junifer 0.0.5.dev131__py3-none-any.whl → 0.0.5.dev145__py3-none-any.whl

junifer/markers/complexity/range_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["RangeEntropy"]
+
+
 @register_marker
 class RangeEntropy(ComplexityBase):
     """Class for range entropy of a time series.

junifer/markers/complexity/range_entropy_auc.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["RangeEntropyAUC"]
+
+
 @register_marker
 class RangeEntropyAUC(ComplexityBase):
     """Class for AUC of range entropy values of a time series over r = 0 to 1.

junifer/markers/complexity/sample_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["SampleEntropy"]
+
+
 @register_marker
 class SampleEntropy(ComplexityBase):
     """Class for sample entropy of a time series.

junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import HurstExponent  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test HurstExponent compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -45,6 +49,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test HurstExponent store().
 

junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import MultiscaleEntropyAUC  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test MultiscaleEntropyAUC compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test MultiscaleEntropyAUC store().
 

junifer/markers/complexity/tests/test_perm_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import PermEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test PermEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test PermEntropy store().
 

junifer/markers/complexity/tests/test_range_entropy.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import RangeEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test RangeEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -45,6 +49,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test RangeEntropy store().
 

junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import RangeEntropyAUC  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test RangeEntropyAUC compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -45,6 +49,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test RangeEntropyAUC store().
 

junifer/markers/complexity/tests/test_sample_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import SampleEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test SampleEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test SampleEntropy store().
 

junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import WeightedPermEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test WeightedPermEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test WeightedPermEntropy store().
 

junifer/markers/complexity/weighted_perm_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["WeightedPermEntropy"]
+
+
 @register_marker
 class WeightedPermEntropy(ComplexityBase):
     """Class for weighted permutation entropy of a time series.

junifer/markers/ets_rss.py

@@ -17,6 +17,9 @@ from .parcel_aggregation import ParcelAggregation
 from .utils import _ets
 
 
+__all__ = ["RSSETSMarker"]
+
+
 @register_marker
 class RSSETSMarker(BaseMarker):
     """Class for root sum of squares of edgewise timeseries.

junifer/markers/falff/__init__.py

@@ -5,3 +5,6 @@
 
 from .falff_parcels import ALFFParcels
 from .falff_spheres import ALFFSpheres
+
+
+__all__ = ["ALFFParcels", "ALFFSpheres"]

junifer/markers/falff/_afni_falff.py

@@ -26,6 +26,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["AFNIALFF"]
+
+
 @singleton
 class AFNIALFF:
     """Class for computing ALFF using AFNI.

junifer/markers/falff/_junifer_falff.py

@@ -27,6 +27,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["JuniferALFF"]
+
+
 @singleton
 class JuniferALFF:
     """Class for computing ALFF using junifer.

junifer/markers/falff/falff_base.py

@@ -29,6 +29,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["ALFFBase"]
+
+
 class ALFFBase(BaseMarker):
     """Base class for (fractional) Amplitude Low Frequency Fluctuation.
 

junifer/markers/falff/falff_parcels.py

@@ -14,6 +14,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .falff_base import ALFFBase
 
 
+__all__ = ["ALFFParcels"]
+
+
 @register_marker
 class ALFFParcels(ALFFBase):
     """Class for ALFF / fALFF on parcels.

junifer/markers/falff/falff_spheres.py

@@ -14,6 +14,9 @@ from ..sphere_aggregation import SphereAggregation
 from .falff_base import ALFFBase
 
 
+__all__ = ["ALFFSpheres"]
+
+
 @register_marker
 class ALFFSpheres(ALFFBase):
     """Class for computing ALFF / fALFF on spheres.

junifer/markers/functional_connectivity/__init__.py

@@ -8,3 +8,12 @@ from .functional_connectivity_spheres import FunctionalConnectivitySpheres
 from .crossparcellation_functional_connectivity import CrossParcellationFC
 from .edge_functional_connectivity_parcels import EdgeCentricFCParcels
 from .edge_functional_connectivity_spheres import EdgeCentricFCSpheres
+
+
+__all__ = [
+    "FunctionalConnectivityParcels",
+    "FunctionalConnectivitySpheres",
+    "CrossParcellationFC",
+    "EdgeCentricFCParcels",
+    "EdgeCentricFCSpheres",
+]

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -15,6 +15,9 @@ from ..parcel_aggregation import ParcelAggregation
 from ..utils import _correlate_dataframes
 
 
+__all__ = ["CrossParcellationFC"]
+
+
 @register_marker
 class CrossParcellationFC(BaseMarker):
     """Class for calculating parcel-wise correlations with 2 parcellations.

