usethis-python · nathanjmcdougall · Mar 21, 2026 · Mar 21, 2026 · Mar 21, 2026 · Mar 21, 2026
diff --git a/src/usethis/_file/ini/io_.py b/src/usethis/_file/ini/io_.py
@@ -147,7 +147,11 @@ def __getitem__(self, item: Sequence[Key]) -> object:
             raise KeyError(msg)
 
     def set_value(
-        self, *, keys: Sequence[Key], value: Any, exists_ok: bool = False
+        self,
+        *,
+        keys: Sequence[Key],
+        value: object,
+        exists_ok: bool = False,
     ) -> None:
         """Set a value in the INI file.
 
@@ -156,19 +160,24 @@ def set_value(
         root = self.get()
 
         if len(keys) == 0:
+            value = TypeAdapter(dict[str, dict[str, str | list[str]]]).validate_python(
+                value
+            )
             self._set_value_in_root(root=root, value=value, exists_ok=exists_ok)
         elif len(keys) == 1:
             (section_key,) = keys
+            value = TypeAdapter(dict[str, str | list[str]]).validate_python(value)
             self._set_value_in_section(
                 root=root, section_key=keys[0], value=value, exists_ok=exists_ok
             )
         elif len(keys) == 2:
             (section_key, option_key) = keys
+            cast_value = TypeAdapter(str | list[str]).validate_python(value)
             self._set_value_in_option(
                 root=root,
                 section_key=section_key,
                 option_key=option_key,
-                value=value,
+                value=cast_value,
                 exists_ok=exists_ok,
             )
         else:
@@ -271,7 +280,7 @@ def _set_value_in_option(
         root: INIDocument,
         section_key: Key,
         option_key: Key,
-        value: str,
+        value: str | list[str],
         exists_ok: bool,
     ) -> None:
         if not isinstance(section_key, str) or not isinstance(option_key, str):
@@ -408,7 +417,7 @@ def _delete_strkeys(self, strkeys: Sequence[str]) -> None:
 
         self.commit(root)
 
-    def extend_list(self, *, keys: Sequence[Key], values: list[str]) -> None:
+    def extend_list(self, *, keys: Sequence[Key], values: Sequence[object]) -> None:
         """Extend a list in the INI file.
 
         An empty list of keys corresponds to the root of the document.
@@ -429,6 +438,7 @@ def extend_list(self, *, keys: Sequence[Key], values: list[str]) -> None:
             raise InvalidINITypeError(msg)
         elif len(keys) == 2:
             section_key, option_key = keys
+            values = TypeAdapter(list[str]).validate_python(values)
             self._extend_list_in_option(
                 root=root, section_key=section_key, option_key=option_key, values=values
             )
@@ -443,7 +453,7 @@ def extend_list(self, *, keys: Sequence[Key], values: list[str]) -> None:
 
     @staticmethod
     def _extend_list_in_option(
-        *, root: INIDocument, section_key: Key, option_key: Key, values: list[str]
+        *, root: INIDocument, section_key: Key, option_key: Key, values: Sequence[str]
     ) -> None:
         for value in values:
             INIFileManager._validated_append(
@@ -452,7 +462,7 @@ def _extend_list_in_option(
 
     @staticmethod
     def _remove_from_list_in_option(
-        *, root: INIDocument, section_key: Key, option_key: Key, values: list[str]
+        *, root: INIDocument, section_key: Key, option_key: Key, values: Sequence[str]
     ) -> None:
         if section_key not in root:
             return
@@ -485,7 +495,9 @@ def _remove_from_list_in_option(
         elif len(new_values) > 1:
             root[section_key][option_key].set_values(new_values)
 
-    def remove_from_list(self, *, keys: Sequence[Key], values: list[str]) -> None:
+    def remove_from_list(
+        self, *, keys: Sequence[Key], values: Sequence[object]
+    ) -> None:
         """Remove values from a list in the INI file.
 
