usethis-python · nathanjmcdougall · Jul 18, 2025 · Jul 17, 2025 · Jul 18, 2025 · Jul 18, 2025
diff --git a/src/usethis/_integrations/file/toml/io_.py b/src/usethis/_integrations/file/toml/io_.py
@@ -167,9 +167,9 @@ def set_value(
         except KeyError:
             _set_value_in_existing(
                 toml_document=toml_document,
-                current_container=d,
+                shared_container=d,
+                shared_keys=shared_keys,
                 keys=keys,
-                current_keys=shared_keys,
                 value=value,
             )
         except ValidationError:
@@ -179,9 +179,9 @@ def set_value(
             else:
                 _set_value_in_existing(
                     toml_document=toml_document,
-                    current_container=d,
+                    shared_keys=shared_keys,
+                    shared_container=d,
                     keys=keys,
-                    current_keys=shared_keys,
                     value=value,
                 )
         else:
@@ -269,12 +269,14 @@ def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
 
         toml_document = copy.copy(self.get())
 
+        shared_keys: list[str] = []
+        d = toml_document
         try:
-            d = toml_document
             for key in keys[:-1]:
                 TypeAdapter(dict).validate_python(d)
                 assert isinstance(d, dict)
                 d = d[key]
+                shared_keys.append(key)
             p_parent = d
             TypeAdapter(dict).validate_python(p_parent)
             assert isinstance(p_parent, dict)
@@ -284,7 +286,13 @@ def extend_list(self, *, keys: Sequence[Key], values: list[Any]) -> None:
             for key in reversed(keys):
                 contents = {key: contents}
             assert isinstance(contents, dict)
-            toml_document = mergedeep.merge(toml_document, contents)
+            _set_value_in_existing(
+                toml_document=toml_document,
+                shared_keys=shared_keys,
+                shared_container=d,
+                keys=keys,
+                value=values,
+            )
             assert isinstance(toml_document, TOMLDocument)
         except ValidationError:
             msg = (
@@ -349,11 +357,20 @@ def remove_from_list(self, *, keys: Sequence[Key], values: Collection[Any]) -> N
 def _set_value_in_existing(
     *,
     toml_document: TOMLDocument,
-    current_container: TOMLDocument | Item | Container,
+    shared_keys: Sequence[Key],
+    shared_container: TOMLDocument | Item | Container,
     keys: Sequence[Key],
-    current_keys: Sequence[Key],
     value: Any,
 ) -> None:
+    """Set a new value in an existing container.
+
+    Args:
+        toml_document: The overall document.
+        shared_keys: Keys to the deepest container that actually exists.
+        shared_container: The shared container itself that needs new contents.
+        keys: Keys to the new value from the root of the document.
+        value: The value at the keys.
+    """
     # The old configuration should be kept for all ID keys except the
     # final/deepest one which shouldn't exist anyway since we checked as much,
     # above. For example, if there is [tool.ruff] then we shouldn't overwrite it
@@ -369,12 +386,12 @@ def _set_value_in_existing(
     else:
         # Note that this alternative logic is just to avoid a bug:
         # https://github.com/usethis-python/usethis-python/issues/507
-        TypeAdapter(dict).validate_python(current_container)
-        assert isinstance(current_container, dict)
+        TypeAdapter(dict).validate_python(shared_container)
+        assert isinstance(shared_container, dict)
 
-        unshared_keys = keys[len(current_keys) :]
+        unshared_keys = keys[len(shared_keys) :]
 
-        if len(current_keys) == 1:
+        if len(shared_keys) == 1:
             # In this case, we need to "seed" the section to avoid another bug:
             # https://github.com/usethis-python/usethis-python/issues/558
 
@@ -385,9 +402,9 @@ def _set_value_in_existing(
             for key in reversed(unshared_keys[1:]):
                 contents = {key: contents}
 
-            current_container[keys[1]] = contents  # type: ignore[reportAssignmentType]
+            shared_container[keys[1]] = contents  # type: ignore[reportAssignmentType]
         else:
-            current_container[_get_unified_key(unshared_keys)] = value
+            shared_container[_get_unified_key(unshared_keys)] = value
 
 
 def _validate_keys(keys: Sequence[Key]) -> list[str]:

diff --git a/src/usethis/_tool/rule.py b/src/usethis/_tool/rule.py
@@ -14,9 +14,8 @@ class RuleConfig(BaseModel):
     """Configuration for linter rules associated with a tool.
 
