Update deprecated typing imports to collections.abc

CHANGELOG.md

@@ -14,6 +14,7 @@
 ### Deprecated
 ### Removed
 ### Fixed
+- Updated deprecated `typing` types to be compliant with Python >=3.11 guidelines (#216)
 
 ## [2.0.0] - 2026-02-10
 

src/opi/execution/base.py

@@ -14,11 +14,12 @@
 import os
 import shutil
 import subprocess
+from collections.abc import Callable, Sequence
 from contextlib import nullcontext
 from io import TextIOWrapper
 from pathlib import Path
 from subprocess import CompletedProcess
-from typing import Any, Callable, Concatenate, ParamSpec, Sequence, TypeVar, cast
+from typing import Any, Concatenate, ParamSpec, TypeVar, cast
 
 from opi import ORCA_MINIMAL_VERSION
 from opi.lib.orca_binary import OrcaBinary

src/opi/execution/core.py

@@ -3,8 +3,8 @@
 """
 
 import json
+from collections.abc import Sequence
 from pathlib import Path
-from typing import Sequence
 
 from opi.execution.base import BaseRunner
 from opi.lib.orca_binary import OrcaBinary

src/opi/input/blocks/block_cpcm.py

@@ -1,4 +1,5 @@
-from typing import Any, Callable, Literal, Union
+from collections.abc import Callable
+from typing import Any, Literal
 
 from pydantic import BaseModel, Field
 
@@ -128,7 +129,7 @@ class BlockCpcm(Block):
     smdsolvent: Solvent | None = None
 
     def format_orca(self) -> str:
-        special_handlers: dict[str, Callable[[Any], Union[str, None]]] = {
+        special_handlers: dict[str, Callable[[Any], str | None]] = {
             "aftercoord": lambda v: None,  # Skip this field
             "radii": lambda v: f"    radii{str(v)}",
             "radius": lambda v: f"    radius{str(v)}",

src/opi/input/blocks/block_frag.py

@@ -1,4 +1,4 @@
-from typing import List, Literal
+from typing import Literal
 
 from pydantic import BaseModel, field_validator
 
@@ -23,7 +23,7 @@ class FragProc(BaseModel):
     Class to model `fragproc` attribute in `BlockFrag`
     """
 
-    flags: List[
+    flags: list[
         Literal[
             "extlib",
             "connectivity",

src/opi/input/structures/properties.py

@@ -1,8 +1,8 @@
 import re
-from collections.abc import Iterator
+from collections.abc import Iterator, Sequence
 from os import PathLike
 from pathlib import Path
-from typing import Literal, Sequence
+from typing import Literal
 
 from opi.utils.tracking_text_io import TrackingTextIO
 

src/opi/input/structures/structure.py

@@ -1,8 +1,8 @@
 import re
-from collections.abc import Iterator
+from collections.abc import Iterable, Iterator, Sequence
 from os import PathLike
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Iterable, Sequence, cast
+from typing import TYPE_CHECKING, Any, cast
 from warnings import warn
 
 import numpy as np

src/opi/output/core.py

@@ -4,9 +4,9 @@
 """
 
 import json
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from pathlib import Path
-from typing import Any, Callable, cast
+from typing import Any, cast
 from warnings import warn
 
 import numpy as np

src/opi/output/cube.py

@@ -1,5 +1,5 @@
+from collections.abc import Iterator
 from pathlib import Path
-from typing import Iterator
 
 
 class CubeOutput:

src/opi/output/grepper/core.py

@@ -1,7 +1,7 @@
-from collections.abc import Iterator
+from collections.abc import Callable, Iterator
 from pathlib import Path
 from re import IGNORECASE, Pattern, RegexFlag, compile, escape, split
-from typing import Any, Callable
+from typing import Any
 
 from opi.output.grepper.pre_condition import (
     ConditionStatus,

src/opi/output/ir_mode.py

@@ -1,5 +1,4 @@
 from dataclasses import dataclass
-from typing import Tuple
 
 
 @dataclass
@@ -17,15 +16,15 @@ class IrMode:
         Partial molar absorptivity (epsilon) of the mode in L/(mol*cm).
     intensity: float
         IR intensity of the mode in km/mol.
-    dipole: Tuple[float, float, float]
+    dipole: tuple[float, float, float]
         Dipole derivatives TX TY TZ in atomic units.
     """
 
     mode: int
     wavenumber: float
     eps: float
     intensity: float
-    dipole: Tuple[float, float, float]
+    dipole: tuple[float, float, float]
 
