Fix bugs in handling of ruff config and rules (#421)

* Fix bugs in handling of ruff config and rules

* Fix incorrect section name in test

* Fix bug in deselection

Author: nathanjmcdougall

src/usethis/_core/tool.py

@@ -304,29 +304,36 @@ def use_ruff(*, remove: bool = False) -> None:
 
     ensure_pyproject_toml()
 
-    rules = [
-        "A",
-        "C4",
-        "E4",
-        "E7",
-        "E9",
-        "EM",
-        "F",
-        "FURB",
-        "I",
-        "PLE",
-        "PLR",
-        "RUF",
-        "SIM",
-        "UP",
-    ]
-    for _tool in ALL_TOOLS:
-        if _tool.is_used():
-            rules += _tool.get_associated_ruff_rules()
-    ignored_rules = [
-        "PLR2004",  # https://github.com/nathanjmcdougall/usethis-python/issues/105
-        "SIM108",  # https://github.com/nathanjmcdougall/usethis-python/issues/118
-    ]
+    # Only add ruff rules if the user doesn't already have a select/ignore list.
+    # Otherwise, we should leave them alone.
+
+    if not RuffTool().get_rules() and not RuffTool().get_ignored_rules():
+        rules = [
+            "A",
+            "C4",
+            "E4",
+            "E7",
+            "E9",
+            "EM",
+            "F",
+            "FURB",
+            "I",
+            "PLE",
+            "PLR",
+            "RUF",
+            "SIM",
+            "UP",
+        ]
+        for _tool in ALL_TOOLS:
+            if _tool.is_used():
+                rules += _tool.get_associated_ruff_rules()
+        ignored_rules = [
+            "PLR2004",  # https://github.com/nathanjmcdougall/usethis-python/issues/105
+            "SIM108",  # https://github.com/nathanjmcdougall/usethis-python/issues/118
+        ]
+    else:
+        rules = []
+        ignored_rules = []
 
     if not remove:
         tool.add_dev_deps()

src/usethis/_tool.py

@@ -385,7 +385,7 @@ def add_configs(self) -> None:
 
             shared_keys = []
             for key in entry.keys:
-                shared_keys += key
+                shared_keys.append(key)
                 new_file_managers = [
                     file_manager
                     for file_manager in file_managers
@@ -397,12 +397,12 @@ def add_configs(self) -> None:
 
             # Now, use the highest-prority file manager to add the config
             (used_file_manager,) = file_managers
-            used_file_manager[entry.keys] = entry.value
             if first_addition:
                 tick_print(
                     f"Adding {self.name} config to '{used_file_manager.relative_path}'."
                 )
                 first_addition = False
+            used_file_manager[entry.keys] = entry.value
 
     def remove_configs(self) -> None:
         """Remove the tool's configuration sections.
@@ -1075,8 +1075,7 @@ def get_dev_deps(self, *, unconditional: bool = False) -> list[Dependency]:
     def get_config_spec(self) -> ConfigSpec:
         # https://docs.astral.sh/ruff/configuration/#config-file-discovery
 
-        root_value = {"line-length": 88}
-        lint_value = {"select": []}
+        line_length = 88
 
         return ConfigSpec.from_flat(
             file_managers=[
@@ -1089,22 +1088,23 @@ def get_config_spec(self) -> ConfigSpec:
                 ConfigItem(
                     description="Overall config",
                     root={
-                        Path(".ruff.toml"): ConfigEntry(keys=[], value=root_value),
-                        Path("ruff.toml"): ConfigEntry(keys=[], value=root_value),
-                        Path("pyproject.toml"): ConfigEntry(
-                            keys=["tool", "ruff"], value=root_value
-                        ),
+                        Path(".ruff.toml"): ConfigEntry(keys=[]),
+                        Path("ruff.toml"): ConfigEntry(keys=[]),
+                        Path("pyproject.toml"): ConfigEntry(keys=["tool", "ruff"]),
                     },
                 ),
                 ConfigItem(
-                    description="Lint config",
+                    description="Line length",
                     root={
                         Path(".ruff.toml"): ConfigEntry(
-                            keys=["lint"], value=lint_value
+                            keys=["line-length"], value=line_length
+                        ),
+                        Path("ruff.toml"): ConfigEntry(
+                            keys=["line-length"], value=line_length
                         ),
-                        Path("ruff.toml"): ConfigEntry(keys=["lint"], value=lint_value),
                         Path("pyproject.toml"): ConfigEntry(
-                            keys=["tool", "ruff", "lint"], value=lint_value
+                            keys=["tool", "ruff", "line-length"],
+                            value=line_length,
                         ),
                     },
                 ),
@@ -1174,10 +1174,11 @@ def select_rules(self, rules: list[str]) -> None:
 