         An empty list of keys corresponds to the root of the document.
@@ -506,6 +518,7 @@ def remove_from_list(self, *, keys: Sequence[Key], values: list[str]) -> None:
             raise InvalidINITypeError(msg)
         elif len(keys) == 2:
             section_key, option_key = keys
+            values = TypeAdapter(list[str]).validate_python(values)
             self._remove_from_list_in_option(
                 root=root, section_key=section_key, option_key=option_key, values=values
             )

diff --git a/src/usethis/_file/merge.py b/src/usethis/_file/merge.py
@@ -1,12 +1,12 @@
 from __future__ import annotations
 
 from collections.abc import MutableMapping
-from typing import Any
+from typing import Any, TypeVar
 
+T = TypeVar("T", bound=MutableMapping[Any, Any])
 
-def _deep_merge(
-    target: MutableMapping[Any, Any], source: MutableMapping[Any, Any]
-) -> MutableMapping[Any, Any]:
+
+def _deep_merge(target: T, source: MutableMapping[Any, Any]) -> T:
     """Recursively merge source into target in place, returning target.
 
     For keys present in both mappings, if both values are mappings the merge is

diff --git a/src/usethis/_file/toml/io_.py b/src/usethis/_file/toml/io_.py
@@ -193,7 +193,7 @@ def set_value(
                 # The configuration is already present, but we're allowed to overwrite it.
                 parent[keys[-1]] = value
 
-        self.commit(toml_document)  # type: ignore[reportAssignmentType]
+        self.commit(toml_document)
 
     def __delitem__(self, keys: Sequence[Key]) -> None:
         """Delete a value in the TOML file.
@@ -262,7 +262,7 @@ def __delitem__(self, keys: Sequence[Key]) -> None:
 
         self.commit(toml_document)
 
-    def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
+    def extend_list(self, *, keys: Sequence[Key], values: Sequence[Any]) -> None:
         if not keys:
             msg = "At least one ID key must be provided."
             raise ValueError(msg)
@@ -311,7 +311,7 @@ def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
                 )
                 raise TOMLValueInvalidError(msg) from None
             assert isinstance(d, list)
-            p_parent[keys[-1]] = d + values
+            p_parent[keys[-1]] = d + list(values)
 
         self.commit(toml_document)
 
@@ -382,7 +382,7 @@ def _set_value_in_existing(
         contents = value
         for key in reversed(keys):
             contents = {key: contents}
-        toml_document = _deep_merge(toml_document, contents)  # type: ignore[reportAssignmentType]
+        toml_document = _deep_merge(toml_document, contents)
         assert isinstance(toml_document, TOMLDocument)
     else:
         # Note that this alternative logic is just to avoid a bug:
@@ -397,13 +397,22 @@ def _set_value_in_existing(
             # https://github.com/usethis-python/usethis-python/issues/558
 
             placeholder = {keys[0]: {keys[1]: {}}}
-            toml_document = _deep_merge(toml_document, placeholder)  # type: ignore[reportArgumentType]
+            toml_document = _deep_merge(toml_document, placeholder)
 
             contents = value
             for key in reversed(unshared_keys[1:]):
                 contents = {key: contents}
 
-            shared_container[keys[1]] = contents  # pyright: ignore[reportArgumentType]
+            # Check it's not a pattern-based key, which isn't supported in TOML files.
+            key = keys[1]
+            if isinstance(key, re.Pattern):
+                msg = (
+                    f"Regex-based keys are not currently supported in TOML files: "
+                    f"{print_keys(keys)}"
+                )
+                raise NotImplementedError(msg)
+
+            shared_container[key] = contents
         else:
             shared_container[_get_unified_key(unshared_keys)] = value
 

diff --git a/src/usethis/_file/yaml/io_.py b/src/usethis/_file/yaml/io_.py
@@ -279,7 +279,7 @@ def __delitem__(self, keys: Sequence[Key]) -> None:
         )
         self.commit(self._content)
 
