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

junifer/storage/utils.py

@@ -6,8 +6,8 @@
 
 import hashlib
 import json
+from collections.abc import Iterable
 from importlib.metadata import PackageNotFoundError, version
-from typing import Dict, Iterable, List, Tuple
 
 import numpy as np
 
@@ -50,7 +50,7 @@ def get_dependency_version(dependency: str) -> str:
     return dep_version
 
 
-def _meta_hash(meta: Dict) -> str:
+def _meta_hash(meta: dict) -> str:
     """Compute the MD5 hash of the metadata.
 
     Parameters
@@ -78,7 +78,7 @@ def _meta_hash(meta: Dict) -> str:
     return meta_md5
 
 
-def process_meta(meta: Dict) -> Tuple[str, Dict, Dict]:
+def process_meta(meta: dict) -> tuple[str, dict, dict]:
     """Process the metadata for storage.
 
     It removes the key "element" and adds the "_element_keys" with the keys
@@ -109,7 +109,7 @@ def process_meta(meta: Dict) -> Tuple[str, Dict, Dict]:
     # Copy the metadata
     t_meta = meta.copy()
     # Remove key "element"
-    element: Dict = t_meta.pop("element", None)
+    element: dict = t_meta.pop("element", None)
     if element is None:
         raise_error(msg="`meta` must contain the key 'element'")
     if "marker" not in t_meta:
@@ -128,7 +128,7 @@ def process_meta(meta: Dict) -> Tuple[str, Dict, Dict]:
     return md5_hash, t_meta, element
 
 
-def element_to_prefix(element: Dict) -> str:
+def element_to_prefix(element: dict) -> str:
     """Convert the element metadata to prefix.
 
     Parameters
@@ -156,7 +156,7 @@ def element_to_prefix(element: Dict) -> str:
 def store_matrix_checks(
     matrix_kind: str,
     diagonal: bool,
-    data_shape: Tuple[int, int],
+    data_shape: tuple[int, int],
     row_names_len: int,
     col_names_len: int,
 ) -> None:
@@ -218,7 +218,7 @@ def matrix_to_vector(
     row_names: Iterable[str],
     matrix_kind: str,
     diagonal: bool,
-) -> Tuple[np.ndarray, List[str]]:
+) -> tuple[np.ndarray, list[str]]:
     """Convert matrix to vector based on parameters.
 
     Parameters

junifer/testing/datagrabbers.py

@@ -6,7 +6,6 @@
 
 import tempfile
 from pathlib import Path
-from typing import Dict, List
 
 import nibabel as nib
 from nilearn import datasets, image
@@ -35,7 +34,7 @@ class OasisVBMTestingDataGrabber(BaseDataGrabber):
         types = ["VBM_GM"]
         super().__init__(types=types, datadir=datadir)
 
-    def get_element_keys(self) -> List[str]:
+    def get_element_keys(self) -> list[str]:
         """Get element keys.
 
         Returns
@@ -46,7 +45,7 @@ class OasisVBMTestingDataGrabber(BaseDataGrabber):
         """
         return ["subject"]
 
-    def get_item(self, subject: str) -> Dict[str, Dict]:
+    def get_item(self, subject: str) -> dict[str, dict]:
         """Implement indexing support.
 
         Parameters
@@ -80,7 +79,7 @@ class OasisVBMTestingDataGrabber(BaseDataGrabber):
         self._dataset = datasets.fetch_oasis_vbm(n_subjects=10)
         return self
 
-    def get_elements(self) -> List[str]:
+    def get_elements(self) -> list[str]:
         """Get elements.
 
         Returns
@@ -106,7 +105,7 @@ class SPMAuditoryTestingDataGrabber(BaseDataGrabber):
         types = ["BOLD", "T1w"]  # TODO: Check that they are T1w
         super().__init__(types=types, datadir=datadir)
 
-    def get_element_keys(self) -> List[str]:
+    def get_element_keys(self) -> list[str]:
         """Get element keys.
 
         Returns
@@ -117,7 +116,7 @@ class SPMAuditoryTestingDataGrabber(BaseDataGrabber):
         """
         return ["subject"]
 
-    def get_elements(self) -> List[str]:
+    def get_elements(self) -> list[str]:
         """Get elements.
 
         Returns
@@ -128,7 +127,7 @@ class SPMAuditoryTestingDataGrabber(BaseDataGrabber):
         """
         return [f"sub{x:03d}" for x in list(range(1, 11))]
 
-    def get_item(self, subject: str) -> Dict[str, Dict]:
+    def get_item(self, subject: str) -> dict[str, dict]:
         """Implement indexing support.
 
         Parameters
@@ -208,7 +207,7 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber):
         )
         return self
 
-    def get_element_keys(self) -> List[str]:
+    def get_element_keys(self) -> list[str]:
         """Get element keys.
 
         Returns
@@ -219,7 +218,7 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber):
         """
         return ["subject"]
 
-    def get_elements(self) -> List[str]:
+    def get_elements(self) -> list[str]:
         """Get elements.
 