     There is a distinction between selected and ignored rules. Selected rules are those
-    which are enabled and will be run by the tool unless ignored. Ignored rules are
-    those which are not run by the tool, even if they are selected. This follows the
-    Ruff paradigm.
+    which are enabled for the tool and will be used unless ignored. Ignored rules are
+    those which are not run, even if they are selected. This follows the Ruff paradigm.
 
     There is also a distinction between managed and unmanaged rule config. Managed
     selections (and ignores) are those which are managed exclusively by the one tool,

diff --git a/tests/usethis/_core/test_core_tool.py b/tests/usethis/_core/test_core_tool.py
@@ -1373,6 +1373,40 @@ def test_inp_rules_not_selected_for_tests_dir(self, tmp_path: Path):
 """
             )
 
+        @pytest.mark.usefixtures("_vary_network_conn")
+        def test_inp_rules_dont_break_config(self, uv_init_dir: Path):
+            # Arrange
+            (uv_init_dir / "pyproject.toml").write_text("""\
+[project]
+name = "test"
+version = "0.1.0"
+
+[tool.ruff]
+line-length = 88
+format.docstring-code-format = true
+lint.select = [ "A", "C4", "E4", "E7", "E9", "F", "FLY", "FURB", "I", "INP", "PLE", "PLR", "PT", "RUF", "SIM", "UP" ]
+lint.ignore = [ "PLR2004", "SIM108" ]
+""")
+
+            with change_cwd(uv_init_dir), files_manager():
+                # Act
+                use_import_linter()
+
+            # Assert
+            contents = (uv_init_dir / "pyproject.toml").read_text()
+            assert contents.startswith("""\
+[project]
+name = "test"
+version = "0.1.0"
+
+[tool.ruff]
+line-length = 88
+format.docstring-code-format = true
+lint.select = [ "A", "C4", "E4", "E7", "E9", "F", "FLY", "FURB", "I", "INP", "PLE", "PLR", "PT", "RUF", "SIM", "UP" ]
+lint.per-file-ignores."tests/**" = ["INP"]
+lint.ignore = [ "PLR2004", "SIM108" ]
+""")
+
         @pytest.mark.usefixtures("_vary_network_conn")
         def test_ruff_passes(self, tmp_path: Path):
             with change_cwd(tmp_path), files_manager():

diff --git a/tests/usethis/_integrations/ci/bitbucket/test_bitbucket_schema.py b/tests/usethis/_integrations/ci/bitbucket/test_bitbucket_schema.py
@@ -9,7 +9,7 @@
 from usethis._integrations.file.pyproject_toml.requires_python import (
     get_requires_python,
 )
-from usethis._test import is_offline
+from usethis._test import change_cwd, is_offline
 
 
 class TestStep2:
@@ -42,7 +42,7 @@ def test_matches_schema_store(self):
         # TIP: go into debug mode to copy-and-paste into updated schema.json
         assert local_schema_json == online_schema_json
 
