junifer 0.0.6.dev201__tar.gz → 0.0.6.dev213__tar.gz

{junifer-0.0.6.dev201 → junifer-0.0.6.dev213}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev201
+Version: 0.0.6.dev213
 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.dev213/docs/changes/newsfragments/386.bugfix

@@ -0,0 +1 @@
+Use the :class:`junifer.pipeline.WorkDirManager` for temporary directories in the :class:`.DataladDataGrabber` by `Fede Raimondo`_

junifer-0.0.6.dev213/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.dev201 → junifer-0.0.6.dev213}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev201'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev201')
+__version__ = version = '0.0.6.dev213'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev213')

junifer-0.0.6.dev213/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/junifer/datagrabber/datalad_base.py

@@ -7,7 +7,6 @@
 
 import atexit
 import os
-import shutil
 import tempfile
 from pathlib import Path
 from typing import Dict, Optional, Tuple, Union
@@ -17,6 +16,7 @@ import datalad.api as dl
 from datalad.support.exceptions import IncompleteResultsError
 from datalad.support.gitrepo import GitRepo
 
+from ..pipeline import WorkDirManager
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseDataGrabber
 
@@ -78,7 +78,8 @@ class DataladDataGrabber(BaseDataGrabber):
         if datadir is None:
             logger.info("`datadir` is None, creating a temporary directory")
             # Create temporary directory
-            tmpdir = Path(tempfile.mkdtemp())
+            tmpdir = WorkDirManager().get_tempdir(prefix="datalad")
+            self._tmpdir = tmpdir
             datadir = tmpdir / "datadir"
             datadir.mkdir(parents=True, exist_ok=False)
             logger.info(f"`datadir` set to {datadir}")
@@ -104,7 +105,6 @@ class DataladDataGrabber(BaseDataGrabber):
                 "Datalad locks set to "
                 f"{datalad.cfg.get('datalad.locations.locks')}"
             )
-            self._tmpdir = tmpdir
             atexit.register(self._rmtmpdir)
         # TODO: uri can be converted to a positional argument
         if uri is None:
@@ -129,7 +129,7 @@ class DataladDataGrabber(BaseDataGrabber):
         """Remove temporary directory if it exists."""
         if self._tmpdir.exists():
             logger.debug("Removing temporary directory")
-            shutil.rmtree(self._tmpdir)
+            WorkDirManager().delete_tempdir(self._tmpdir)
 
     @property
     def datadir(self) -> Path:

{junifer-0.0.6.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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.dev201 → junifer-0.0.6.dev213}/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

{junifer-0.0.6.dev201/junifer/pipeline → junifer-0.0.6.dev213/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.dev201 → junifer-0.0.6.dev213}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev201
+Version: 0.0.6.dev213
 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.dev201 → junifer-0.0.6.dev213}/junifer.egg-info/SOURCES.txt

@@ -84,8 +84,10 @@ docs/changes/newsfragments/380.misc
 docs/changes/newsfragments/382.misc
 docs/changes/newsfragments/383.misc
 docs/changes/newsfragments/384.misc
+docs/changes/newsfragments/386.bugfix
 docs/changes/newsfragments/387.change
 docs/changes/newsfragments/387.feature
+docs/changes/newsfragments/391.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst
@@ -124,6 +126,7 @@ 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
@@ -394,7 +397,6 @@ 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
@@ -461,6 +463,7 @@ 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