-    def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
+    def extend_list(self, *, keys: Sequence[Key], values: Sequence[Any]) -> None:
         """Extend a list in the configuration file."""
         if not keys:
             msg = "At least one ID key must be provided."
@@ -317,7 +317,7 @@ def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
             TypeAdapter(list).validate_python(d)
             assert isinstance(p_parent, dict)
             assert isinstance(d, list)
-            p_parent[keys[-1]] = d + values
+            p_parent[keys[-1]] = d + list(values)
 
         assert self._content is not None  # We have called .get() already.
         update_ruamel_yaml_map(
@@ -327,7 +327,7 @@ def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
         )
         self.commit(self._content)
 
-    def remove_from_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
+    def remove_from_list(self, *, keys: Sequence[Key], values: Sequence[Any]) -> None:
         """Remove values from a list in the configuration file."""
         if not keys:
             msg = "At least one ID key must be provided."
@@ -386,7 +386,7 @@ def _set_value_in_existing(
     contents = value
     for key in reversed(keys):
         contents = {key: contents}
-    content = _deep_merge(content, contents)  # type: ignore[reportAssignmentType]
+    content = _deep_merge(content, contents)
 
 
 def _validate_keys(keys: Sequence[Key]) -> list[str]:

diff --git a/src/usethis/_file/yaml/update.py b/src/usethis/_file/yaml/update.py
@@ -8,11 +8,12 @@
 )
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
     from typing import Any
 
     from usethis._file.yaml.typing_ import YAMLLiteral
 
-_T = TypeVar("_T")
+_T = TypeVar("_T", bound=object)
 
 
 def update_ruamel_yaml_map(
@@ -116,7 +117,7 @@ def lcs_list_update(original: list[_T], new: list[_T]) -> None:
                 original_idx += 1
 
 
-def _shared_id_sequences(*seqs: list[Any]) -> list[list[int]]:
+def _shared_id_sequences(*seqs: Sequence[object]) -> Sequence[list[int]]:
     """Map list elements to integers which are equal iff the objects are with __eq__."""
     # Don't use "in" because that would mean the elements must be hashable,
     # which we don't want to require. This means we have to loop over every element,

diff --git a/src/usethis/_io.py b/src/usethis/_io.py
@@ -2,7 +2,7 @@
 
 import re
 from abc import ABCMeta, abstractmethod
-from typing import TYPE_CHECKING, Generic, TypeAlias, TypeVar
+from typing import TYPE_CHECKING, Any, Generic, TypeAlias, TypeVar
 
 from typing_extensions import assert_never
 
@@ -13,7 +13,7 @@
     from collections.abc import Sequence
     from pathlib import Path
     from types import TracebackType
-    from typing import Any, ClassVar
+    from typing import ClassVar
 
     from typing_extensions import Self
 
@@ -192,7 +192,7 @@ def __contains__(self, keys: Sequence[Key]) -> bool:
     def __getitem__(self, keys: Sequence[Key]) -> object:
         raise NotImplementedError
 
-    def __setitem__(self, keys: Sequence[Key], value: Any) -> None:
+    def __setitem__(self, keys: Sequence[Key], value: object) -> None:
         """Set a value in the configuration file."""
         return self.set_value(keys=keys, value=value, exists_ok=True)
 
@@ -202,21 +202,23 @@ def __delitem__(self, keys: Sequence[Key]) -> None:
 
     @abstractmethod
     def set_value(
-        self, *, keys: Sequence[Key], value: Any, exists_ok: bool = False
+        self, *, keys: Sequence[Key], value: object, exists_ok: bool = False
     ) -> None:
         """Set a value in the configuration file."""
         raise NotImplementedError
 
     @abstractmethod
-    def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
+    def extend_list(self, *, keys: Sequence[Key], values: Sequence[object]) -> None:
         """Extend a list in the configuration file.
 
