junifer 0.0.7.dev332__tar.gz → 0.0.8.dev12__tar.gz

junifer-0.0.8.dev12/.python-version

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

{junifer-0.0.7.dev332 → junifer-0.0.8.dev12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev332
+Version: 0.0.8.dev12
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -19,26 +19,26 @@ Classifier: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.9
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
-Requires-Dist: numpy<2.0.0,>=1.26.0
-Requires-Dist: scipy<=1.15.0,>=1.10.0
-Requires-Dist: datalad<1.2.0,>=1.0.0
-Requires-Dist: pandas<2.3.0,>=2.0.0
+Requires-Dist: numpy<2.4.0,>=1.26.0
+Requires-Dist: scipy<1.17.0,>=1.10.0
+Requires-Dist: datalad<1.3.0,>=1.0.0
+Requires-Dist: pandas<2.4.0,>=2.0.0
 Requires-Dist: nibabel<5.4.0,>=5.2.0
 Requires-Dist: nilearn<=0.10.4,>=0.10.3
 Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
 Requires-Dist: ruamel.yaml<0.19,>=0.17
 Requires-Dist: h5py>=3.10
-Requires-Dist: tqdm<4.67.0,>=4.66.1
+Requires-Dist: tqdm<4.68.0,>=4.66.1
 Requires-Dist: templateflow<25.0.0,>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0
 Requires-Dist: lazy_loader==0.4
@@ -62,15 +62,15 @@ Requires-Dist: ruff; extra == "dev"
 Requires-Dist: towncrier; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
-Requires-Dist: sphinx<8.1.0,>=7.3.0; extra == "docs"
-Requires-Dist: sphinx-gallery<0.18.0,>=0.17.0; extra == "docs"
-Requires-Dist: furo<2024.9.0,>=2024.4.27; extra == "docs"
-Requires-Dist: numpydoc<1.9.0,>=1.6.0; extra == "docs"
+Requires-Dist: sphinx<8.4.0,>=7.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.20.0,>=0.17.0; extra == "docs"
+Requires-Dist: furo<2025.10.0,>=2024.4.27; extra == "docs"
+Requires-Dist: numpydoc<=1.9.0,>=1.6.0; extra == "docs"
 Requires-Dist: julearn==0.3.3; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
-Requires-Dist: towncrier<24.7.0,>=23.10.0; extra == "docs"
-Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
-Requires-Dist: sphinxcontrib-towncrier==0.4.0a0; extra == "docs"
+Requires-Dist: towncrier<=25.8.0,>=24.7.0; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid<=1.0.0,>=0.8.1; extra == "docs"
+Requires-Dist: sphinxcontrib-towncrier==0.5.0a0; extra == "docs"
 Requires-Dist: setuptools-scm>=8; extra == "docs"
 Dynamic: license-file
 

junifer-0.0.8.dev12/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-0.0.7.dev332 → junifer-0.0.8.dev12}/docs/whats_new.rst

