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

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -31,7 +31,7 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 )
 def test_DataladAOMICID1000(
     type_: str,
-    nested_types: Optional[List[str]],
+    nested_types: Optional[list[str]],
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber.
 
@@ -87,7 +87,7 @@ def test_DataladAOMICID1000(
     ],
 )
 def test_DataladAOMICID1000_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber partial data access.
 

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -40,8 +40,8 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 )
 def test_DataladAOMICPIOP1(
     type_: str,
-    nested_types: Optional[List[str]],
-    tasks: Optional[List[str]],
+    nested_types: Optional[list[str]],
+    tasks: Optional[list[str]],
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
 
@@ -117,7 +117,7 @@ def test_DataladAOMICPIOP1(
     ],
 )
 def test_DataladAOMICPIOP1_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber partial data access.
 

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -35,8 +35,8 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
 )
 def test_DataladAOMICPIOP2(
     type_: str,
-    nested_types: Optional[List[str]],
-    tasks: Optional[List[str]],
+    nested_types: Optional[list[str]],
+    tasks: Optional[list[str]],
 ) -> None:
     """Test DataladAOMICPIOP2 DataGrabber.
 
@@ -97,7 +97,7 @@ def test_DataladAOMICPIOP2(
     ],
 )
 def test_DataladAOMICPIOP2_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICPIOP2 DataGrabber partial data access.
 

junifer/datagrabber/base.py

@@ -6,8 +6,9 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
+from collections.abc import Iterator
 from pathlib import Path
-from typing import Dict, Iterator, List, Tuple, Union
+from typing import Union
 
 from ..pipeline import UpdateMetaMixin
 from ..utils import logger, raise_error
@@ -36,7 +37,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
 
     """
 
-    def __init__(self, types: List[str], datadir: Union[str, Path]) -> None:
+    def __init__(self, types: list[str], datadir: Union[str, Path]) -> None:
         # Validate types
         if not isinstance(types, list):
             raise_error(msg="`types` must be a list", klass=TypeError)
@@ -67,8 +68,8 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         yield from self.get_elements()
 
     def __getitem__(
-        self, element: Union[str, Tuple[str, ...]]
-    ) -> Dict[str, Dict]:
+        self, element: Union[str, tuple[str, ...]]
+    ) -> dict[str, dict]:
         """Enable indexing support.
 
         Parameters
@@ -89,7 +90,7 @@ 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))
         logger.debug(f"Named element: {named_element}")
         # Fetch element
         out = self.get_item(**named_element)
@@ -113,7 +114,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         """Context exit."""
         return None
 
-    def get_types(self) -> List[str]:
+    def get_types(self) -> list[str]:
         """Get types.
 
         Returns
@@ -136,7 +137,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         """
         return self._datadir
 
-    def filter(self, selection: List[Union[str, Tuple[str]]]) -> Iterator:
+    def filter(self, selection: list[Union[str, tuple[str]]]) -> Iterator:
         """Filter elements to be grabbed.
 
         Parameters
@@ -151,7 +152,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
 
         """
 
-        def filter_func(element: Union[str, Tuple[str]]) -> bool:
+        def filter_func(element: Union[str, tuple[str]]) -> bool:
             """Filter element based on selection.
 
             Parameters
@@ -182,7 +183,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         yield from filter(filter_func, self.get_elements())
 
     @abstractmethod
-    def get_element_keys(self) -> List[str]:
+    def get_element_keys(self) -> list[str]:
         """Get element keys.
 
         For each item in the ``element`` tuple passed to ``__getitem__()``,
@@ -200,7 +201,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         )  # pragma: no cover
 
     @abstractmethod
-    def get_elements(self) -> List[Union[str, Tuple[str]]]:
+    def get_elements(self) -> list[Union[str, tuple[str]]]:
         """Get elements.
 
