README.md

@@ -39,6 +39,7 @@ The documentation is available at [https://juaml.github.io/junifer](https://juam
   * `preprocess`: Preprocessing module.
   * `storage`: Storage module.
   * `testing`: Testing components module.
+  * `typing`: Type hints module.
   * `utils`: Utilities module (e.g. logging).
 
 ## Installation

docs/changes/newsfragments/392.feature

@@ -0,0 +1 @@
+Introduce ``junifer.typing`` sub-module to organise internal and external type hints by `Synchon Mandal`_

docs/extending/dependencies.rst

@@ -28,7 +28,7 @@ component depends on. For example, for :class:`.RSSETSMarker`, we have:
 
 .. code-block:: python
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
 The type annotation is for documentation and static type checking purposes.
 Although not required, we highly recommend you use them, your future self
@@ -44,7 +44,7 @@ by having a class attribute like so:
 
 .. code-block:: python
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "afni",
             "commands": ["3dReHo", "3dAFNItoNIFTI"],
@@ -78,7 +78,7 @@ that it shows the problem a bit better and how we solve it:
 
     class SpaceWarper(BasePreprocessor):
         # docstring
-        _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "fsl",
                 "depends_on": FSLWarper,
@@ -115,14 +115,14 @@ similar. ``FSLWarper`` looks like this (only the relevant part is shown here):
     class FSLWarper:
         # docstring
 
-        _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,

docs/extending/marker.rst

@@ -196,15 +196,16 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
     from junifer.api.decorators import register_marker
     from junifer.data import get_parcellation
     from junifer.markers import BaseMarker
+    from junifer.typing import Dependencies, MarkerInOutMappings
     from nilearn.maskers import NiftiLabelsMasker
 
 
     @register_marker
     class ParcelMean(BaseMarker):
 
-        _DEPENDENCIES = {"nilearn", "numpy"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "numpy"}
 
-        _MARKER_INOUT_MAPPINGS: ClassVar[dict[str, dict[str, str]]] = {
+        _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
             "BOLD": {
                 "parcel_mean": "timeseries",
             },

junifer/__init__.pyi

@@ -13,6 +13,7 @@ __all__ = [
     "external",
     "onthefly",
     "testing",
+    "typing",
     "__version__",
 ]
 
@@ -30,6 +31,7 @@ from . import (
     utils,
     external,
     testing,
+    typing,
     onthefly,
 )
 from ._version import __version__

junifer/api/decorators.py

@@ -8,6 +8,7 @@
 from typing import Type
 
 from ..pipeline import PipelineComponentRegistry
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 
 
 __all__ = [
@@ -19,7 +20,7 @@ __all__ = [
 ]
 
 
-def register_datagrabber(klass: Type) -> Type:
+def register_datagrabber(klass: DataGrabberLike) -> DataGrabberLike:
     """Register DataGrabber.
 
     Registers the DataGrabber so it can be used by name.
@@ -73,7 +74,7 @@ def register_datareader(klass: Type) -> Type:
     return klass
 
 
-def register_preprocessor(klass: Type) -> Type:
+def register_preprocessor(klass: PreprocessorLike) -> PreprocessorLike:
     """Preprocessor registration decorator.
 
     Registers the preprocessor so it can be used by name.
@@ -96,7 +97,7 @@ def register_preprocessor(klass: Type) -> Type:
     return klass
 
 
-def register_marker(klass: Type) -> Type:
+def register_marker(klass: MarkerLike) -> MarkerLike:
     """Marker registration decorator.
 
     Registers the marker so it can be used by name.
@@ -119,7 +120,7 @@ def register_marker(klass: Type) -> Type:
     return klass
 
 
-def register_storage(klass: Type) -> Type:
+def register_storage(klass: StorageLike) -> StorageLike:
     """Storage registration decorator.
 
     Registers the storage so it can be used by name.

junifer/api/functions.py

@@ -11,22 +11,23 @@ from pathlib import Path
 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 ..datagrabber import BaseDataGrabber
+from ..markers import BaseMarker
 from ..pipeline import (
     MarkerCollection,
     PipelineComponentRegistry,
     WorkDirManager,
 )
-from ..preprocess.base import BasePreprocessor
-from ..storage.base import BaseFeatureStorage
+from ..preprocess import BasePreprocessor
+from ..storage import BaseFeatureStorage
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error, yaml
 
 
 __all__ = ["run", "collect", "queue", "reset", "list_elements"]
 
 
-def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
+def _get_datagrabber(datagrabber_config: Dict) -> DataGrabberLike:
     """Get DataGrabber.
 
