junifer 0.0.6.dev205__tar.gz → 0.0.6.dev219__tar.gz

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev205
+Version: 0.0.6.dev219
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.6.dev219/docs/changes/newsfragments/389.enh

@@ -0,0 +1 @@
+Add a ``cleanup`` parameter to the :class:`junifer.pipeline.WorkDirManager`, which allows to disable cleaning up temporary directories by `Fede Raimondo`_

junifer-0.0.6.dev219/docs/changes/newsfragments/391.misc

@@ -0,0 +1 @@
+Refactor ``Singleton`` class to use a metaclass instead of a class decorator by `Fede Raimondo`_

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev205'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev205')
+__version__ = version = '0.0.6.dev219'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev219')

junifer-0.0.6.dev219/junifer/conftest.py

@@ -0,0 +1,25 @@
+"""Provide conftest for pytest."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+# License: AGPL
+
+import pytest
+
+from junifer.utils.singleton import Singleton
+
+
+@pytest.fixture(autouse=True)
+def reset_singletons() -> None:
+    """Reset all singletons."""
+    to_clean = ["WorkDirManager"]
+    to_remove = [
+        v for k, v in Singleton.instances.items() if k.__name__ in to_clean
+    ]
+    Singleton.instances = {
+        k: v
+        for k, v in Singleton.instances.items()
+        if k.__name__ not in to_clean
+    }
+    # Force deleting the singletons
+    for elem in to_remove:
+        del elem

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/data/coordinates/_coordinates.py

@@ -11,8 +11,8 @@ import numpy as np
 import pandas as pd
 from numpy.typing import ArrayLike
 
-from ...pipeline.singleton import singleton
 from ...utils import logger, raise_error
+from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
 from ._fsl_coordinates_warper import FSLCoordinatesWarper
@@ -21,8 +21,7 @@ from ._fsl_coordinates_warper import FSLCoordinatesWarper
 __all__ = ["CoordinatesRegistry"]
 
 
-@singleton
-class CoordinatesRegistry(BasePipelineDataRegistry):
+class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
     """Class for coordinates data registry.
 
     This class is a singleton and is used for managing available coordinates

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/data/masks/_masks.py

@@ -25,8 +25,8 @@ from nilearn.masking import (
     intersect_masks,
 )
 
-from ...pipeline.singleton import singleton
 from ...utils import logger, raise_error
+from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
 from ..utils import closest_resolution
@@ -126,8 +126,7 @@ def compute_brain_mask(
     return new_img_like(target_img, mask)  # type: ignore
 
 
-@singleton
-class MaskRegistry(BasePipelineDataRegistry):
+class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
     """Class for mask data registry.
 
     This class is a singleton and is used for managing available mask

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/data/parcellations/_parcellations.py

@@ -20,8 +20,8 @@ import numpy as np
 import pandas as pd
 from nilearn import datasets, image
 
-from ...pipeline.singleton import singleton
 from ...utils import logger, raise_error, warn_with_log
+from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import closest_resolution
 from ._ants_parcellation_warper import ANTsParcellationWarper
@@ -38,8 +38,7 @@ __all__ = [
 ]
 
 
-@singleton
-class ParcellationRegistry(BasePipelineDataRegistry):
+class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
     """Class for parcellation data registry.
 
     This class is a singleton and is used for managing available parcellation

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/data/pipeline_data_registry_base.py

@@ -7,12 +7,13 @@ from abc import ABC, abstractmethod
 from typing import Any, List, Mapping
 
 from ..utils import raise_error
+from ..utils.singleton import ABCSingleton
 
 
 __all__ = ["BasePipelineDataRegistry"]
 
 
-class BasePipelineDataRegistry(ABC):
+class BasePipelineDataRegistry(ABC, metaclass=ABCSingleton):
     """Abstract base class for pipeline data registry.
 
     For every interface that is required, one needs to provide a concrete

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/datagrabber/hcp1200/tests/test_hcp1200.py

@@ -3,6 +3,9 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import shutil
+import tempfile
+from pathlib import Path
 from typing import Iterable, Optional
 
 import pytest
@@ -17,7 +20,8 @@ URI = "https://gin.g-node.org/juaml/datalad-example-hcp1200"
 @pytest.fixture(scope="module")
 def hcpdg() -> Iterable[DataladHCP1200]:
     """Return a HCP1200 DataGrabber."""
-    dg = DataladHCP1200()
+    tmpdir = Path(tempfile.gettempdir())
+    dg = DataladHCP1200(datadir=tmpdir / "datadir")
     # Set URI to Gin
     dg.uri = URI
     # Set correct root directory
@@ -26,6 +30,7 @@ def hcpdg() -> Iterable[DataladHCP1200]:
         for t_elem in dg.get_elements():
             dg[t_elem]
         yield dg
+    shutil.rmtree(tmpdir / "datadir", ignore_errors=True)
 
 
 @pytest.mark.parametrize(

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/markers/falff/_afni_falff.py

@@ -18,8 +18,8 @@ from typing import (
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...pipeline.singleton import singleton
 from ...utils import logger, run_ext_cmd
+from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
@@ -29,8 +29,7 @@ if TYPE_CHECKING:
 __all__ = ["AFNIALFF"]
 
 
-@singleton
-class AFNIALFF:
+class AFNIALFF(metaclass=Singleton):
     """Class for computing ALFF using AFNI.
 
