[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

src/pleiades/core/data_manager.py

@@ -73,9 +73,7 @@ def get_file_path(self, category: DataCategory, filename: str) -> Path:
 
         file_path = Path(filename)
         if file_path.suffix not in self._VALID_EXTENSIONS[category]:
-            raise ValueError(
-                f"Invalid file extension for {category}. " f"Allowed extensions: {self._VALID_EXTENSIONS[category]}"
-            )
+            raise ValueError(f"Invalid file extension for {category}. " f"Allowed extensions: {self._VALID_EXTENSIONS[category]}")
 
         try:
             with resources.path(f"pleiades.data.{self._get_category_path(category)}", filename) as path:

src/pleiades/core/models.py

@@ -231,9 +231,7 @@ def areal_density(self) -> float:
         if self.thickness_unit == "mm":
             thickness_cm /= 10.0
 
-        return (
-            thickness_cm * self.density * CONSTANTS.avogadro_number / self.atomic_mass.value / 1e24
-        )  # Convert to atoms/barn
+        return thickness_cm * self.density * CONSTANTS.avogadro_number / self.atomic_mass.value / 1e24  # Convert to atoms/barn
 
 
 # Unit conversion functions

src/pleiades/sammy/backends/docker.py

@@ -48,9 +48,7 @@ def prepare_environment(self, files: SammyFiles) -> None:
                 raise EnvironmentPreparationError("Docker not found in PATH")
 
             # Verify docker image exists
-            result = subprocess.run(
-                ["docker", "image", "inspect", self.config.image_name], capture_output=True, text=True
-            )
+            result = subprocess.run(["docker", "image", "inspect", self.config.image_name], capture_output=True, text=True)
             if result.returncode != 0:
                 raise EnvironmentPreparationError(f"Docker image not found: {self.config.image_name}")
 

src/pleiades/sammy/backends/local.py

@@ -81,10 +81,7 @@ def execute_sammy(self, files: SammyFiles) -> SammyExecutionResult:
 
             if not success:
                 logger.error(f"SAMMY execution failed for {execution_id}")
-                error_message = (
-                    f"SAMMY execution failed with return code {process.returncode}. "
-                    "Check console output for details."
-                )
+                error_message = f"SAMMY execution failed with return code {process.returncode}. " "Check console output for details."
             else:
                 logger.info(f"SAMMY execution completed successfully for {execution_id}")
                 error_message = None

src/pleiades/sammy/factory.py

@@ -105,9 +105,7 @@ def list_available_backends() -> Dict[BackendType, bool]:
         return available
 
     @classmethod
-    def create_runner(
-        cls, backend_type: str, working_dir: Path, output_dir: Optional[Path] = None, **kwargs
-    ) -> SammyRunner:
+    def create_runner(cls, backend_type: str, working_dir: Path, output_dir: Optional[Path] = None, **kwargs) -> SammyRunner:
         """
         Create a SAMMY runner with the specified backend and configuration.
 
@@ -295,9 +293,7 @@ def process_config(cfg):
             backend_config = config.get(backend_type, {})
 
             # Create runner using create_runner
-            return cls.create_runner(
-                backend_type=backend_type, working_dir=working_dir, output_dir=output_dir, **backend_config
-            )
+            return cls.create_runner(backend_type=backend_type, working_dir=working_dir, output_dir=output_dir, **backend_config)
 
         except Exception as e:
             if not isinstance(e, (ConfigurationError, BackendNotAvailableError)):
@@ -347,9 +343,7 @@ def auto_select(
                 preferred = BackendType(preferred_backend.lower())
                 if available[preferred]:
                     logger.info(f"Using preferred backend: {preferred.value}")
-                    return cls.create_runner(
-                        backend_type=preferred.value, working_dir=working_dir, output_dir=output_dir, **kwargs
-                    )
+                    return cls.create_runner(backend_type=preferred.value, working_dir=working_dir, output_dir=output_dir, **kwargs)
                 else:
                     logger.warning(f"Preferred backend {preferred.value} not available, " "trying alternatives")
             except ValueError:
@@ -367,9 +361,7 @@ def auto_select(
             if available[backend]:
                 try:
                     logger.info(f"Attempting to use {backend.value} backend")
-                    return cls.create_runner(
-                        backend_type=backend.value, working_dir=working_dir, output_dir=output_dir, **kwargs
-                    )
+                    return cls.create_runner(backend_type=backend.value, working_dir=working_dir, output_dir=output_dir, **kwargs)
                 except Exception as e:
                     logger.warning(f"Failed to configure {backend.value} backend: {str(e)}")
                     errors.append(f"{backend.value}: {str(e)}")

tests/unit/pleiades/sammy/backends/test_docker.py

@@ -124,9 +124,7 @@ def test_execute_sammy_success(self, docker_config, mock_sammy_files, mock_subpr
         assert "Normal finish to SAMMY" in result.console_output
         assert result.error_message is None
 
-    def test_execute_sammy_failure(
-        self, docker_config, mock_sammy_files, mock_subprocess_docker_fail, mock_docker_command
-    ):
+    def test_execute_sammy_failure(self, docker_config, mock_sammy_files, mock_subprocess_docker_fail, mock_docker_command):
         """Should handle SAMMY execution failure in container."""
         _ = mock_docker_command  # implicitly used via fixture
         _ = mock_subprocess_docker_fail  # implicitly used via fixture
@@ -139,9 +137,7 @@ def test_execute_sammy_failure(
         assert not result.success
         assert "Docker execution failed" in result.error_message
 
