Remove pyproject.toml config when removing deptry (#266)

* Rmeove pyproject.toml config when removing deptry

* Fix accidental change to removal message

* Don't report null removals

Author: nathanjmcdougall

.gitignore

@@ -160,3 +160,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# Windsurf config
+.windsurfrules

doc/lessons.md

@@ -0,0 +1,56 @@
+# Lessons Learned
+
+## Test Driven Development
+
+- ALWAYS write tests before implementing functionality. This helps ensure the code meets requirements and avoids unnecessary complexity.
+- When implementing a new feature, first write a failing test that describes the desired behavior.
+- Tests should be specific and focused on one piece of functionality.
+- After implementing changes, run the full test suite and code quality checks to catch any regressions.
+- Test classes should be at the root level of the test file, not nested within other test classes, to ensure proper test discovery and organization.
+- When running pytest for a specific test class, use the format `pytest path/to/test.py::TestClassName -v`
+- For efficiency, run only the specific tests you need:
+  - For a single test: `pytest path/to/test.py::TestClass::test_name`
+  - For a test in a nested class: `pytest path/to/test.py::TestClass::TestNestedClass::test_name`
+  - For a parameterized test: `pytest path/to/test.py::test_name`
+- Structure tests with explicit comments to improve readability:
+  ```python
+  def test_something(self):
+      # Arrange - set up test data and conditions
+      
+      # Act - perform the action being tested
+      
+      # Assert - verify the results
+  ```
+
+## Code Quality
+
+- Avoid code duplication in error handling paths. When you see similar error handling repeated, consider consolidating the logic:
+  1. Collect all items to process up front
+  2. Use a single loop to handle common operations and error cases
+  3. Consolidate status messages or logging
+- Keep docstrings focused on interface behavior, not implementation details
+- Never make changes unrelated to the current task or failing test
+- Keep a clear separation between interface documentation (docstrings) and implementation notes (comments)
+- Run pre-commit checks after making changes to ensure code quality and formatting standards are met
+- Never include type information in docstrings when it's already present in type annotations
+- ALWAYS run pre-commit checks after any code changes are considered complete:
+  1. Run `uv run pre-commit run --all-files`
+  2. If any checks modify files, run the checks again to ensure everything is clean
+  3. Never consider a change complete until all pre-commit checks pass
+- Use `contextlib.suppress` instead of empty try-except blocks:
+  ```python
+  # Instead of:
+  try:
+      do_something()
+  except SomeError:
+      pass
+      
+  # Use:
+  from contextlib import suppress
+  with suppress(SomeError):
+      do_something()
+  ```
+- Display user feedback messages:
+  1. Use present tense ("Removing..." not "Removed...")
+  2. Show messages as soon as possible, don't wait until after the operation
+  3. Use a flag like `first_removal` to ensure messages are shown exactly once

src/usethis/_core/tool.py

@@ -90,8 +90,8 @@ def use_deptry(*, remove: bool = False) -> None:
         box_print("Run 'deptry src' to run deptry.")
     else:
         tool.remove_pre_commit_repo_configs()
+        tool.remove_pyproject_configs()
         remove_bitbucket_step_from_default(get_bitbucket_deptry_step())
-
         remove_deps_from_group(tool.dev_deps, "dev")
 
 

src/usethis/_tool.py

@@ -59,7 +59,11 @@ def get_pre_commit_repos(self) -> list[LocalRepo | UriRepo]:
         return []
 
     def get_pyproject_configs(self) -> list[PyProjectConfig]:
-        """Get the pyproject configurations for the tool."""
+        """Get the pyproject configurations for the tool.
+
+        All configuration keys returned by this method must be sub-keys of the
+        keys returned by get_pyproject_id_keys().
+        """
         return []
 
     def get_associated_ruff_rules(self) -> list[str]:
@@ -155,15 +159,21 @@ def add_pyproject_configs(self) -> None:
                     first_addition = False
 
     def remove_pyproject_configs(self) -> None:
-        """Remove the tool's pyproject.toml configuration."""
-        configs = self.get_pyproject_configs()
-        if not configs:
-            return
+        """Remove all pyproject.toml configurations associated with this tool.
 
+        This includes any tool-specific sections in the pyproject.toml file.
+        If no configurations exist, this method has no effect.
+        """
+        # Collect all keys to remove
+        keys_to_remove = [
+            config.id_keys for config in self.get_pyproject_configs()
+        ] + self.get_pyproject_id_keys()
+
+        # Try to remove the first key to trigger the message
         first_removal = True
-        for config in configs:
+        for keys in keys_to_remove:
             try:
-                remove_config_value(config.id_keys)
+                remove_config_value(keys)
             except PyProjectTOMLValueMissingError:
                 pass
             else:
@@ -238,6 +248,9 @@ def get_pre_commit_repos(self) -> list[LocalRepo | UriRepo]:
             )
         ]
 
+    def get_pyproject_id_keys(self) -> list[list[str]]:
+        return [["tool", "deptry"]]
+
 
 class PreCommitTool(Tool):
     @property

tests/usethis/_core/test_tool.py

@@ -323,6 +323,21 @@ def test_bitbucket_integration(self, uv_init_repo_dir: Path):
             contents = (uv_init_repo_dir / "bitbucket-pipelines.yml").read_text()
             assert "deptry" not in contents
 