     @classmethod
     def from_string(cls, line: str) -> "IrMode":

src/opi/output/models/base/get_item.py

@@ -1,7 +1,8 @@
 import re
 import typing
 from abc import ABC
-from typing import Any, Union, get_args, get_origin
+from types import UnionType
+from typing import Any, get_args, get_origin
 
 from pydantic import BaseModel
 
@@ -12,7 +13,7 @@ def get_clean_type_name(t: Any) -> str:
     origin = get_origin(t)
     # > If the type is a Union we have to dissect it
     # > typically it will be Union[Something | None] so we do not want the None part
-    if origin is Union:
+    if origin is UnionType:
         # > Generate a list of the types in the Union
         args = [a for a in get_args(t) if a is not type(None)]
         # > recursively call the function on the first argument

src/opi/output/models/base/strict_types.py

@@ -1,4 +1,4 @@
-from typing import Literal, Union
+from typing import Literal
 
 from pydantic import Field, FiniteFloat, NonNegativeInt, PositiveInt, Strict
 from typing_extensions import Annotated
@@ -16,9 +16,7 @@
 StrictNegativeFloat = Annotated[FiniteFloat, Strict(), Field(lt=0)]
 
 StrictPositiveFloatOrMinusOne = Annotated[
-    Union[
-        Annotated[FiniteFloat, Strict(), Field(gt=0)],  # Positive float
-        Literal[-1],
-    ],
+    Annotated[FiniteFloat, Strict(), Field(gt=0)]  # Positive float
+    | Literal[-1],
     Field(description="Positive float or -1"),
 ]

src/opi/output/models/json/property/properties/energy_list.py

@@ -1,4 +1,5 @@
-from typing import ClassVar, Iterator
+from collections.abc import Iterator
+from typing import ClassVar
 
 from pydantic import ConfigDict, RootModel
 

src/opi/utils/misc.py

@@ -1,8 +1,9 @@
 import os
 import platform
 import sys
+from collections.abc import Mapping, Sequence
 from pathlib import Path
-from typing import Any, Mapping, Sequence, cast
+from typing import Any, cast
 
 from opi import ORCA_MINIMAL_VERSION
 from opi.lib.orca_binary import OrcaBinary

src/opi/utils/tracking_text_io.py

@@ -1,6 +1,6 @@
 import types
 from io import StringIO
-from typing import Any, Optional, TextIO, Type
+from typing import Any, TextIO
 
 
 class TrackingTextIO:
@@ -20,9 +20,9 @@ def __enter__(self) -> "TrackingTextIO":
 
     def __exit__(
         self,
-        _exc_type: Optional[Type[BaseException]],
-        _exc_value: Optional[BaseException],
-        _traceback: Optional[types.TracebackType],
+        _exc_type: type[BaseException] | None,
+        _exc_value: BaseException | None,
+        _traceback: types.TracebackType | None,
     ) -> bool | None:
         self._stream.close()
         return None

tests/conftest.py

@@ -9,7 +9,7 @@
 from collections.abc import Generator
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Any, Optional, cast
+from typing import Any, cast
 
 import pytest
 from _pytest._code.code import ExceptionRepr
@@ -119,7 +119,7 @@ def pytest_runtest_makereport(
         funcargs = cast(dict[str, Any], getattr(item, "funcargs", {}))
 
         # > if `tmp_path` is in the functions signature
-        tmp = cast(Optional[Path], funcargs.get("tmp_path"))
+        tmp = cast(Path | None, funcargs.get("tmp_path"))
         if tmp is not None:
             # > make mypy happy by making sure `when` is not None
             when = rep.when or "call"

tests/fixtures/example_input_file.py

@@ -1,6 +1,6 @@
 import inspect
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable
 
 import pytest
 

tests/fixtures/output_object.py

@@ -1,5 +1,5 @@
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable
 
 import pytest
 

tests/unit/test_output_attributes.py

@@ -1,6 +1,6 @@
 import inspect
 from pathlib import Path
-from typing import Any, Set, get_args, get_origin
+from typing import Any, get_args, get_origin
 
 import pytest
 from pydantic import BaseModel
@@ -89,8 +89,8 @@ def test_attributes(self, tmp_path: Path, json_dir: Path, json_file_list: list[P
         assert not output_attr
 
     def get_all_attributes(
-        self, model: type[BaseModel], visited: Set[type] = None, prefix: str = ""
-    ) -> Set[str]:
+        self, model: type[BaseModel], visited: set[type] = None, prefix: str = ""
+    ) -> set[str]:
         """
         Recursively get all attribute names from a Pydantic model, including nested custom types.
         Attribute names include their parent class prefix (e.g., "A.attr1.attr2").
@@ -164,7 +164,7 @@ def collect_non_none_attrs(
         depth: int = -1,
         prefix: str | None = None,
         _visited=None,
-    ) -> Set[str]:
+    ) -> set[str]:
         """
         Collect a set of attribute paths whose values are not None.
         - Accepts a single object or a list of objects