@@ -10,6 +10,125 @@ What's new
 
 .. towncrier release notes start
 
+Junifer 0.0.7 (2026-03-04)
+--------------------------
+
+Bugfixes
+^^^^^^^^
+
+- Allow ``timeseries_2d`` storage for :class:`.HDF5FeatureStorage` by `Fede
+  Raimondo`_ (:gh:`444`)
+- Fix FSL presence checking status code by `Fede Raimondo`_ (:gh:`454`)
+- Bypass warper check for callable masks on native data by `Synchon Mandal`_
+  (:gh:`481`)
+- Fix mask specification check involving dicts in
+  :class:`junifer.data.MaskRegistry` when working in native space by `Synchon
+  Mandal`_ (:gh:`487`)
+
+
+API Changes
+^^^^^^^^^^^
+
+- ``fname``, ``overwrite`` and ``output_format`` have been removed from
+  :func:`.configure_logging` by `Synchon Mandal`_ (:gh:`231`)
+- ``ParcellationRegistry.get`` now returns labels as dictionary mapping from
+  values to labels instead of a list of labels by `Synchon Mandal`_ (:gh:`257`)
+- :func:`.read_transform` has a new parameter ``nan_policy`` to handle NaN
+  values when transforming feature data by `Fede Raimondo`_ (:gh:`429`)
+- :func:`.get_data`, :func:`.load_data`, :func:`.list_data`,
+  :func:`.register_data` and :func:`.deregister_data` now support ``"maps"`` as
+  a valid argument for ``kind`` by `Synchon Mandal`_ (:gh:`458`)
+
+
+Improved Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+- Add documentation on extending data registries by `Synchon Mandal`_
+  (:gh:`450`)
+- Add documentation on adding data types by `Synchon Mandal`_ (:gh:`451`)
+- Add documentation on :class:`.ConfigManager`, dumping data object and
+  extending data dump assets by `Synchon Mandal`_ (:gh:`452`)
+
+
+Enhancements
+^^^^^^^^^^^^
+
+- Allow parcellation registration with non-continuous ranges as values by
+  `Synchon Mandal`_ (:gh:`257`)
+- Add support for Chatterjee's xi correlation in
+  :class:`.JuniferConnectivityMeasure` by `Synchon Mandal`_ (:gh:`333`)
+- Implement a NaN policy for :func:`.read_transform` by `Fede Raimondo`_
+  (:gh:`429`)
+- Add FreeSurfer 7.4.1 aseg parcellation to :class:`.ParcellationRegistry` by
+  `Synchon Mandal`_ (:gh:`470`)
+- Simplify ``Storage`` interface and implementations by `Synchon Mandal`_
+  (:gh:`472`)
+- Simplify ``Preprocess`` interface and implementations by `Synchon Mandal`_
+  (:gh:`473`)
+- Simplify :class:`.PipelineStepMixin` interface by `Synchon Mandal`_
+  (:gh:`476`)
+- Improve ``Marker`` interface and implementations by `Synchon Mandal`_
+  (:gh:`477`)
+- Add Glasser and Julich-Brain parcellations to :class:`.ParcellationRegistry`
+  by `Synchon Mandal`_ (:gh:`486`)
+
+
+Features
+^^^^^^^^
+
+- Introduce :class:`.TemporalFilter` preprocessor for temporally filtering BOLD
+  data by `Fede Raimondo`_ (:gh:`432`)
+- Introduce :class:`.TemporalSlicer` preprocessor for temporally slicing BOLD
+  data by `Synchon Mandal`_ (:gh:`443`)
+- Enable data registries to be extended by exposing
+  :class:`.BasePipelineDataRegistry` and introducing
+  :func:`.register_data_registry` decorator by `Synchon Mandal`_ (:gh:`450`)
+- Enable data types to be added by introducing :func:`.register_data_type` by
+  `Synchon Mandal`_ (:gh:`451`)
+- Allow pipeline data object to be dumped by introducing
+  :class:`.DataObjectDumper` and available dumping / loading assets to be
+  extended by introducing :func:`.register_data_dump_asset` decorator by
+  `Synchon Mandal`_ (:gh:`452`)
+- Introduce :class:`.MapsRegistry` to centralise probabilistic atlas (maps)
+  data management by `Synchon Mandal`_ (:gh:`458`)
+- Introduce :class:`.MapsAggregation`, :class:`.FunctionalConnectivityMaps`,
+  :class:`.EdgeCentricFCMaps`, :class:`.ReHoMaps`, :class:`.ALFFMaps` and
+  :class:`.TemporalSNRMaps` by `Synchon Mandal`_ (:gh:`460`)
+- Enable :class:`.SpaceWarper` to warp data from native space to template
+  spaces via both FSL and ANTs by `Synchon Mandal`_ (:gh:`462`)
+
+
+Miscellaneous
+^^^^^^^^^^^^^
+
+- Adopt ``structlog`` for logging infrastructure by `Synchon Mandal`_
+  (:gh:`231`)
+- Regular repository maintenance by updating ``.pre-commit-config.yaml``,
+  replacing ``black`` with ``ruff-format`` and updating tool configs by
+  `Synchon Mandal`_ (:gh:`441`)
+- Bump ``junifer-data`` to ``v3`` for Docker images by `Synchon Mandal`_
+  (:gh:`456`)
+- Bump ``junifer-data`` to ``v3`` by `Synchon Mandal`_ (:gh:`457`)
+- Constrain ``templateflow`` version to ``>=23.0.0,<25.0.0`` by `Synchon
+  Mandal`_ (:gh:`458`)
+- Add a new GitHub Action to mark stale issues by `Synchon Mandal`_ (:gh:`464`)
+- Bump ``junifer-data`` to ``v4`` for Docker images by `Synchon Mandal`_
+  (:gh:`465`)
+- Bump ``junifer-data`` to ``v4`` by `Synchon Mandal`_ (:gh:`466`)
+- Disable FSL installation for ``junifer-ci`` Docker image build with
+  ``junifer-data`` v4 by `Synchon Mandal`_ (:gh:`467`)
+- Pin ``junifer-ci`` Docker image to ``python:3.12-slim-bookworm`` and
+  re-enable FSL installation by `Synchon Mandal`_ (:gh:`468`)
+- Bump ``junifer-data`` to ``v5`` by `Synchon Mandal`_ (:gh:`470`)
+- Bump ``junifer-data`` to ``v6`` for Docker images by `Synchon Mandal`_
+  (:gh:`483`)
+- Bump ``junifer-data`` to ``v7`` for Docker images by `Synchon Mandal`_
+  (:gh:`485`)
+- Bump ``junifer-data`` to ``v7`` by `Synchon Mandal`_ (:gh:`486`)
+- Add Dockerfile and a corresponding action for building and publishing the
+  image by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`489`)
+
+
 Junifer 0.0.6 (2025-03-24)
 --------------------------
 