+        def test_use_deptry_removes_config(self, tmp_path: Path):
+            """Test that use_deptry removes the tool's config when removing."""
+            # Arrange
+            pyproject = tmp_path / "pyproject.toml"
+            pyproject.write_text("""[tool.deptry]
+ignore_missing = ["pytest"]
+""")
+
+            # Act
+            with change_cwd(tmp_path):
+                use_deptry(remove=True)
+
+            # Assert
+            assert "[tool.deptry]" not in pyproject.read_text()
+
     class TestPreCommitIntegration:
         @pytest.mark.usefixtures("_vary_network_conn")
         def test_pre_commit_first(
@@ -606,14 +621,14 @@ def test_requirements_txt_used(
                 # Act
                 use_pre_commit(remove=True)
 
-            # Assert
-            out, _ = capfd.readouterr()
-            assert out == (
-                "✔ Ensuring pre-commit hooks are uninstalled.\n"
-                "✔ Removing '.pre-commit-config.yaml'.\n"
-                "✔ Removing dependency 'pre-commit' from the 'dev' group in 'pyproject.toml'.\n"
-                "☐ Run 'uv export --no-dev --output-file=requirements.txt' to write \n'requirements.txt'.\n"
-            )
+                # Assert
+                out, _ = capfd.readouterr()
+                assert out == (
+                    "✔ Ensuring pre-commit hooks are uninstalled.\n"
+                    "✔ Removing '.pre-commit-config.yaml'.\n"
+                    "✔ Removing dependency 'pre-commit' from the 'dev' group in 'pyproject.toml'.\n"
+                    "☐ Run 'uv export --no-dev --output-file=requirements.txt' to write \n'requirements.txt'.\n"
+                )
 
         @pytest.mark.usefixtures("_vary_network_conn")
         def test_pyproject_fmt_used(
@@ -628,15 +643,15 @@ def test_pyproject_fmt_used(
                 # Act
                 use_pre_commit(remove=True)
 
-            # Assert
-            out, _ = capfd.readouterr()
-            assert out == (
-                "✔ Ensuring pre-commit hooks are uninstalled.\n"
-                "✔ Removing '.pre-commit-config.yaml'.\n"
-                "✔ Removing dependency 'pre-commit' from the 'dev' group in 'pyproject.toml'.\n"
-                "✔ Adding dependency 'pyproject-fmt' to the 'dev' group in 'pyproject.toml'.\n"
-                "☐ Run 'pyproject-fmt pyproject.toml' to run pyproject-fmt.\n"
-            )
+                # Assert
+                out, _ = capfd.readouterr()
+                assert out == (
+                    "✔ Ensuring pre-commit hooks are uninstalled.\n"
+                    "✔ Removing '.pre-commit-config.yaml'.\n"
+                    "✔ Removing dependency 'pre-commit' from the 'dev' group in 'pyproject.toml'.\n"
+                    "✔ Adding dependency 'pyproject-fmt' to the 'dev' group in 'pyproject.toml'.\n"
+                    "☐ Run 'pyproject-fmt pyproject.toml' to run pyproject-fmt.\n"
+                )
 
     class TestBitbucketCIIntegration:
         def test_prexisting(self, uv_init_repo_dir: Path):

tests/usethis/test_tool.py

@@ -8,7 +8,7 @@
 from usethis._integrations.pyproject.core import set_config_value
 from usethis._integrations.uv.deps import Dependency, add_deps_to_group
 from usethis._test import change_cwd
-from usethis._tool import Tool
+from usethis._tool import ALL_TOOLS, DeptryTool, Tool
 
 
 class DefaultTool(Tool):
@@ -669,3 +669,64 @@ def get_pyproject_configs(self) -> list[PyProjectConfig]:
             out, err = capfd.readouterr()
             assert not err
             assert out == "✔ Adding mytool config to 'pyproject.toml'.\n"
+
+
+class TestDeptryTool:
+    """Tests for DeptryTool."""
+
+    def test_get_pyproject_id_keys(self):
+        """Test that get_pyproject_id_keys returns the correct keys."""
+        # Arrange
+        tool = DeptryTool()
+
+        # Act
+        result = tool.get_pyproject_id_keys()
+
+        # Assert
+        assert result == [["tool", "deptry"]]
+
+    def test_remove_pyproject_configs_removes_deptry_section(self, tmp_path: Path):
+        """Test that remove_pyproject_configs removes the deptry section."""
+        # Arrange
+        pyproject = tmp_path / "pyproject.toml"
+        pyproject.write_text("""[tool.deptry]
+ignore_missing = ["pytest"]
+""")
+
+        # Act
+        with change_cwd(tmp_path):
+            tool = DeptryTool()
+            tool.remove_pyproject_configs()
+
+        # Assert
+        assert "[tool.deptry]" not in pyproject.read_text()
+        assert "ignore_missing" not in pyproject.read_text()
+
+    def test_config_keys_are_subkeys_of_id_keys(self):
+        """Test that all config keys are subkeys of id keys."""
+        # Arrange
+        tool = DeptryTool()
+
+        # Act
+        id_keys = tool.get_pyproject_id_keys()
+        configs = tool.get_pyproject_configs()
+
+        # Assert
+        for config in configs:
+            # For each config, check if its keys are a subset of any id_keys
+            assert any(config.id_keys[: len(id_key)] == id_key for id_key in id_keys), (
+                f"Config keys {config.id_keys} not covered by ID keys {id_keys}"
+            )
+
+
+@pytest.mark.parametrize("tool", ALL_TOOLS)
+def test_all_tools_config_keys_are_subkeys_of_id_keys(tool: Tool):
+    """Test that all tools' config keys are subkeys of their ID keys."""
+    id_keys = tool.get_pyproject_id_keys()
+    configs = tool.get_pyproject_configs()
+
+    for config in configs:
+        # For each config, check if its keys are a subset of any id_keys
+        assert any(config.id_keys[: len(id_key)] == id_key for id_key in id_keys), (
+            f"Config keys {config.id_keys} not covered by ID keys in {tool.name}"
+        )