junifer 0.0.6.dev248__py3-none-any.whl → 0.0.6.dev258__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev248'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev248')
+__version__ = version = '0.0.6.dev258'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev258')

junifer/api/decorators.py

@@ -5,7 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Type
 
 from ..pipeline import PipelineComponentRegistry
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
@@ -47,7 +46,7 @@ def register_datagrabber(klass: DataGrabberLike) -> DataGrabberLike:
     return klass
 
 
-def register_datareader(klass: Type) -> Type:
+def register_datareader(klass: type) -> type:
     """Register DataReader.
 
     Registers the DataReader so it can be used by name.

junifer/api/functions.py

@@ -8,7 +8,7 @@
 import os
 import shutil
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from ..datagrabber import BaseDataGrabber
@@ -27,7 +27,7 @@ from ..utils import logger, raise_error, yaml
 __all__ = ["run", "collect", "queue", "reset", "list_elements"]
 
 
-def _get_datagrabber(datagrabber_config: Dict) -> DataGrabberLike:
+def _get_datagrabber(datagrabber_config: dict) -> DataGrabberLike:
     """Get DataGrabber.
 
     Parameters
@@ -49,7 +49,7 @@ def _get_datagrabber(datagrabber_config: Dict) -> DataGrabberLike:
     )
 
 
-def _get_preprocessor(preprocessing_config: Dict) -> PreprocessorLike:
+def _get_preprocessor(preprocessing_config: dict) -> PreprocessorLike:
     """Get Preprocessor.
 
     Parameters
@@ -71,7 +71,7 @@ def _get_preprocessor(preprocessing_config: Dict) -> PreprocessorLike:
     )
 
 
-def _get_marker(marker_config: Dict) -> MarkerLike:
+def _get_marker(marker_config: dict) -> MarkerLike:
     """Get Marker.
 
     Parameters
@@ -93,7 +93,7 @@ def _get_marker(marker_config: Dict) -> MarkerLike:
     )
 
 
-def _get_storage(storage_config: Dict) -> StorageLike:
+def _get_storage(storage_config: dict) -> StorageLike:
     """Get Storage.
 
     Parameters
@@ -117,11 +117,11 @@ def _get_storage(storage_config: Dict) -> StorageLike:
 
 def run(
     workdir: Union[str, Path],
-    datagrabber: Dict,
-    markers: List[Dict],
-    storage: Dict,
-    preprocessors: Optional[List[Dict]] = None,
-    elements: Union[str, List[Union[str, Tuple]], Tuple, None] = None,
+    datagrabber: dict,
+    markers: list[dict],
+    storage: dict,
+    preprocessors: Optional[list[dict]] = None,
+    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
 ) -> None:
     """Run the pipeline on the selected element.
 
@@ -202,7 +202,7 @@ def run(
                 mc.fit(datagrabber_object[t_element])
 
 
-def collect(storage: Dict) -> None:
+def collect(storage: dict) -> None:
     """Collect and store data.
 
     Parameters
@@ -224,12 +224,12 @@ def collect(storage: Dict) -> None:
 
 
 def queue(
-    config: Dict,
+    config: dict,
     kind: str,
     jobname: str = "junifer_job",
     overwrite: bool = False,
-    elements: Union[str, List[Union[str, Tuple]], Tuple, None] = None,
-    **kwargs: Union[str, int, bool, Dict, Tuple, List],
+    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
+    **kwargs: Union[str, int, bool, dict, tuple, list],
 ) -> None:
     """Queue a job to be executed later.
 
@@ -316,7 +316,7 @@ def queue(
                 elements = dg.get_elements()
     # Listify elements
     if not isinstance(elements, list):
-        elements: List[Union[str, Tuple]] = [elements]
+        elements: list[Union[str, tuple]] = [elements]
 
     # Check job queueing system
     adapter = None
@@ -341,7 +341,7 @@ def queue(
     logger.info("Queue done")
 
 
-def reset(config: Dict) -> None:
+def reset(config: dict) -> None:
     """Reset the storage and jobs directory.
 
     Parameters
@@ -380,8 +380,8 @@ def reset(config: Dict) -> None:
 
 
 def list_elements(
-    datagrabber: Dict,
-    elements: Union[str, List[Union[str, Tuple]], Tuple, None] = None,
+    datagrabber: dict,
+    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
 ) -> str:
     """List elements of the datagrabber filtered using `elements`.
 

