fix: RUF012 fixes across codebase

junifer/markers/ets_rss.py

@@ -6,7 +6,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
 import numpy as np
 
@@ -42,7 +42,7 @@ class RSSETSMarker(BaseMarker):
 
     """
 
-    _DEPENDENCIES = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
 
     def __init__(
         self,

junifer/markers/falff/falff_base.py

@@ -6,7 +6,7 @@
 # License: AGPL
 
 from abc import abstractmethod
-from typing import Dict, List, Optional
+from typing import ClassVar, Dict, List, Optional, Union
 
 from ...utils.logging import raise_error
 from ..base import BaseMarker
@@ -44,7 +44,9 @@ class ALFFBase(BaseMarker):
 
     """
 
-    _EXT_DEPENDENCIES = [
+    _EXT_DEPENDENCIES: ClassVar[
+        List[Dict[str, Union[str, bool, List[str]]]]
+    ] = [
         {
             "name": "afni",
             "optional": True,

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -4,7 +4,7 @@
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
 import pandas as pd
 
@@ -39,7 +39,7 @@ class CrossParcellationFC(BaseMarker):
         (default None).
     """
 
-    _DEPENDENCIES = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
 
     def __init__(
         self,

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -5,7 +5,7 @@
 
 
 from abc import abstractmethod
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
 from nilearn.connectome import ConnectivityMeasure
 from sklearn.covariance import EmpiricalCovariance
@@ -42,7 +42,7 @@ class FunctionalConnectivityBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES = {"nilearn", "scikit-learn"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "scikit-learn"}
 
     def __init__(
         self,

junifer/markers/parcel_aggregation.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
 import numpy as np
 from nilearn.image import math_img, resample_to_img
@@ -51,7 +51,7 @@ class ParcelAggregation(BaseMarker):
         None).
     """
 
-    _DEPENDENCIES = {"nilearn", "numpy"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
 
     def __init__(
         self,

junifer/markers/reho/reho_base.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import TYPE_CHECKING, Any, Dict, List, Optional
+from typing import TYPE_CHECKING, Any, ClassVar, Dict, List, Optional, Union
 
 from ...utils import logger, raise_error
 from ..base import BaseMarker
@@ -29,7 +29,9 @@ class ReHoBase(BaseMarker):
 
     """
 
-    _EXT_DEPENDENCIES = [
+    _EXT_DEPENDENCIES: ClassVar[
+        List[Dict[str, Union[str, bool, List[str]]]]
+    ] = [
         {
             "name": "afni",
             "optional": True,

junifer/markers/sphere_aggregation.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
 from ..api.decorators import register_marker
 from ..data import get_mask, load_coordinates
@@ -57,7 +57,7 @@ class SphereAggregation(BaseMarker):
 
     """
 
-    _DEPENDENCIES = {"nilearn", "numpy"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
 
     def __init__(
         self,

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -5,7 +5,7 @@
 
 
 from abc import abstractmethod
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Union
 
 from nilearn import image as nimg
 
@@ -34,7 +34,7 @@ class TemporalSNRBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
 
     def __init__(
         self,

junifer/pipeline/tests/test_pipeline_step_mixin.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 import warnings
-from typing import Dict, List
+from typing import ClassVar, Dict, List, Set, Union
 
 import pytest
 
@@ -30,7 +30,7 @@ def test_pipeline_step_mixin_validate_correct_dependencies() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _DEPENDENCIES = {"setuptools"}
+        _DEPENDENCIES: ClassVar[Set[str]] = {"setuptools"}
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -51,7 +51,7 @@ def test_pipeline_step_mixin_validate_incorrect_dependencies() -> None:
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _DEPENDENCIES = {"foobar"}
+        _DEPENDENCIES: ClassVar[Set[str]] = {"foobar"}
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -76,7 +76,9 @@ def test_pipeline_step_mixin_validate_correct_ext_dependencies() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES = [{"name": "afni", "optional": False}]
+        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, bool]]]] = [
+            {"name": "afni", "optional": False}
+        ]
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -100,9 +102,9 @@ def test_pipeline_step_mixin_validate_ext_deps_correct_commands() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES = [
-            {"name": "afni", "optional": False, "commands": ["3dReHo"]}
-        ]
+        _EXT_DEPENDENCIES: ClassVar[
+            List[Dict[str, Union[str, bool, List[str]]]]
+        ] = [{"name": "afni", "optional": False, "commands": ["3dReHo"]}]
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -128,9 +130,9 @@ def test_pipeline_step_mixin_validate_ext_deps_incorrect_commands() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES = [
-            {"name": "afni", "optional": False, "commands": ["3d"]}
-        ]
+        _EXT_DEPENDENCIES: ClassVar[
+            List[Dict[str, Union[str, bool, List[str]]]]
+        ] = [{"name": "afni", "optional": False, "commands": ["3d"]}]
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -152,7 +154,9 @@ def test_pipeline_step_mixin_validate_incorrect_ext_dependencies() -> None:
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES = [{"name": "foobar", "optional": True}]
+        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, bool]]]] = [
+            {"name": "foobar", "optional": True}
+        ]
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -5,7 +5,17 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Union
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Optional,
+    Set,
+    Tuple,
+    Union,
+)
 
 import numpy as np
 import pandas as pd
@@ -141,7 +151,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
 
     """
 
-    _DEPENDENCIES = {"numpy", "nilearn"}
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nilearn"}
 
     def __init__(
         self,