junifer 0.0.6.dev213__py3-none-any.whl → 0.0.6.dev227__py3-none-any.whl

junifer/pipeline/marker_collection.py

@@ -5,20 +5,14 @@
 # License: AGPL
 
 from collections import Counter
-from typing import TYPE_CHECKING, Dict, List, Optional
+from typing import Dict, List, Optional
 
 from ..datareader import DefaultDataReader
 from ..pipeline import PipelineStepMixin, WorkDirManager
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error
 
 
-if TYPE_CHECKING:
-    from junifer.datagrabber import BaseDataGrabber
-    from junifer.markers import BaseMarker
-    from junifer.preprocess import BasePreprocessor
-    from junifer.storage import BaseFeatureStorage
-
-
 __all__ = ["MarkerCollection"]
 
 
@@ -45,10 +39,10 @@ class MarkerCollection:
 
     def __init__(
         self,
-        markers: List["BaseMarker"],
+        markers: List[MarkerLike],
         datareader: Optional[PipelineStepMixin] = None,
-        preprocessors: Optional[List["BasePreprocessor"]] = None,
-        storage: Optional["BaseFeatureStorage"] = None,
+        preprocessors: Optional[List[PreprocessorLike]] = None,
+        storage: Optional[StorageLike] = None,
     ):
         # Check that the markers have different names
         marker_names = [m.name for m in markers]
@@ -111,7 +105,7 @@ class MarkerCollection:
 
         return None if self._storage else out
 
-    def validate(self, datagrabber: "BaseDataGrabber") -> None:
+    def validate(self, datagrabber: DataGrabberLike) -> None:
         """Validate the pipeline.
 
         Without doing any computation, check if the marker collection can

junifer/pipeline/pipeline_component_registry.py

@@ -6,18 +6,13 @@
 # License: AGPL
 
 import importlib
-from typing import TYPE_CHECKING, Dict, List, Mapping, Optional, Union
+from typing import Dict, List, Mapping, Optional, Union
 
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error
 from ..utils.singleton import Singleton
 
 
-if TYPE_CHECKING:
-    from ..datagrabber import BaseDataGrabber
-    from ..storage import BaseFeatureStorage
-    from .pipeline_step_mixin import PipelineStepMixin
-
-
 __all__ = ["PipelineComponentRegistry"]
 
 
@@ -241,7 +236,7 @@ class PipelineComponentRegistry(metaclass=Singleton):
         name: str,
         baseclass: type,
         init_params: Optional[Dict] = None,
-    ) -> Union["BaseDataGrabber", "PipelineStepMixin", "BaseFeatureStorage"]:
+    ) -> Union[DataGrabberLike, PreprocessorLike, MarkerLike, StorageLike]:
         """Build an instance of class registered as ``name``.
 
         Parameters

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, Dict, List
 
 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:
@@ -19,7 +24,7 @@ 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]:
             return input
@@ -40,7 +45,7 @@ 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]:
             return input
@@ -65,7 +70,7 @@ 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]:
             return input
@@ -89,7 +94,7 @@ 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"]}
         ]
 
@@ -117,7 +122,7 @@ 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"]}
         ]
 
@@ -141,7 +146,7 @@ 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}
         ]
 
@@ -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,
@@ -196,14 +199,12 @@ 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,
@@ -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,

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/workdir_manager.py

@@ -39,15 +39,20 @@ class WorkDirManager(metaclass=Singleton):
         The path to the element directory.
     root_tempdir : pathlib.Path or None
         The path to the root 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).
 
     """
 
-    def __init__(self, workdir: Optional[Union[str, Path]] = None) -> None:
+    def __init__(
+        self, workdir: Optional[Union[str, Path]] = None, cleanup=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:
@@ -72,6 +77,9 @@ class WorkDirManager(metaclass=Singleton):
 
     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
@@ -171,6 +179,8 @@ class WorkDirManager(metaclass=Singleton):
             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)
 
@@ -182,6 +192,9 @@ class WorkDirManager(metaclass=Singleton):
         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 "
@@ -244,5 +257,7 @@ class WorkDirManager(metaclass=Singleton):
             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/confounds/fmriprep_confound_remover.py

@@ -11,7 +11,6 @@ from typing import (
     Dict,
     List,
     Optional,
-    Set,
     Tuple,
     Union,
 )
@@ -23,6 +22,7 @@ from nilearn._utils.niimg_conversions import check_niimg_4d
 
 from ...api.decorators import register_preprocessor
 from ...data import get_data
+from ...typing import Dependencies
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 
@@ -152,7 +152,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nilearn"}
 
     def __init__(
         self,

junifer/preprocess/smoothing/_afni_smoothing.py

@@ -6,20 +6,18 @@
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Dict,
-    List,
-    Set,
     Union,
 )
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies, ExternalDependencies
 from ...utils import logger, run_ext_cmd
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["AFNISmoothing"]
@@ -32,14 +30,14 @@ class AFNISmoothing:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "afni",
             "commands": ["3dBlurToFWHM"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nibabel"}
 