         Returns
@@ -230,7 +229,7 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber):
         """
         return [f"sub-{x:02d}" for x in list(range(1, 11))]
 
-    def get_item(self, subject: str) -> Dict[str, Dict]:
+    def get_item(self, subject: str) -> dict[str, dict]:
         """Implement indexing support.
 
         Parameters

junifer/tests/test_stats.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, Optional
+from typing import Optional
 
 import numpy as np
 import pytest
@@ -25,7 +25,7 @@ from junifer.stats import count, get_aggfunc_by_name, select, winsorized_mean
         ("mode", {"keepdims": True}),
     ],
 )
-def test_get_aggfunc_by_name(name: str, params: Optional[Dict]) -> None:
+def test_get_aggfunc_by_name(name: str, params: Optional[dict]) -> None:
     """Test aggregation function retrieval by name.
 
     Parameters

junifer/typing/_typing.py

@@ -3,12 +3,9 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+from collections.abc import MutableMapping, Sequence
 from typing import (
     TYPE_CHECKING,
-    AbstractSet,
-    MutableMapping,
-    Sequence,
-    Type,
     Union,
 )
 
@@ -34,10 +31,10 @@ __all__ = [
 ]
 
 
-DataGrabberLike = Type["BaseDataGrabber"]
-PreprocessorLike = Type["BasePreprocessor"]
-MarkerLike = Type["BaseMarker"]
-StorageLike = Type["BaseFeatureStorage"]
+DataGrabberLike = type["BaseDataGrabber"]
+PreprocessorLike = type["BasePreprocessor"]
+MarkerLike = type["BaseMarker"]
+StorageLike = type["BaseFeatureStorage"]
 PipelineComponent = Union[
     "DataGrabberLike",
     "DefaultDataReader",
@@ -45,7 +42,7 @@ PipelineComponent = Union[
     "MarkerLike",
     "StorageLike",
 ]
-Dependencies = AbstractSet[str]
+Dependencies = set[str]
 ConditionalDependencies = Sequence[
     MutableMapping[
         str,

junifer/utils/helpers.py

@@ -6,7 +6,6 @@
 import collections.abc
 import subprocess
 import sys
-from typing import Dict, List
 
 from .logging import logger, raise_error
 
@@ -14,7 +13,7 @@ from .logging import logger, raise_error
 __all__ = ["run_ext_cmd", "deep_update"]
 
 
-def run_ext_cmd(name: str, cmd: List[str]) -> None:
+def run_ext_cmd(name: str, cmd: list[str]) -> None:
     """Run external command via subprocess.
 
     Parameters
@@ -58,7 +57,7 @@ def run_ext_cmd(name: str, cmd: List[str]) -> None:
         )
 
 
-def deep_update(d: Dict, u: Dict) -> Dict:
+def deep_update(d: dict, u: dict) -> dict:
     """Deep update `d` with `u`.
 
     From: "https://stackoverflow.com/questions/3232943/update-value-of-a-nested

junifer/utils/logging.py

@@ -16,7 +16,7 @@ import logging
 import warnings
 from pathlib import Path
 from subprocess import PIPE, Popen, TimeoutExpired
-from typing import Dict, NoReturn, Optional, Type, Union
+from typing import NoReturn, Optional, Union
 from warnings import warn
 
 import datalad
@@ -119,7 +119,7 @@ def _get_git_head(path: Path) -> str:
     return proc_stdout
 
 
-def get_versions() -> Dict:
+def get_versions() -> dict:
     """Import stuff and get versions if module.
 
     Returns
@@ -189,7 +189,7 @@ def _close_handlers(logger: logging.Logger) -> None:
             logger.removeHandler(handler)
 
 
-def _safe_log(versions: Dict, name: str) -> None:
+def _safe_log(versions: dict, name: str) -> None:
     """Log with safety.
 
     Parameters
@@ -308,7 +308,7 @@ def configure_logging(
 
 def raise_error(
     msg: str,
-    klass: Type[Exception] = ValueError,
+    klass: type[Exception] = ValueError,
     exception: Optional[Exception] = None,
 ) -> NoReturn:
     """Raise error, but first log it.
@@ -331,7 +331,7 @@ def raise_error(
 
 
 def warn_with_log(
-    msg: str, category: Optional[Type[Warning]] = RuntimeWarning
+    msg: str, category: Optional[type[Warning]] = RuntimeWarning
 ) -> None:
     """Warn, but first log it.
 

junifer/utils/singleton.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from abc import ABCMeta
-from typing import Any, ClassVar, Dict, Type
+from typing import Any, ClassVar
 
 
 __all__ = ["Singleton", "ABCSingleton"]
@@ -21,9 +21,9 @@ class Singleton(type):
 
     """
 
-    instances: ClassVar[Dict] = {}
+    instances: ClassVar[dict] = {}
 
-    def __call__(cls, *args: Any, **kwargs: Any) -> Type:
+    def __call__(cls, *args: Any, **kwargs: Any) -> type:
         """Get the only instance for a class.
 
         Parameters

{junifer-0.0.6.dev248.dist-info → junifer-0.0.6.dev258.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev248
+Version: 0.0.6.dev258
 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>
@@ -24,7 +24,7 @@ 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: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst