junifer 0.0.6.dev248__py3-none-any.whl → 0.0.6.dev252__py3-none-any.whl

junifer/onthefly/read_transform.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 
-from typing import Dict, Optional, Tuple
+from typing import Optional
 
 import pandas as pd
 
@@ -20,8 +20,8 @@ def read_transform(
     transform: str,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,
-    transform_args: Optional[Tuple] = None,
-    transform_kw_args: Optional[Dict] = None,
+    transform_args: Optional[tuple] = None,
+    transform_kw_args: Optional[dict] = None,
 ) -> pd.DataFrame:
     """Read stored feature and transform to specific statistical output.
 

junifer/pipeline/marker_collection.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from collections import Counter
-from typing import Dict, List, Optional
+from typing import Optional
 
 from ..datareader import DefaultDataReader
 from ..pipeline import PipelineStepMixin, WorkDirManager
@@ -39,9 +39,9 @@ class MarkerCollection:
 
     def __init__(
         self,
-        markers: List[MarkerLike],
+        markers: list[MarkerLike],
         datareader: Optional[PipelineStepMixin] = None,
-        preprocessors: Optional[List[PreprocessorLike]] = None,
+        preprocessors: Optional[list[PreprocessorLike]] = None,
         storage: Optional[StorageLike] = None,
     ):
         # Check that the markers have different names
@@ -59,7 +59,7 @@ class MarkerCollection:
         self._preprocessors = preprocessors
         self._storage = storage
 
-    def fit(self, input: Dict[str, Dict]) -> Optional[Dict]:
+    def fit(self, input: dict[str, dict]) -> Optional[dict]:
         """Fit the pipeline.
 
         Parameters

junifer/pipeline/pipeline_component_registry.py

@@ -6,7 +6,8 @@
 # License: AGPL
 
 import importlib
-from typing import Dict, List, Mapping, Optional, Union
+from collections.abc import Mapping
+from typing import Optional, Union
 
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error
@@ -111,7 +112,7 @@ class PipelineComponentRegistry(metaclass=Singleton):
             raise_error(msg=f"Invalid step: {step}", klass=ValueError)
 
     @property
-    def steps(self) -> List[str]:
+    def steps(self) -> list[str]:
         """Get valid pipeline steps."""
         return self._steps
 
@@ -166,7 +167,7 @@ class PipelineComponentRegistry(metaclass=Singleton):
         logger.info(f"De-registering {name} in {step}")
         _ = self._components[step].pop(name)
 
-    def step_components(self, step: str) -> List[str]:
+    def step_components(self, step: str) -> list[str]:
         """Get registered components for ``step``.
 
         Parameters
@@ -235,7 +236,7 @@ class PipelineComponentRegistry(metaclass=Singleton):
         step: str,
         name: str,
         baseclass: type,
-        init_params: Optional[Dict] = None,
+        init_params: Optional[dict] = None,
     ) -> Union[DataGrabberLike, PreprocessorLike, MarkerLike, StorageLike]:
         """Build an instance of class registered as ``name``.
 

junifer/pipeline/pipeline_step_mixin.py

@@ -15,7 +15,7 @@ else:
 
 from importlib.util import find_spec
 from itertools import chain
-from typing import Any, Dict, List
+from typing import Any
 
 from ..utils import raise_error
 from .utils import check_ext_dependencies
@@ -27,7 +27,7 @@ __all__ = ["PipelineStepMixin"]
 class PipelineStepMixin:
     """Mixin class for a pipeline step."""
 
-    def validate_input(self, input: List[str]) -> List[str]:
+    def validate_input(self, input: list[str]) -> list[str]:
         """Validate the input to the pipeline step.
 
         Parameters
@@ -74,8 +74,8 @@ class PipelineStepMixin:
 
     def _fit_transform(
         self,
-        input: Dict[str, Dict],
-    ) -> Dict[str, Dict]:
+        input: dict[str, dict],
+    ) -> dict[str, dict]:
         """Fit and transform.
 
         Parameters
@@ -94,7 +94,7 @@ class PipelineStepMixin:
             klass=NotImplementedError,
         )  # pragma: no cover
 
-    def validate(self, input: List[str]) -> List[str]:
+    def validate(self, input: list[str]) -> list[str]:
         """Validate the the pipeline step.
 
         Parameters
@@ -228,8 +228,8 @@ class PipelineStepMixin:
         return outputs
 
     def fit_transform(
-        self, input: Dict[str, Dict], **kwargs: Any
-    ) -> Dict[str, Dict]:
+        self, input: dict[str, dict], **kwargs: Any
+    ) -> dict[str, dict]:
         """Fit and transform.
 
         Parameters

junifer/pipeline/tests/test_pipeline_component_registry.py

@@ -7,7 +7,6 @@
 
 import logging
 from abc import ABC
-from typing import Type
 
 import pytest
 
@@ -61,7 +60,7 @@ def test_pipeline_component_registry_components():
     ],
 )
 def test_pipeline_component_registry_register(
-    caplog: pytest.LogCaptureFixture, step: str, klass: Type
+    caplog: pytest.LogCaptureFixture, step: str, klass: type
 ) -> None:
     """Test register for PipelineComponentRegistry.
 
@@ -90,7 +89,7 @@ def test_pipeline_component_registry_register(
     ],
 )
 def test_pipeline_component_registry_deregister(
-    caplog: pytest.LogCaptureFixture, step: str, klass: Type
+    caplog: pytest.LogCaptureFixture, step: str, klass: type
 ) -> None:
     """Test de-register for PipelineComponentRegistry.
 

junifer/pipeline/tests/test_pipeline_step_mixin.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 import warnings
-from typing import ClassVar, Dict, List
+from typing import ClassVar
 
 import pytest
 
@@ -26,13 +26,13 @@ def test_PipelineStepMixin_correct_dependencies() -> None:
 
         _DEPENDENCIES: ClassVar[Dependencies] = {"math"}
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -47,13 +47,13 @@ def test_PipelineStepMixin_incorrect_dependencies() -> None:
 
         _DEPENDENCIES: ClassVar[Dependencies] = {"foobar"}
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = IncorrectMixer()
@@ -72,13 +72,13 @@ def test_PipelineStepMixin_correct_ext_dependencies() -> None:
 
         _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [{"name": "afni"}]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -98,13 +98,13 @@ def test_PipelineStepMixin_ext_deps_correct_commands() -> None:
             {"name": "afni", "commands": ["3dReHo"]}
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -126,13 +126,13 @@ def test_PipelineStepMixin_ext_deps_incorrect_commands() -> None:
             {"name": "afni", "commands": ["3d"]}
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -150,13 +150,13 @@ def test_PipelineStepMixin_incorrect_ext_dependencies() -> None:
             {"name": "foobar", "optional": True}
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = IncorrectMixer()
@@ -182,13 +182,13 @@ def test_PipelineStepMixin_correct_conditional_dependencies() -> None:
 
         using = "math"
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()
@@ -211,13 +211,13 @@ def test_PipelineStepMixin_incorrect_conditional_dependencies() -> None:
             },
         ]
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = IncorrectMixer()
@@ -246,13 +246,13 @@ def test_PipelineStepMixin_correct_conditional_ext_dependencies() -> None:
 
         using = "afni"
 
-        def validate_input(self, input: List[str]) -> List[str]:
+        def validate_input(self, input: list[str]) -> list[str]:
             return input
 
         def get_output_type(self, input_type: str) -> str:
             return input_type
 
-        def _fit_transform(self, input: Dict[str, Dict]) -> Dict[str, Dict]:
+        def _fit_transform(self, input: dict[str, dict]) -> dict[str, dict]:
             return {"input": input}
 
     mixer = CorrectMixer()

junifer/pipeline/tests/test_update_meta_mixin.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, List, Set, Union
+from typing import Union
 
 import pytest
 
@@ -21,10 +21,10 @@ from junifer.pipeline.update_meta_mixin import UpdateMetaMixin
     ],
 )
 def test_UpdateMetaMixin(
-    input: Dict,
+    input: dict,
     step_name: str,
-    dependencies: Union[Set, List, str, None],
-    expected: Set,
+    dependencies: Union[set, list, str, None],
+    expected: set,
 ) -> None:
     """Test UpdateMetaMixin.
 

