Merge pull request #392 from juaml/style/typing

[ENH]: Introduce `junfer.typing` module

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 @@
 ]
 
 
-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 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 @@ def store(
         type_: str,
         feature: str,
         out: Dict[str, Any],
-        storage: "BaseFeatureStorage",
+        storage: StorageLike,
     ) -> None:
         """Store.
 
@@ -182,7 +179,7 @@ def store(
     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 @@
     Dict,
     List,
     Optional,
-    Set,
     Union,
 )
 
@@ -25,6 +24,7 @@
 )
 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 @@
     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 <[email protected]>
 # 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 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 @@
     TYPE_CHECKING,
     ClassVar,
     Optional,
-    Set,
     Tuple,
 )
 
@@ -19,12 +18,13 @@
 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."""