         Returns
@@ -217,7 +218,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         )  # pragma: no cover
 
     @abstractmethod
-    def get_item(self, **element: Dict) -> Dict[str, Dict]:
+    def get_item(self, **element: dict) -> dict[str, dict]:
         """Get the specified item from the dataset.
 
         Parameters

junifer/datagrabber/datalad_base.py

@@ -9,7 +9,7 @@ import atexit
 import os
 import tempfile
 from pathlib import Path
-from typing import Dict, Optional, Tuple, Union
+from typing import Optional, Union
 
 import datalad
 import datalad.api as dl
@@ -165,7 +165,7 @@ class DataladDataGrabber(BaseDataGrabber):
             raise_error("Could not get dataset ID from remote")
         return remote_id
 
-    def _dataset_get(self, out: Dict) -> Dict:
+    def _dataset_get(self, out: dict) -> dict:
         """Get the dataset found from the path in ``out``.
 
         Parameters
@@ -283,7 +283,7 @@ class DataladDataGrabber(BaseDataGrabber):
                 logger.debug(f"Dropping {f}")
                 self._dataset.drop(f, result_renderer="disabled")
 
-    def __getitem__(self, element: Union[str, Tuple]) -> Dict:
+    def __getitem__(self, element: Union[str, tuple]) -> dict:
         """Implement single element indexing in the Datalad database.
 
         It will first obtain the paths from the parent class and then

junifer/datagrabber/dmcc13_benchmark.py

@@ -5,7 +5,7 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Union
 
 from ..api.decorators import register_datagrabber
 from ..utils import raise_error
@@ -59,11 +59,11 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
     def __init__(
         self,
         datadir: Union[str, Path, None] = None,
-        types: Union[str, List[str], None] = None,
-        sessions: Union[str, List[str], None] = None,
-        tasks: Union[str, List[str], None] = None,
-        phase_encodings: Union[str, List[str], None] = None,
-        runs: Union[str, List[str], None] = None,
+        types: Union[str, list[str], None] = None,
+        sessions: Union[str, list[str], None] = None,
+        tasks: Union[str, list[str], None] = None,
+        phase_encodings: Union[str, list[str], None] = None,
+        runs: Union[str, list[str], None] = None,
         native_t1w: bool = False,
     ) -> None:
         # Declare all sessions
@@ -271,7 +271,7 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
         task: str,
         phase_encoding: str,
         run: str,
-    ) -> Dict:
+    ) -> dict:
         """Index one element in the dataset.
 
         Parameters
@@ -309,7 +309,7 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
         )
         return out
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Implement fetching list of subjects in the dataset.
 
         Returns

junifer/datagrabber/hcp1200/datalad_hcp1200.py

@@ -6,7 +6,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List, Union
+from typing import Union
 
 from junifer.datagrabber.datalad_base import DataladDataGrabber
 
@@ -50,8 +50,8 @@ class DataladHCP1200(DataladDataGrabber, HCP1200):
     def __init__(
         self,
         datadir: Union[str, Path, None] = None,
-        tasks: Union[str, List[str], None] = None,
-        phase_encodings: Union[str, List[str], None] = None,
+        tasks: Union[str, list[str], None] = None,
+        phase_encodings: Union[str, list[str], None] = None,
         ica_fix: bool = False,
     ) -> None:
         uri = (

junifer/datagrabber/hcp1200/hcp1200.py

@@ -7,7 +7,7 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -48,8 +48,8 @@ class HCP1200(PatternDataGrabber):
     def __init__(
         self,
         datadir: Union[str, Path],
-        tasks: Union[str, List[str], None] = None,
-        phase_encodings: Union[str, List[str], None] = None,
+        tasks: Union[str, list[str], None] = None,
+        phase_encodings: Union[str, list[str], None] = None,
         ica_fix: bool = False,
     ) -> None:
         # All tasks
@@ -66,10 +66,10 @@ class HCP1200(PatternDataGrabber):
         ]
         # Set default tasks
         if tasks is None:
-            self.tasks: List[str] = all_tasks
+            self.tasks: list[str] = all_tasks
         # Convert single task into list
         else:
-            if not isinstance(tasks, List):
+            if not isinstance(tasks, list):
                 tasks = [tasks]
             # Check for invalid task(s)
             for task in tasks:
@@ -78,7 +78,7 @@ class HCP1200(PatternDataGrabber):
                         f"'{task}' is not a valid HCP-YA fMRI task input. "
                         f"Valid task values can be any or all of {all_tasks}."
                     )
-            self.tasks: List[str] = tasks
+            self.tasks: list[str] = tasks
 