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -12,6 +12,9 @@ from ..utils import _ets
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["EdgeCentricFCParcels"]
+
+
 @register_marker
 class EdgeCentricFCParcels(FunctionalConnectivityBase):
     """Class for edge-centric FC using parcellations.

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -12,6 +12,9 @@ from ..utils import _ets, raise_error
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["EdgeCentricFCSpheres"]
+
+
 @register_marker
 class EdgeCentricFCSpheres(FunctionalConnectivityBase):
     """Class for edge-centric FC using coordinates (spheres).

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -14,6 +14,9 @@ from ...utils import raise_error
 from ..base import BaseMarker
 
 
+__all__ = ["FunctionalConnectivityBase"]
+
+
 class FunctionalConnectivityBase(BaseMarker):
     """Abstract base class for functional connectivity markers.
 

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -12,6 +12,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["FunctionalConnectivityParcels"]
+
+
 @register_marker
 class FunctionalConnectivityParcels(FunctionalConnectivityBase):
     """Class for functional connectivity using parcellations.

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -13,6 +13,9 @@ from ..utils import raise_error
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["FunctionalConnectivitySpheres"]
+
+
 @register_marker
 class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
     """Class for functional connectivity using coordinates (spheres).

junifer/markers/parcel_aggregation.py

@@ -17,6 +17,9 @@ from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
 
+__all__ = ["ParcelAggregation"]
+
+
 @register_marker
 class ParcelAggregation(BaseMarker):
     """Class for parcel aggregation.

junifer/markers/reho/__init__.py

@@ -5,3 +5,6 @@
 
 from .reho_parcels import ReHoParcels
 from .reho_spheres import ReHoSpheres
+
+
+__all__ = ["ReHoParcels", "ReHoSpheres"]

junifer/markers/reho/_afni_reho.py

@@ -26,6 +26,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["AFNIReHo"]
+
+
 @singleton
 class AFNIReHo:
     """Class for computing ReHo using AFNI.

junifer/markers/reho/_junifer_reho.py

@@ -28,6 +28,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["JuniferReHo"]
+
+
 @singleton
 class JuniferReHo:
     """Class for computing ReHo using junifer.

junifer/markers/reho/reho_base.py

@@ -26,6 +26,8 @@ from ._junifer_reho import JuniferReHo
 if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
+__all__ = ["ReHoBase"]
+
 
 class ReHoBase(BaseMarker):
     """Base class for regional homogeneity computation.

junifer/markers/reho/reho_parcels.py

@@ -14,6 +14,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .reho_base import ReHoBase
 
 
+__all__ = ["ReHoParcels"]
+
+
 @register_marker
 class ReHoParcels(ReHoBase):
     """Class for regional homogeneity on parcels.

junifer/markers/reho/reho_spheres.py

@@ -14,6 +14,9 @@ from ..sphere_aggregation import SphereAggregation
 from .reho_base import ReHoBase
 
 
+__all__ = ["ReHoSpheres"]
+
+
 @register_marker
 class ReHoSpheres(ReHoBase):
     """Class for regional homogeneity on spheres.

junifer/markers/sphere_aggregation.py

@@ -14,6 +14,9 @@ from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
 
+__all__ = ["SphereAggregation"]
+
+
 @register_marker
 class SphereAggregation(BaseMarker):
     """Class for sphere aggregation.

junifer/markers/temporal_snr/__init__.py

@@ -5,3 +5,6 @@
 
 from .temporal_snr_parcels import TemporalSNRParcels
 from .temporal_snr_spheres import TemporalSNRSpheres
+
+
+__all__ = ["TemporalSNRParcels", "TemporalSNRSpheres"]

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -13,6 +13,9 @@ from ...utils import raise_error
 from ..base import BaseMarker
 
 
+__all__ = ["TemporalSNRBase"]
+
+
 class TemporalSNRBase(BaseMarker):
     """Abstract base class for temporal SNR markers.
 

junifer/markers/temporal_snr/temporal_snr_parcels.py

@@ -10,6 +10,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .temporal_snr_base import TemporalSNRBase
 