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -6,7 +6,7 @@
 import shutil
 import textwrap
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 from ...utils import logger, make_executable, raise_error, run_ext_cmd
 from .queue_context_adapter import QueueContextAdapter
@@ -60,10 +60,10 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         job_name: str,
         job_dir: Path,
         yaml_config_path: Path,
-        elements: List[Union[str, Tuple]],
+        elements: list[Union[str, tuple]],
         pre_run: Optional[str] = None,
         pre_collect: Optional[str] = None,
-        env: Optional[Dict[str, str]] = None,
+        env: Optional[dict[str, str]] = None,
         verbose: str = "info",
         submit: bool = False,
     ) -> None:
@@ -86,7 +86,7 @@ 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: Optional[dict[str, str]]) -> None:
         """Check value of env parameter on init.
 
         Parameters

junifer/api/queue_context/htcondor_adapter.py

@@ -6,7 +6,7 @@
 import shutil
 import textwrap
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 from ...utils import logger, make_executable, raise_error, run_ext_cmd
 from .queue_context_adapter import QueueContextAdapter
@@ -78,10 +78,10 @@ class HTCondorAdapter(QueueContextAdapter):
         job_name: str,
         job_dir: Path,
         yaml_config_path: Path,
-        elements: List[Union[str, Tuple]],
+        elements: list[Union[str, tuple]],
         pre_run: Optional[str] = None,
         pre_collect: Optional[str] = None,
-        env: Optional[Dict[str, str]] = None,
+        env: Optional[dict[str, str]] = None,
         verbose: str = "info",
         cpus: int = 1,
         mem: str = "8G",
@@ -115,7 +115,7 @@ 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: Optional[dict[str, str]]) -> None:
         """Check value of env parameter on init.
 
         Parameters

junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py

@@ -5,7 +5,7 @@
 
 import logging
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -44,7 +44,7 @@ def test_GnuParallelLocalAdapter_env_shell_error() -> None:
     ],
 )
 def test_GnuParallelLocalAdapter_elements(
-    elements: List[Union[str, Tuple]],
+    elements: list[Union[str, tuple]],
     expected_text: str,
 ) -> None:
     """Test GnuParallelLocalAdapter elements().
@@ -177,7 +177,7 @@ def test_GnuParallelLocalAdapter_prepare(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    env: Dict[str, str],
+    env: dict[str, str],
 ) -> None:
     """Test GnuParallelLocalAdapter prepare().
 

junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -5,7 +5,7 @@
 
 import logging
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -181,7 +181,7 @@ def test_HTCondorAdapter_run_collect(
     ],
 )
 def test_HTCondor_dag(
-    elements: List[Union[str, Tuple]], collect: str, expected_text: str
+    elements: list[Union[str, tuple]], collect: str, expected_text: str
 ) -> None:
     """Test HTCondorAdapter dag().
 
@@ -218,7 +218,7 @@ def test_HTCondorAdapter_prepare(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    env: Dict[str, str],
+    env: dict[str, str],
 ) -> None:
     """Test HTCondorAdapter prepare().
 

junifer/api/tests/test_functions.py

@@ -7,7 +7,7 @@
 
 import logging
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import pytest
 from ruamel.yaml import YAML
@@ -26,7 +26,7 @@ yaml.indent(mapping=2, sequence=4, offset=2)
 
 
 @pytest.fixture
-def datagrabber() -> Dict[str, str]:
+def datagrabber() -> dict[str, str]:
     """Return a datagrabber as a dictionary."""
     return {
         "kind": "PartlyCloudyTestingDataGrabber",
@@ -34,7 +34,7 @@ def datagrabber() -> Dict[str, str]:
 
 
 @pytest.fixture
-def markers() -> List[Dict[str, str]]:
+def markers() -> list[dict[str, str]]:
     """Return markers as a list of dictionary."""
     return [
         {
@@ -53,7 +53,7 @@ def markers() -> List[Dict[str, str]]:
 
 
 @pytest.fixture
-def storage() -> Dict[str, str]:
+def storage() -> dict[str, str]:
     """Return a storage as a dictionary."""
     return {
         "kind": "SQLiteFeatureStorage",
@@ -62,9 +62,9 @@ def storage() -> Dict[str, str]:
 
 def test_run_single_element(
     tmp_path: Path,
-    datagrabber: Dict[str, str],
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    datagrabber: dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
 ) -> None:
     """Test run function with single element.
 
@@ -97,8 +97,8 @@ def test_run_single_element(
 
 def test_run_single_element_with_preprocessing(
     tmp_path: Path,
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
 ) -> None:
     """Test run function with single element and pre-processing.
 
