junifer 0.0.6.dev51__tar.gz → 0.0.6.dev91__tar.gz

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev51
+Version: 0.0.6.dev91
 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>
@@ -42,6 +42,7 @@ Requires-Dist: httpx[http2]==0.26.0
 Requires-Dist: tqdm==4.66.1
 Requires-Dist: templateflow>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0
+Requires-Dist: lazy_loader==0.4
 Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all

junifer-0.0.6.dev91/docs/changes/newsfragments/355.misc

@@ -0,0 +1 @@
+Adopt lazy-import mechanism for the package by `Synchon Mandal`_

junifer-0.0.6.dev91/docs/changes/newsfragments/369.bugfix

@@ -0,0 +1 @@
+Correct listing for :class:`.fMRIPrepConfoundRemover` in ``junifer.pipeline.registry`` by `Synchon Mandal`_

junifer-0.0.6.dev91/junifer/__init__.py

@@ -0,0 +1,10 @@
+"""Provide imports for junifer package."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/__init__.py → junifer-0.0.6.dev91/junifer/__init__.pyi

@@ -1,12 +1,22 @@
-"""Provide imports for junifer package."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = [
+    "api",
+    "configs",
+    "data",
+    "datagrabber",
+    "datareader",
+    "markers",
+    "pipeline",
+    "preprocess",
+    "stats",
+    "storage",
+    "utils",
+    "external",
+    "onthefly",
+    "__version__",
+]
 
 from . import (
     api,
-    cli,
     configs,
     data,
     datagrabber,
@@ -21,21 +31,3 @@ from . import (
     onthefly,
 )
 from ._version import __version__
-
-
-__all__ = [
-    "api",
-    "cli",
-    "configs",
-    "data",
-    "datagrabber",
-    "datareader",
-    "markers",
-    "pipeline",
-    "preprocess",
-    "stats",
-    "storage",
-    "utils",
-    "external",
-    "onthefly",
-]

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev51'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev51')
+__version__ = version = '0.0.6.dev91'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev91')

junifer-0.0.6.dev91/junifer/api/__init__.py

@@ -0,0 +1,10 @@
+"""Public API components."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/api/__init__.py → junifer-0.0.6.dev91/junifer/api/__init__.pyi

@@ -1,11 +1,4 @@
-"""Public API components."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = ["decorators", "collect", "queue", "run", "reset", "list_elements"]
 
 from . import decorators
 from .functions import collect, list_elements, reset, run, queue
-
-
-__all__ = ["decorators", "collect", "queue", "run", "reset", "list_elements"]

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/api/functions.py

@@ -14,8 +14,7 @@ from typing import Dict, List, Optional, Tuple, Union
 from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from ..datagrabber.base import BaseDataGrabber
 from ..markers.base import BaseMarker
-from ..markers.collection import MarkerCollection
-from ..pipeline import WorkDirManager
+from ..pipeline import MarkerCollection, WorkDirManager
 from ..pipeline.registry import build
 from ..preprocess.base import BasePreprocessor
 from ..storage.base import BaseFeatureStorage

junifer-0.0.6.dev91/junifer/api/queue_context/__init__.py

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

junifer-0.0.6.dev51/junifer/api/queue_context/__init__.py → junifer-0.0.6.dev91/junifer/api/queue_context/__init__.pyi

@@ -1,11 +1,5 @@
-"""Context adapters for queueing."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = ["QueueContextAdapter", "HTCondorAdapter", "GnuParallelLocalAdapter"]
 
 from .queue_context_adapter import QueueContextAdapter
 from .htcondor_adapter import HTCondorAdapter
 from .gnu_parallel_local_adapter import GnuParallelLocalAdapter
-
-
-__all__ = ["QueueContextAdapter", "HTCondorAdapter", "GnuParallelLocalAdapter"]

junifer-0.0.6.dev91/junifer/cli/__init__.py

@@ -0,0 +1,9 @@
+"""Junifer CLI components."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev91/junifer/cli/__init__.pyi