 
+__all__ = ["TemporalSNRParcels"]
+
+
 @register_marker
 class TemporalSNRParcels(TemporalSNRBase):
     """Class for temporal signal-to-noise ratio using parcellations.

junifer/markers/temporal_snr/temporal_snr_spheres.py

@@ -11,6 +11,9 @@ from ..utils import raise_error
 from .temporal_snr_base import TemporalSNRBase
 
 
+__all__ = ["TemporalSNRSpheres"]
+
+
 @register_marker
 class TemporalSNRSpheres(TemporalSNRBase):
     """Class for temporal signal-to-noise ratio using coordinates (spheres).

junifer/onthefly/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from .read_transform import read_transform
+
+
+__all__ = ["read_transform"]

junifer/onthefly/read_transform.py

@@ -15,6 +15,9 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
+__all__ = ["read_transform"]
+
+
 def read_transform(
     storage: Type["BaseFeatureStorage"],
     transform: str,

junifer/pipeline/__init__.py

@@ -7,3 +7,11 @@ from . import registry
 from .pipeline_step_mixin import PipelineStepMixin
 from .update_meta_mixin import UpdateMetaMixin
 from .workdir_manager import WorkDirManager
+
+
+__all__ = [
+    "registry",
+    "PipelineStepMixin",
+    "UpdateMetaMixin",
+    "WorkDirManager",
+]

junifer/pipeline/pipeline_step_mixin.py

@@ -17,6 +17,9 @@ from ..utils import raise_error
 from .utils import check_ext_dependencies
 
 
+__all__ = ["PipelineStepMixin"]
+
+
 class PipelineStepMixin:
     """Mixin class for a pipeline step."""
 

junifer/pipeline/registry.py

@@ -16,6 +16,9 @@ if TYPE_CHECKING:
     from .pipeline_step_mixin import PipelineStepMixin
 
 
+__all__ = ["register", "get_step_names", "get_class", "build"]
+
+
 # Define valid steps for operation
 _VALID_STEPS: List[str] = [
     "datagrabber",

junifer/pipeline/singleton.py

@@ -6,6 +6,9 @@
 from typing import Any, Dict, Type
 
 
+__all__ = ["singleton"]
+
+
 def singleton(cls: Type) -> Type:
     """Make a class singleton.
 

junifer/pipeline/update_meta_mixin.py

@@ -7,6 +7,9 @@
 from typing import Dict
 
 
+__all__ = ["UpdateMetaMixin"]
+
+
 class UpdateMetaMixin:
     """Mixin class for updating meta."""
 

junifer/pipeline/utils.py

@@ -10,6 +10,9 @@ from typing import Any, List, Optional
 from junifer.utils.logging import raise_error, warn_with_log
 
 
+__all__ = ["check_ext_dependencies"]
+
+
 def check_ext_dependencies(
     name: str, optional: bool = False, **kwargs: Any
 ) -> bool:

junifer/pipeline/workdir_manager.py

@@ -13,6 +13,9 @@ from ..utils import logger
 from .singleton import singleton
 
 
+__all__ = ["WorkDirManager"]
+
+
 @singleton
 class WorkDirManager:
     """Class for working directory manager.

junifer/preprocess/__init__.py

@@ -9,3 +9,11 @@ from .base import BasePreprocessor
 from .confounds import fMRIPrepConfoundRemover
 from .warping import SpaceWarper
 from .smoothing import Smoothing
+
+
+__all__ = [
+    "BasePreprocessor",
+    "fMRIPrepConfoundRemover",
+    "SpaceWarper",
+    "Smoothing",
+]

junifer/preprocess/base.py

@@ -11,6 +11,9 @@ from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils import logger, raise_error
 
 
+__all__ = ["BasePreprocessor"]
+
+
 class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
     """Abstract base class for all preprocessors.
 
@@ -136,7 +139,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
             A single input from the Junifer Data object to preprocess.
         extra_input : dict, optional
             The other fields in the Junifer Data object. Useful for accessing
-            other data kind that needs to be used in the computation. For
+            other data type that needs to be used in the computation. For
             example, the confound removers can make use of the
             confounds if available (default None).
 

junifer/preprocess/confounds/__init__.py

@@ -5,3 +5,6 @@
 # License: AGPL
 
 from .fmriprep_confound_remover import fMRIPrepConfoundRemover
+
+
+__all__ = ["fMRIPrepConfoundRemover"]