.python-version

@@ -0,0 +1 @@
+3.12

docs/changes/newsfragments/474.misc

@@ -0,0 +1 @@
+Drop Python 3.9 and add Python 3.14 support, upgrade codebase to follow modern syntax, bump dependencies and add ``uv`` support.

junifer/api/functions.py

@@ -8,7 +8,6 @@
 import os
 import shutil
 from pathlib import Path
-from typing import Optional, Union
 
 from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from ..datagrabber import BaseDataGrabber
@@ -122,12 +121,12 @@ def _get_storage(storage_config: dict) -> StorageLike:
 
 
 def run(
-    workdir: Union[str, Path, dict],
+    workdir: str | Path | dict,
     datagrabber: dict,
     markers: list[dict],
     storage: dict,
-    preprocessors: Optional[list[dict]] = None,
+    preprocessors: list[dict] | None = None,
-    elements: Optional[Elements] = None,
+    elements: Elements | None = None,
 ) -> None:
     """Run the pipeline on the selected element.
 
@@ -166,7 +165,7 @@ def run(
 
     """
     # Conditional to handle workdir config
-    if isinstance(workdir, (str, Path)):
+    if isinstance(workdir, str | Path):
         if isinstance(workdir, str):
             workdir = {"workdir": Path(workdir), "cleanup": True}
         else:
@@ -263,8 +262,8 @@ def queue(
     kind: str,
     jobname: str = "junifer_job",
     overwrite: bool = False,
-    elements: Optional[Elements] = None,
+    elements: Elements | None = None,
-    **kwargs: Union[str, int, bool, dict, tuple, list],
+    **kwargs: str | int | bool | dict | tuple | list,
 ) -> None:
     """Queue a job to be executed later.
 
@@ -425,7 +424,7 @@ def reset(config: dict) -> None:
 
 def list_elements(
     datagrabber: dict,
-    elements: Optional[Elements] = None,
+    elements: Elements | None = None,
 ) -> str:
     """List elements of the datagrabber filtered using `elements`.
 

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -6,7 +6,6 @@
 import shutil
 import textwrap
 from pathlib import Path
-from typing import Optional
 
 from ...typing import Elements
 from ...utils import logger, make_executable, raise_error, run_ext_cmd
@@ -65,11 +64,11 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         job_dir: Path,
         yaml_config_path: Path,
         elements: Elements,
-        pre_run: Optional[str] = None,
+        pre_run: str | None = None,
-        pre_collect: Optional[str] = None,
+        pre_collect: str | None = None,
-        env: Optional[dict[str, str]] = None,
+        env: dict[str, str] | None = None,
         verbose: str = "info",
-        verbose_datalad: Optional[str] = None,
+        verbose_datalad: str | None = None,
         submit: bool = False,
     ) -> None:
         """Initialize the class."""
@@ -92,7 +91,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         self._run_joblog_path = self._job_dir / f"run_{self._job_name}_joblog"
         self._elements_file_path = self._job_dir / "elements"
 
-    def _check_env(self, env: Optional[dict[str, str]]) -> None:
+    def _check_env(self, env: dict[str, str] | None) -> None:
         """Check value of env parameter on init.
 
         Parameters

junifer/api/queue_context/htcondor_adapter.py

@@ -6,7 +6,6 @@
 import shutil
 import textwrap
 from pathlib import Path
-from typing import Optional
 
 from ...typing import Elements
 from ...utils import logger, make_executable, raise_error, run_ext_cmd
@@ -83,15 +82,15 @@ class HTCondorAdapter(QueueContextAdapter):
         job_dir: Path,
         yaml_config_path: Path,
         elements: Elements,
-        pre_run: Optional[str] = None,
+        pre_run: str | None = None,
-        pre_collect: Optional[str] = None,
+        pre_collect: str | None = None,
-        env: Optional[dict[str, str]] = None,
+        env: dict[str, str] | None = None,
         verbose: str = "info",
-        verbose_datalad: Optional[str] = None,
+        verbose_datalad: str | None = None,
         cpus: int = 1,
         mem: str = "8G",
         disk: str = "1G",
-        extra_preamble: Optional[str] = None,
+        extra_preamble: str | None = None,
         collect: str = "yes",
         submit: bool = False,
     ) -> None:
@@ -121,7 +120,7 @@ class HTCondorAdapter(QueueContextAdapter):
         )
         self._dag_path = self._job_dir / f"{self._job_name}.dag"
 
-    def _check_env(self, env: Optional[dict[str, str]]) -> None:
+    def _check_env(self, env: dict[str, str] | None) -> None:
         """Check value of env parameter on init.
 
         Parameters

junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py

@@ -5,7 +5,6 @@
 
 import logging
 from pathlib import Path
-from typing import Optional, Union
 
 import pytest
 
@@ -44,7 +43,7 @@ def test_GnuParallelLocalAdapter_env_shell_error() -> None:
     ],
 )
 def test_GnuParallelLocalAdapter_elements(
-    elements: list[Union[str, tuple]],
+    elements: list[str | tuple],
     expected_text: str,
 ) -> None:
     """Test GnuParallelLocalAdapter elements().
@@ -76,7 +75,7 @@ def test_GnuParallelLocalAdapter_elements(
     ],
 )
 def test_GnuParallelLocalAdapter_pre_run(
-    pre_run: Optional[str],
+    pre_run: str | None,
     expected_text: str,
     shell: str,
 ) -> None:
@@ -114,7 +113,7 @@ def test_GnuParallelLocalAdapter_pre_run(
     ],
 )
 def test_GnuParallelLocalAdapter_pre_collect(
-    pre_collect: Optional[str],
+    pre_collect: str | None,
     expected_text: str,
     shell: str,
 ) -> None:

junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -5,7 +5,6 @@
 
 import logging
 from pathlib import Path
-from typing import Optional, Union
 
 import pytest
 
@@ -58,7 +57,7 @@ def test_HTCondorAdapter_collect_error() -> None:
     ],
 )
 def test_HTCondorAdapter_pre_run(
-    pre_run: Optional[str],
+    pre_run: str | None,
     expected_text: str,
     shell: str,
 ) -> None:
@@ -100,7 +99,7 @@ def test_HTCondorAdapter_pre_run(
     ],
 )
 def test_HTCondorAdapter_pre_collect(
-    pre_collect: Optional[str],
+    pre_collect: str | None,
     expected_text: str,
     collect: str,
     shell: str,
@@ -140,7 +139,7 @@ def test_HTCondorAdapter_pre_collect(
     ],
 )
 def test_HTCondorAdapter_run_collect(
-    extra_preamble: Optional[str], expected_text: str
+    extra_preamble: str | None, expected_text: str
 ) -> None:
     """Test HTCondorAdapter run() and collect().
 
@@ -181,7 +180,7 @@ def test_HTCondorAdapter_run_collect(
     ],
 )
 def test_HTCondor_dag(
-    elements: list[Union[str, tuple]], collect: str, expected_text: str
+    elements: list[str | tuple], collect: str, expected_text: str
 ) -> None:
     """Test HTCondorAdapter dag().
 

junifer/api/tests/test_functions.py

@@ -8,7 +8,7 @@
 import logging
 from contextlib import AbstractContextManager, nullcontext
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any
 
 import pytest
 from nibabel.filebasedimages import ImageFileError
@@ -516,7 +516,7 @@ def test_queue_with_imports(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    with_: Union[str, list[str]],
+    with_: str | list[str],
 ) -> None:
     """Test queue with `with` imports.
 
@@ -742,7 +742,7 @@ def test_reset_queue(
 )
 def test_list_elements(
     datagrabber: dict[str, str],
-    elements: Optional[list[tuple[str, ...]]],
+    elements: list[tuple[str, ...]] | None,
 ) -> None:
     """Test elements listing.
 

junifer/cli/cli.py

@@ -8,7 +8,6 @@ import pathlib
 import subprocess
 import sys
 from pathlib import Path
-from typing import Optional, Union
 
 import click
 
@@ -46,7 +45,7 @@ __all__ = [
 
 
 def _validate_optional_verbose(
-    ctx: click.Context, param: str, value: Optional[str]
+    ctx: click.Context, param: str, value: str | None
 ):
     """Validate optional verbose option.
 
@@ -71,9 +70,7 @@ def _validate_optional_verbose(
         return _validate_verbose(ctx, param, value)
 
 
-def _validate_verbose(
+def _validate_verbose(ctx: click.Context, param: str, value: str) -> str | int:
-    ctx: click.Context, param: str, value: str
-) -> Union[str, int]:
     """Validate verbose option.
 
     Parameters
@@ -142,8 +139,8 @@ def cli() -> None:  # pragma: no cover
 def run(
     filepath: click.Path,
     element: tuple[str],
-    verbose: Union[str, int],
+    verbose: str | int,
-    verbose_datalad: Optional[Union[str, int]],
+    verbose_datalad: str | int | None,
 ) -> None:
     """Run feature extraction.
 
@@ -214,8 +211,8 @@ def run(
 )
 def collect(
     filepath: click.Path,
-    verbose: Union[str, int],
+    verbose: str | int,
-    verbose_datalad: Union[str, int, None],
+    verbose_datalad: str | int | None,
 ) -> None:
     """Collect extracted features.
 
@@ -270,8 +267,8 @@ def queue(
     element: tuple[str],
     overwrite: bool,
     submit: bool,
-    verbose: Union[str, int],
+    verbose: str | int,
-    verbose_datalad: Union[str, int, None],
+    verbose_datalad: str | int | None,
 ) -> None:
     """Queue feature extraction.
 
@@ -433,8 +430,8 @@ def selftest(subpkg: str) -> None:
 )
 def reset(
     filepath: click.Path,
-    verbose: Union[str, int],
+    verbose: str | int,
-    verbose_datalad: Union[str, int, None],
+    verbose_datalad: str | int | None,
 ) -> None:
     """Reset generated assets.
 