junifer/pipeline/update_meta_mixin.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, List, Union
+from typing import Union
 
 
 __all__ = ["UpdateMetaMixin"]
@@ -15,7 +15,7 @@ class UpdateMetaMixin:
 
     def update_meta(
         self,
-        input: Union[Dict, List[Dict]],
+        input: Union[dict, list[dict]],
         step_name: str,
     ) -> None:
         """Update metadata.

junifer/pipeline/utils.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 import subprocess
-from typing import Any, List, Optional
+from typing import Any, Optional
 
 from junifer.utils.logging import raise_error, warn_with_log
 
@@ -71,7 +71,7 @@ def check_ext_dependencies(
     return found
 
 
-def _check_afni(commands: Optional[List[str]] = None) -> bool:
+def _check_afni(commands: Optional[list[str]] = None) -> bool:
     """Check if AFNI is present in the system.
 
     Parameters
@@ -131,7 +131,7 @@ def _check_afni(commands: Optional[List[str]] = None) -> bool:
     return afni_found
 
 
-def _check_fsl(commands: Optional[List[str]] = None) -> bool:
+def _check_fsl(commands: Optional[list[str]] = None) -> bool:
     """Check if FSL is present in the system.
 
     Parameters
@@ -193,7 +193,7 @@ def _check_fsl(commands: Optional[List[str]] = None) -> bool:
     return fsl_found
 
 
-def _check_ants(commands: Optional[List[str]] = None) -> bool:
+def _check_ants(commands: Optional[list[str]] = None) -> bool:
     """Check if ANTs is present in the system.
 
     Parameters
@@ -253,7 +253,7 @@ def _check_ants(commands: Optional[List[str]] = None) -> bool:
     return ants_found
 
 
-def _check_freesurfer(commands: Optional[List[str]] = None) -> bool:
+def _check_freesurfer(commands: Optional[list[str]] = None) -> bool:
     """Check if FreeSurfer is present in the system.
 
     Parameters

junifer/preprocess/base.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any, Optional, Union
 
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils import logger, raise_error
@@ -38,8 +38,8 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
 
     def __init__(
         self,
-        on: Optional[Union[List[str], str]] = None,
-        required_data_types: Optional[Union[List[str], str]] = None,
+        on: Optional[Union[list[str], str]] = None,
+        required_data_types: Optional[Union[list[str], str]] = None,
     ) -> None:
         """Initialize the class."""
         # Use all data types if not provided
@@ -60,7 +60,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
         else:
             self._required_data_types = required_data_types
 
-    def validate_input(self, input: List[str]) -> List[str]:
+    def validate_input(self, input: list[str]) -> list[str]:
         """Validate input.
 
         Parameters
@@ -90,7 +90,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
         return [x for x in self._on if x in input]
 
     @abstractmethod
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid data types for input.
 
         Returns
@@ -128,9 +128,9 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
     @abstractmethod
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[dict[str, Any], Optional[dict[str, dict[str, Any]]]]:
         """Preprocess.
 
         Parameters
@@ -160,8 +160,8 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
 
     def _fit_transform(
         self,
-        input: Dict[str, Dict],
-    ) -> Dict:
+        input: dict[str, dict],
+    ) -> dict:
         """Fit and transform.
 
         Parameters

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -8,10 +8,7 @@
 from typing import (
     Any,
     ClassVar,
-    Dict,
-    List,
     Optional,
-    Tuple,
     Union,
 )
 
@@ -156,14 +153,14 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
 
     def __init__(
         self,
-        strategy: Optional[Dict[str, str]] = None,
+        strategy: Optional[dict[str, str]] = None,
         spike: Optional[float] = None,
         detrend: bool = True,
         standardize: bool = True,
         low_pass: Optional[float] = None,
         high_pass: Optional[float] = None,
         t_r: Optional[float] = None,
-        masks: Union[str, Dict, List[Union[Dict, str]], None] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
     ) -> None:
         """Initialize the class."""
         if strategy is None:
@@ -211,7 +208,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
             )
         super().__init__(on="BOLD", required_data_types=["BOLD"])
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid data types for input.
 