@@ -137,9 +137,9 @@ def test_run_single_element_with_preprocessing(
 
 def test_run_multi_element_multi_output(
     tmp_path: Path,
-    datagrabber: Dict[str, str],
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    datagrabber: dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
 ) -> None:
     """Test run function with multi element and multi output.
 
@@ -173,9 +173,9 @@ def test_run_multi_element_multi_output(
 
 def test_run_multi_element_single_output(
     tmp_path: Path,
-    datagrabber: Dict[str, str],
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    datagrabber: dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
 ) -> None:
     """Test run function with multi element and single output.
 
@@ -210,9 +210,9 @@ def test_run_multi_element_single_output(
 
 def test_run_and_collect(
     tmp_path: Path,
-    datagrabber: Dict[str, str],
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    datagrabber: dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
 ) -> None:
     """Test run and collect functions.
 
@@ -259,9 +259,9 @@ def test_queue_correct_yaml_config(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    datagrabber: Dict[str, str],
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    datagrabber: dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
 ) -> None:
     """Test proper YAML config generation for queueing.
 
@@ -426,7 +426,7 @@ def test_queue_with_imports(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    with_: Union[str, List[str]],
+    with_: Union[str, list[str]],
 ) -> None:
     """Test queue with `with` imports.
 
@@ -477,7 +477,7 @@ def test_queue_with_elements(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    elements: Union[str, List[Union[str, Tuple[str]]], Tuple[str]],
+    elements: Union[str, list[Union[str, tuple[str]]], tuple[str]],
 ) -> None:
     """Test queue with elements.
 
@@ -508,7 +508,7 @@ def test_queue_without_elements(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    datagrabber: Dict[str, str],
+    datagrabber: dict[str, str],
 ) -> None:
     """Test queue without elements.
 
@@ -536,9 +536,9 @@ def test_queue_without_elements(
 
 def test_reset_run(
     tmp_path: Path,
-    datagrabber: Dict[str, str],
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    datagrabber: dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
 ) -> None:
     """Test reset function for run.
 
@@ -580,9 +580,9 @@ def test_reset_run(
 def test_reset_queue(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
-    datagrabber: Dict[str, str],
-    markers: List[Dict[str, str]],
-    storage: Dict[str, str],
+    datagrabber: dict[str, str],
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
     job_name: str,
 ) -> None:
     """Test reset function for queue.
@@ -647,8 +647,8 @@ def test_reset_queue(
     ],
 )
 def test_list_elements(
-    datagrabber: Dict[str, str],
-    elements: Optional[List[str]],
+    datagrabber: dict[str, str],
+    elements: Optional[list[str]],
 ) -> None:
     """Test elements listing.
 

junifer/cli/cli.py

@@ -8,7 +8,7 @@ import pathlib
 import subprocess
 import sys
 from pathlib import Path
-from typing import Optional, Tuple, Union
+from typing import Optional, Union
 
 import click
 
@@ -106,7 +106,7 @@ def cli() -> None:  # pragma: no cover
     default="info",
 )
 def run(
-    filepath: click.Path, element: Tuple[str], verbose: Union[str, int]
+    filepath: click.Path, element: tuple[str], verbose: Union[str, int]
 ) -> None:
     """Run feature extraction.
 
@@ -395,7 +395,7 @@ def reset(
 )
 def list_elements(
     filepath: click.Path,
-    element: Tuple[str],
+    element: tuple[str],
     output_file: Optional[click.Path],
     verbose: Union[str, int],
 ) -> None:

junifer/cli/parser.py

@@ -8,7 +8,7 @@ import importlib
 import importlib.util
 import sys
 from pathlib import Path
-from typing import Dict, List, Tuple, Union
+from typing import Union
 
 import pandas as pd
 
@@ -18,7 +18,7 @@ from ..utils import logger, raise_error, warn_with_log, yaml
 __all__ = ["parse_yaml", "parse_elements"]
 
 
-def parse_yaml(filepath: Union[str, Path]) -> Dict:  # noqa: C901
+def parse_yaml(filepath: Union[str, Path]) -> dict:  # noqa: C901
     """Parse YAML.
 
     Parameters
@@ -140,7 +140,7 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:  # noqa: C901
     return contents
 
 
-def parse_elements(element: Tuple[str], config: Dict) -> Union[List, None]:
+def parse_elements(element: tuple[str], config: dict) -> Union[list, None]:
     """Parse elements from cli.
 
