junifer 0.0.5.dev242__py3-none-any.whl → 0.0.6__py3-none-any.whl

junifer/pipeline/workdir_manager.py

@@ -10,14 +10,13 @@ from pathlib import Path
 from typing import Optional, Union
 
 from ..utils import logger
-from .singleton import singleton
+from ..utils.singleton import Singleton
 
 
 __all__ = ["WorkDirManager"]
 
 
-@singleton
-class WorkDirManager:
+class WorkDirManager(metaclass=Singleton):
     """Class for working directory manager.
 
     This class is a singleton and is used for managing temporary and working
@@ -31,6 +30,9 @@ class WorkDirManager:
     workdir : str or pathlib.Path, optional
         The path to the super-directory. If None, "TMPDIR/junifer" is used
         where TMPDIR is the platform-dependent temporary directory.
+    cleanup : bool, optional
+        If False, the directories are not cleaned up after the object is
+        destroyed. This is useful for debugging purposes (default True).
 
     Attributes
     ----------
@@ -43,12 +45,14 @@ class WorkDirManager:
 
     """
 
-    def __init__(self, workdir: Optional[Union[str, Path]] = None) -> None:
+    def __init__(
+        self, workdir: Optional[Union[str, Path]] = None, cleanup: bool = True
+    ) -> None:
         """Initialize the class."""
         self._workdir = Path(workdir) if isinstance(workdir, str) else workdir
         self._elementdir = None
         self._root_tempdir = None
-
+        self._cleanup_dirs = cleanup
         self._set_default_workdir()
 
     def _set_default_workdir(self) -> None:
@@ -73,6 +77,9 @@ class WorkDirManager:
 
     def _cleanup(self) -> None:
         """Clean up the element and temporary directories."""
+        if self._cleanup_dirs is False:
+            self._root_tempdir = None
+            return
         # Remove element directory
         self.cleanup_elementdir()
         # Remove root temporary directory
@@ -172,6 +179,8 @@ class WorkDirManager:
             The temporary directory path to be deleted.
 
         """
+        if self._cleanup_dirs is False:
+            return
         logger.debug(f"Deleting element temporary directory at {tempdir}")
         shutil.rmtree(tempdir, ignore_errors=True)
 
@@ -183,6 +192,9 @@ class WorkDirManager:
         can lead to required intermediate files not being found.
 
         """
+        if self._cleanup_dirs is False:
+            self._elementdir = None
+            return
         if self._elementdir is not None:
             logger.debug(
                 "Deleting element directory at "
@@ -245,5 +257,7 @@ class WorkDirManager:
             The temporary directory path to be deleted.
 
         """
+        if self._cleanup_dirs is False:
+            return
         logger.debug(f"Deleting temporary directory at {tempdir}")
         shutil.rmtree(tempdir, ignore_errors=True)

junifer/preprocess/__init__.py

@@ -5,15 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .base import BasePreprocessor
-from .confounds import fMRIPrepConfoundRemover
-from .warping import SpaceWarper
-from .smoothing import Smoothing
+import lazy_loader as lazy
 
 
-__all__ = [
-    "BasePreprocessor",
-    "fMRIPrepConfoundRemover",
-    "SpaceWarper",
-    "Smoothing",
-]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/preprocess/__init__.pyi

@@ -0,0 +1,11 @@
+__all__ = [
+    "BasePreprocessor",
+    "fMRIPrepConfoundRemover",
+    "SpaceWarper",
+    "Smoothing",
+]
+
+from .base import BasePreprocessor
+from .confounds import fMRIPrepConfoundRemover
+from .warping import SpaceWarper
+from .smoothing import Smoothing

junifer/preprocess/base.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any, Optional, Union
 
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils import logger, raise_error
@@ -38,8 +38,8 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
 
     def __init__(
         self,
-        on: Optional[Union[List[str], str]] = None,
-        required_data_types: Optional[Union[List[str], str]] = None,
+        on: Optional[Union[list[str], str]] = None,
+        required_data_types: Optional[Union[list[str], str]] = None,
     ) -> None:
         """Initialize the class."""
         # Use all data types if not provided
@@ -60,7 +60,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
         else:
             self._required_data_types = required_data_types
 
-    def validate_input(self, input: List[str]) -> List[str]:
+    def validate_input(self, input: list[str]) -> list[str]:
         """Validate input.
 
         Parameters
@@ -90,7 +90,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
         return [x for x in self._on if x in input]
 
     @abstractmethod
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid data types for input.
 
         Returns
@@ -128,9 +128,9 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
     @abstractmethod
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[dict[str, Any], Optional[dict[str, dict[str, Any]]]]:
         """Preprocess.
 
         Parameters
@@ -160,8 +160,8 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
 
     def _fit_transform(
         self,
-        input: Dict[str, Dict],
-    ) -> Dict:
+        input: dict[str, dict],
+    ) -> dict:
         """Fit and transform.
 
         Parameters

junifer/preprocess/confounds/__init__.py

@@ -4,7 +4,7 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from .fmriprep_confound_remover import fMRIPrepConfoundRemover
+import lazy_loader as lazy
 
 
-__all__ = ["fMRIPrepConfoundRemover"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/preprocess/confounds/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["fMRIPrepConfoundRemover"]
+
+from .fmriprep_confound_remover import fMRIPrepConfoundRemover