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

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/cli/cli.py

@@ -28,6 +28,23 @@ from .utils import (
 )
 
 
+__all__ = [
+    "cli",
+    "run",
+    "collect",
+    "queue",
+    "wtf",
+    "selftest",
+    "reset",
+    "list_elements",
+    "setup",
+    "afni_docker",
+    "fsl_docker",
+    "ants_docker",
+    "freesurfer_docker",
+]
+
+
 def _validate_verbose(
     ctx: click.Context, param: str, value: str
 ) -> Union[str, int]:

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/cli/tests/test_cli_utils.py

@@ -47,6 +47,7 @@ def test_get_dependency_information_short() -> None:
         "tqdm",
         "templateflow",
         "lapy",
+        "lazy_loader",
         "looseversion",
     ]
 
@@ -76,6 +77,7 @@ def test_get_dependency_information_long() -> None:
         "tqdm",
         "templateflow",
         "lapy",
+        "lazy_loader",
     ]
     for key in dependency_list:
         assert key in dependency_information_keys

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/configs/juseless/__init__.py

@@ -3,7 +3,7 @@
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-from . import datagrabbers
+import lazy_loader as lazy
 
 
-__all__ = ["datagrabbers"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev91/junifer/configs/juseless/__init__.pyi

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

junifer-0.0.6.dev91/junifer/configs/juseless/datagrabbers/__init__.py

@@ -0,0 +1,11 @@
+"""Custom DataGrabbers for FZJ INM-7's beloved juseless."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/configs/juseless/datagrabbers/__init__.py → junifer-0.0.6.dev91/junifer/configs/juseless/datagrabbers/__init__.pyi

@@ -1,17 +1,3 @@
-"""Custom DataGrabbers for FZJ INM-7's beloved juseless."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-from .aomic_id1000_vbm import JuselessDataladAOMICID1000VBM
-from .camcan_vbm import JuselessDataladCamCANVBM
-from .ixi_vbm import JuselessDataladIXIVBM
-from .ucla import JuselessUCLA
-from .ukb_vbm import JuselessDataladUKBVBM
-
-
 __all__ = [
     "JuselessDataladAOMICID1000VBM",
     "JuselessDataladCamCANVBM",
@@ -19,3 +5,9 @@ __all__ = [
     "JuselessUCLA",
     "JuselessDataladUKBVBM",
 ]
+
+from .aomic_id1000_vbm import JuselessDataladAOMICID1000VBM
+from .camcan_vbm import JuselessDataladCamCANVBM
+from .ixi_vbm import JuselessDataladIXIVBM
+from .ucla import JuselessUCLA
+from .ukb_vbm import JuselessDataladUKBVBM

junifer-0.0.6.dev91/junifer/data/__init__.py

@@ -0,0 +1,10 @@
+"""Parcellations, coordinates and masks."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/data/__init__.py → junifer-0.0.6.dev91/junifer/data/__init__.pyi

@@ -1,8 +1,21 @@
-"""Parcellations, coordinates and masks."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = [
+    "list_coordinates",
+    "load_coordinates",
+    "register_coordinates",
+    "get_coordinates",
+    "list_parcellations",
+    "load_parcellation",
+    "register_parcellation",
+    "merge_parcellations",
+    "get_parcellation",
+    "list_masks",
+    "load_mask",
+    "register_mask",
+    "get_mask",
+    "get_template",
+    "get_xfm",
+    "utils",
+]
 
 from .coordinates import (
     list_coordinates,
@@ -28,23 +41,3 @@ from .masks import (
 from .template_spaces import get_template, get_xfm
 
 from . import utils
-
-
-__all__ = [
-    "list_coordinates",
-    "load_coordinates",
-    "register_coordinates",
-    "get_coordinates",
-    "list_parcellations",
-    "load_parcellation",
-    "register_parcellation",
-    "merge_parcellations",
-    "get_parcellation",
-    "list_masks",
-    "load_mask",
-    "register_mask",
-    "get_mask",
-    "get_template",
-    "get_xfm",
-    "utils",
-]

junifer-0.0.6.dev91/junifer/datagrabber/__init__.py

@@ -0,0 +1,11 @@
+"""DataGrabbers for datasets' data description."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/datagrabber/__init__.py → junifer-0.0.6.dev91/junifer/datagrabber/__init__.pyi

