junifer 0.0.6.dev227__py3-none-any.whl → 0.0.6.dev252__py3-none-any.whl

junifer/storage/sqlite.py

@@ -6,7 +6,7 @@
 
 import json
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
+from typing import TYPE_CHECKING, Any, Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -92,7 +92,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         # Set upsert
         self._upsert = upsert
 
-    def get_engine(self, element: Optional[Dict] = None) -> "Engine":
+    def get_engine(self, element: Optional[dict] = None) -> "Engine":
         """Get engine.
 
         Parameters
@@ -209,7 +209,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
                         msg=f"Invalid option {if_exists} for if_exists."
                     )
 
-    def list_features(self) -> Dict[str, Dict[str, Any]]:
+    def list_features(self) -> dict[str, dict[str, Any]]:
         """List the features in the storage.
 
         Returns
@@ -229,7 +229,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         # Format index names for retrieved data
         meta_df.index = meta_df.index.str.replace(r"meta_", "")
         # Convert dataframe to dictionary
-        out: Dict[str, Dict[str, str]] = meta_df.to_dict(
+        out: dict[str, dict[str, str]] = meta_df.to_dict(
             orient="index"
         )  # type: ignore
         # Format output
@@ -242,8 +242,8 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         self,
         feature_name: Optional[str] = None,
         feature_md5: Optional[str] = None,
-    ) -> Dict[
-        str, Union[str, List[Union[int, str, Dict[str, str]]], np.ndarray]
+    ) -> dict[
+        str, Union[str, list[Union[int, str, dict[str, str]]], np.ndarray]
     ]:
         """Read stored feature.
 
@@ -358,7 +358,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         df = df.set_index(index_names)
         return df
 
-    def store_metadata(self, meta_md5: str, element: Dict, meta: Dict) -> None:
+    def store_metadata(self, meta_md5: str, element: dict, meta: dict) -> None:
         """Implement metadata storing in the storage.
 
         Parameters
@@ -381,7 +381,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
             self._save_upsert(meta_df, "meta", engine)
 
     def store_df(
-        self, meta_md5: str, element: Dict, df: Union[pd.DataFrame, pd.Series]
+        self, meta_md5: str, element: dict, df: Union[pd.DataFrame, pd.Series]
     ) -> None:
         """Implement pandas DataFrame storing.
 
@@ -434,10 +434,10 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
     def store_matrix(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
-        col_names: Optional[List[str]] = None,
-        row_names: Optional[List[str]] = None,
+        col_names: Optional[list[str]] = None,
+        row_names: Optional[list[str]] = None,
         matrix_kind: str = "full",
         diagonal: bool = True,
     ) -> None:

junifer/storage/tests/test_hdf5.py

@@ -6,7 +6,6 @@
 
 from copy import deepcopy
 from pathlib import Path
-from typing import Dict, Tuple
 
 import h5py
 import numpy as np
@@ -874,7 +873,7 @@ def test_store_scalar_table(tmp_path: Path) -> None:
     assert_array_equal(read_df.values, data)
 
 
-def _create_data_to_store(n_elements: int, kind: str) -> Tuple[str, Dict]:
+def _create_data_to_store(n_elements: int, kind: str) -> tuple[str, dict]:
     """Create data to store.
 
     Parameters

junifer/storage/tests/test_sqlite.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List, Union
+from typing import Union
 
 import numpy as np
 import pandas as pd
@@ -56,7 +56,7 @@ df_ignore = pd.DataFrame(
 
 
 def _read_sql(
-    table_name: str, uri: str, index_col: Union[str, List[str]]
+    table_name: str, uri: str, index_col: Union[str, list[str]]
 ) -> pd.DataFrame:
     """Read database table into a pandas DataFrame.
 

junifer/storage/tests/test_utils.py

@@ -4,7 +4,8 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict, Iterable, List, Tuple, Union
+from collections.abc import Iterable
+from typing import Union
 
 import numpy as np
 import pytest
@@ -198,7 +199,7 @@ def test_process_meta_invalid_metadata_key() -> None:
         ),
     ],
 )
-def test_process_meta_element(meta: Dict, elements: List[str]) -> None:
+def test_process_meta_element(meta: dict, elements: list[str]) -> None:
     """Test metadata element after processing.
 
     Parameters
@@ -215,7 +216,7 @@ def test_process_meta_element(meta: Dict, elements: List[str]) -> None:
     assert "A" in processed_meta
     assert "B" in processed_meta
     assert "element" not in processed_meta
-    assert isinstance(processed_meta["dependencies"], Dict)
+    assert isinstance(processed_meta["dependencies"], dict)
     assert all(
         x in processed_meta["dependencies"] for x in meta["dependencies"]
     )
@@ -232,7 +233,7 @@ def test_process_meta_element(meta: Dict, elements: List[str]) -> None:
         ({"subject": 1, "session": 2}, "element_1_2_"),
     ],
 )
-def test_element_to_prefix(element: Dict, prefix: str) -> None:
+def test_element_to_prefix(element: dict, prefix: str) -> None:
     """Test converting element to prefix (for file naming).
 
     Parameters
@@ -320,7 +321,7 @@ def test_element_to_prefix_invalid_type() -> None:
     ],
 )
 def test_store_matrix_checks(
-    params: Dict[str, Union[str, bool, Tuple[int, int], int]], err_msg: str
+    params: dict[str, Union[str, bool, tuple[int, int], int]], err_msg: str
 ) -> None:
     """Test matrix storing parameter checks.
 
@@ -401,9 +402,9 @@ def test_store_matrix_checks(
     ],
 )
 def test_matrix_to_vector(
-    params: Dict[str, Union[np.ndarray, Iterable[str], str, bool]],
+    params: dict[str, Union[np.ndarray, Iterable[str], str, bool]],
     expected_data: np.ndarray,
-    expected_columns: List[str],
+    expected_columns: list[str],
 ) -> None:
     """Test matrix to vector.
 

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.dev227.dist-info → junifer-0.0.6.dev252.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev227
+Version: 0.0.6.dev252
 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