     Parameters
@@ -48,7 +49,7 @@ def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
     )
 
 
-def _get_preprocessor(preprocessing_config: Dict) -> BasePreprocessor:
+def _get_preprocessor(preprocessing_config: Dict) -> PreprocessorLike:
     """Get Preprocessor.
 
     Parameters
@@ -70,7 +71,7 @@ def _get_preprocessor(preprocessing_config: Dict) -> BasePreprocessor:
     )
 
 
-def _get_marker(marker_config: Dict) -> BaseMarker:
+def _get_marker(marker_config: Dict) -> MarkerLike:
     """Get Marker.
 
     Parameters
@@ -92,7 +93,7 @@ def _get_marker(marker_config: Dict) -> BaseMarker:
     )
 
 
-def _get_storage(storage_config: Dict) -> BaseFeatureStorage:
+def _get_storage(storage_config: Dict) -> StorageLike:
     """Get Storage.
 
     Parameters

junifer/datagrabber/multiple.py

@@ -8,6 +8,7 @@
 from typing import Dict, List, Tuple, Union
 
 from ..api.decorators import register_datagrabber
+from ..typing import DataGrabberLike
 from ..utils import deep_update, raise_error
 from .base import BaseDataGrabber
 
@@ -37,7 +38,7 @@ class MultipleDataGrabber(BaseDataGrabber):
 
     """
 
-    def __init__(self, datagrabbers: List[BaseDataGrabber], **kwargs) -> None:
+    def __init__(self, datagrabbers: List[DataGrabberLike], **kwargs) -> None:
         # Check datagrabbers consistency
         # Check for same element keys
         first_keys = datagrabbers[0].get_element_keys()

junifer/markers/base.py

@@ -6,16 +6,13 @@
 
 from abc import ABC, abstractmethod
 from copy import deepcopy
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
+from typing import Any, Dict, List, Optional, Union
 
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
+from ..typing import StorageLike
 from ..utils import logger, raise_error
 
 
-if TYPE_CHECKING:
-    from junifer.storage import BaseFeatureStorage
-
-
 __all__ = ["BaseMarker"]
 
 
@@ -159,7 +156,7 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
         type_: str,
         feature: str,
         out: Dict[str, Any],
-        storage: "BaseFeatureStorage",
+        storage: StorageLike,
     ) -> None:
         """Store.
 
@@ -182,7 +179,7 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
     def _fit_transform(
         self,
         input: Dict[str, Dict],
-        storage: Optional["BaseFeatureStorage"] = None,
+        storage: Optional[StorageLike] = None,
     ) -> Dict:
         """Fit and transform.
 

junifer/markers/brainprint.py

@@ -11,7 +11,6 @@ from typing import (
     Dict,
     List,
     Optional,
-    Set,
     Union,
 )
 
@@ -25,6 +24,7 @@ from ..external.BrainPrint.brainprint.brainprint import (
 )
 from ..external.BrainPrint.brainprint.surfaces import surf_to_vtk
 from ..pipeline import WorkDirManager
+from ..typing import Dependencies, ExternalDependencies, MarkerInOutMappings
 from ..utils import logger, run_ext_cmd
 from .base import BaseMarker
 
@@ -68,7 +68,7 @@ class BrainPrint(BaseMarker):
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "freesurfer",
             "commands": [
@@ -80,9 +80,9 @@ class BrainPrint(BaseMarker):
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"lapy", "numpy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"lapy", "numpy"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "FreeSurfer": {
             "eigenvalues": "scalar_table",
             "areas": "vector",

junifer/markers/complexity/complexity_base.py

@@ -11,10 +11,10 @@ from typing import (
     Dict,
     List,
     Optional,
-    Set,
     Union,
 )
 
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import raise_error
 from ..base import BaseMarker
 from ..parcel_aggregation import ParcelAggregation
@@ -51,9 +51,9 @@ class ComplexityBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "neurokit2"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "neurokit2"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "complexity": "vector",
         },

junifer/markers/ets_rss.py

@@ -6,11 +6,12 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 import numpy as np
 
 from ..api.decorators import register_marker
+from ..typing import Dependencies, MarkerInOutMappings
 from ..utils import logger
 from .base import BaseMarker
 from .parcel_aggregation import ParcelAggregation
@@ -45,9 +46,9 @@ class RSSETSMarker(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "rss_ets": "timeseries",
         },

junifer/markers/falff/_afni_falff.py

@@ -8,22 +8,20 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Dict,
-    List,
     Optional,
     Tuple,
-    Union,
 )
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import ExternalDependencies
 from ...utils import logger, run_ext_cmd
 from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["AFNIALFF"]
@@ -37,7 +35,7 @@ class AFNIALFF(metaclass=Singleton):
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "afni",
             "commands": ["3dRSFC", "3dAFNItoNIFTI"],

junifer/markers/falff/_junifer_falff.py

@@ -9,7 +9,6 @@ from typing import (
     TYPE_CHECKING,
     ClassVar,
     Optional,
-    Set,
     Tuple,
 )
 