@@ -487,9 +484,9 @@ def reset(
 def list_elements(
     filepath: click.Path,
     element: tuple[str],
-    output_file: Optional[click.Path],
+    output_file: click.Path | None,
-    verbose: Union[str, int],
+    verbose: str | int,
-    verbose_datalad: Union[str, int, None],
+    verbose_datalad: str | int | None,
 ) -> None:
     """List elements of a dataset.
 

junifer/cli/parser.py

@@ -8,7 +8,6 @@ import importlib
 import importlib.util
 import sys
 from pathlib import Path
-from typing import Union
 
 import pandas as pd
 
@@ -19,7 +18,7 @@ from ..utils import logger, raise_error, warn_with_log, yaml
 __all__ = ["parse_elements", "parse_yaml"]
 
 
-def parse_yaml(filepath: Union[str, Path]) -> dict:  # noqa: C901
+def parse_yaml(filepath: str | Path) -> dict:  # noqa: C901
     """Parse YAML.
 
     Parameters
@@ -141,9 +140,7 @@ def parse_yaml(filepath: Union[str, Path]) -> dict:  # noqa: C901
     return contents
 
 
-def parse_elements(
+def parse_elements(element: tuple[str, ...], config: dict) -> Elements | None:
-    element: tuple[str, ...], config: dict
-) -> Union[Elements, None]:
     """Parse elements from cli.
 
     Parameters

junifer/cli/tests/test_cli.py

@@ -4,8 +4,8 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable
 
 import pytest
 from click.testing import CliRunner

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -5,7 +5,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
 
 from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
@@ -29,7 +28,7 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
 
     """
 
-    def __init__(self, datadir: Union[str, Path, None] = None) -> None:
+    def __init__(self, datadir: str | Path | None = None) -> None:
         uri = "https://gin.g-node.org/felixh/ds003097_ReproVBM"
         types = ["VBM_GM"]
         replacements = ["subject"]

junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
 
 from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
@@ -30,7 +29,7 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
 
     """
 
-    def __init__(self, datadir: Union[str, Path, None] = None) -> None:
+    def __init__(self, datadir: str | Path | None = None) -> None:
         uri = (
             "ria+http://cat_12.5.ds.inm7.de"
             "#a139b26a-8406-11ea-8f94-a0369f287950"

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
 
 from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
@@ -36,8 +35,8 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
 
     def __init__(
         self,
-        datadir: Union[str, Path, None] = None,
+        datadir: str | Path | None = None,
-        sites: Union[str, list[str], None] = None,
+        sites: str | list[str] | None = None,
     ) -> None:
         uri = (
             "ria+http://cat_12.5.ds.inm7.de"

junifer/configs/juseless/datagrabbers/tests/test_ucla.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 import socket
-from typing import Optional, Union
 
 import pytest
 
@@ -53,7 +52,7 @@ def test_JuselessUCLA() -> None:
     ],
 )
 def test_JuselessUCLA_partial_data_access(
-    types: Union[str, list[str]],
+    types: str | list[str],
 ) -> None:
     """Test JuselessUCLA DataGrabber partial data access.
 
@@ -92,7 +91,7 @@ def test_JuselessUCLA_incorrect_data_type() -> None:
     "tasks",
     [None, "rest", ["rest", "stopsignal"]],
 )
-def test_JuselessUCLA_task_params(tasks: Optional[str]) -> None:
+def test_JuselessUCLA_task_params(tasks: str | None) -> None:
     """Test JuselessUCLA with different task parameters.
 
     Parameters

junifer/configs/juseless/datagrabbers/ucla.py

@@ -5,7 +5,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
 
 from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataGrabber
@@ -40,11 +39,9 @@ class JuselessUCLA(PatternDataGrabber):
 
     def __init__(
         self,
-        datadir: Union[
+        datadir: str | Path = "/data/project/psychosis_thalamus/data/fmriprep",
-            str, Path
+        types: str | list[str] | None = None,
-        ] = "/data/project/psychosis_thalamus/data/fmriprep",
+        tasks: str | list[str] | None = None,
-        types: Union[str, list[str], None] = None,
-        tasks: Union[str, list[str], None] = None,
     ) -> None:
         # Declare all tasks
         all_tasks = [

junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
 
 from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
@@ -30,7 +29,7 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber):
 
     """
 
-    def __init__(self, datadir: Union[str, Path, None] = None) -> None:
+    def __init__(self, datadir: str | Path | None = None) -> None:
         uri = "ria+http://ukb.ds.inm7.de#~cat_m0wp1"
         rootdir = "m0wp1"
         types = ["VBM_GM"]

junifer/data/_dispatch.py

@@ -3,12 +3,11 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from collections.abc import Iterator, MutableMapping
+from collections.abc import Callable, Iterator, MutableMapping
 from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     Any,
-    Callable,
     Optional,
     Union,
 )
@@ -110,14 +109,9 @@ class DataDispatcher(MutableMapping):
 
 def get_data(
     kind: str,
-    names: Union[
+    names: str | list[str] | dict | list[dict],
-        str,  # coordinates, parcellation, mask
-        list[str],  # parcellation, mask
-        dict,  # mask
-        list[dict],  # mask
-    ],
     target_data: dict[str, Any],
-    extra_input: Optional[dict[str, Any]] = None,
+    extra_input: dict[str, Any] | None = None,
 ) -> Union[
     tuple[ArrayLike, list[str]],  # coordinates
     tuple["Nifti1Image", dict[int, str]],  # parcellation
@@ -196,15 +190,11 @@ def load_data(
     kind: str,
     name: str,
     **kwargs,
-) -> Union[
+) -> (
-    tuple[ArrayLike, list[str], str],  # coordinates
+    tuple[ArrayLike, list[str], str]
-    tuple[
+    | tuple[Optional["Nifti1Image"], list[str], Path, str]
-        Optional["Nifti1Image"], list[str], Path, str
+    | tuple[Union["Nifti1Image", Callable] | None, Path | None, str]
-    ],  # parcellation / maps
+):
-    tuple[
-        Optional[Union["Nifti1Image", Callable]], Optional[Path], str
-    ],  # mask
-]:
     """Load ``kind`` named ``name``.
 
     Parameters

junifer/data/coordinates/_coordinates.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Any, Optional
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -135,7 +135,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry):
         coordinates: ArrayLike,
         voi_names: list[str],
         space: str,
-        overwrite: Optional[bool] = False,
+        overwrite: bool | None = False,
     ) -> None:
         """Register a custom user coordinates.
 
@@ -302,7 +302,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry):
         self,
         coords: str,
         target_data: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> tuple[ArrayLike, list[str]]:
         """Get coordinates, tailored for the target data.
 

junifer/data/maps/_ants_maps_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Optional
+from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
 
@@ -34,7 +34,7 @@ class ANTsMapsWarper:
         src: str,
         dst: str,
         target_data: dict[str, Any],
-        warp_data: Optional[dict[str, Any]],
+        warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":
         """Warp ``maps_img`` to correct space.
 

junifer/data/maps/_maps.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Optional, Union
+from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
 import nilearn.image as nimg
@@ -74,7 +74,7 @@ class MapsRegistry(BasePipelineDataRegistry):
     def register(
         self,
         name: str,
-        maps_path: Union[str, Path],
+        maps_path: str | Path,
         maps_labels: list[str],
         space: str,
         overwrite: bool = False,
@@ -156,7 +156,7 @@ class MapsRegistry(BasePipelineDataRegistry):
         self,
         name: str,
         target_space: str,
-        resolution: Optional[float] = None,
+        resolution: float | None = None,
         path_only: bool = False,
     ) -> tuple[Optional["Nifti1Image"], list[str], Path, str]:
         """Load map(s) and labels.
@@ -251,7 +251,7 @@ class MapsRegistry(BasePipelineDataRegistry):
         self,
         maps: str,
         target_data: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> tuple["Nifti1Image", list[str]]:
         """Get map(s), tailored for the target image.
 
@@ -376,9 +376,9 @@ class MapsRegistry(BasePipelineDataRegistry):
 
 
 def _retrieve_smith(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
-    components: Optional[str] = None,
+    components: str | None = None,
-    dimension: Optional[int] = None,
+    dimension: int | None = None,
 ) -> tuple[Path, list[str]]:
     """Retrieve Smith maps.
 

junifer/data/masks/_ants_mask_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Optional
+from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
 import numpy as np
@@ -55,7 +55,7 @@ class ANTsMaskWarper:
         src: str,
         dst: str,
         target_data: dict[str, Any],
-        warp_data: Optional[dict[str, Any]],
+        warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":  # pragma: no cover
         """Warp ``mask_img`` to correct space.
 

junifer/data/masks/_masks.py

@@ -4,12 +4,11 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+from collections.abc import Callable
 from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     Any,
-    Callable,
-    Optional,
     Union,
 )
 
@@ -45,12 +44,12 @@ __all__ = ["MaskRegistry", "compute_brain_mask"]
 
 def compute_brain_mask(
     target_data: dict[str, Any],
-    warp_data: Optional[dict[str, Any]] = None,
+    warp_data: dict[str, Any] | None = None,
     mask_type: str = "brain",
     threshold: float = 0.5,
     source: str = "template",
-    template_space: Optional[str] = None,
+    template_space: str | None = None,
-    extra_input: Optional[dict[str, Any]] = None,
+    extra_input: dict[str, Any] | None = None,
 ) -> "Nifti1Image":
     """Compute the whole-brain, grey-matter or white-matter mask.
 
@@ -281,7 +280,7 @@ class MaskRegistry(BasePipelineDataRegistry):
     def register(
         self,
         name: str,
-        mask_path: Union[str, Path],
+        mask_path: str | Path,
         space: str,
         overwrite: bool = False,
     ) -> None:
@@ -355,9 +354,9 @@ class MaskRegistry(BasePipelineDataRegistry):
     def load(
         self,
         name: str,
-        resolution: Optional[float] = None,
+        resolution: float | None = None,
         path_only: bool = False,
-    ) -> tuple[Optional[Union["Nifti1Image", Callable]], Optional[Path], str]:
+    ) -> tuple[Union["Nifti1Image", Callable] | None, Path | None, str]:
         """Load mask.
 
         Parameters
@@ -428,9 +427,9 @@ class MaskRegistry(BasePipelineDataRegistry):
 
     def get(  # noqa: C901
         self,
-        masks: Union[str, dict, list[Union[dict, str]]],
+        masks: str | dict | list[dict | str],
         target_data: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> "Nifti1Image":
         """Get mask, tailored for the target image.
 