         # All phase encodings
         all_phase_encodings = ["LR", "RL"]
@@ -150,7 +150,7 @@ class HCP1200(PatternDataGrabber):
             replacements=replacements,
         )
 
-    def get_item(self, subject: str, task: str, phase_encoding: str) -> Dict:
+    def get_item(self, subject: str, task: str, phase_encoding: str) -> dict:
         """Implement single element indexing in the database.
 
         Parameters
@@ -180,7 +180,7 @@ class HCP1200(PatternDataGrabber):
             subject=subject, task=new_task, phase_encoding=phase_encoding
         )
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Implement fetching list of elements in the dataset.
 
         Returns

junifer/datagrabber/hcp1200/tests/test_hcp1200.py

@@ -5,8 +5,9 @@
 
 import shutil
 import tempfile
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Iterable, Optional
+from typing import Optional
 
 import pytest
 

junifer/datagrabber/multiple.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, List, Tuple, Union
+from typing import Union
 
 from ..api.decorators import register_datagrabber
 from ..typing import DataGrabberLike
@@ -38,7 +38,7 @@ class MultipleDataGrabber(BaseDataGrabber):
 
     """
 
-    def __init__(self, datagrabbers: List[DataGrabberLike], **kwargs) -> None:
+    def __init__(self, datagrabbers: list[DataGrabberLike], **kwargs) -> None:
         # Check datagrabbers consistency
         # Check for same element keys
         first_keys = datagrabbers[0].get_element_keys()
@@ -79,7 +79,7 @@ class MultipleDataGrabber(BaseDataGrabber):
                 )
         self._datagrabbers = datagrabbers
 
-    def __getitem__(self, element: Union[str, Tuple]) -> Dict:
+    def __getitem__(self, element: Union[str, tuple]) -> dict:
         """Implement indexing.
 
         Parameters
@@ -127,7 +127,7 @@ class MultipleDataGrabber(BaseDataGrabber):
             dg.__exit__(exc_type, exc_value, exc_traceback)
 
     # TODO: return type should be List[List[str]], but base type is List[str]
-    def get_types(self) -> List[str]:
+    def get_types(self) -> list[str]:
         """Get types.
 
         Returns
@@ -139,7 +139,7 @@ class MultipleDataGrabber(BaseDataGrabber):
         types = [x for dg in self._datagrabbers for x in dg.get_types()]
         return types
 
-    def get_element_keys(self) -> List[str]:
+    def get_element_keys(self) -> list[str]:
         """Get element keys.
 
         For each item in the ``element`` tuple passed to ``__getitem__()``,
@@ -153,7 +153,7 @@ class MultipleDataGrabber(BaseDataGrabber):
         """
         return self._datagrabbers[0].get_element_keys()
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Get elements.
 
         Returns
@@ -171,7 +171,7 @@ class MultipleDataGrabber(BaseDataGrabber):
             elements.intersection_update(s)
         return list(elements)
 
-    def get_item(self, **_: Dict) -> Dict[str, Dict]:
+    def get_item(self, **_: dict) -> dict[str, dict]:
         """Get the specified item from the dataset.
 
