[MAINT]: Drop Python 3.9 and add Python 3.14 support

.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,
-    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/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 @@ def __init__(
         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 @@ def __init__(
         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 @@ def __init__(
         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 @@ def __init__(
         )
         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 subprocess
 import sys
 from pathlib import Path
-from typing import Optional, Union
 
 import click
 
@@ -46,7 +45,7 @@
 
 
 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/cli/parser.py

@@ -8,7 +8,6 @@
 import importlib.util
 import sys
 from pathlib import Path
-from typing import Union
 
 import pandas as pd
 
@@ -19,7 +18,7 @@
 __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/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"