     def preprocess(
         self,

junifer/preprocess/smoothing/_fsl_smoothing.py

@@ -6,20 +6,17 @@
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Dict,
-    List,
-    Set,
-    Union,
 )
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies, ExternalDependencies
 from ...utils import logger, run_ext_cmd
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["FSLSmoothing"]
@@ -32,14 +29,14 @@ class FSLSmoothing:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "fsl",
             "commands": ["susan"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nibabel"}
 
     def preprocess(
         self,

junifer/preprocess/smoothing/_nilearn_smoothing.py

@@ -7,18 +7,18 @@ from typing import (
     TYPE_CHECKING,
     ClassVar,
     Literal,
-    Set,
     Union,
 )
 
 from nilearn import image as nimg
 from numpy.typing import ArrayLike
 
+from ...typing import Dependencies
 from ...utils import logger
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["NilearnSmoothing"]
@@ -31,7 +31,7 @@ class NilearnSmoothing:
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
     def preprocess(
         self,

junifer/preprocess/smoothing/smoothing.py

@@ -3,9 +3,10 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Type, Union
+from typing import Any, ClassVar, Dict, List, Optional, Tuple, Union
 
 from ...api.decorators import register_preprocessor
+from ...typing import ConditionalDependencies
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 from ._afni_smoothing import AFNISmoothing
@@ -67,7 +68,7 @@ class Smoothing(BasePreprocessor):
 
     """
 
-    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+    _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
         {
             "using": "nilearn",
             "depends_on": NilearnSmoothing,

junifer/preprocess/warping/_ants_warper.py

@@ -7,9 +7,6 @@ from typing import (
     Any,
     ClassVar,
     Dict,
-    List,
-    Set,
-    Union,
 )
 
 import nibabel as nib
@@ -17,6 +14,7 @@ import numpy as np
 
 from ...data import get_template, get_xfm
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies, ExternalDependencies
 from ...utils import logger, run_ext_cmd
 
 
@@ -31,14 +29,14 @@ class ANTsWarper:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "ants",
             "commands": ["ResampleImage", "antsApplyTransforms"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nibabel"}
 
     def preprocess(
         self,

junifer/preprocess/warping/_fsl_warper.py

@@ -7,15 +7,13 @@ from typing import (
     Any,
     ClassVar,
     Dict,
-    List,
-    Set,
-    Union,
 )
 
 import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies, ExternalDependencies
 from ...utils import logger, run_ext_cmd
 
 
@@ -30,14 +28,14 @@ class FSLWarper:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "fsl",
             "commands": ["flirt", "applywarp"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nibabel"}
 
     def preprocess(
         self,

junifer/preprocess/warping/space_warper.py

@@ -3,11 +3,12 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Type, Union
+from typing import Any, ClassVar, Dict, List, Optional, Tuple, Union
 
 from templateflow import api as tflow
 
 from ...api.decorators import register_preprocessor
+from ...typing import ConditionalDependencies
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 from ._ants_warper import ANTsWarper
@@ -46,7 +47,7 @@ class SpaceWarper(BasePreprocessor):
 
     """
 
-    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+    _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
         {
             "using": "fsl",
             "depends_on": FSLWarper,

junifer/preprocess/warping/tests/test_space_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import socket
-from typing import TYPE_CHECKING, Tuple, Type
+from typing import Tuple, Type
 
 import pytest
 from numpy.testing import assert_array_equal, assert_raises
@@ -14,10 +14,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.pipeline.utils import _check_ants, _check_fsl
 from junifer.preprocess import SpaceWarper
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
-
-
-if TYPE_CHECKING:
-    from junifer.datagrabber import BaseDataGrabber
+from junifer.typing import DataGrabberLike
 
 
 @pytest.mark.parametrize(
@@ -99,7 +96,7 @@ def test_SpaceWarper_errors(
     reason="only for juseless",
 )
 def test_SpaceWarper_native(
-    datagrabber: "BaseDataGrabber", element: Tuple[str, ...], using: str
+    datagrabber: DataGrabberLike, element: Tuple[str, ...], using: str
 ) -> None:
     """Test SpaceWarper for native space warping.
 
@@ -162,7 +159,7 @@ def test_SpaceWarper_native(
     _check_ants() is False, reason="requires ANTs to be in PATH"
 )
 def test_SpaceWarper_multi_mni(
-    datagrabber: "BaseDataGrabber",
+    datagrabber: DataGrabberLike,
     element: Tuple[str, ...],
     space: str,
 ) -> None:

junifer/typing/__init__.py

@@ -0,0 +1,9 @@
+"""Type hints for internal and external use."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/typing/__init__.pyi

@@ -0,0 +1,23 @@
+__all__ = [
+    "DataGrabberLike",
+    "PreprocessorLike",
+    "MarkerLike",
+    "StorageLike",
+    "PipelineComponent",
+    "Dependencies",
+    "ConditionalDependencies",
+    "ExternalDependencies",
+    "MarkerInOutMappings",
+]
+
+from ._typing import (
+    DataGrabberLike,
+    PreprocessorLike,
+    MarkerLike,
+    StorageLike,
+    PipelineComponent,
+    Dependencies,
+    ConditionalDependencies,
+    ExternalDependencies,
+    MarkerInOutMappings,
+)