-    def test_target_python_version(self):
+    def test_target_python_version(self, usethis_dev_dir: Path):
         # If this test fails, we should bump the version in the command in schema.py
-        with PyprojectTOMLManager():
+        with change_cwd(usethis_dev_dir), PyprojectTOMLManager():
             assert get_requires_python() == ">=3.10"
diff --git a/tests/usethis/_integrations/file/pyproject_toml/test_pyproject_toml_io_.py b/tests/usethis/_integrations/file/pyproject_toml/test_pyproject_toml_io_.py
@@ -392,5 +392,32 @@ def test_add_one(self, tmp_path: Path):
                 == """\
 [tool.usethis]
 key = ["value1", "value2"]
+"""
+            )
+
+        def test_deep_nesting_doesnt_break_config(self, tmp_path: Path):
+            # https://github.com/usethis-python/usethis-python/issues/862
+            # The issue is basically the same as this one though:
+            # https://github.com/usethis-python/usethis-python/issues/507
+            (tmp_path / "pyproject.toml").write_text("""\
+[tool.ruff]
+lint.select = [ "INP" ]
+""")
+
+            with change_cwd(tmp_path), PyprojectTOMLManager() as mgr:
+                # Act
+                mgr.extend_list(
+                    keys=["tool", "ruff", "lint", "per-file-ignores", "tests/**"],
+                    values=["INP"],
+                )
+
+            # Assert
+            contents = (tmp_path / "pyproject.toml").read_text()
+            assert (
+                contents
+                == """\
+[tool.ruff]
+lint.select = [ "INP" ]
+lint.per-file-ignores."tests/**" = ["INP"]
 """
             )
diff --git a/tests/usethis/_integrations/pre_commit/test_pre_commit_schema.py b/tests/usethis/_integrations/pre_commit/test_pre_commit_schema.py
@@ -9,7 +9,7 @@
     get_requires_python,
 )
 from usethis._integrations.pre_commit.schema import HookDefinition, LocalRepo
-from usethis._test import is_offline
+from usethis._test import change_cwd, is_offline
 
 
 def test_multiple_per_repo():
@@ -44,7 +44,7 @@ def test_matches_schema_store(self):
         # TIP: go into debug mode to copy-and-paste into updated schema.json
         assert local_schema_json == online_schema_json.replace("\r\n", "\n\n")
 
-    def test_target_python_version(self):
+    def test_target_python_version(self, usethis_dev_dir: Path):
         # If this test fails, we should bump the version in the command in schema.py
-        with PyprojectTOMLManager():
+        with change_cwd(usethis_dev_dir), PyprojectTOMLManager():
             assert get_requires_python() == ">=3.10"
diff --git a/tests/usethis/_interface/test_lint.py b/tests/usethis/_interface/test_lint.py
@@ -23,5 +23,5 @@ def test_dependencies_added(self, tmp_path: Path):
 
         # Check Ruff formatter is not added
         txt = (tmp_path / "pyproject.toml").read_text()
-        assert "ruff.format" not in txt
-        assert "ruff.lint" in txt
+        assert "format" not in txt
+        assert "lint" in txt
diff --git a/tests/usethis/_tool/impl/test_ruff.py b/tests/usethis/_tool/impl/test_ruff.py
@@ -312,3 +312,29 @@ def test_ruff_toml(self, tmp_path: Path):
             # Act
             with change_cwd(tmp_path), DotRuffTOMLManager():
                 assert RuffTool().is_formatter_used()
+
+    class TestIgnoreRulesInGlob:
+        def test_dont_break_config(self, tmp_path: Path):
+            # https://github.com/usethis-python/usethis-python/issues/862
+            # The issue is basically the same as this one though:
+            # https://github.com/usethis-python/usethis-python/issues/507
+            # Arrange
+            (tmp_path / "pyproject.toml").write_text("""\
+[tool.ruff]
+lint.select = [ "INP" ]
+""")
+
+            with change_cwd(tmp_path), files_manager():
+                # Act
+                RuffTool().ignore_rules_in_glob(["INP"], glob="tests/**")
+
+            # Assert
+            contents = (tmp_path / "pyproject.toml").read_text()
+            assert (
+                contents
+                == """\
+[tool.ruff]
+lint.select = [ "INP" ]
+lint.per-file-ignores."tests/**" = ["INP"]
+"""
+            )