@@ -1,24 +1,3 @@
-"""DataGrabbers for datasets' data description."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-
-# These 4 need to be in this order, otherwise it is a circular import
-from .base import BaseDataGrabber
-from .datalad_base import DataladDataGrabber
-from .pattern import PatternDataGrabber
-from .pattern_datalad import PatternDataladDataGrabber
-
-from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
-from .hcp1200 import HCP1200, DataladHCP1200
-from .multiple import MultipleDataGrabber
-from .dmcc13_benchmark import DMCC13Benchmark
-
-from .pattern_validation_mixin import PatternValidationMixin
-
 __all__ = [
     "BaseDataGrabber",
     "DataladDataGrabber",
@@ -33,3 +12,16 @@ __all__ = [
     "DMCC13Benchmark",
     "PatternValidationMixin",
 ]
+
+# These 4 need to be in this order, otherwise it is a circular import
+from .base import BaseDataGrabber
+from .datalad_base import DataladDataGrabber
+from .pattern import PatternDataGrabber
+from .pattern_datalad import PatternDataladDataGrabber
+
+from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
+from .hcp1200 import HCP1200, DataladHCP1200
+from .multiple import MultipleDataGrabber
+from .dmcc13_benchmark import DMCC13Benchmark
+
+from .pattern_validation_mixin import PatternValidationMixin

junifer-0.0.6.dev91/junifer/datagrabber/aomic/__init__.py

@@ -0,0 +1,10 @@
+"""Provide imports for aomic sub-package."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/datagrabber/aomic/__init__.py → junifer-0.0.6.dev91/junifer/datagrabber/aomic/__init__.pyi

@@ -1,12 +1,5 @@
-"""Provide imports for aomic sub-package."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-# License: AGPL
+__all__ = ["DataladAOMICID1000", "DataladAOMICPIOP1", "DataladAOMICPIOP2"]
 
 from .id1000 import DataladAOMICID1000
 from .piop1 import DataladAOMICPIOP1
 from .piop2 import DataladAOMICPIOP2
-
-
-__all__ = ["DataladAOMICID1000", "DataladAOMICPIOP1", "DataladAOMICPIOP2"]

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/datagrabber/hcp1200/__init__.py

@@ -3,8 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .hcp1200 import HCP1200
-from .datalad_hcp1200 import DataladHCP1200
+import lazy_loader as lazy
 
 
-__all__ = ["HCP1200", "DataladHCP1200"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev91/junifer/datagrabber/hcp1200/__init__.pyi

@@ -0,0 +1,4 @@
+__all__ = ["HCP1200", "DataladHCP1200"]
+
+from .hcp1200 import HCP1200
+from .datalad_hcp1200 import DataladHCP1200

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/datareader/__init__.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .default import DefaultDataReader
+import lazy_loader as lazy
 
 
-__all__ = ["DefaultDataReader"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev91/junifer/datareader/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["DefaultDataReader"]
+
+from .default import DefaultDataReader

junifer-0.0.6.dev91/junifer/external/nilearn/__init__.py

@@ -0,0 +1,9 @@
+"""Custom objects adapted from nilearn."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/external/nilearn/__init__.py → junifer-0.0.6.dev91/junifer/external/nilearn/__init__.pyi

@@ -1,10 +1,4 @@
-"""Custom objects adapted from nilearn."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = ["JuniferNiftiSpheresMasker", "JuniferConnectivityMeasure"]
 
 from .junifer_nifti_spheres_masker import JuniferNiftiSpheresMasker
 from .junifer_connectivity_measure import JuniferConnectivityMeasure
-
-
-__all__ = ["JuniferNiftiSpheresMasker", "JuniferConnectivityMeasure"]

junifer-0.0.6.dev91/junifer/markers/__init__.py

@@ -0,0 +1,11 @@
+"""Markers for feature extraction."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev51/junifer/markers/__init__.py → junifer-0.0.6.dev91/junifer/markers/__init__.pyi