     This class uses AFNI's 3dRSFC to compute ALFF. It's designed as a singleton

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/markers/falff/_junifer_falff.py

@@ -19,8 +19,8 @@ import scipy as sp
 from nilearn import image as nimg
 
 from ...pipeline import WorkDirManager
-from ...pipeline.singleton import singleton
 from ...utils import logger
+from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
@@ -30,8 +30,7 @@ if TYPE_CHECKING:
 __all__ = ["JuniferALFF"]
 
 
-@singleton
-class JuniferALFF:
+class JuniferALFF(metaclass=Singleton):
     """Class for computing ALFF using junifer.
 
     It's designed as a singleton with caching for efficient computation.

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/markers/reho/_afni_reho.py

@@ -18,8 +18,8 @@ from typing import (
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...pipeline.singleton import singleton
 from ...utils import logger, run_ext_cmd
+from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
@@ -29,8 +29,7 @@ if TYPE_CHECKING:
 __all__ = ["AFNIReHo"]
 
 
-@singleton
-class AFNIReHo:
+class AFNIReHo(metaclass=Singleton):
     """Class for computing ReHo using AFNI.
 
     This class uses AFNI's 3dReHo to compute ReHo. It's designed as a singleton

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/markers/reho/_junifer_reho.py

@@ -20,8 +20,8 @@ from nilearn import image as nimg
 from nilearn import masking as nmask
 
 from ...pipeline import WorkDirManager
-from ...pipeline.singleton import singleton
 from ...utils import logger, raise_error
+from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
@@ -31,8 +31,7 @@ if TYPE_CHECKING:
 __all__ = ["JuniferReHo"]
 
 
-@singleton
-class JuniferReHo:
+class JuniferReHo(metaclass=Singleton):
     """Class for computing ReHo using junifer.
 
     It's designed as a singleton with caching for efficient computation.

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/pipeline/pipeline_component_registry.py

@@ -9,7 +9,7 @@ import importlib
 from typing import TYPE_CHECKING, Dict, List, Mapping, Optional, Union
 
 from ..utils import logger, raise_error
-from .singleton import singleton
+from ..utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
@@ -21,8 +21,7 @@ if TYPE_CHECKING:
 __all__ = ["PipelineComponentRegistry"]
 
 
-@singleton
-class PipelineComponentRegistry:
+class PipelineComponentRegistry(metaclass=Singleton):
     """Class for pipeline component registry.
 
     This class is a singleton and is used for managing pipeline components.

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer/pipeline/tests/test_workdir_manager.py

@@ -102,3 +102,45 @@ 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-0.0.6.dev205 → junifer-0.0.6.dev219}/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
@@ -40,15 +39,20 @@ class WorkDirManager:
         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:
@@ -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-0.0.6.dev205/junifer/pipeline → junifer-0.0.6.dev219/junifer/utils}/singleton.py

@@ -1,15 +1,17 @@
 """Provide a singleton class to be used by pipeline components."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+#          Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, Type
+from abc import ABCMeta
+from typing import Any, ClassVar, Dict, Type
 
 
-__all__ = ["singleton"]
+__all__ = ["Singleton", "ABCSingleton"]
 
 
-def singleton(cls: Type) -> Type:
+class Singleton(type):
     """Make a class singleton.
 
     Parameters
@@ -17,15 +19,11 @@ def singleton(cls: Type) -> Type:
     cls : class
         The class to designate as singleton.
 
-    Returns
-    -------
-    class
-        The only instance of the class.
-
     """
-    instances: Dict = {}
 
-    def get_instance(*args: Any, **kwargs: Any) -> Type:
+    instances: ClassVar[Dict] = {}
+
+    def __call__(cls, *args: Any, **kwargs: Any) -> Type:
         """Get the only instance for a class.
 
         Parameters
@@ -41,8 +39,15 @@ def singleton(cls: Type) -> Type:
             The only instance of the class.
 
         """
-        if cls not in instances:
-            instances[cls] = cls(*args, **kwargs)
-        return instances[cls]
+        if cls not in cls.instances:
+            cls.instances[cls] = super(Singleton, cls).__call__(  # noqa: UP008
+                *args, **kwargs
+            )
+
+        return cls.instances[cls]
+
+
+class ABCSingleton(ABCMeta, Singleton):
+    """Make an abstract class a singleton."""
 
-    return get_instance
+    pass

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev205
+Version: 0.0.6.dev219
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.6.dev205 → junifer-0.0.6.dev219}/junifer.egg-info/SOURCES.txt

@@ -87,6 +87,8 @@ docs/changes/newsfragments/384.misc
 docs/changes/newsfragments/386.bugfix
 docs/changes/newsfragments/387.change
 docs/changes/newsfragments/387.feature
+docs/changes/newsfragments/389.enh
+docs/changes/newsfragments/391.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst
@@ -125,6 +127,7 @@ examples/yamls/ukb_gmd_mean.yaml
 junifer/__init__.py
 junifer/__init__.pyi
 junifer/_version.py
+junifer/conftest.py
 junifer/py.typed
 junifer/stats.py
 junifer.egg-info/PKG-INFO
@@ -395,7 +398,6 @@ junifer/pipeline/marker_collection.py
 junifer/pipeline/pipeline_component_registry.py
 junifer/pipeline/pipeline_step_mixin.py
 junifer/pipeline/py.typed
-junifer/pipeline/singleton.py
 junifer/pipeline/update_meta_mixin.py
 junifer/pipeline/utils.py
 junifer/pipeline/workdir_manager.py
@@ -462,6 +464,7 @@ junifer/utils/fs.py
 junifer/utils/helpers.py
 junifer/utils/logging.py
 junifer/utils/py.typed
+junifer/utils/singleton.py
 junifer/utils/tests/test_fs.py
 junifer/utils/tests/test_helpers.py
 junifer/utils/tests/test_logging.py