@@ -718,7 +717,7 @@ class MaskRegistry(BasePipelineDataRegistry):
 
 def _load_vickery_patil_mask(
     name: str,
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
 ) -> Path:
     """Load Vickery-Patil mask.
 

junifer/data/masks/tests/test_masks.py

@@ -6,8 +6,8 @@
 # License: AGPL
 
 import socket
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable, Optional, Union
 
 import nibabel as nib
 import numpy as np
@@ -264,7 +264,7 @@ def test_load_incorrect() -> None:
 )
 def test_vickery_patil(
     name: str,
-    resolution: Optional[float],
+    resolution: float | None,
     pixdim: list[float],
     fname: str,
 ) -> None:
@@ -417,7 +417,7 @@ def test_get_errors() -> None:
 def test_nilearn_compute_masks(
     mask_name: str,
     function: Callable,
-    params: Union[dict, None],
+    params: dict | None,
     resample: bool,
 ) -> None:
     """Test using nilearn compute mask functions.
@@ -502,7 +502,7 @@ def test_get_inherit() -> None:
     ],
 )
 def test_get_multiple(
-    masks: Union[str, dict, list[Union[dict, str]]], params: dict
+    masks: str | dict | list[dict | str], params: dict
 ) -> None:
     """Test getting multiple masks.
 

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Optional
+from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
 
@@ -34,7 +34,7 @@ class ANTsParcellationWarper:
         src: str,
         dst: str,
         target_data: dict[str, Any],
-        warp_data: Optional[dict[str, Any]],
+        warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":
         """Warp ``parcellation_img`` to correct space.
 

junifer/data/parcellations/_parcellations.py

@@ -7,7 +7,7 @@
 
 from itertools import product
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Optional, Union
+from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
 import nilearn.image as nimg
@@ -226,7 +226,7 @@ class ParcellationRegistry(BasePipelineDataRegistry):
     def register(
         self,
         name: str,
-        parcellation_path: Union[str, Path],
+        parcellation_path: str | Path,
         parcels_labels: list[str],
         space: str,
         overwrite: bool = False,
@@ -309,7 +309,7 @@ class ParcellationRegistry(BasePipelineDataRegistry):
         self,
         name: str,
         target_space: str,
-        resolution: Optional[float] = None,
+        resolution: float | None = None,
         path_only: bool = False,
     ) -> tuple[Optional["Nifti1Image"], list[str], Path, str]:
         """Load parcellation and labels.
@@ -463,9 +463,9 @@ class ParcellationRegistry(BasePipelineDataRegistry):
 
     def get(
         self,
-        parcellations: Union[str, list[str]],
+        parcellations: str | list[str],
         target_data: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> tuple["Nifti1Image", dict[int, str]]:
         """Get parcellation, tailored for the target image.
 
@@ -608,6 +608,7 @@ class ParcellationRegistry(BasePipelineDataRegistry):
                         )
                     ),
                     all_labels[0],
+                    strict=False,
                 )
             )
         # Parcellations are already transformed to target standard space
@@ -623,8 +624,8 @@ class ParcellationRegistry(BasePipelineDataRegistry):
 
 
 def _retrieve_schaefer(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
-    n_rois: Optional[int] = None,
+    n_rois: int | None = None,
     yeo_networks: int = 7,
 ) -> tuple[Path, list[str]]:
     """Retrieve Schaefer parcellation.
@@ -707,8 +708,8 @@ def _retrieve_schaefer(
 
 
 def _retrieve_tian(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
-    scale: Optional[int] = None,
+    scale: int | None = None,
     space: str = "MNI152NLin6Asym",
     magneticfield: str = "3T",
 ) -> tuple[Path, list[str]]:
@@ -847,7 +848,7 @@ def _retrieve_tian(
 
 
 def _retrieve_suit(
-    resolution: Optional[float],
+    resolution: float | None,
     space: str = "MNI152NLin6Asym",
 ) -> tuple[Path, list[str]]:
     """Retrieve SUIT parcellation.
@@ -919,7 +920,7 @@ def _retrieve_suit(
 
 
 def _retrieve_aicha(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
     version: int = 2,
 ) -> tuple[Path, list[str]]:
     """Retrieve AICHA parcellation.
@@ -1013,7 +1014,7 @@ def _retrieve_aicha(
 
 
 def _retrieve_shen(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
     year: int = 2015,
     n_rois: int = 268,
 ) -> tuple[Path, list[str]]:
@@ -1139,10 +1140,10 @@ def _retrieve_shen(
 
 
 def _retrieve_yan(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
-    n_rois: Optional[int] = None,
+    n_rois: int | None = None,
-    yeo_networks: Optional[int] = None,
+    yeo_networks: int | None = None,
-    kong_networks: Optional[int] = None,
+    kong_networks: int | None = None,
 ) -> tuple[Path, list[str]]:
     """Retrieve Yan parcellation.
 
@@ -1264,8 +1265,8 @@ def _retrieve_yan(
 
 
 def _retrieve_brainnetome(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
-    threshold: Optional[int] = None,
+    threshold: int | None = None,
 ) -> tuple[Path, list[str]]:
     """Retrieve Brainnetome parcellation.
 
@@ -1355,7 +1356,7 @@ def _retrieve_brainnetome(
 
 
 def _retrieve_aseg(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
 ) -> tuple[Path, list[str]]:
     """Retrieve aseg generated from FreeSurfer 7.4.1 .
 
@@ -1455,7 +1456,7 @@ def _retrieve_aseg(
 
 
 def _retrieve_glasser(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
 ) -> tuple[Path, list[str]]:
     """Retrieve Glasser v1.0 .
 
@@ -1499,7 +1500,7 @@ def _retrieve_glasser(
 
 
 def _retrieve_julich_brain(
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
     version: str = "v3_1",
 ) -> tuple[Path, list[str]]:
     """Retrieve Julich-Brain labelled parcellations.
@@ -1613,11 +1614,12 @@ def merge_parcellations(
         zip(
             np.trim_zeros(np.unique(ref_parc_data.astype(int))),
             labels_lists[0],
+            strict=False,
         ),
     )
 
     for idx, (parc, labs) in enumerate(
-        zip(parcellations_list[1:], labels_lists[1:])
+        zip(parcellations_list[1:], labels_lists[1:], strict=False)
     ):
         # Resample to reference (1st in the list) parcellation
         if parc.shape != ref_parc.shape:
@@ -1637,7 +1639,13 @@ def merge_parcellations(
         # and update label mapping
         parc_data[parc_data != 0] += (idx + 1) * max_val
         val_label_map.update(
-            dict(zip(np.trim_zeros(np.unique(parc_data.astype(int))), labs))
+            dict(
+                zip(
+                    np.trim_zeros(np.unique(parc_data.astype(int))),
+                    labs,
+                    strict=False,
+                )
+            )
         )
         # Only set new values for the voxels that are 0
         # This makes sure that the voxels that are in multiple

junifer/data/template_spaces.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, Union
 
 import nibabel as nib
 import numpy as np
@@ -47,9 +47,9 @@ def get_xfm(src: str, dst: str) -> Path:  # pragma: no cover
 def get_template(
     space: str,
     target_img: nib.Nifti1Image,
-    extra_input: Optional[dict[str, Any]] = None,
+    extra_input: dict[str, Any] | None = None,
     template_type: str = "T1w",
-    resolution: Optional[Union[int, "str"]] = None,
+    resolution: Union[int, "str"] | None = None,
 ) -> nib.Nifti1Image:
     """Get template for the space, tailored for the target image.
 

junifer/data/utils.py

@@ -6,7 +6,6 @@
 
 from collections.abc import MutableMapping
 from pathlib import Path
-from typing import Optional, Union
 
 import numpy as np
 
@@ -36,9 +35,9 @@ JUNIFER_DATA_PARAMS = {
 
 
 def closest_resolution(
-    resolution: Optional[Union[float, int]],
+    resolution: float | int | None,
-    valid_resolution: Union[list[float], list[int], np.ndarray],
+    valid_resolution: list[float] | list[int] | np.ndarray,
-) -> Union[float, int]:
+) -> float | int:
     """Find the closest resolution.
 
     Parameters
@@ -136,7 +135,7 @@ def get_native_warper(
     return possible_warpers[0]
 
 
-def get_dataset_path() -> Optional[Path]:
+def get_dataset_path() -> Path | None:
     """Get junifer-data dataset path.
 
     Returns

junifer/datagrabber/aomic/id1000.py

@@ -8,7 +8,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -45,8 +44,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
 
     def __init__(
         self,
-        datadir: Union[str, Path, None] = None,
+        datadir: str | Path | None = None,
-        types: Union[str, list[str], None] = None,
+        types: str | list[str] | None = None,
         space: str = "MNI152NLin2009cAsym",
     ) -> None:
         valid_spaces = ["native", "MNI152NLin2009cAsym"]

junifer/datagrabber/aomic/piop1.py

@@ -9,7 +9,6 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -51,9 +50,9 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
 
     def __init__(
         self,
-        datadir: Union[str, Path, None] = None,
+        datadir: str | Path | None = None,
-        types: Union[str, list[str], None] = None,
+        types: str | list[str] | None = None,
-        tasks: Union[str, list[str], None] = None,
+        tasks: str | list[str] | None = None,
         space: str = "MNI152NLin2009cAsym",
     ) -> None:
         valid_spaces = ["native", "MNI152NLin2009cAsym"]

junifer/datagrabber/aomic/piop2.py

@@ -9,7 +9,6 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -51,9 +50,9 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
 
     def __init__(
         self,
-        datadir: Union[str, Path, None] = None,
+        datadir: str | Path | None = None,
-        types: Union[str, list[str], None] = None,
+        types: str | list[str] | None = None,
-        tasks: Union[str, list[str], None] = None,
+        tasks: str | list[str] | None = None,
         space: str = "MNI152NLin2009cAsym",
     ) -> None:
         valid_spaces = ["native", "MNI152NLin2009cAsym"]

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -7,8 +7,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import pytest
 
 from junifer.datagrabber.aomic.id1000 import DataladAOMICID1000
@@ -35,7 +33,7 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 )
 def test_DataladAOMICID1000(
     type_: str,
-    nested_types: Optional[list[str]],
+    nested_types: list[str] | None,
     space: str,
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber.
@@ -94,7 +92,7 @@ def test_DataladAOMICID1000(
     ],
 )
 def test_DataladAOMICID1000_partial_data_access(
-    types: Union[str, list[str]],
+    types: str | list[str],
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber partial data access.
 