@@ -19,12 +18,13 @@ import scipy as sp
 from nilearn import image as nimg
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies
 from ...utils import logger
 from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["JuniferALFF"]
@@ -37,7 +37,7 @@ class JuniferALFF(metaclass=Singleton):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nilearn", "scipy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nilearn", "scipy"}
 
     def __del__(self) -> None:
         """Terminate the class."""

junifer/markers/falff/falff_base.py

@@ -12,13 +12,11 @@ from typing import (
     Any,
     ClassVar,
     Dict,
-    List,
     Optional,
     Tuple,
-    Type,
-    Union,
 )
 
+from ...typing import ConditionalDependencies, MarkerInOutMappings
 from ...utils.logging import logger, raise_error
 from ..base import BaseMarker
 from ._afni_falff import AFNIALFF
@@ -26,7 +24,7 @@ from ._junifer_falff import JuniferALFF
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["ALFFBase"]
@@ -72,7 +70,7 @@ class ALFFBase(BaseMarker):
 
     """
 
-    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+    _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
         {
             "using": "afni",
             "depends_on": AFNIALFF,
@@ -83,7 +81,7 @@ class ALFFBase(BaseMarker):
         },
     ]
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "alff": "vector",
             "falff": "vector",

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -4,11 +4,12 @@
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 import pandas as pd
 
 from ...api.decorators import register_marker
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import logger, raise_error
 from ..base import BaseMarker
 from ..parcel_aggregation import ParcelAggregation
@@ -49,9 +50,9 @@ class CrossParcellationFC(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "functional_connectivity": "matrix",
         },

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -5,11 +5,12 @@
 
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
 from ...external.nilearn import JuniferConnectivityMeasure
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import raise_error
 from ..base import BaseMarker
 
@@ -51,9 +52,9 @@ class FunctionalConnectivityBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "scikit-learn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "scikit-learn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "functional_connectivity": "matrix",
         },

junifer/markers/parcel_aggregation.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 import numpy as np
 from nilearn.image import math_img
@@ -13,6 +13,7 @@ from nilearn.maskers import NiftiMasker
 from ..api.decorators import register_marker
 from ..data import get_data
 from ..stats import get_aggfunc_by_name
+from ..typing import Dependencies, MarkerInOutMappings
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
@@ -61,9 +62,9 @@ class ParcelAggregation(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "numpy"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "T1w": {
             "aggregation": "vector",
         },

junifer/markers/reho/_afni_reho.py

@@ -8,22 +8,20 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Dict,
-    List,
     Optional,
     Tuple,
-    Union,
 )
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import ExternalDependencies
 from ...utils import logger, run_ext_cmd
 from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["AFNIReHo"]
@@ -37,7 +35,7 @@ class AFNIReHo(metaclass=Singleton):
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "afni",
             "commands": ["3dReHo", "3dAFNItoNIFTI"],

junifer/markers/reho/_junifer_reho.py

@@ -9,7 +9,6 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Set,
     Tuple,
 )
 
@@ -20,12 +19,13 @@ from nilearn import image as nimg
 from nilearn import masking as nmask
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies
 from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["JuniferReHo"]
@@ -38,7 +38,7 @@ class JuniferReHo(metaclass=Singleton):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nilearn", "scipy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nilearn", "scipy"}
 
     def __del__(self) -> None:
         """Terminate the class."""

junifer/markers/reho/reho_base.py

@@ -10,13 +10,11 @@ from typing import (
     Any,
     ClassVar,
     Dict,
-    List,
     Optional,
     Tuple,
-    Type,
-    Union,
 )
 
+from ...typing import ConditionalDependencies, MarkerInOutMappings
 from ...utils import logger, raise_error
 from ..base import BaseMarker
 from ._afni_reho import AFNIReHo
@@ -24,7 +22,7 @@ from ._junifer_reho import JuniferReHo
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 __all__ = ["ReHoBase"]
 