         Returns
@@ -240,7 +237,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
         # Does not add any new keys
         return input_type
 
-    def _map_adhoc_to_fmriprep(self, input: Dict[str, Any]) -> None:
+    def _map_adhoc_to_fmriprep(self, input: dict[str, Any]) -> None:
         """Map the adhoc format to the fmpriprep format spec.
 
         Based on the spec, map the column names to match the fmriprep format.
@@ -270,8 +267,8 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
         confounds_df.rename(columns=confounds_mapping, inplace=True)
 
     def _process_fmriprep_spec(
-        self, input: Dict[str, Any]
-    ) -> Tuple[List[str], Dict[str, str], Dict[str, str], str]:
+        self, input: dict[str, Any]
+    ) -> tuple[list[str], dict[str, str], dict[str, str], str]:
         """Process the fmpriprep format spec from the specified file.
 
         Based on the strategy, find the relevant column names in the dataframe,
@@ -359,7 +356,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
         out = to_select, squares_to_compute, derivatives_to_compute, spike_name
         return out
 
-    def _pick_confounds(self, input: Dict[str, Any]) -> pd.DataFrame:
+    def _pick_confounds(self, input: dict[str, Any]) -> pd.DataFrame:
         """Select relevant confounds from the specified file.
 
         Parameters
@@ -418,7 +415,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
 
     def _validate_data(
         self,
-        input: Dict[str, Any],
+        input: dict[str, Any],
     ) -> None:
         """Validate input data.
 
@@ -506,9 +503,9 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[dict[str, Any], Optional[dict[str, dict[str, Any]]]]:
         """Preprocess.
 
         Parameters

junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py

@@ -5,7 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List
 
 import numpy as np
 import pandas as pd
@@ -47,7 +46,7 @@ def test_fMRIPrepConfoundRemover_init() -> None:
         ["T1w", "BOLD"],
     ],
 )
-def test_fMRIPrepConfoundRemover_validate_input(input_: List[str]) -> None:
+def test_fMRIPrepConfoundRemover_validate_input(input_: list[str]) -> None:
     """Test fMRIPrepConfoundRemover validate_input.
 
     Parameters

junifer/preprocess/smoothing/smoothing.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Union
+from typing import Any, ClassVar, Optional, Union
 
 from ...api.decorators import register_preprocessor
 from ...typing import ConditionalDependencies
@@ -86,8 +86,8 @@ class Smoothing(BasePreprocessor):
     def __init__(
         self,
         using: str,
-        on: Union[List[str], str],
-        smoothing_params: Optional[Dict] = None,
+        on: Union[list[str], str],
+        smoothing_params: Optional[dict] = None,
     ) -> None:
         """Initialize the class."""
         # Validate `using` parameter
@@ -102,7 +102,7 @@ class Smoothing(BasePreprocessor):
         )
         super().__init__(on=on)
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid data types for input.
 
         Returns
@@ -133,9 +133,9 @@ class Smoothing(BasePreprocessor):
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[dict[str, Any], Optional[dict[str, dict[str, Any]]]]:
         """Preprocess.
 
         Parameters

junifer/preprocess/warping/_ants_warper.py

@@ -6,7 +6,6 @@
 from typing import (
     Any,
     ClassVar,
-    Dict,
 )
 
 import nibabel as nib
@@ -40,10 +39,10 @@ class ANTsWarper:
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        input: dict[str, Any],
+        extra_input: dict[str, Any],
         reference: str,
-    ) -> Dict[str, Any]:
+    ) -> dict[str, Any]:
         """Preprocess using ANTs.
 
         Parameters

junifer/preprocess/warping/_fsl_warper.py

@@ -6,7 +6,6 @@
 from typing import (
     Any,
     ClassVar,
-    Dict,
 )
 
 import nibabel as nib
@@ -39,9 +38,9 @@ class FSLWarper:
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Dict[str, Any],
-    ) -> Dict[str, Any]:
+        input: dict[str, Any],
+        extra_input: dict[str, Any],
+    ) -> dict[str, Any]:
         """Preprocess using FSL.
 
         Parameters