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -7,8 +7,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import pytest
 
 from junifer.datagrabber import DataladAOMICPIOP1
@@ -71,8 +69,8 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 )
 def test_DataladAOMICPIOP1(
     type_: str,
-    nested_types: Optional[list[str]],
+    nested_types: list[str] | None,
-    tasks: Optional[list[str]],
+    tasks: list[str] | None,
     space: str,
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
@@ -151,7 +149,7 @@ def test_DataladAOMICPIOP1(
     ],
 )
 def test_DataladAOMICPIOP1_partial_data_access(
-    types: Union[str, list[str]],
+    types: str | list[str],
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber partial data access.
 

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -7,8 +7,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import pytest
 
 from junifer.datagrabber import DataladAOMICPIOP2
@@ -65,8 +63,8 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
 )
 def test_DataladAOMICPIOP2(
     type_: str,
-    nested_types: Optional[list[str]],
+    nested_types: list[str] | None,
-    tasks: Optional[list[str]],
+    tasks: list[str] | None,
     space: str,
 ) -> None:
     """Test DataladAOMICPIOP2 DataGrabber.
@@ -130,7 +128,7 @@ def test_DataladAOMICPIOP2(
     ],
 )
 def test_DataladAOMICPIOP2_partial_data_access(
-    types: Union[str, list[str]],
+    types: str | list[str],
 ) -> None:
     """Test DataladAOMICPIOP2 DataGrabber partial data access.
 

junifer/datagrabber/base.py

@@ -8,7 +8,6 @@
 from abc import ABC, abstractmethod
 from collections.abc import Iterator
 from pathlib import Path
-from typing import Union
 
 from ..pipeline import UpdateMetaMixin
 from ..typing import Element, Elements
@@ -38,7 +37,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
 
     """
 
-    def __init__(self, types: list[str], datadir: Union[str, Path]) -> None:
+    def __init__(self, types: list[str], datadir: str | Path) -> None:
         # Validate types
         if not isinstance(types, list):
             raise_error(msg="`types` must be a list", klass=TypeError)
@@ -89,7 +88,9 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
             element = (element,)
         # Zip through element keys and actual values to construct element
         # access dictionary
-        named_element: dict = dict(zip(self.get_element_keys(), element))
+        named_element: dict = dict(
+            zip(self.get_element_keys(), element, strict=False)
+        )
         logger.debug(f"Named element: {named_element}")
         # Fetch element
         out = self.get_item(**named_element)

junifer/datagrabber/datalad_base.py

@@ -9,7 +9,6 @@ import atexit
 import os
 import tempfile
 from pathlib import Path
-from typing import Optional, Union
 
 import datalad
 import datalad.api as dl
@@ -71,9 +70,9 @@ class DataladDataGrabber(BaseDataGrabber):
 
     def __init__(
         self,
-        rootdir: Union[str, Path] = ".",
+        rootdir: str | Path = ".",
-        datadir: Union[str, Path, None] = None,
+        datadir: str | Path | None = None,
-        uri: Optional[str] = None,
+        uri: str | None = None,
         **kwargs,
     ):
         if datadir is None:

junifer/datagrabber/dmcc13_benchmark.py

@@ -5,7 +5,6 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Union
 
 from ..api.decorators import register_datagrabber
 from ..utils import raise_error
@@ -58,12 +57,12 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
 
     def __init__(
         self,
-        datadir: Union[str, Path, None] = None,
+        datadir: str | Path | None = None,
-        types: Union[str, list[str], None] = None,
+        types: str | list[str] | None = None,
-        sessions: Union[str, list[str], None] = None,
+        sessions: str | list[str] | None = None,
-        tasks: Union[str, list[str], None] = None,
+        tasks: str | list[str] | None = None,
-        phase_encodings: Union[str, list[str], None] = None,
+        phase_encodings: str | list[str] | None = None,
-        runs: Union[str, list[str], None] = None,
+        runs: str | list[str] | None = None,
         native_t1w: bool = False,
     ) -> None:
         # Declare all sessions

junifer/datagrabber/hcp1200/datalad_hcp1200.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
 
 from junifer.datagrabber.datalad_base import DataladDataGrabber
 
@@ -49,9 +48,9 @@ class DataladHCP1200(DataladDataGrabber, HCP1200):
 
     def __init__(
         self,
-        datadir: Union[str, Path, None] = None,
+        datadir: str | Path | None = None,
-        tasks: Union[str, list[str], None] = None,
+        tasks: str | list[str] | None = None,
-        phase_encodings: Union[str, list[str], None] = None,
+        phase_encodings: str | list[str] | None = None,
         ica_fix: bool = False,
     ) -> None:
         uri = (

junifer/datagrabber/hcp1200/hcp1200.py

@@ -7,7 +7,6 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -47,9 +46,9 @@ class HCP1200(PatternDataGrabber):
 
     def __init__(
         self,
-        datadir: Union[str, Path],
+        datadir: str | Path,
-        tasks: Union[str, list[str], None] = None,
+        tasks: str | list[str] | None = None,
-        phase_encodings: Union[str, list[str], None] = None,
+        phase_encodings: str | list[str] | None = None,
         ica_fix: bool = False,
     ) -> None:
         # All tasks

junifer/datagrabber/hcp1200/tests/test_hcp1200.py

@@ -7,7 +7,6 @@ import shutil
 import tempfile
 from collections.abc import Iterable
 from pathlib import Path
-from typing import Optional
 
 import pytest
 
@@ -64,8 +63,8 @@ def hcpdg() -> Iterable[DataladHCP1200]:
 )
 def test_HCP1200(
     hcpdg: DataladHCP1200,
-    tasks: Optional[str],
+    tasks: str | None,
-    phase_encodings: Optional[str],
+    phase_encodings: str | None,
     ica_fix: bool,
     expected_path_name: str,
 ) -> None:
@@ -140,8 +139,8 @@ def test_HCP1200(
 )
 def test_HCP1200_single_access(
     hcpdg: DataladHCP1200,
-    tasks: Optional[str],
+    tasks: str | None,
-    phase_encodings: Optional[str],
+    phase_encodings: str | None,
 ) -> None:
     """Test HCP1200 DataGrabber single access.
 
@@ -180,8 +179,8 @@ def test_HCP1200_single_access(
 )
 def test_HCP1200_multi_access(
     hcpdg: DataladHCP1200,
-    tasks: Optional[str],
+    tasks: str | None,
-    phase_encodings: Optional[str],
+    phase_encodings: str | None,
 ) -> None:
     """Test HCP1200 DataGrabber multiple access.
 
@@ -275,8 +274,8 @@ def test_HCP1200_multi_access_phase_simple(
     ],
 )
 def test_HCP1200_incorrect_access_task(
-    tasks: Optional[str],
+    tasks: str | None,
-    phase_encodings: Optional[str],
+    phase_encodings: str | None,
 ) -> None:
     """Test HCP1200 DataGrabber incorrect access for task.
 
@@ -307,8 +306,8 @@ def test_HCP1200_incorrect_access_task(
     ],
 )
 def test_HCP1200_incorrect_access_phase(
-    tasks: Optional[str],
+    tasks: str | None,
-    phase_encodings: Optional[str],
+    phase_encodings: str | None,
 ) -> None:
     """Test HCP1200 DataGrabber incorrect access for phase.
 
@@ -374,7 +373,7 @@ def test_HCP1200_elements(
     ],
 )
 def test_HCP1200_incorrect_access_icafix(
-    tasks: Optional[str], ica_fix: bool
+    tasks: str | None, ica_fix: bool
 ) -> None:
     """Test HCP1200 DataGrabber incorrect access for icafix.
 

junifer/datagrabber/multiple.py

@@ -5,8 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Union
-
 from ..api.decorators import register_datagrabber
 from ..typing import DataGrabberLike
 from ..utils import deep_update, raise_error
@@ -79,7 +77,7 @@ class MultipleDataGrabber(BaseDataGrabber):
                 )
         self._datagrabbers = datagrabbers
 
-    def __getitem__(self, element: Union[str, tuple]) -> dict:
+    def __getitem__(self, element: str | tuple) -> dict:
         """Implement indexing.
 
         Parameters

junifer/datagrabber/pattern.py

@@ -8,7 +8,6 @@
 import re
 from copy import deepcopy
 from pathlib import Path
-from typing import Optional, Union
 
 import numpy as np
 
@@ -173,9 +172,9 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
         self,
         types: list[str],
         patterns: DataGrabberPatterns,
-        replacements: Union[list[str], str],
+        replacements: list[str] | str,
-        datadir: Union[str, Path],
+        datadir: str | Path,
-        confounds_format: Optional[str] = None,
+        confounds_format: str | None = None,
         partial_pattern_ok: bool = False,
     ) -> None:
         # Convert replacements to list if not already

junifer/datagrabber/tests/test_dmcc13_benchmark.py

@@ -3,8 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import pytest
 
 from junifer.datagrabber import DMCC13Benchmark
@@ -48,10 +46,10 @@ URI = "https://gin.g-node.org/synchon/datalad-example-dmcc13-benchmark"
     ],
 )
 def test_DMCC13Benchmark(
-    sessions: Optional[str],
+    sessions: str | None,
-    tasks: Optional[str],
+    tasks: str | None,
-    phase_encodings: Optional[str],
+    phase_encodings: str | None,
-    runs: Optional[str],
+    runs: str | None,
     native_t1w: bool,
 ) -> None:
     """Test DMCC13Benchmark DataGrabber.
@@ -129,7 +127,9 @@ def test_DMCC13Benchmark(
                 "sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz"
             )
 
-        for data_type, data_file_name in zip(data_types, data_file_names):
+        for data_type, data_file_name in zip(
+            data_types, data_file_names, strict=False
+        ):
             # Assert data type
             assert data_type in out
             # Conditional for Warp
@@ -166,6 +166,7 @@ def test_DMCC13Benchmark(
                     "desc-confounds_regressors.tsv"
                 ),
             ),
+            strict=False,
         ):
             # Assert data type
             assert type_ in out["BOLD"]
@@ -218,7 +219,7 @@ def test_DMCC13Benchmark(
     ],
 )
 def test_DMCC13Benchmark_partial_data_access(
-    types: Union[str, list[str]],
+    types: str | list[str],
     native_t1w: bool,
 ) -> None:
     """Test DMCC13Benchmark DataGrabber partial data access.

junifer/datagrabber/tests/test_pattern_validation_mixin.py

@@ -5,7 +5,6 @@
 # License: AGPL
 
 from contextlib import AbstractContextManager, nullcontext
-from typing import Union
 
 import pytest
 
@@ -289,9 +288,9 @@ def test_register_data_type() -> None:
     ],
 )
 def test_PatternValidationMixin(
-    types: Union[str, list[str], list[int]],
+    types: str | list[str] | list[int],
-    replacements: Union[str, list[str], list[int]],
+    replacements: str | list[str] | list[int],
-    patterns: Union[str, dict[str, dict[str, str]]],
+    patterns: str | dict[str, dict[str, str]],
     expect: AbstractContextManager,
 ) -> None:
     """Test validation.

junifer/datareader/default.py

@@ -5,7 +5,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Optional, Union
 
 import nibabel as nib
 import pandas as pd
@@ -59,7 +58,7 @@ class DefaultDataReader(PipelineStepMixin, UpdateMetaMixin):
     def _fit_transform(
         self,
         input: dict[str, dict],
-        params: Optional[dict] = None,
+        params: dict | None = None,
     ) -> dict:
         """Fit and transform.
 
