junifer 0.0.5.dev240__py3-none-any.whl → 0.0.6__py3-none-any.whl

junifer/pipeline/tests/test_pipeline_component_registry.py

@@ -0,0 +1,200 @@
+"""Provide tests for PipelineComponentRegistry."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import logging
+from abc import ABC
+
+import pytest
+
+from junifer.datagrabber.pattern import PatternDataGrabber
+from junifer.pipeline.pipeline_component_registry import (
+    PipelineComponentRegistry,
+)
+from junifer.storage import SQLiteFeatureStorage
+
+
+def test_pipeline_component_registry_singleton() -> None:
+    """Test that PipelineComponentRegistry is a singleton."""
+    registry_1 = PipelineComponentRegistry()
+    registry_2 = PipelineComponentRegistry()
+    assert id(registry_1) == id(registry_2)
+
+
+def test_pipeline_component_registry_register_invalid_step():
+    """Test invalid step name during component registration."""
+    with pytest.raises(ValueError, match="Invalid step:"):
+        PipelineComponentRegistry().register(step="foo", klass=str)
+
+
+def test_pipeline_component_registry_steps():
+    """Test steps for PipelineComponentRegistry."""
+    assert set(PipelineComponentRegistry().steps) == {
+        "datagrabber",
+        "datareader",
+        "preprocessing",
+        "marker",
+        "storage",
+    }
+
+
+def test_pipeline_component_registry_components():
+    """Test components for PipelineComponentRegistry."""
+    assert set(PipelineComponentRegistry().steps) == {
+        "datagrabber",
+        "datareader",
+        "preprocessing",
+        "marker",
+        "storage",
+    }
+
+
+@pytest.mark.parametrize(
+    "step, klass",
+    [
+        ("datagrabber", PatternDataGrabber),
+        ("storage", SQLiteFeatureStorage),
+    ],
+)
+def test_pipeline_component_registry_register(
+    caplog: pytest.LogCaptureFixture, step: str, klass: type
+) -> None:
+    """Test register for PipelineComponentRegistry.
+
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+    step : str
+        The parametrized name of the step.
+    klass : str
+        The parametrized name of the class.
+
+    """
+    with caplog.at_level(logging.INFO):
+        # Register
+        PipelineComponentRegistry().register(step=step, klass=klass)
+        # Check logging message
+        assert "Registering" in caplog.text
+
+
+@pytest.mark.parametrize(
+    "step, klass",
+    [
+        ("datagrabber", PatternDataGrabber),
+        ("storage", SQLiteFeatureStorage),
+    ],
+)
+def test_pipeline_component_registry_deregister(
+    caplog: pytest.LogCaptureFixture, step: str, klass: type
+) -> None:
+    """Test de-register for PipelineComponentRegistry.
+
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+    step : str
+        The parametrized name of the step.
+    klass : str
+        The parametrized name of the class.
+
+    """
+    with caplog.at_level(logging.INFO):
+        # Register
+        PipelineComponentRegistry().deregister(step=step, klass=klass)
+        # Check logging message
+        assert "De-registering" in caplog.text
+
+
+def test_pipeline_component_registry_step_components() -> None:
+    """Test step components for PipelineComponentRegistry."""
+    # Check absent name
+    assert "fizz" not in PipelineComponentRegistry().step_components(
+        step="datagrabber"
+    )
+
+    # Create new class
+    class fizz(str):
+        pass
+
+    # Register datagrabber
+    PipelineComponentRegistry().register(step="datagrabber", klass=fizz)
+    # Check registered component
+    assert "fizz" in PipelineComponentRegistry().step_components(
+        step="datagrabber"
+    )
+
+
+def test_pipeline_component_registry_get_class_invalid_name() -> None:
+    """Test get class invalid name for PipelineComponentRegistry."""
+    with pytest.raises(ValueError, match="Invalid name:"):
+        PipelineComponentRegistry().get_class(step="datagrabber", name="foo")
+
+
+def test_pipeline_component_registry_get_class():
+    """Test get class for PipelineComponentRegistry."""
+
+    # Create new class
+    class bar(str):
+        pass
+
+    # Register datagrabber
+    PipelineComponentRegistry().register(step="datagrabber", klass=bar)
+    # Get class
+    obj = PipelineComponentRegistry().get_class(step="datagrabber", name="bar")
+    assert isinstance(obj, type(bar))
+
+
+def test_pipeline_component_registry_build():
+    """Test component instance building for PipelineComponentRegistry."""
+    import numpy as np
+
+    # Define abstract base class
+    class SuperClass(ABC):
+        pass
+
+    # Define concrete class
+    class ConcreteClass(SuperClass):
+        def __init__(self, value=1):
+            self.value = value
+
+    # Register
+    PipelineComponentRegistry().register(
+        step="datagrabber", klass=ConcreteClass
+    )
+
+    # Build
+    obj = PipelineComponentRegistry().build_component_instance(
+        step="datagrabber", name="ConcreteClass", baseclass=SuperClass
+    )
+    assert isinstance(obj, ConcreteClass)
+    assert obj.value == 1
+
+    # Build
+    obj = PipelineComponentRegistry().build_component_instance(
+        step="datagrabber",
+        name="ConcreteClass",
+        baseclass=SuperClass,
+        init_params={"value": 2},
+    )
+    assert isinstance(obj, ConcreteClass)
+    assert obj.value == 2
+
+    # Check error
+    with pytest.raises(ValueError, match="Must inherit"):
+        PipelineComponentRegistry().build_component_instance(
+            step="datagrabber", name="ConcreteClass", baseclass=np.ndarray
+        )
+
+    # Check error
+    with pytest.raises(RuntimeError, match="Failed to create"):
+        PipelineComponentRegistry().build_component_instance(
+            step="datagrabber",
+            name="ConcreteClass",
+            baseclass=SuperClass,
+            init_params={"wrong": 2},
+        )