         Parameters

junifer/datagrabber/pattern.py

@@ -8,7 +8,7 @@
 import re
 from copy import deepcopy
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import numpy as np
 
@@ -170,9 +170,9 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
 
     def __init__(
         self,
-        types: List[str],
-        patterns: Dict[str, Dict[str, str]],
-        replacements: Union[List[str], str],
+        types: list[str],
+        patterns: dict[str, dict[str, str]],
+        replacements: Union[list[str], str],
         datadir: Union[str, Path],
         confounds_format: Optional[str] = None,
         partial_pattern_ok: bool = False,
@@ -215,7 +215,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
 
     def _replace_patterns_regex(
         self, pattern: str
-    ) -> Tuple[str, str, List[str]]:
+    ) -> tuple[str, str, list[str]]:
         """Replace the patterns in ``pattern`` with the named groups.
 
         It allows elements to be obtained from the filesystem.
@@ -261,7 +261,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
 
         return re_pattern, glob_pattern, t_replacements
 
-    def _replace_patterns_glob(self, element: Dict, pattern: str) -> str:
+    def _replace_patterns_glob(self, element: dict, pattern: str) -> str:
         """Replace ``pattern`` with the ``element`` so it can be globbed.
 
         Parameters
@@ -294,7 +294,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
         return pattern.format(**element)
 
     def _get_path_from_patterns(
-        self, element: Dict, pattern: str, data_type: str
+        self, element: dict, pattern: str, data_type: str
     ) -> Path:
         """Get path from resolved patterns.
 
@@ -351,7 +351,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
 
         return path
 
-    def get_element_keys(self) -> List[str]:
+    def get_element_keys(self) -> list[str]:
         """Get element keys.
 
         For each item in the "element" tuple, this functions returns the
@@ -366,7 +366,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
         """
         return self.replacements
 
-    def get_item(self, **element: str) -> Dict[str, Dict]:
+    def get_item(self, **element: str) -> dict[str, dict]:
         """Implement single element indexing for the datagrabber.
 
         This method constructs a real path to the requested item's data, by
@@ -449,7 +449,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
 
         return out
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Implement fetching list of elements in the dataset.
 
         It will use regex to search for "replacements" in the "patterns" and

junifer/datagrabber/pattern_validation_mixin.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, List, Union
+from typing import Union
 
 from ..utils import logger, raise_error, warn_with_log
 
@@ -72,7 +72,7 @@ PATTERNS_SCHEMA = {
 class PatternValidationMixin:
     """Mixin class for pattern validation."""
 
-    def _validate_types(self, types: List[str]) -> None:
+    def _validate_types(self, types: list[str]) -> None:
         """Validate the types.
 
         Parameters
@@ -95,8 +95,8 @@ class PatternValidationMixin:
 
     def _validate_replacements(
         self,
-        replacements: List[str],
-        patterns: Dict[str, Union[Dict[str, str], List[Dict[str, str]]]],
+        replacements: list[str],
+        patterns: dict[str, Union[dict[str, str], list[dict[str, str]]]],
         partial_pattern_ok: bool,
     ) -> None:
         """Validate the replacements.
@@ -181,8 +181,8 @@ class PatternValidationMixin:
 
     def _validate_mandatory_keys(
         self,
-        keys: List[str],
-        schema: List[str],
+        keys: list[str],
+        schema: list[str],
         data_type: str,
         partial_pattern_ok: bool = False,
     ) -> None:
@@ -230,7 +230,7 @@ class PatternValidationMixin:
                 logger.debug(f"Mandatory key: `{key}` found for {data_type}.")
 
     def _identify_stray_keys(
-        self, keys: List[str], schema: List[str], data_type: str
+        self, keys: list[str], schema: list[str], data_type: str
     ) -> None:
         """Identify stray keys.
 