@@ -149,7 +148,7 @@ class DefaultDataReader(PipelineStepMixin, UpdateMetaMixin):
 
 def _read_data(
     data_type: str, path: Path, read_params: dict
-) -> Union[nib.Nifti1Image, pd.DataFrame, None]:
+) -> nib.Nifti1Image | pd.DataFrame | None:
     """Read data for data type.
 
     Parameters

junifer/external/nilearn/junifer_connectivity_measure.py

@@ -3,9 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import sys
+from collections.abc import Callable
 from itertools import product
-from typing import Callable, Optional
 
 import numpy as np
 from nilearn import signal
@@ -189,9 +188,9 @@ def _map_eigenvalues(
 
 def _geometric_mean(
     matrices: list[np.ndarray],
-    init: Optional[np.ndarray] = None,
+    init: np.ndarray | None = None,
     max_iter: int = 10,
-    tol: Optional[float] = 1e-7,
+    tol: float | None = 1e-7,
 ) -> np.ndarray:
     """Compute the geometric mean of symmetric positive definite matrices.
 
@@ -431,14 +430,6 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
 
             connectivities = [cov_to_corr(cov) for cov in covariances_std]
         elif self.kind == "xi correlation":
-            if sys.version_info < (3, 10):  # pragma: no cover
-                raise_error(
-                    klass=RuntimeError,
-                    msg=(
-                        "scipy.stats.chatterjeexi is available from "
-                        "scipy 1.15.0 and that requires Python 3.10 and above."
-                    ),
-                )
             connectivities = []
             for x in X:
                 n_rois = x.shape[1]

junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -3,7 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import TYPE_CHECKING, Callable, Optional, Union
+from collections.abc import Callable
+from typing import TYPE_CHECKING, Union
 
 import numpy as np
 from nilearn import image, masking
@@ -133,7 +134,7 @@ def _apply_mask_and_get_affinity(
             interpolation="nearest",
         )
         mask, _ = masking.load_mask_img(mask_img)
-        mask_coords = list(zip(*np.where(mask != 0)))
+        mask_coords = list(zip(*np.where(mask != 0), strict=False))
 
         X = masking.apply_mask_fmri(niimg, mask_img)
 
@@ -166,7 +167,7 @@ def _apply_mask_and_get_affinity(
         except ValueError:
             nearests.append(None)
 
-    mask_coords = np.asarray(list(zip(*mask_coords)))
+    mask_coords = np.asarray(list(zip(*mask_coords, strict=False)))
     mask_coords = image.resampling.coord_transform(
         mask_coords[0], mask_coords[1], mask_coords[2], affine
     )
@@ -255,7 +256,7 @@ class _JuniferExtractionFunctor:
     def __init__(
         self,
         seeds_: "ArrayLike",
-        radius: Optional[float],
+        radius: float | None,
         mask_img: Union["Nifti1Image", "Nifti2Image", None],
         agg_func: Callable,
         allow_overlap: bool,
@@ -352,7 +353,7 @@ class JuniferNiftiSpheresMasker(NiftiSpheresMasker):
     def __init__(
         self,
         seeds: "ArrayLike",
-        radius: Optional[float] = None,
+        radius: float | None = None,
         mask_img: Union["Nifti1Image", "Nifti2Image", None] = None,
         agg_func: Callable = np.mean,
         allow_overlap: bool = False,

junifer/external/nilearn/tests/test_junifer_connectivity_measure.py

@@ -7,7 +7,7 @@ import copy
 import sys
 import warnings
 from math import cosh, exp, log, sinh, sqrt
-from typing import TYPE_CHECKING, Optional, Union
+from typing import TYPE_CHECKING, Optional
 
 import numpy as np
 import pytest
@@ -88,7 +88,7 @@ def random_diagonal(
     p: int,
     v_min: float = 1.0,
     v_max: float = 2.0,
-    random_state: Union[int, np.random.RandomState] = 0,
+    random_state: int | np.random.RandomState = 0,
 ) -> np.ndarray:
     """Generate a random diagonal matrix.
 
@@ -120,7 +120,7 @@ def random_spd(
     p: int,
     eig_min: float,
     cond: float,
-    random_state: Union[int, np.random.RandomState] = 0,
+    random_state: int | np.random.RandomState = 0,
 ) -> np.ndarray:
     """Generate a random symmetric positive definite matrix.
 
@@ -190,7 +190,7 @@ def signals() -> list[np.ndarray]:
 
 @pytest.fixture
 def signals_and_covariances(
-    cov_estimator: Union[LedoitWolf, EmpiricalCovariance],
+    cov_estimator: LedoitWolf | EmpiricalCovariance,
 ) -> tuple[list[np.ndarray], list[float]]:
     """Return signals and covariances for a covariance estimator.
 
@@ -343,7 +343,7 @@ def test_geometric_mean_properties() -> None:
 
     # Generic
     assert isinstance(spds, list)
-    for spd, input_spd in zip(spds, input_spds):
+    for spd, input_spd in zip(spds, input_spds, strict=False):
         assert_array_equal(spd, input_spd)
     assert is_spd(gmean, decimal=7)
 
@@ -352,7 +352,7 @@ def random_non_singular(
     p: int,
     sing_min: float = 1.0,
     sing_max: float = 2.0,
-    random_state: Union[int, np.random.RandomState] = 0,
+    random_state: int | np.random.RandomState = 0,
 ) -> np.ndarray:
     """Generate a random nonsingular matrix.
 
@@ -669,7 +669,7 @@ def _assert_connectivity_tangent(connectivities, conn_measure, covs) -> None:
 
     """
     for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
+        covs, connectivities, strict=False
     ):
         assert_array_almost_equal(
             estimated_covariance_matrix, estimated_covariance_matrix.T
@@ -701,7 +701,7 @@ def _assert_connectivity_precision(connectivities, covs) -> None:
 
     """
     for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
+        covs, connectivities, strict=False
     ):
         assert is_spd(estimated_covariance_matrix, decimal=7)
         assert_array_almost_equal(
@@ -729,7 +729,7 @@ def _assert_connectivity_correlation(
 
     """
     for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
+        covs, connectivities, strict=False
     ):
         assert is_spd(estimated_covariance_matrix, decimal=7)
 
@@ -750,7 +750,7 @@ def _assert_connectivity_correlation(
 def _assert_connectivity_partial_correlation(connectivities, covs) -> None:
     """Assert partial correlation connectivity matrix."""
     for true_covariance_matrix, estimated_covariance_matrix in zip(
-        covs, connectivities
+        covs, connectivities, strict=False
     ):
         precision_matrix = linalg.inv(true_covariance_matrix)
 

junifer/markers/base.py

@@ -6,7 +6,7 @@
 
 from abc import ABC, abstractmethod
 from copy import deepcopy
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..typing import MarkerInOutMappings, StorageLike
@@ -44,8 +44,8 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
 
     def __init__(
         self,
-        on: Optional[Union[list[str], str]] = None,
+        on: list[str] | str | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Check for missing mapping attribute
         if not hasattr(self, "_MARKER_INOUT_MAPPINGS"):
@@ -126,7 +126,7 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
         return self._MARKER_INOUT_MAPPINGS[input_type][output_feature]
 
     @abstractmethod
-    def compute(self, input: dict, extra_input: Optional[dict] = None) -> dict:
+    def compute(self, input: dict, extra_input: dict | None = None) -> dict:
         """Compute.
 
         Parameters
@@ -181,7 +181,7 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
     def _fit_transform(
         self,
         input: dict[str, dict],
-        storage: Optional[StorageLike] = None,
+        storage: StorageLike | None = None,
     ) -> dict:
         """Fit and transform.
 

junifer/markers/brainprint.py

@@ -8,8 +8,6 @@ from pathlib import Path
 from typing import (
     Any,
     ClassVar,
-    Optional,
-    Union,
 )
 
 import numpy as np
@@ -99,7 +97,7 @@ class BrainPrint(BaseMarker):
         asymmetry: bool = False,
         asymmetry_distance: str = "euc",
         use_cholmod: bool = False,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.num = num
         self.skip_cortex = skip_cortex
@@ -307,7 +305,7 @@ class BrainPrint(BaseMarker):
 
     def _fix_nan(
         self,
-        input_data: list[Union[float, str, npt.ArrayLike]],
+        input_data: list[float | str | npt.ArrayLike],
     ) -> np.ndarray:  # pragma: no cover
         """Convert BrainPrint output with string NaN to ``numpy.nan``.
 