         rules_str = ", ".join([f"'{rule}'" for rule in rules])
         s = "" if len(rules) == 1 else "s"
-        tick_print(f"Enabling Ruff rule{s} {rules_str} in 'pyproject.toml'.")
 
         (file_manager,) = self.get_active_config_file_managers()
-        file_manager.extend_list(keys=["tool", "ruff", "lint", "select"], values=rules)
+        tick_print(f"Enabling Ruff rule{s} {rules_str} in '{file_manager.name}'.")
+        keys = self._get_select_keys(file_manager)
+        file_manager.extend_list(keys=keys, values=rules)
 
     def ignore_rules(self, rules: list[str]) -> None:
         """Ignore Ruff rules in the project."""
@@ -1188,10 +1189,11 @@ def ignore_rules(self, rules: list[str]) -> None:
 
         rules_str = ", ".join([f"'{rule}'" for rule in rules])
         s = "" if len(rules) == 1 else "s"
-        tick_print(f"Ignoring Ruff rule{s} {rules_str} in 'pyproject.toml'.")
 
         (file_manager,) = self.get_active_config_file_managers()
-        file_manager.extend_list(keys=["tool", "ruff", "lint", "ignore"], values=rules)
+        tick_print(f"Ignoring Ruff rule{s} {rules_str} in '{file_manager.name}'.")
+        keys = self._get_ignore_keys(file_manager)
+        file_manager.extend_list(keys=keys, values=rules)
 
     def deselect_rules(self, rules: list[str]) -> None:
         """Ensure Ruff rules are not selected in the project."""
@@ -1202,18 +1204,18 @@ def deselect_rules(self, rules: list[str]) -> None:
 
         rules_str = ", ".join([f"'{rule}'" for rule in rules])
         s = "" if len(rules) == 1 else "s"
-        tick_print(f"Disabling Ruff rule{s} {rules_str} in 'pyproject.toml'.")
 
         (file_manager,) = self.get_active_config_file_managers()
-        file_manager.remove_from_list(
-            keys=["tool", "ruff", "lint", "select"], values=rules
-        )
+        tick_print(f"Disabling Ruff rule{s} {rules_str} in '{file_manager.name}'.")
+        keys = self._get_select_keys(file_manager)
+        file_manager.remove_from_list(keys=keys, values=rules)
 
     def get_rules(self) -> list[str]:
         """Get the Ruff rules selected in the project."""
         (file_manager,) = self.get_active_config_file_managers()
+        keys = self._get_select_keys(file_manager)
         try:
-            rules: list[str] = file_manager[["tool", "ruff", "lint", "select"]]
+            rules: list[str] = file_manager[keys]
         except KeyError:
             rules = []
 