@@ -261,9 +261,9 @@ class PatternValidationMixin:
 
     def validate_patterns(
         self,
-        types: List[str],
-        replacements: List[str],
-        patterns: Dict[str, Union[Dict[str, str], List[Dict[str, str]]]],
+        types: list[str],
+        replacements: list[str],
+        patterns: dict[str, Union[dict[str, str], list[dict[str, str]]]],
         partial_pattern_ok: bool = False,
     ) -> None:
         """Validate the patterns.

junifer/datagrabber/tests/test_datalad_base.py

@@ -4,7 +4,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Type
 
 import datalad.api as dl
 import pytest
@@ -27,7 +26,7 @@ _testing_dataset = {
 
 
 @pytest.fixture
-def concrete_datagrabber() -> Type[DataladDataGrabber]:
+def concrete_datagrabber() -> type[DataladDataGrabber]:
     """Return a concrete datalad-based DataGrabber.
 
     Returns
@@ -69,7 +68,7 @@ def concrete_datagrabber() -> Type[DataladDataGrabber]:
 
 
 def test_DataladDataGrabber_install_errors(
-    tmp_path: Path, concrete_datagrabber: Type
+    tmp_path: Path, concrete_datagrabber: type
 ) -> None:
     """Test DataladDataGrabber install errors / warnings.
 
@@ -108,7 +107,7 @@ def test_DataladDataGrabber_install_errors(
 
 
 def test_DataladDataGrabber_clone_cleanup(
-    tmp_path: Path, concrete_datagrabber: Type
+    tmp_path: Path, concrete_datagrabber: type
 ) -> None:
     """Test DataladDataGrabber clone and remove.
 
@@ -157,7 +156,7 @@ def test_DataladDataGrabber_clone_cleanup(
 
 
 def test_DataladDataGrabber_clone_create_cleanup(
-    concrete_datagrabber: Type,
+    concrete_datagrabber: type,
 ) -> None:
     """Test DataladDataGrabber tempdir clone and remove.
 
@@ -203,7 +202,7 @@ def test_DataladDataGrabber_clone_create_cleanup(
 
 
 def test_DataladDataGrabber_previously_cloned(
-    tmp_path: Path, concrete_datagrabber: Type
+    tmp_path: Path, concrete_datagrabber: type
 ) -> None:
     """Test DataladDataGrabber on cloned dataset.
 
@@ -272,7 +271,7 @@ def test_DataladDataGrabber_previously_cloned(
 
 
 def test_DataladDataGrabber_previously_cloned_and_get(
-    tmp_path: Path, concrete_datagrabber: Type
+    tmp_path: Path, concrete_datagrabber: type
 ) -> None:
     """Test DataladDataGrabber on cloned dataset with files present.
 
@@ -355,7 +354,7 @@ def test_DataladDataGrabber_previously_cloned_and_get(
 
 
 def test_DataladDataGrabber_previously_cloned_and_get_dirty(
-    tmp_path: Path, concrete_datagrabber: Type
+    tmp_path: Path, concrete_datagrabber: type
 ) -> None:
     """Test DataladDataGrabber on a dirty cloned dataset.
 

junifer/datagrabber/tests/test_dmcc13_benchmark.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -218,7 +218,7 @@ def test_DMCC13Benchmark(
     ],
 )
 def test_DMCC13Benchmark_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
     native_t1w: bool,
 ) -> None:
     """Test DMCC13Benchmark DataGrabber partial data access.

junifer/datagrabber/tests/test_pattern_validation_mixin.py

@@ -4,8 +4,8 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from contextlib import nullcontext
-from typing import ContextManager, Dict, List, Union
+from contextlib import AbstractContextManager, nullcontext
+from typing import Union
 
 import pytest
 
@@ -186,10 +186,10 @@ from junifer.datagrabber.pattern_validation_mixin import PatternValidationMixin
     ],
 )
 def test_PatternValidationMixin(
-    types: Union[str, List[str], List[int]],
-    replacements: Union[str, List[str], List[int]],
-    patterns: Union[str, Dict[str, Dict[str, str]]],
-    expect: ContextManager,
+    types: Union[str, list[str], list[int]],
+    replacements: Union[str, list[str], list[int]],
+    patterns: Union[str, dict[str, dict[str, str]]],
+    expect: AbstractContextManager,
 ) -> None:
     """Test validation.