@@ -329,7 +327,7 @@ class BrainPrint(BaseMarker):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict] = None,
+        extra_input: dict | None = None,
     ) -> dict:  # pragma: no cover
         """Compute.
 

junifer/markers/complexity/complexity_base.py

@@ -8,8 +8,6 @@ from typing import (
     TYPE_CHECKING,
     Any,
     ClassVar,
-    Optional,
-    Union,
 )
 
 from ...typing import Dependencies, MarkerInOutMappings
@@ -59,11 +57,11 @@ class ComplexityBase(BaseMarker):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.parcellation = parcellation
         self.agg_method = agg_method
@@ -85,7 +83,7 @@ class ComplexityBase(BaseMarker):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 

junifer/markers/complexity/hurst_exponent.py

@@ -4,8 +4,6 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import neurokit2 as nk
 import numpy as np
 
@@ -55,12 +53,12 @@ class HurstExponent(ComplexityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        params: Optional[dict] = None,
+        params: dict | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         super().__init__(
             parcellation=parcellation,

junifer/markers/complexity/multiscale_entropy_auc.py

@@ -4,8 +4,6 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import neurokit2 as nk
 import numpy as np
 
@@ -56,12 +54,12 @@ class MultiscaleEntropyAUC(ComplexityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        params: Optional[dict] = None,
+        params: dict | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         super().__init__(
             parcellation=parcellation,

junifer/markers/complexity/perm_entropy.py

@@ -4,8 +4,6 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import neurokit2 as nk
 import numpy as np
 
@@ -56,12 +54,12 @@ class PermEntropy(ComplexityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        params: Optional[dict] = None,
+        params: dict | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         super().__init__(
             parcellation=parcellation,

junifer/markers/complexity/range_entropy.py

@@ -4,8 +4,6 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import neurokit2 as nk
 import numpy as np
 
@@ -56,12 +54,12 @@ class RangeEntropy(ComplexityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        params: Optional[dict] = None,
+        params: dict | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         super().__init__(
             parcellation=parcellation,

junifer/markers/complexity/range_entropy_auc.py

@@ -4,8 +4,6 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import neurokit2 as nk
 import numpy as np
 
@@ -56,12 +54,12 @@ class RangeEntropyAUC(ComplexityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        params: Optional[dict] = None,
+        params: dict | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         super().__init__(
             parcellation=parcellation,
@@ -138,7 +136,11 @@ class RangeEntropyAUC(ComplexityBase):
                 range_ent_vec[idx_r] = range_en_auc_roi_tmp[0]
                 idx_r = idx_r + 1
 
-            range_en_auc_roi[idx_roi] = np.trapz(range_ent_vec)
+            range_en_auc_roi[idx_roi] = (
+                np.trapezoid(range_ent_vec)
+                if int(np.__version__[0]) > 1
+                else np.trapz(range_ent_vec)
+            )
 
         range_en_auc_roi = range_en_auc_roi / n_r
 

junifer/markers/complexity/sample_entropy.py

@@ -4,8 +4,6 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import neurokit2 as nk
 import numpy as np
 
@@ -57,12 +55,12 @@ class SampleEntropy(ComplexityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        params: Optional[dict] = None,
+        params: dict | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         super().__init__(
             parcellation=parcellation,

junifer/markers/complexity/weighted_perm_entropy.py

@@ -4,8 +4,6 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional, Union
-
 import neurokit2 as nk
 import numpy as np
 
@@ -57,12 +55,12 @@ class WeightedPermEntropy(ComplexityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        params: Optional[dict] = None,
+        params: dict | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         super().__init__(
             parcellation=parcellation,

junifer/markers/ets_rss.py

@@ -6,7 +6,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 import numpy as np
 
@@ -56,11 +56,11 @@ class RSSETSMarker(BaseMarker):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.parcellation = parcellation
         self.agg_method = agg_method
@@ -71,7 +71,7 @@ class RSSETSMarker(BaseMarker):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict] = None,
+        extra_input: dict | None = None,
     ) -> dict:
         """Compute.
 

junifer/markers/falff/_afni_falff.py

@@ -8,7 +8,6 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Optional,
 )
 
 import nibabel as nib
@@ -53,7 +52,7 @@ class AFNIALFF(metaclass=Singleton):
         input_path: Path,
         highpass: float,
         lowpass: float,
-        tr: Optional[float],
+        tr: float | None,
     ) -> tuple["Nifti1Image", "Nifti1Image", Path, Path]:
         """Compute ALFF + fALFF map.
 

junifer/markers/falff/_junifer_falff.py

@@ -8,7 +8,6 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Optional,
 )
 
 import nibabel as nib
@@ -50,7 +49,7 @@ class JuniferALFF(metaclass=Singleton):
         input_path: Path,
         highpass: float,
         lowpass: float,
-        tr: Optional[float],
+        tr: float | None,
     ) -> tuple["Nifti1Image", "Nifti1Image", Path, Path]:
         """Compute ALFF + fALFF map.
 

junifer/markers/falff/falff_base.py

@@ -11,7 +11,6 @@ from typing import (
     TYPE_CHECKING,
     Any,
     ClassVar,
-    Optional,
 )
 
 from ...typing import ConditionalDependencies, MarkerInOutMappings
@@ -91,8 +90,8 @@ class ALFFBase(BaseMarker):
         highpass: float,
         lowpass: float,
         using: str,
-        tr: Optional[float] = None,
+        tr: float | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         if highpass < 0:
             raise_error("Highpass must be positive or 0")

junifer/markers/falff/falff_maps.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ...utils import logger
@@ -65,9 +65,9 @@ class ALFFMaps(ALFFBase):
         using: str,
         highpass: float = 0.01,
         lowpass: float = 0.1,
-        tr: Optional[float] = None,
+        tr: float | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(
@@ -83,7 +83,7 @@ class ALFFMaps(ALFFBase):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 

junifer/markers/falff/falff_parcels.py

@@ -6,7 +6,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ...utils import logger
@@ -70,15 +70,15 @@ class ALFFParcels(ALFFBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         using: str,
         highpass: float = 0.01,
         lowpass: float = 0.1,
-        tr: Optional[float] = None,
+        tr: float | None = None,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(
@@ -96,7 +96,7 @@ class ALFFParcels(ALFFBase):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 

junifer/markers/falff/falff_spheres.py

@@ -6,7 +6,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ...utils import logger
@@ -79,15 +79,15 @@ class ALFFSpheres(ALFFBase):
         self,
         coords: str,
         using: str,
-        radius: Optional[float] = None,
+        radius: float | None = None,
         allow_overlap: bool = False,
         highpass: float = 0.01,
         lowpass: float = 0.1,
-        tr: Optional[float] = None,
+        tr: float | None = None,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(
@@ -107,7 +107,7 @@ class ALFFSpheres(ALFFBase):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 

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, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 import pandas as pd
 
@@ -63,10 +63,10 @@ class CrossParcellationFC(BaseMarker):
         parcellation_one: str,
         parcellation_two: str,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
         corr_method: str = "pearson",
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         if parcellation_one == parcellation_two:
             raise_error(
@@ -83,7 +83,7 @@ class CrossParcellationFC(BaseMarker):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict] = None,
+        extra_input: dict | None = None,
     ) -> dict:
         """Compute.
 

junifer/markers/functional_connectivity/edge_functional_connectivity_maps.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..maps_aggregation import MapsAggregation
@@ -54,9 +54,9 @@ class EdgeCentricFCMaps(FunctionalConnectivityBase):
         self,
         maps: str,
         conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
+        conn_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.maps = maps
         super().__init__(
@@ -67,7 +67,7 @@ class EdgeCentricFCMaps(FunctionalConnectivityBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform maps aggregation and ETS computation.
 

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..parcel_aggregation import ParcelAggregation
@@ -61,13 +61,13 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
+        conn_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.parcellation = parcellation
         super().__init__(
@@ -80,7 +80,7 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform parcel aggregation and ETS computation.
 

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..sphere_aggregation import SphereAggregation
@@ -70,14 +70,14 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
     def __init__(
         self,
         coords: str,
-        radius: Optional[float] = None,
+        radius: float | None = None,
         allow_overlap: bool = False,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
+        conn_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.coords = coords
         self.radius = radius
@@ -94,7 +94,7 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform sphere aggregation and ETS computation.
 

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
@@ -62,11 +62,11 @@ class FunctionalConnectivityBase(BaseMarker):
     def __init__(
         self,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
+        conn_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.agg_method = agg_method
         self.agg_method_params = agg_method_params
@@ -83,7 +83,7 @@ class FunctionalConnectivityBase(BaseMarker):
     def aggregate(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Perform aggregation."""
         raise_error(
@@ -94,7 +94,7 @@ class FunctionalConnectivityBase(BaseMarker):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict] = None,
+        extra_input: dict | None = None,
     ) -> dict:
         """Compute.
 

junifer/markers/functional_connectivity/functional_connectivity_maps.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..maps_aggregation import MapsAggregation
@@ -47,9 +47,9 @@ class FunctionalConnectivityMaps(FunctionalConnectivityBase):
         self,
         maps: str,
         conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
+        conn_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.maps = maps
         super().__init__(
@@ -60,7 +60,7 @@ class FunctionalConnectivityMaps(FunctionalConnectivityBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform maps aggregation.
 

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..parcel_aggregation import ParcelAggregation
@@ -55,13 +55,13 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
+        conn_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.parcellation = parcellation
         super().__init__(
@@ -74,7 +74,7 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform parcel aggregation.
 