     Parameters
@@ -201,7 +201,7 @@ def parse_elements(element: Tuple[str], config: Dict) -> Union[List, None]:
     return elements
 
 
-def _parse_elements_file(filepath: Path) -> List[Tuple[str, ...]]:
+def _parse_elements_file(filepath: Path) -> list[tuple[str, ...]]:
     """Parse elements from file.
 
     Parameters

junifer/cli/tests/test_cli.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Callable, List, Tuple
+from typing import Callable
 
 import pytest
 from click.testing import CliRunner
@@ -42,7 +42,7 @@ runner = CliRunner()
     ],
 )
 def test_run_and_collect_commands(
-    tmp_path: Path, elements: Tuple[str, ...]
+    tmp_path: Path, elements: tuple[str, ...]
 ) -> None:
     """Test run and collect commands.
 
@@ -175,7 +175,7 @@ def test_run_using_element_file(tmp_path: Path, elements: str) -> None:
     ],
 )
 def test_multi_element_access(
-    tmp_path: Path, elements: str, expected_list: List[Tuple[str, ...]]
+    tmp_path: Path, elements: str, expected_list: list[tuple[str, ...]]
 ) -> None:
     """Test mulit-element parsing.
 
@@ -306,7 +306,7 @@ def test_reset(
     ],
 )
 def test_list_elements_stdout(
-    elements: Tuple[str, ...],
+    elements: tuple[str, ...],
 ) -> None:
     """Test elements listing to stdout.
 
@@ -344,7 +344,7 @@ def test_list_elements_stdout(
 )
 def test_list_elements_output_file(
     tmp_path: Path,
-    elements: Tuple[str, ...],
+    elements: tuple[str, ...],
 ) -> None:
     """Test elements listing to output file.
 

junifer/cli/utils.py

@@ -7,13 +7,12 @@ import os
 import platform as pl
 import re
 from importlib.metadata import distribution
-from typing import Dict
 
 from .._version import __version__
 from ..utils.logging import get_versions
 
 
-def _get_junifer_version() -> Dict[str, str]:
+def _get_junifer_version() -> dict[str, str]:
     """Get junifer version information.
 
     Returns
@@ -27,7 +26,7 @@ def _get_junifer_version() -> Dict[str, str]:
     }
 
 
-def _get_python_information() -> Dict[str, str]:
+def _get_python_information() -> dict[str, str]:
     """Get installed Python information.
 
     Parameters
@@ -42,7 +41,7 @@ def _get_python_information() -> Dict[str, str]:
     }
 
 
-def _get_dependency_information(long_: bool) -> Dict[str, str]:
+def _get_dependency_information(long_: bool) -> dict[str, str]:
     """Get Python environment dependency information.
 
     Parameters
@@ -87,7 +86,7 @@ def _get_dependency_information(long_: bool) -> Dict[str, str]:
     return pruned_dependency_versions
 
 
-def _get_system_information() -> Dict[str, str]:
+def _get_system_information() -> dict[str, str]:
     """Get system information.
 
     Returns
@@ -101,7 +100,7 @@ def _get_system_information() -> Dict[str, str]:
     }
 
 
-def _get_environment_information(long_: bool) -> Dict[str, str]:
+def _get_environment_information(long_: bool) -> dict[str, str]:
     """Get system environment information.
 
     Parameters

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -6,7 +6,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List, Union
+from typing import Union
 
 from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
@@ -37,7 +37,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
     def __init__(
         self,
         datadir: Union[str, Path, None] = None,
-        sites: Union[str, List[str], None] = None,
+        sites: Union[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 +6,7 @@
 # License: AGPL
 
 import socket
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -53,7 +53,7 @@ def test_JuselessUCLA() -> None:
     ],
 )
 def test_JuselessUCLA_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test JuselessUCLA DataGrabber partial data access.
 

junifer/configs/juseless/datagrabbers/ucla.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List, Union
+from typing import Union
 
 from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataGrabber
@@ -43,8 +43,8 @@ class JuselessUCLA(PatternDataGrabber):
         datadir: Union[
             str, Path
         ] = "/data/project/psychosis_thalamus/data/fmriprep",
-        types: Union[str, List[str], None] = None,
-        tasks: Union[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 = [
@@ -136,7 +136,7 @@ class JuselessUCLA(PatternDataGrabber):
             confounds_format="fmriprep",
         )
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Implement fetching list of elements in the dataset.
 
         Returns