@@ -1222,13 +1224,42 @@ def get_rules(self) -> list[str]:
     def get_ignored_rules(self) -> list[str]:
         """Get the Ruff rules ignored in the project."""
         (file_manager,) = self.get_active_config_file_managers()
+        keys = self._get_ignore_keys(file_manager)
         try:
-            rules: list[str] = file_manager[["tool", "ruff", "lint", "ignore"]]
+            rules: list[str] = file_manager[keys]
         except KeyError:
             rules = []
 
         return rules
 
+    @staticmethod
+    def _get_select_keys(file_manager: KeyValueFileManager) -> list[str]:
+        """Get the keys for the select rules in the given file manager."""
+        if isinstance(file_manager, PyprojectTOMLManager):
+            return ["tool", "ruff", "lint", "select"]
+        elif isinstance(file_manager, RuffTOMLManager | DotRuffTOMLManager):
+            return ["lint", "select"]
+        else:
+            msg = (
+                f"Unknown location for selected ruff rules for file manager "
+                f"'{file_manager.name}' of type {file_manager.__class__.__name__}."
+            )
+            raise NotImplementedError(msg)
+
+    @staticmethod
+    def _get_ignore_keys(file_manager: KeyValueFileManager) -> list[str]:
+        """Get the keys for the ignored rules in the given file manager."""
+        if isinstance(file_manager, PyprojectTOMLManager):
+            return ["tool", "ruff", "lint", "ignore"]
+        elif isinstance(file_manager, RuffTOMLManager | DotRuffTOMLManager):
+            return ["lint", "ignore"]
+        else:
+            msg = (
+                f"Unknown location for ignored ruff rules for file manager "
+                f"'{file_manager.name}' of type {file_manager.__class__.__name__}."
+            )
+            raise NotImplementedError(msg)
+
 
 ALL_TOOLS: list[Tool] = [
     CodespellTool(),

tests/usethis/_core/test_core_tool.py

@@ -1694,6 +1694,51 @@ def test_creates_pyproject_toml(
             assert not err
             assert out.startswith("✔ Writing 'pyproject.toml'.\n")
 
+        def test_existing_ruff_toml(
+            self, uv_init_dir: Path, capfd: pytest.CaptureFixture[str]
+        ):
+            # https://github.com/nathanjmcdougall/usethis-python/issues/420
+
+            # Arrange
+            (uv_init_dir / "ruff.toml").write_text("""\
+namespace-packages = ["src/usethis/namespace"]
+
+[lint]
+select = [ "ALL" ]
+ignore = [ "EM", "T20", "TRY003", "S603" ]
+
+[lint.extend-per-file-ignores]
+"__main__.py" = [ "BLE001" ]
+""")
+
+            # Act
+            with change_cwd(uv_init_dir), files_manager():
+                use_ruff()
+
+            # Assert
+            out, err = capfd.readouterr()
+            assert not err
+            assert out == (
+                "✔ Adding dependency 'ruff' to the 'dev' group in 'pyproject.toml'.\n"
+                "☐ Install the dependency 'ruff'.\n"
+                "✔ Adding Ruff config to 'ruff.toml'.\n"
+                "☐ Run 'ruff check --fix' to run the Ruff linter with autofixes.\n"
+                "☐ Run 'ruff format' to run the Ruff formatter.\n"
+            )
+            assert (uv_init_dir / "ruff.toml").read_text() == (
+                """\
+namespace-packages = ["src/usethis/namespace"]
+line-length = 88
+
+[lint]
+select = [ "ALL" ]
+ignore = [ "EM", "T20", "TRY003", "S603" ]
+
+[lint.extend-per-file-ignores]
+"__main__.py" = [ "BLE001" ]
+"""
+            )
+
     class TestRemove:
         @pytest.mark.usefixtures("_vary_network_conn")
         def test_config_file(self, uv_init_dir: Path):

tests/usethis/test_usethis_tool.py

@@ -966,7 +966,7 @@ def test_ruff_toml(self, tmp_path: Path):
             # Arrange
             (tmp_path / "ruff.toml").write_text(
                 """
-[tool.ruff.lint]
+[lint]
 select = ["A", "B"]
 """
             )
@@ -1053,7 +1053,7 @@ def test_ruff_toml(self, tmp_path: Path):
             # Arrange
             (tmp_path / ".ruff.toml").write_text(
                 """\
-[tool.ruff.lint]
+[lint]
 select = ["A", "B"]
 """
             )