@@ -1,12 +1,23 @@
-"""Markers for feature extraction."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = [
+    "BaseMarker",
+    "RSSETSMarker",
+    "ParcelAggregation",
+    "SphereAggregation",
+    "FunctionalConnectivityParcels",
+    "FunctionalConnectivitySpheres",
+    "CrossParcellationFC",
+    "EdgeCentricFCParcels",
+    "EdgeCentricFCSpheres",
+    "ReHoParcels",
+    "ReHoSpheres",
+    "ALFFParcels",
+    "ALFFSpheres",
+    "TemporalSNRParcels",
+    "TemporalSNRSpheres",
+    "BrainPrint",
+]
 
 from .base import BaseMarker
-from .collection import MarkerCollection
 from .ets_rss import RSSETSMarker
 from .parcel_aggregation import ParcelAggregation
 from .sphere_aggregation import SphereAggregation
@@ -24,24 +35,3 @@ from .temporal_snr import (
     TemporalSNRSpheres,
 )
 from .brainprint import BrainPrint
-
-
-__all__ = [
-    "BaseMarker",
-    "MarkerCollection",
-    "RSSETSMarker",
-    "ParcelAggregation",
-    "SphereAggregation",
-    "FunctionalConnectivityParcels",
-    "FunctionalConnectivitySpheres",
-    "CrossParcellationFC",
-    "EdgeCentricFCParcels",
-    "EdgeCentricFCSpheres",
-    "ReHoParcels",
-    "ReHoSpheres",
-    "ALFFParcels",
-    "ALFFSpheres",
-    "TemporalSNRParcels",
-    "TemporalSNRSpheres",
-    "BrainPrint",
-]

junifer-0.0.6.dev91/junifer/markers/complexity/__init__.py

@@ -0,0 +1,21 @@
+"""Provide imports for complexity sub-package."""
+
+# Authors: Amir Omidvarnia <a.omidvarnia@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from importlib.util import find_spec
+
+from ..utils import raise_error
+
+
+# Check if neurokit2 is found
+if find_spec("neurokit2") is None:
+    raise_error(
+        msg="Could not find `neurokit2`, make sure the package is installed.",
+        klass=ImportError,
+    )
+else:
+    import lazy_loader as lazy
+
+    __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev91/junifer/markers/complexity/__init__.pyi

@@ -0,0 +1,17 @@
+__all__ = [
+    "HurstExponent",
+    "RangeEntropy",
+    "RangeEntropyAUC",
+    "PermEntropy",
+    "WeightedPermEntropy",
+    "SampleEntropy",
+    "MultiscaleEntropyAUC",
+]
+
+from .hurst_exponent import HurstExponent
+from .range_entropy import RangeEntropy
+from .range_entropy_auc import RangeEntropyAUC
+from .perm_entropy import PermEntropy
+from .weighted_perm_entropy import WeightedPermEntropy
+from .sample_entropy import SampleEntropy
+from .multiscale_entropy_auc import MultiscaleEntropyAUC

{junifer-0.0.6.dev51 → junifer-0.0.6.dev91}/junifer/markers/falff/__init__.py

@@ -3,8 +3,7 @@
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-from .falff_parcels import ALFFParcels
-from .falff_spheres import ALFFSpheres
+import lazy_loader as lazy
 
 
-__all__ = ["ALFFParcels", "ALFFSpheres"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev91/junifer/markers/falff/__init__.pyi

@@ -0,0 +1,4 @@
+__all__ = ["ALFFParcels", "ALFFSpheres"]
+
+from .falff_parcels import ALFFParcels
+from .falff_spheres import ALFFSpheres

junifer-0.0.6.dev91/junifer/markers/functional_connectivity/__init__.py

@@ -0,0 +1,9 @@
+"""Provide imports for functional connectivity sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)