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..sphere_aggregation import SphereAggregation
@@ -65,14 +65,14 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
     def __init__(
         self,
         coords: str,
-        radius: Optional[float] = None,
+        radius: float | None = None,
         allow_overlap: bool = False,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
         conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
+        conn_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.coords = coords
         self.radius = radius
@@ -89,7 +89,7 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform sphere aggregation.
 

junifer/markers/maps_aggregation.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 from nilearn.maskers import NiftiMapsMasker
 
@@ -88,11 +88,11 @@ class MapsAggregation(BaseMarker):
     def __init__(
         self,
         maps: str,
-        time_method: Optional[str] = None,
+        time_method: str | None = None,
-        time_method_params: Optional[dict[str, Any]] = None,
+        time_method_params: dict[str, Any] | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        on: Union[list[str], str, None] = None,
+        on: list[str] | str | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.maps = maps
         self.masks = masks
@@ -113,7 +113,7 @@ class MapsAggregation(BaseMarker):
         self.time_method_params = time_method_params or {}
 
     def compute(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Compute.
 

junifer/markers/parcel_aggregation.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 import numpy as np
 from nilearn.image import math_img
@@ -96,14 +96,14 @@ class ParcelAggregation(BaseMarker):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         method: str,
-        method_params: Optional[dict[str, Any]] = None,
+        method_params: dict[str, Any] | None = None,
-        time_method: Optional[str] = None,
+        time_method: str | None = None,
-        time_method_params: Optional[dict[str, Any]] = None,
+        time_method_params: dict[str, Any] | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        on: Union[list[str], str, None] = None,
+        on: list[str] | str | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         if not isinstance(parcellation, list):
             parcellation = [parcellation]
@@ -128,7 +128,7 @@ class ParcelAggregation(BaseMarker):
         self.time_method_params = time_method_params or {}
 
     def compute(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Compute.
 

junifer/markers/reho/_afni_reho.py

@@ -8,7 +8,6 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Optional,
 )
 
 import nibabel as nib
@@ -52,14 +51,14 @@ class AFNIReHo(metaclass=Singleton):
         self,
         input_path: Path,
         nneigh: int = 27,
-        neigh_rad: Optional[float] = None,
+        neigh_rad: float | None = None,
-        neigh_x: Optional[float] = None,
+        neigh_x: float | None = None,
-        neigh_y: Optional[float] = None,
+        neigh_y: float | None = None,
-        neigh_z: Optional[float] = None,
+        neigh_z: float | None = None,
-        box_rad: Optional[int] = None,
+        box_rad: int | None = None,
-        box_x: Optional[int] = None,
+        box_x: int | None = None,
-        box_y: Optional[int] = None,
+        box_y: int | None = None,
-        box_z: Optional[int] = None,
+        box_z: int | None = None,
     ) -> tuple["Nifti1Image", Path]:
         """Compute ReHo map.
 

junifer/markers/reho/reho_base.py

@@ -8,7 +8,6 @@ from typing import (
     TYPE_CHECKING,
     Any,
     ClassVar,
-    Optional,
 )
 
 from ...typing import ConditionalDependencies, MarkerInOutMappings
@@ -66,7 +65,7 @@ class ReHoBase(BaseMarker):
     def __init__(
         self,
         using: str,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Validate `using` parameter
         valid_using = [dep["using"] for dep in self._CONDITIONAL_DEPENDENCIES]

junifer/markers/reho/reho_maps.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 import numpy as np
 
@@ -87,9 +87,9 @@ class ReHoMaps(ReHoBase):
         self,
         maps: str,
         using: str,
-        reho_params: Optional[dict] = None,
+        reho_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(using=using, name=name)
@@ -100,7 +100,7 @@ class ReHoMaps(ReHoBase):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 

junifer/markers/reho/reho_parcels.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 import numpy as np
 
@@ -91,13 +91,13 @@ class ReHoParcels(ReHoBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         using: str,
-        reho_params: Optional[dict] = None,
+        reho_params: dict | None = None,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(using=using, name=name)
@@ -110,7 +110,7 @@ class ReHoParcels(ReHoBase):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 

junifer/markers/reho/reho_spheres.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 import numpy as np
 
@@ -104,13 +104,13 @@ class ReHoSpheres(ReHoBase):
         self,
         coords: str,
         using: str,
-        radius: Optional[float] = None,
+        radius: float | None = None,
         allow_overlap: bool = False,
-        reho_params: Optional[dict] = None,
+        reho_params: dict | None = None,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(using=using, name=name)
@@ -125,7 +125,7 @@ class ReHoSpheres(ReHoBase):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Compute.
 

junifer/markers/sphere_aggregation.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 from ..api.decorators import register_marker
 from ..data import get_data
@@ -102,15 +102,15 @@ class SphereAggregation(BaseMarker):
     def __init__(
         self,
         coords: str,
-        radius: Optional[float] = None,
+        radius: float | None = None,
         allow_overlap: bool = False,
         method: str = "mean",
-        method_params: Optional[dict[str, Any]] = None,
+        method_params: dict[str, Any] | None = None,
-        time_method: Optional[str] = None,
+        time_method: str | None = None,
-        time_method_params: Optional[dict[str, Any]] = None,
+        time_method_params: dict[str, Any] | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        on: Union[list[str], str, None] = None,
+        on: list[str] | str | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.coords = coords
         self.radius = radius
@@ -137,7 +137,7 @@ class SphereAggregation(BaseMarker):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict] = None,
+        extra_input: dict | None = None,
     ) -> dict:
         """Compute.
 

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 from nilearn import image as nimg
 
@@ -48,9 +48,9 @@ class TemporalSNRBase(BaseMarker):
     def __init__(
         self,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.agg_method = agg_method
         self.agg_method_params = agg_method_params
@@ -59,7 +59,7 @@ class TemporalSNRBase(BaseMarker):
 
     @abstractmethod
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict[str, Any]:
         """Perform aggregation."""
         raise_error(
@@ -70,7 +70,7 @@ class TemporalSNRBase(BaseMarker):
     def compute(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict] = None,
+        extra_input: dict | None = None,
     ) -> dict:
         """Compute.
 

junifer/markers/temporal_snr/temporal_snr_maps.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..maps_aggregation import MapsAggregation
@@ -35,8 +35,8 @@ class TemporalSNRMaps(TemporalSNRBase):
     def __init__(
         self,
         maps: str,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.maps = maps
         super().__init__(
@@ -45,7 +45,7 @@ class TemporalSNRMaps(TemporalSNRBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform maps aggregation.
 

junifer/markers/temporal_snr/temporal_snr_parcels.py

@@ -3,7 +3,7 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..parcel_aggregation import ParcelAggregation
@@ -40,11 +40,11 @@ class TemporalSNRParcels(TemporalSNRBase):
 
     def __init__(
         self,
-        parcellation: Union[str, list[str]],
+        parcellation: str | list[str],
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.parcellation = parcellation
         super().__init__(
@@ -55,7 +55,7 @@ class TemporalSNRParcels(TemporalSNRBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform parcel aggregation.
 

junifer/markers/temporal_snr/temporal_snr_spheres.py

@@ -3,7 +3,7 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any
 
 from ...api.decorators import register_marker
 from ..sphere_aggregation import SphereAggregation
@@ -50,12 +50,12 @@ class TemporalSNRSpheres(TemporalSNRBase):
     def __init__(
         self,
         coords: str,
-        radius: Optional[float] = None,
+        radius: float | None = None,
         allow_overlap: bool = False,
         agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
+        agg_method_params: dict | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
-        name: Optional[str] = None,
+        name: str | None = None,
     ) -> None:
         self.coords = coords
         self.radius = radius
@@ -70,7 +70,7 @@ class TemporalSNRSpheres(TemporalSNRBase):
         )
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform sphere aggregation.
 

junifer/markers/utils.py

@@ -8,7 +8,7 @@
 #          Amir Omidvarnia <a.omidvarnia@fz-juelich.de>
 # License: AGPL
 
-from typing import Callable, Optional, Union
+from collections.abc import Callable
 
 import numpy as np
 import pandas as pd
@@ -19,8 +19,8 @@ from ..utils import raise_error
 
 def _ets(
     bold_ts: np.ndarray,
-    roi_names: Union[None, list[str]] = None,
+    roi_names: None | list[str] = None,
-) -> tuple[np.ndarray, Optional[list[str]]]:
+) -> tuple[np.ndarray, list[str] | None]:
     """Compute the edge-wise time series based on BOLD time series.
 
     Take a timeseries of brain areas, and calculate timeseries for each
@@ -73,7 +73,8 @@ def _ets(
             )
         _roi_names = np.array(roi_names)
         edge_names = [
-            "~".join([x, y]) for x, y in zip(_roi_names[u], _roi_names[v])
+            "~".join([x, y])
+            for x, y in zip(_roi_names[u], _roi_names[v], strict=False)
         ]
         return ets, edge_names
 
@@ -81,7 +82,7 @@ def _ets(
 def _correlate_dataframes(
     df1: pd.DataFrame,
     df2: pd.DataFrame,
-    method: Union[str, Callable] = "pearson",
+    method: str | Callable = "pearson",
 ) -> pd.DataFrame:
     """Column-wise correlations between two dataframes.
 

junifer/onthefly/_brainprint.py

@@ -3,8 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional
-
 import numpy as np
 import pandas as pd
 
@@ -17,7 +15,7 @@ __all__ = ["normalize", "reweight"]
 
 def normalize(
     storage: StorageLike,
-    features: dict[str, dict[str, Optional[str]]],
+    features: dict[str, dict[str, str | None]],
     kind: str,
 ) -> pd.DataFrame:  # pragma: no cover
     """Read stored brainprint data and normalize either surfaces or volumes.
@@ -87,8 +85,8 @@ def normalize(
 
 def reweight(
     storage: StorageLike,
-    feature_name: Optional[str] = None,
+    feature_name: str | None = None,
-    feature_md5: Optional[str] = None,
+    feature_md5: str | None = None,
 ) -> pd.DataFrame:  # pragma: no cover
     """Read stored brainprint data and reweight eigenvalues.
 

junifer/onthefly/read_transform.py

@@ -3,8 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional
-
 import numpy as np
 import pandas as pd
 
@@ -18,11 +16,11 @@ __all__ = ["read_transform"]
 def read_transform(
     storage: StorageLike,
     transform: str,
-    feature_name: Optional[str] = None,
+    feature_name: str | None = None,
-    feature_md5: Optional[str] = None,
+    feature_md5: str | None = None,
-    nan_policy: Optional[str] = "bypass",
+    nan_policy: str | None = "bypass",
-    transform_args: Optional[tuple] = None,
+    transform_args: tuple | None = None,
-    transform_kw_args: Optional[dict] = None,
+    transform_kw_args: dict | None = None,
 ) -> pd.DataFrame:
     """Read stored feature and transform to specific statistical output.
 

junifer/pipeline/marker_collection.py

@@ -6,7 +6,6 @@
 
 from collections import Counter
 from pathlib import Path
-from typing import Optional
 
 from ..datareader import DefaultDataReader
 from ..pipeline import DataObjectDumper, PipelineStepMixin, WorkDirManager
@@ -41,9 +40,9 @@ class MarkerCollection:
     def __init__(
         self,
         markers: list[MarkerLike],
-        datareader: Optional[PipelineStepMixin] = None,
+        datareader: PipelineStepMixin | None = None,
-        preprocessors: Optional[list[PreprocessorLike]] = None,
+        preprocessors: list[PreprocessorLike] | None = None,
-        storage: Optional[StorageLike] = None,
+        storage: StorageLike | None = None,
     ):
         # Check that the markers have different names
         marker_names = [m.name for m in markers]
@@ -60,7 +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]) -> dict | None:
         """Fit the pipeline.
 