@@ -51,7 +49,7 @@ class ReHoBase(BaseMarker):
 
     """
 
-    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+    _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
         {
             "using": "afni",
             "depends_on": AFNIReHo,
@@ -62,7 +60,7 @@ class ReHoBase(BaseMarker):
         },
     ]
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "reho": "vector",
         },

junifer/markers/sphere_aggregation.py

@@ -4,12 +4,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from ..api.decorators import register_marker
 from ..data import get_data
 from ..external.nilearn import JuniferNiftiSpheresMasker
 from ..stats import get_aggfunc_by_name
+from ..typing import Dependencies, MarkerInOutMappings
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
@@ -66,9 +67,9 @@ class SphereAggregation(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "numpy"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "T1w": {
             "aggregation": "vector",
         },

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -5,10 +5,11 @@
 
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from nilearn import image as nimg
 
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import raise_error
 from ..base import BaseMarker
 
@@ -37,9 +38,9 @@ class TemporalSNRBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "tsnr": "vector",
         },

junifer/onthefly/_brainprint.py

@@ -3,23 +3,20 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import TYPE_CHECKING, Dict, Optional, Type
+from typing import Dict, Optional
 
 import numpy as np
 import pandas as pd
 
+from ..typing import StorageLike
 from ..utils import raise_error
 
 
-if TYPE_CHECKING:
-    from junifer.storage import BaseFeatureStorage
-
-
 __all__ = ["normalize", "reweight"]
 
 
 def normalize(
-    storage: Type["BaseFeatureStorage"],
+    storage: StorageLike,
     features: Dict[str, Dict[str, Optional[str]]],
     kind: str,
 ) -> pd.DataFrame:
@@ -89,7 +86,7 @@ def normalize(
 
 
 def reweight(
-    storage: Type["BaseFeatureStorage"],
+    storage: StorageLike,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,
 ) -> pd.DataFrame:

junifer/onthefly/read_transform.py

@@ -4,22 +4,19 @@
 # License: AGPL
 
 
-from typing import TYPE_CHECKING, Dict, Optional, Tuple, Type
+from typing import Dict, Optional, Tuple
 
 import pandas as pd
 
+from ..typing import StorageLike
 from ..utils import logger, raise_error, warn_with_log
 
 
-if TYPE_CHECKING:
-    from junifer.storage import BaseFeatureStorage
-
-
 __all__ = ["read_transform"]
 
 
 def read_transform(
-    storage: Type["BaseFeatureStorage"],
+    storage: StorageLike,
     transform: str,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,

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

@@ -103,6 +103,7 @@ def test_workdir_manager_get_and_delete_tempdir(tmp_path: Path) -> None:
     # 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.
 

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,
+)

junifer/typing/_typing.py

@@ -0,0 +1,61 @@
+"""Provide type hints for internal and external use."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    TYPE_CHECKING,
+    AbstractSet,
+    MutableMapping,
+    Sequence,
+    Type,
+    Union,
+)
+
+
+if TYPE_CHECKING:
+    from ..datagrabber import BaseDataGrabber
+    from ..datareader import DefaultDataReader
+    from ..markers import BaseMarker
+    from ..preprocess import BasePreprocessor
+    from ..storage import BaseFeatureStorage
+
+
+__all__ = [
+    "DataGrabberLike",
+    "PreprocessorLike",
+    "MarkerLike",
+    "StorageLike",
+    "PipelineComponent",
+    "Dependencies",
+    "ConditionalDependencies",
+    "ExternalDependencies",
+    "MarkerInOutMappings",
+]
+
+
+DataGrabberLike = Type["BaseDataGrabber"]
+PreprocessorLike = Type["BasePreprocessor"]
+MarkerLike = Type["BaseMarker"]
+StorageLike = Type["BaseFeatureStorage"]
+PipelineComponent = Union[
+    "DataGrabberLike",
+    "DefaultDataReader",
+    "PreprocessorLike",
+    "MarkerLike",
+    "StorageLike",
+]
+Dependencies = AbstractSet[str]
+ConditionalDependencies = Sequence[
+    MutableMapping[
+        str,
+        Union[
+            str,
+            PipelineComponent,
+            Sequence[str],
+            Sequence[PipelineComponent],
+        ],
+    ]
+]
+ExternalDependencies = Sequence[MutableMapping[str, Union[str, Sequence[str]]]]
+MarkerInOutMappings = MutableMapping[str, MutableMapping[str, str]]