         This method will always extend the list, even if it results in duplicates.
         """
         raise NotImplementedError
 
     @abstractmethod
-    def remove_from_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
+    def remove_from_list(
+        self, *, keys: Sequence[Key], values: Sequence[object]
+    ) -> None:
         """Remove values from a list in the configuration file."""
         raise NotImplementedError
 

diff --git a/src/usethis/_pipeweld/containers.py b/src/usethis/_pipeweld/containers.py
@@ -1,13 +1,7 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
-
 from pydantic import BaseModel, RootModel
 
-if TYPE_CHECKING:
-    from typing import Any
-
-
 _HASH_SALT = "e6fdde87-adc6-42f6-8e66-4aabe4ba05f2"
 
 
@@ -21,7 +15,7 @@ def __getitem__(self, item: int) -> Series | Parallel | DepGroup | str:
     def __setitem__(self, item: int, value: Series | Parallel | DepGroup | str) -> None:
         self.root[item] = value
 
-    def __eq__(self, other: Any):
+    def __eq__(self, other: object):
         if not isinstance(other, Series):
             return False
         return self.root == other.root
@@ -37,7 +31,7 @@ def __hash__(self):
     def __or__(self, other: Parallel) -> Parallel:
         return Parallel(self.root | other.root)
 
-    def __eq__(self, other: Any):
+    def __eq__(self, other: object):
         if not isinstance(other, Parallel):
             return False
 

diff --git a/src/usethis/_test.py b/src/usethis/_test.py
@@ -4,7 +4,7 @@
 import socket
 from contextlib import contextmanager
 from pathlib import Path
-from typing import IO, TYPE_CHECKING, Any
+from typing import IO, TYPE_CHECKING
 
 from typer.testing import CliRunner as TyperCliRunner  # noqa: TID251
 
@@ -47,10 +47,10 @@ def invoke_safe(
         self,
         app: Typer,
         args: str | Sequence[str] | None = None,
-        input: bytes | str | IO[Any] | None = None,  # noqa: A002
+        input: bytes | str | IO[str] | None = None,  # noqa: A002
         env: Mapping[str, str] | None = None,
         color: bool = False,
-        **extra: Any,
+        **extra: object,
     ) -> Result:
         return self.invoke(
             app,
@@ -66,11 +66,11 @@ def invoke(  # noqa: PLR0913
         self,
         app: Typer,
         args: str | Sequence[str] | None = None,
-        input: bytes | str | IO[Any] | None = None,  # noqa: A002
+        input: bytes | str | IO[str] | None = None,  # noqa: A002
         env: Mapping[str, str] | None = None,
         catch_exceptions: bool = True,
         color: bool = False,
-        **extra: Any,
+        **extra: object,
     ) -> Result:
         if catch_exceptions:
             msg = "`catch_exceptions=True` is forbidden in usethis tests. Use `.invoke_safe()` instead."

diff --git a/src/usethis/_tool/base.py b/src/usethis/_tool/base.py
@@ -38,6 +38,8 @@
 )
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+
     from usethis._io import KeyValueFileManager
     from usethis._tool.config import ConfigItem
     from usethis._tool.rule import Rule
@@ -549,7 +551,7 @@ def _get_select_keys(self, file_manager: KeyValueFileManager[object]) -> list[st
         )
         raise UnhandledConfigEntryError(msg)
 
-    def select_rules(self, rules: list[Rule]) -> bool:
+    def select_rules(self, rules: Sequence[Rule]) -> bool:
         """Select the rules managed by the tool.
 
         These rules are not validated; it is assumed they are valid rules for the tool,
@@ -598,7 +600,7 @@ def _get_ignore_keys(self, file_manager: KeyValueFileManager[object]) -> list[st
         )
         raise UnhandledConfigEntryError(msg)
 
-    def ignore_rules(self, rules: list[Rule]) -> bool:
+    def ignore_rules(self, rules: Sequence[Rule]) -> bool:
         """Ignore rules managed by the tool.
 
         Ignoring a rule is different from deselecting it - it means that even if it
@@ -664,7 +666,7 @@ def unignore_rules(self, rules: list[str]) -> bool:
 
         return True
 
-    def deselect_rules(self, rules: list[Rule]) -> bool:
+    def deselect_rules(self, rules: Sequence[Rule]) -> bool:
         """Deselect the rules managed by the tool.
 
         Any rules that aren't already selected are ignored.