         Parameters

junifer/pipeline/pipeline_component_registry.py

@@ -7,7 +7,6 @@
 
 import importlib
 from collections.abc import Mapping
-from typing import Optional, Union
 
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error
@@ -119,7 +118,7 @@ class PipelineComponentRegistry(metaclass=Singleton):
         return self._steps
 
     @property
-    def components(self) -> Mapping[str, Mapping[str, Union[str, type]]]:
+    def components(self) -> Mapping[str, Mapping[str, str | type]]:
         """Get registered components for valid pipeline steps."""
         return self._components
 
@@ -238,8 +237,8 @@ class PipelineComponentRegistry(metaclass=Singleton):
         step: str,
         name: str,
         baseclass: type,
-        init_params: Optional[dict] = None,
+        init_params: dict | None = None,
-    ) -> Union[DataGrabberLike, PreprocessorLike, MarkerLike, StorageLike]:
+    ) -> DataGrabberLike | PreprocessorLike | MarkerLike | StorageLike:
         """Build an instance of class registered as ``name``.
 
         Parameters

junifer/pipeline/tests/test_data_object_dumper.py

@@ -5,7 +5,6 @@
 
 import pickle
 from pathlib import Path
-from typing import Union
 
 import nibabel
 import pytest
@@ -36,9 +35,9 @@ from junifer.utils import config
     ],
 )
 def test_dispatcher_addition_errors(
-    dispatcher: Union[AssetDumperDispatcher, AssetLoaderDispatcher],
+    dispatcher: AssetDumperDispatcher | AssetLoaderDispatcher,
-    inbuilt_key: Union[str, type],
+    inbuilt_key: str | type,
-    ext_key: Union[str, type],
+    ext_key: str | type,
     val: type,
 ) -> None:
     """Test asset dumper / loader addition errors.
@@ -70,9 +69,9 @@ def test_dispatcher_addition_errors(
     ],
 )
 def test_dispatcher_removal_errors(
-    dispatcher: Union[AssetDumperDispatcher, AssetLoaderDispatcher],
+    dispatcher: AssetDumperDispatcher | AssetLoaderDispatcher,
-    inbuilt_key: Union[str, type],
+    inbuilt_key: str | type,
-    ext_key: Union[str, type],
+    ext_key: str | type,
 ) -> None:
     """Test asset dumper / loader removal errors.
 

junifer/pipeline/tests/test_update_meta_mixin.py

@@ -4,8 +4,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Union
-
 import pytest
 
 from junifer.pipeline.update_meta_mixin import UpdateMetaMixin
@@ -23,7 +21,7 @@ from junifer.pipeline.update_meta_mixin import UpdateMetaMixin
 def test_UpdateMetaMixin(
     input: dict,
     step_name: str,
-    dependencies: Union[set, list, str, None],
+    dependencies: set | list | str | None,
     expected: set,
 ) -> None:
     """Test UpdateMetaMixin.

junifer/pipeline/update_meta_mixin.py

@@ -4,9 +4,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Union
-
-
 __all__ = ["UpdateMetaMixin"]
 
 
@@ -15,7 +12,7 @@ class UpdateMetaMixin:
 
     def update_meta(
         self,
-        input: Union[dict, list[dict]],
+        input: dict | list[dict],
         step_name: str,
     ) -> None:
         """Update metadata.
@@ -51,6 +48,6 @@ class UpdateMetaMixin:
             # Update step dependencies
             dependencies = getattr(self, "_DEPENDENCIES", set())
             if dependencies is not None:
-                if not isinstance(dependencies, (set, list)):
+                if not isinstance(dependencies, set | list):
                     dependencies = {dependencies}
                 entry["meta"]["dependencies"].update(dependencies)

junifer/pipeline/utils.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 import subprocess
-from typing import Any, Optional
+from typing import Any
 
 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: list[str] | None = 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: list[str] | None = None) -> bool:
     """Check if FSL is present in the system.
 
     Parameters
@@ -195,7 +195,7 @@ 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: list[str] | None = None) -> bool:
     """Check if ANTs is present in the system.
 
     Parameters
@@ -255,7 +255,7 @@ 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: list[str] | None = None) -> bool:
     """Check if FreeSurfer is present in the system.
 
     Parameters

junifer/pipeline/workdir_manager.py

@@ -7,7 +7,6 @@
 import shutil
 import tempfile
 from pathlib import Path
-from typing import Optional, Union
 
 from ..utils import logger
 from ..utils.singleton import Singleton
@@ -46,7 +45,7 @@ class WorkDirManager(metaclass=Singleton):
     """
 
     def __init__(
-        self, workdir: Optional[Union[str, Path]] = None, cleanup: bool = True
+        self, workdir: str | Path | None = None, cleanup: bool = True
     ) -> None:
         """Initialize the class."""
         self._workdir = Path(workdir) if isinstance(workdir, str) else workdir
@@ -97,7 +96,7 @@ class WorkDirManager(metaclass=Singleton):
         return self._workdir  # type: ignore
 
     @workdir.setter
-    def workdir(self, path: Union[str, Path]) -> None:
+    def workdir(self, path: str | Path) -> None:
         """Set working directory.
 
         The directory path is created if it doesn't exist yet.
@@ -130,7 +129,7 @@ class WorkDirManager(metaclass=Singleton):
         return self._elementdir  # type: ignore
 
     def get_element_tempdir(
-        self, prefix: Optional[str] = None, suffix: Optional[str] = None
+        self, prefix: str | None = None, suffix: str | None = None
     ) -> Path:
         """Get an element-scoped temporary directory.
 
@@ -203,12 +202,12 @@ class WorkDirManager(metaclass=Singleton):
             self._elementdir = None
 
     @property
-    def root_tempdir(self) -> Optional[Path]:
+    def root_tempdir(self) -> Path | None:
         """Get root temporary directory."""
         return self._root_tempdir
 
     def get_tempdir(
-        self, prefix: Optional[str] = None, suffix: Optional[str] = None
+        self, prefix: str | None = None, suffix: str | None = None
     ) -> Path:
         """Get a component-scoped temporary directory.
 

junifer/preprocess/_temporal_filter.py

@@ -9,8 +9,6 @@ from collections.abc import Sequence
 from typing import (
     Any,
     ClassVar,
-    Optional,
-    Union,
 )
 
 import nibabel as nib
@@ -63,10 +61,10 @@ class TemporalFilter(BasePreprocessor):
         self,
         detrend: bool = True,
         standardize: bool = True,
-        low_pass: Optional[float] = None,
+        low_pass: float | None = None,
-        high_pass: Optional[float] = None,
+        high_pass: float | None = None,
-        t_r: Optional[float] = None,
+        t_r: float | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
     ) -> None:
         """Initialize the class."""
         self.detrend = detrend
@@ -102,7 +100,7 @@ class TemporalFilter(BasePreprocessor):
     def preprocess(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Preprocess.
 

junifer/preprocess/_temporal_slicer.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 from collections.abc import Sequence
-from typing import Any, ClassVar, Optional
+from typing import Any, ClassVar
 
 import nibabel as nib
 import nilearn.image as nimg
@@ -51,9 +51,9 @@ class TemporalSlicer(BasePreprocessor):
     def __init__(
         self,
         start: float,
-        stop: Optional[float],
+        stop: float | None,
-        duration: Optional[float] = None,
+        duration: float | None = None,
-        t_r: Optional[float] = None,
+        t_r: float | None = None,
     ) -> None:
         """Initialize the class."""
         if start < 0:
@@ -68,7 +68,7 @@ class TemporalSlicer(BasePreprocessor):
     def preprocess(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Preprocess.
 

junifer/preprocess/base.py

@@ -6,7 +6,7 @@
 
 from abc import ABC, abstractmethod
 from collections.abc import Sequence
-from typing import Any, ClassVar, Optional, Union
+from typing import Any, ClassVar
 
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils import logger, raise_error
@@ -43,8 +43,8 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
 
     def __init__(
         self,
-        on: Optional[Union[list[str], str]] = None,
+        on: list[str] | str | None = None,
-        required_data_types: Optional[Union[list[str], str]] = None,
+        required_data_types: list[str] | str | None = None,
     ) -> None:
         """Initialize the class."""
         # Check for missing data types attributes
@@ -119,7 +119,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
     def preprocess(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Preprocess.
 

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -9,8 +9,6 @@ from collections.abc import Sequence
 from typing import (
     Any,
     ClassVar,
-    Optional,
-    Union,
 )
 
 import nibabel as nib
@@ -180,17 +178,17 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
 
     def __init__(
         self,
-        strategy: Optional[dict[str, Union[str, bool]]] = None,
+        strategy: dict[str, str | bool] | None = None,
-        spike: Optional[float] = None,
+        spike: float | None = None,
-        scrub: Optional[int] = None,
+        scrub: int | None = None,
-        fd_threshold: Optional[float] = None,
+        fd_threshold: float | None = None,
-        std_dvars_threshold: Optional[float] = None,
+        std_dvars_threshold: float | None = None,
         detrend: bool = True,
         standardize: bool = True,
-        low_pass: Optional[float] = None,
+        low_pass: float | None = None,
-        high_pass: Optional[float] = None,
+        high_pass: float | None = None,
-        t_r: Optional[float] = None,
+        t_r: float | None = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+        masks: str | dict | list[dict | str] | None = None,
     ) -> None:
         """Initialize the class."""
         if strategy is None:
@@ -593,7 +591,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
     def preprocess(
         self,
         input: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         """Preprocess.
 

junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py

@@ -83,7 +83,7 @@ def test_fMRIPrepConfoundRemover__map_adhoc_to_fmriprep() -> None:
     ]
 
     # Build mappings dictionary
-    mappings = dict(zip(adhoc_names, fmriprep_names))
+    mappings = dict(zip(adhoc_names, fmriprep_names, strict=False))
     input = {
         "mappings": {"fmriprep": mappings},
         "data": adhoc_df,
@@ -238,7 +238,7 @@ def test_fMRIPrepConfoundRemover__pick_confounds_adhoc() -> None:
     ]
 
     # Build mappings dictionary
-    mappings = dict(zip(adhoc_names, fmriprep_names))
+    mappings = dict(zip(adhoc_names, fmriprep_names, strict=False))
     input = {
         "mappings": {"fmriprep": mappings},
         "data": adhoc_df,