-    def test_collect_outputs(
-        self, docker_config, mock_sammy_files, mock_subprocess_docker, mock_docker_command, mock_sammy_results
-    ):
+    def test_collect_outputs(self, docker_config, mock_sammy_files, mock_subprocess_docker, mock_docker_command, mock_sammy_results):
         """Should collect output files from container."""
         _ = mock_docker_command  # implicitly used via fixture
         _ = mock_subprocess_docker  # implicitly used via fixture

tests/unit/pleiades/sammy/test_config.py

@@ -24,9 +24,7 @@ def test_create_with_valid_paths(self, temp_working_dir):
 
     def test_create_with_defaults(self, temp_working_dir):
         """Should create config with default values."""
-        config = LocalSammyConfig(
-            working_dir=temp_working_dir, output_dir=temp_working_dir / "output", sammy_executable=Path("sammy")
-        )
+        config = LocalSammyConfig(working_dir=temp_working_dir, output_dir=temp_working_dir / "output", sammy_executable=Path("sammy"))
         assert config.shell_path == Path("/bin/bash")
 
     def test_validate_sammy_in_path(self, temp_working_dir, monkeypatch):
@@ -37,18 +35,14 @@ def mock_which(path):
 
         monkeypatch.setattr("shutil.which", mock_which)
 
-        config = LocalSammyConfig(
-            working_dir=temp_working_dir, output_dir=temp_working_dir / "output", sammy_executable=Path("sammy")
-        )
+        config = LocalSammyConfig(working_dir=temp_working_dir, output_dir=temp_working_dir / "output", sammy_executable=Path("sammy"))
         assert config.validate()
 
     def test_validate_sammy_not_in_path(self, temp_working_dir, monkeypatch):
         """Should raise error if SAMMY not in PATH."""
         monkeypatch.setattr("shutil.which", lambda _: None)
 
-        config = LocalSammyConfig(
-            working_dir=temp_working_dir, output_dir=temp_working_dir / "output", sammy_executable=Path("sammy")
-        )
+        config = LocalSammyConfig(working_dir=temp_working_dir, output_dir=temp_working_dir / "output", sammy_executable=Path("sammy"))
         with pytest.raises(ConfigurationError) as exc:
             config.validate()
         assert "not found" in str(exc.value)
@@ -171,9 +165,7 @@ def test_validate_invalid_url(self, temp_working_dir):
 
     def test_empty_url(self, temp_working_dir):
         """Should raise error for empty URL."""
-        config = NovaSammyConfig(
-            working_dir=temp_working_dir, output_dir=temp_working_dir / "output", url="", api_key="valid_api_key"
-        )
+        config = NovaSammyConfig(working_dir=temp_working_dir, output_dir=temp_working_dir / "output", url="", api_key="valid_api_key")
         with pytest.raises(ConfigurationError) as exc:
             config.validate()
         assert "NOVA service URL cannot be empty" in str(exc.value)

tests/unit/pleiades/sammy/test_factory.py

@@ -73,9 +73,7 @@ def _mock_run(*args, **kwargs):
 @pytest.fixture
 def mock_subprocess_run_docker_fail(monkeypatch):
     """Mock subprocess.run to simulate docker info failure."""
-    monkeypatch.setattr(
-        subprocess, "run", lambda *args, **kwargs: subprocess.CompletedProcess(args=args, returncode=1, **kwargs)
-    )
+    monkeypatch.setattr(subprocess, "run", lambda *args, **kwargs: subprocess.CompletedProcess(args=args, returncode=1, **kwargs))
 
 
 # Mock SammyRunner creation for runner tests
@@ -100,9 +98,7 @@ def test_list_available_backends_all_available(self, mock_which, mock_subprocess
             BackendType.NOVA: True,
         }
 
-    def test_list_available_backends_none_available(
-        self, monkeypatch, mock_which_unavailable, mock_subprocess_run_docker_fail
-    ):
+    def test_list_available_backends_none_available(self, monkeypatch, mock_which_unavailable, mock_subprocess_run_docker_fail):
         """No backends should be available."""
         _ = mock_which_unavailable, mock_subprocess_run_docker_fail  # implicitly used by the fixture
         # remove NOVA env vars to simulate unavailability
@@ -218,9 +214,7 @@ def test_auto_select_local(self, mock_which, mock_subprocess_run, mock_sammy_run
         assert isinstance(runner, LocalSammyRunner)
         assert "Attempting to use local backend" in caplog.text
 
-    def test_auto_select_docker(
-        self, monkeypatch, mock_which_unavailable, mock_subprocess_run, mock_sammy_runner, tmp_path, caplog
-    ):
+    def test_auto_select_docker(self, monkeypatch, mock_which_unavailable, mock_subprocess_run, mock_sammy_runner, tmp_path, caplog):
         """Should auto-select docker backend if local unavailable."""
         _ = mock_which_unavailable, mock_subprocess_run, mock_sammy_runner  # implicitly used by the fixture
         # remove NOVA env vars to simulate unavailability
@@ -240,9 +234,7 @@ def test_auto_select_preferred(self, mock_which, mock_subprocess_run, mock_sammy
         assert isinstance(runner, DockerSammyRunner)
         assert "Using preferred backend: docker" in caplog.text
 
-    def test_auto_select_none_available(
-        self, monkeypatch, mock_which_unavailable, mock_subprocess_run_docker_fail, tmp_path, caplog
-    ):
+    def test_auto_select_none_available(self, monkeypatch, mock_which_unavailable, mock_subprocess_run_docker_fail, tmp_path, caplog):
         """Should raise error if no backends available."""
         _ = mock_which_unavailable, mock_subprocess_run_docker_fail  # implicitly used by the fixture
         # remove NOVA env vars to simulate unavailability