{junifer-0.0.7.dev332 → junifer-0.0.8.dev12}/junifer/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.7.dev332'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev332')
+__version__ = version = '0.0.8.dev12'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev12')
 
-__commit_id__ = commit_id = 'g52d8784c5'
+__commit_id__ = commit_id = 'gbb6de25ad'

{junifer-0.0.7.dev332 → junifer-0.0.8.dev12}/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,
-    elements: Optional[Elements] = None,
+    preprocessors: list[dict] | None = 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,
-    **kwargs: Union[str, int, bool, dict, tuple, list],
+    elements: Elements | None = None,
+    **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-0.0.7.dev332 → junifer-0.0.8.dev12}/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_collect: Optional[str] = None,
-        env: Optional[dict[str, str]] = None,
+        pre_run: str | None = None,
+        pre_collect: str | None = 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-0.0.7.dev332 → junifer-0.0.8.dev12}/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_collect: Optional[str] = None,
-        env: Optional[dict[str, str]] = None,
+        pre_run: str | None = None,
+        pre_collect: str | None = 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-0.0.7.dev332 → junifer-0.0.8.dev12}/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-0.0.7.dev332 → junifer-0.0.8.dev12}/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-0.0.7.dev332 → junifer-0.0.8.dev12}/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-0.0.7.dev332 → junifer-0.0.8.dev12}/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(
-    ctx: click.Context, param: str, value: str
-) -> Union[str, int]:
+def _validate_verbose(ctx: click.Context, param: str, value: str) -> 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_datalad: Optional[Union[str, int]],
+    verbose: 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_datalad: Union[str, int, None],
+    verbose: str | int,
+    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_datalad: Union[str, int, None],
+    verbose: str | int,
+    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_datalad: Union[str, int, None],
+    verbose: str | int,
+    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],
-    verbose: Union[str, int],
-    verbose_datalad: Union[str, int, None],
+    output_file: click.Path | None,
+    verbose: str | int,
+    verbose_datalad: str | int | None,
 ) -> None:
     """List elements of a dataset.
 

{junifer-0.0.7.dev332 → junifer-0.0.8.dev12}/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(
-    element: tuple[str, ...], config: dict
-) -> Union[Elements, None]:
+def parse_elements(element: tuple[str, ...], config: dict) -> Elements | None:
     """Parse elements from cli.
 
     Parameters

{junifer-0.0.7.dev332 → junifer-0.0.8.dev12}/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-0.0.7.dev332 → junifer-0.0.8.dev12}/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-0.0.7.dev332 → junifer-0.0.8.dev12}/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-0.0.7.dev332 → junifer-0.0.8.dev12}/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,
-        sites: Union[str, list[str], None] = None,
+        datadir: str | Path | None = None,
+        sites: str | list[str] | None = None,
     ) -> None:
         uri = (
             "ria+http://cat_12.5.ds.inm7.de"

{junifer-0.0.7.dev332 → junifer-0.0.8.dev12}/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-0.0.7.dev332 → junifer-0.0.8.dev12}/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[
-            str, Path
-        ] = "/data/project/psychosis_thalamus/data/fmriprep",
-        types: Union[str, list[str], None] = None,
-        tasks: Union[str, list[str], None] = None,
+        datadir: str | Path = "/data/project/psychosis_thalamus/data/fmriprep",
+        types: str | list[str] | None = None,
+        tasks: str | list[str] | None = None,
     ) -> None:
         # Declare all tasks
         all_tasks = [