junifer/pipeline/tests/test_pipeline_step_mixin.py

@@ -5,12 +5,17 @@
 # License: AGPL
 
 import warnings
-from typing import ClassVar, Dict, List, Set, Type, Union
+from typing import ClassVar
 
 import pytest
 
 from junifer.pipeline.pipeline_step_mixin import PipelineStepMixin
 from junifer.pipeline.utils import _check_afni
+from junifer.typing import (
+    ConditionalDependencies,
+    Dependencies,
+    ExternalDependencies,
+)
 
 
 def test_PipelineStepMixin_correct_dependencies() -> None:
@@ -19,15 +24,15 @@ def test_PipelineStepMixin_correct_dependencies() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _DEPENDENCIES: ClassVar[Set[str]] = {"math"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"math"}
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -40,15 +45,15 @@ def test_PipelineStepMixin_incorrect_dependencies() -> None:
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _DEPENDENCIES: ClassVar[Set[str]] = {"foobar"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"foobar"}
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = IncorrectMixer()
@@ -65,15 +70,15 @@ def test_PipelineStepMixin_correct_ext_dependencies() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, str]]] = [{"name": "afni"}]
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [{"name": "afni"}]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -89,17 +94,17 @@ def test_PipelineStepMixin_ext_deps_correct_commands() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
             {"name": "afni", "commands": ["3dReHo"]}
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -117,17 +122,17 @@ def test_PipelineStepMixin_ext_deps_incorrect_commands() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
             {"name": "afni", "commands": ["3d"]}
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -141,17 +146,17 @@ def test_PipelineStepMixin_incorrect_ext_dependencies() -> None:
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, bool]]]] = [
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
             {"name": "foobar", "optional": True}
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = IncorrectMixer()
@@ -163,14 +168,12 @@ def test_PipelineStepMixin_correct_conditional_dependencies() -> None:
     """Test fit-transform with correct conditional dependencies."""
 
     class Dependency:
-        _DEPENDENCIES: ClassVar[Set[str]] = {"math"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"math"}
 
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _CONDITIONAL_DEPENDENCIES: ClassVar[
-            List[Dict[str, Union[str, Type]]]
-        ] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "math",
                 "depends_on": Dependency,
@@ -179,13 +182,13 @@ def test_PipelineStepMixin_correct_conditional_dependencies() -> None:
 
         using = "math"
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -196,27 +199,25 @@ def test_PipelineStepMixin_incorrect_conditional_dependencies() -> None:
     """Test fit-transform with incorrect conditional dependencies."""
 
     class Dependency:
-        _DEPENDENCIES: ClassVar[Set[str]] = {"math"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"math"}
 
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _CONDITIONAL_DEPENDENCIES: ClassVar[
-            List[Dict[str, Union[str, Type]]]
-        ] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "math",
                 "depends_on": Dependency,
             },
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = IncorrectMixer()
@@ -231,14 +232,12 @@ def test_PipelineStepMixin_correct_conditional_ext_dependencies() -> None:
     """Test fit-transform with correct conditional external dependencies."""
 
     class ExternalDependency:
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, str]]] = [{"name": "afni"}]
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [{"name": "afni"}]
 
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _CONDITIONAL_DEPENDENCIES: ClassVar[
-            List[Dict[str, Union[str, Type]]]
-        ] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "afni",
                 "depends_on": ExternalDependency,
@@ -247,13 +246,13 @@ def test_PipelineStepMixin_correct_conditional_ext_dependencies() -> None:
 
         using = "afni"
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()

junifer/pipeline/tests/test_update_meta_mixin.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, List, Set, Union
+from typing import Union
 
 import pytest
 
@@ -21,10 +21,10 @@ from junifer.pipeline.update_meta_mixin import UpdateMetaMixin
     ],
 )
 def test_UpdateMetaMixin(
-    input: Dict,
+    input: dict,
     step_name: str,
-    dependencies: Union[Set, List, str, None],
-    expected: Set,
+    dependencies: Union[set, list, str, None],
+    expected: set,
 ) -> None:
     """Test UpdateMetaMixin.
 

junifer/pipeline/tests/test_workdir_manager.py

@@ -102,3 +102,46 @@ def test_workdir_manager_get_and_delete_tempdir(tmp_path: Path) -> None:
     workdir_mgr._cleanup()
     # Should remove temporary directory
     assert workdir_mgr.root_tempdir is None
+
+
+def test_workdir_manager_no_cleanup(tmp_path: Path) -> None:
+    """Test WorkDirManager correctly bypasses cleanup.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    workdir_mgr = WorkDirManager(cleanup=False)
+    workdir_mgr.workdir = tmp_path
+    # Check no root temporary directory
+    assert workdir_mgr.root_tempdir is None
+
+    tempdir = workdir_mgr.get_tempdir()
+    assert tempdir.exists()
+    # Should create a temporary directory
+    assert workdir_mgr.root_tempdir is not None
+
+    workdir_mgr.delete_tempdir(tempdir)
+    workdir_mgr._cleanup()
+
+    # Should remove temporary directory
+    assert workdir_mgr.root_tempdir is None
+    # But the temporary directory should still exist
+    assert tempdir.exists()
+
+    # Now the same but for the element directory
+
+    # Check no element directory
+    assert workdir_mgr.elementdir is None
+
+    tempdir = workdir_mgr.get_element_tempdir()
+    # Should create a temporary directory
+    assert workdir_mgr.elementdir is not None
+
+    workdir_mgr.cleanup_elementdir()
+    # Should remove temporary directory
+    assert workdir_mgr.elementdir is None
+    # But the temporary directory should still exist
+    assert tempdir.exists()

junifer/pipeline/update_meta_mixin.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict
+from typing import Union
 
 
 __all__ = ["UpdateMetaMixin"]
@@ -15,14 +15,14 @@ class UpdateMetaMixin:
 
     def update_meta(
         self,
-        input: Dict,
+        input: Union[dict, list[dict]],
         step_name: str,
     ) -> None:
         """Update metadata.
 
         Parameters
         ----------
-        input : dict
+        input : dict or list of dict
             The data object to update.
         step_name : str
             The name of the pipeline step.
@@ -36,17 +36,21 @@ class UpdateMetaMixin:
         for k, v in vars(self).items():
             if not k.startswith("_"):
                 t_meta[k] = v
-        # Add "meta" to the step's local context dict
-        if "meta" not in input:
-            input["meta"] = {}
-        # Add step name
-        input["meta"][step_name] = t_meta
-        # Add step dependencies
-        if "dependencies" not in input["meta"]:
-            input["meta"]["dependencies"] = set()
-        # Update step dependencies
-        dependencies = getattr(self, "_DEPENDENCIES", set())
-        if dependencies is not None:
-            if not isinstance(dependencies, (set, list)):
-                dependencies = {dependencies}
-            input["meta"]["dependencies"].update(dependencies)
+        # Conditional for list dtype vals like Warp
+        if not isinstance(input, list):
+            input = [input]
+        for entry in input:
+            # Add "meta" to the step's entry's local context dict
+            if "meta" not in entry:
+                entry["meta"] = {}
+            # Add step name
+            entry["meta"][step_name] = t_meta
+            # Add step dependencies
+            if "dependencies" not in entry["meta"]:
+                entry["meta"]["dependencies"] = set()
+            # Update step dependencies
+            dependencies = getattr(self, "_DEPENDENCIES", set())
+            if dependencies is not None:
+                if not isinstance(dependencies, (set, list)):
+                    dependencies = {dependencies}
+                entry["meta"]["dependencies"].update(dependencies)

junifer/pipeline/utils.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 import subprocess
-from typing import Any, List, Optional
+from typing import Any, Optional
 
 from junifer.utils.logging import raise_error, warn_with_log
 
@@ -71,7 +71,7 @@ def check_ext_dependencies(
     return found
 
 
-def _check_afni(commands: Optional[List[str]] = None) -> bool:
+def _check_afni(commands: Optional[list[str]] = None) -> bool:
     """Check if AFNI is present in the system.
 
     Parameters
@@ -131,7 +131,7 @@ def _check_afni(commands: Optional[List[str]] = None) -> bool:
     return afni_found
 
 
-def _check_fsl(commands: Optional[List[str]] = None) -> bool:
+def _check_fsl(commands: Optional[list[str]] = None) -> bool:
     """Check if FSL is present in the system.
 
     Parameters
@@ -193,7 +193,7 @@ def _check_fsl(commands: Optional[List[str]] = None) -> bool:
     return fsl_found
 
 
-def _check_ants(commands: Optional[List[str]] = None) -> bool:
+def _check_ants(commands: Optional[list[str]] = None) -> bool:
     """Check if ANTs is present in the system.
 
     Parameters
@@ -237,7 +237,7 @@ def _check_ants(commands: Optional[List[str]] = None) -> bool:
                 shell=True,  # is unsafe but kept for resolution via PATH
                 check=False,
             )
-            command_found = command_process.returncode == 0
+            command_found = command_process.returncode == 1
             commands_found_results[command] = (
                 "found" if command_found else "not found"
             )
@@ -253,7 +253,7 @@ def _check_ants(commands: Optional[List[str]] = None) -> bool:
     return ants_found
 
 
-def _check_freesurfer(commands: Optional[List[str]] = None) -> bool:
+def _check_freesurfer(commands: Optional[list[str]] = None) -> bool:
     """Check if FreeSurfer is present in the system.
 
     Parameters