junifer/api/__init__.py

@@ -7,4 +7,3 @@
 from .cli import cli
 from .functions import run, collect
 from . import decorators
-from . import registry

junifer/api/decorators.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .registry import register
+from ..pipeline.registry import register
 
 
 def register_datagrabber(klass: type) -> type:

junifer/api/functions.py

@@ -16,10 +16,10 @@ import yaml
 from ..datagrabber.base import BaseDataGrabber
 from ..markers.base import BaseMarker
 from ..markers.collection import MarkerCollection
+from ..pipeline.registry import build
 from ..storage.base import BaseFeatureStorage
 from ..utils import logger, raise_error
 from ..utils.fs import make_executable
-from .registry import build
 
 
 def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:

junifer/api/tests/test_functions.py

@@ -11,8 +11,8 @@ import pytest
 
 import junifer.testing.registry  # noqa: F401
 from junifer.api.functions import collect, run
-from junifer.api.registry import build
 from junifer.datagrabber.base import BaseDataGrabber
+from junifer.pipeline.registry import build
 
 
 # Define datagrabber

junifer/pipeline/registry.py

@@ -11,12 +11,13 @@ from ..utils.logging import logger, raise_error
 
 
 if TYPE_CHECKING:
-    from ..datagrabber.base import BaseDataGrabber
+    from ..datagrabber import BaseDataGrabber
-    from ..pipeline import PipelineStepMixin
+    from ..storage import BaseFeatureStorage
-    from ..storage.base import BaseFeatureStorage
+    from .pipeline_step_mixin import PipelineStepMixin
+
 
 # Define valid steps for operation
-_valid_steps = [
+_VALID_STEPS: List[str] = [
     "datagrabber",
     "datareader",
     "preprocessing",
@@ -25,7 +26,7 @@ _valid_steps = [
 ]
 
 # Define registry for valid steps
-_registry = {x: {} for x in _valid_steps}
+_REGISTRY: Dict[str, Dict[str, type]] = {x: {} for x in _VALID_STEPS}
 
 
 def register(step: str, name: str, klass: type) -> None:
@@ -42,14 +43,14 @@ def register(step: str, name: str, klass: type) -> None:
 
     """
     # Verify step
-    if step not in _valid_steps:
+    if step not in _VALID_STEPS:
         raise_error(msg=f"Invalid step: {step}", klass=ValueError)
 
     logger.info(f"Registering {name} in {step}")
-    _registry[step][name] = klass
+    _REGISTRY[step][name] = klass
 
 
-def get_step_names(step: str) -> List:
+def get_step_names(step: str) -> List[str]:
     """Get the names of the registered functions for a given step.
 
     Parameters
@@ -64,10 +65,10 @@ def get_step_names(step: str) -> List:
 
     """
     # Verify step
-    if step not in _valid_steps:
+    if step not in _VALID_STEPS:
         raise_error(msg=f"Invalid step: {step}", klass=ValueError)
 
-    return list(_registry[step].keys())
+    return list(_REGISTRY[step].keys())
 
 
 def get_class(step: str, name: str) -> type:
@@ -87,13 +88,13 @@ def get_class(step: str, name: str) -> type:
 
     """
     # Verify step
-    if step not in _valid_steps:
+    if step not in _VALID_STEPS:
         raise_error(msg=f"Invalid step: {step}", klass=ValueError)
     # Verify step name
-    if name not in _registry[step]:
+    if name not in _REGISTRY[step]:
         raise_error(msg=f"Invalid name: {name}", klass=ValueError)
 
-    return _registry[step][name]
+    return _REGISTRY[step][name]
 
 
 def build(

junifer/pipeline/tests/test_registry.py

@@ -10,8 +10,13 @@ from typing import Type
 
 import pytest
 
-from junifer.api.registry import build, get_class, get_step_names, register
 from junifer.datagrabber import PatternDataGrabber
+from junifer.pipeline.registry import (
+    build,
+    get_class,
+    get_step_names,
+    register,
+)
 from junifer.storage import SQLiteFeatureStorage
 
 

junifer/testing/registry.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from ..api.registry import register
+from ..pipeline.registry import register
 from .datagrabbers import (
     OasisVBMTestingDatagrabber,
     SPMAuditoryTestingDatagrabber,

junifer/testing/tests/test_testing_registry.py

@@ -2,14 +2,14 @@
 
 import importlib
 
-from junifer.api.registry import get_step_names
+from junifer.pipeline.registry import get_step_names
 
 
 def test_testing_registry() -> None:
     """Test testing registry."""
     import junifer
 
-    importlib.reload(junifer.api.registry)
+    importlib.reload(junifer.pipeline.registry)
     importlib.reload(junifer)
 
     assert "OasisVBMTestingDatagrabber" not in get_step_names("datagrabber")