: int) -> float:
         if descr > len(self.arr):
             raise KeyError(f"Out of array. {descr} > {len(self.arr)}")
 

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/dto/pest_type/PestTypeCoefficient.py

@@ -22,7 +22,7 @@ class PestTypeCoefficient(BaseModel):
                 raise ValueError("Expected 6 items: mwH, logpH, hbaH, hbdH, rbH, arRCH")
 
             keys = ("mwH", "logpH", "hbaH", "hbdH", "rbH", "arRCH")
-            return dict(zip(keys, data))
+            return dict(zip(keys, data, strict=True))
 
         raise TypeError("Expected a dict or a 6-item tuple/list")
 

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/gui/actions/actions_other.py

@@ -22,7 +22,7 @@ class GUIActionsOther:
             return
 
         try:
-            with open(file_path, "r", encoding="utf-8") as file:
+            with open(file_path, encoding="utf-8") as file:
                 self.data_manager.clear_file()
                 self.data_tree.delete(*self.data_tree.get_children())
 

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/gui/utility/DataManager.py

@@ -26,7 +26,7 @@ class DataManager(metaclass=DataManagerMeta):
         return self
 
     def add(self, lst, entry):
-        if not entry in lst:
+        if entry not in lst:
             lst.append(entry)
         return self
 

pythonqepest-2.0.0a5/pythonQEPest/helpers/get_values_from_line.py

@@ -0,0 +1,2 @@
+def get_values_from_line(lst: list | tuple | set) -> list[float]:
+    return [float(x) for x in lst[1:]]

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/helpers/norm.py

@@ -1,7 +1,4 @@
-from typing import Union
-
-
-def norm(arr: Union[list, tuple], d: Union[int, float], descr: int) -> float:
+def norm(arr: list | tuple, d: int | float, descr: int) -> float:
     if descr > len(arr):
         raise KeyError(f"Out of array. {descr} > {len(arr)}")
 
@@ -9,7 +6,7 @@ def norm(arr: Union[list, tuple], d: Union[int, float], descr: int) -> float:
     return d / max_val if max_val != 0 else 0.0
 
 
-def norm_h(d: Union[int, float], descr: int) -> float:
+def norm_h(d: int | float, descr: int) -> float:
     return norm(
         (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213),
         d,
@@ -17,7 +14,7 @@ def norm_h(d: Union[int, float], descr: int) -> float:
     )
 
 
-def norm_i(d: Union[int, float], descr: int) -> float:
+def norm_i(d: int | float, descr: int) -> float:
     return norm(
         (78.2919965, 71.2829691, 133.9224801, 331.170104, 70.5540709, 193.0023343),
         d,
@@ -25,7 +22,7 @@ def norm_i(d: Union[int, float], descr: int) -> float:
     )
 
 
-def norm_f(d: Union[int, float], descr: int) -> float:
+def norm_f(d: int | float, descr: int) -> float:
     return norm(
         (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319),
         d,

pythonqepest-2.0.0a5/pythonQEPest/helpers/round_to_4digs.py

@@ -0,0 +1,2 @@
+def round_to_4digs(q) -> float:
+    return float(f"{q:.4f}")

{pythonqepest-2.0.0a4 → pythonqepest-2.0.0a5}/pythonQEPest/services/QEPestFileService.py

@@ -11,7 +11,6 @@ logger = logging.getLogger(__name__)
 
 
 class QEPestFileService:
-
     def __init__(self, qepest: QEPestMeta, qepest_file: QEPestFile):
         self.qepest = qepest
         self.qepest_file = qepest_file
@@ -59,7 +58,7 @@ class QEPestFileService:
 
     def _read_smiles_file(self) -> None:
         try:
-            with open(self.qepest_file.input_file, "r") as f:
+            with open(self.qepest_file.input_file) as f:
                 lines = f.readlines()
 
             with open(self.qepest_file.output_file, "w") as wr:
@@ -91,7 +90,7 @@ class QEPestFileService:
 
     def _read_descriptor_file(self) -> None:
         try:
-            with open(self.qepest_file.input_file, "r") as f:
+            with open(self.qepest_file.input_file) as f:
                 lines = f.readlines()
 
             with open(self.qepest_file.output_file, "w") as wr:

pythonqepest-2.0.0a4/pythonQEPest/helpers/get_values_from_line.py

@@ -1,5 +0,0 @@
-from typing import Union
-
-
-def get_values_from_line(lst: Union[list, tuple, set]) -> list[float]:
-    return [float(x) for x in lst[1:]]

pythonqepest-2.0.0a4/pythonQEPest/helpers/round_to_4digs.py

@@ -1,2 +0,0 @@
-def round_to_4digs(q) -> float:
-    return float("{:.4f}".format(q))