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

junifer/preprocess/warping/_ants_warper.py

@@ -6,7 +6,6 @@
 from typing import (
     Any,
     ClassVar,
-    Dict,
 )
 
 import nibabel as nib
@@ -40,10 +39,10 @@ class ANTsWarper:
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        input: dict[str, Any],
+        extra_input: dict[str, Any],
         reference: str,
-    ) -> Dict[str, Any]:
+    ) -> dict[str, Any]:
         """Preprocess using ANTs.
 
         Parameters

junifer/preprocess/warping/_fsl_warper.py

@@ -6,7 +6,6 @@
 from typing import (
     Any,
     ClassVar,
-    Dict,
 )
 
 import nibabel as nib
@@ -39,9 +38,9 @@ class FSLWarper:
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Dict[str, Any],
-    ) -> Dict[str, Any]:
+        input: dict[str, Any],
+        extra_input: dict[str, Any],
+    ) -> dict[str, Any]:
         """Preprocess using FSL.
 
         Parameters

junifer/preprocess/warping/space_warper.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Union
+from typing import Any, ClassVar, Optional, Union
 
 from templateflow import api as tflow
 
@@ -64,7 +64,7 @@ class SpaceWarper(BasePreprocessor):
     ]
 
     def __init__(
-        self, using: str, reference: str, on: Union[List[str], str]
+        self, using: str, reference: str, on: Union[list[str], str]
     ) -> None:
         """Initialize the class."""
         # Validate `using` parameter
@@ -94,7 +94,7 @@ class SpaceWarper(BasePreprocessor):
         else:
             raise_error(f"Unknown reference: {self.reference}")
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid data types for input.
 
         Returns
@@ -135,9 +135,9 @@ class SpaceWarper(BasePreprocessor):
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[dict[str, Any], Optional[dict[str, dict[str, Any]]]]:
         """Preprocess.
 
         Parameters

junifer/preprocess/warping/tests/test_space_warper.py

@@ -4,7 +4,6 @@
 # License: AGPL
 
 import socket
-from typing import Tuple, Type
 
 import pytest
 from numpy.testing import assert_array_equal, assert_raises
@@ -29,7 +28,7 @@ from junifer.typing import DataGrabberLike
 def test_SpaceWarper_errors(
     using: str,
     reference: str,
-    error_type: Type[Exception],
+    error_type: type[Exception],
     error_msg: str,
 ) -> None:
     """Test SpaceWarper errors.
@@ -96,7 +95,7 @@ def test_SpaceWarper_errors(
     reason="only for juseless",
 )
 def test_SpaceWarper_native(
-    datagrabber: DataGrabberLike, element: Tuple[str, ...], using: str
+    datagrabber: DataGrabberLike, element: tuple[str, ...], using: str
 ) -> None:
     """Test SpaceWarper for native space warping.
 
@@ -160,7 +159,7 @@ def test_SpaceWarper_native(
 )
 def test_SpaceWarper_multi_mni(
     datagrabber: DataGrabberLike,
-    element: Tuple[str, ...],
+    element: tuple[str, ...],
     space: str,
 ) -> None:
     """Test SpaceWarper for MNI space warping.

junifer/stats.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Callable, Dict, List, Optional
+from typing import Any, Callable, Optional
 
 import numpy as np
 from scipy.stats import mode, trim_mean
@@ -17,7 +17,7 @@ __all__ = ["get_aggfunc_by_name", "count", "winsorized_mean", "select"]
 
 
 def get_aggfunc_by_name(
-    name: str, func_params: Optional[Dict[str, Any]] = None
+    name: str, func_params: Optional[dict[str, Any]] = None
 ) -> Callable:
     """Get an aggregation function by its name.
 
@@ -169,8 +169,8 @@ def winsorized_mean(
 def select(
     data: np.ndarray,
     axis: int = 0,
-    pick: Optional[List[int]] = None,
-    drop: Optional[List[int]] = None,
+    pick: Optional[list[int]] = None,
+    drop: Optional[list[int]] = None,
 ) -> np.ndarray:
     """Select a subset of the data.
 

junifer/storage/base.py

@@ -5,8 +5,9 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Optional, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -43,7 +44,7 @@ class BaseFeatureStorage(ABC):
     def __init__(
         self,
         uri: Union[str, Path],
-        storage_types: Union[List[str], str],
+        storage_types: Union[list[str], str],
         single_output: bool = True,
     ) -> None:
         self.uri = uri
@@ -61,7 +62,7 @@ class BaseFeatureStorage(ABC):
         self._valid_inputs = storage_types
         self.single_output = single_output
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid storage types for input.
 
         Returns
@@ -76,7 +77,7 @@ class BaseFeatureStorage(ABC):
             klass=NotImplementedError,
         )
 
-    def validate(self, input_: List[str]) -> None:
+    def validate(self, input_: list[str]) -> None:
         """Validate the input to the pipeline step.
 
         Parameters
@@ -98,7 +99,7 @@ class BaseFeatureStorage(ABC):
             )
 
     @abstractmethod
-    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
@@ -119,8 +120,8 @@ class BaseFeatureStorage(ABC):
         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.
 
@@ -169,7 +170,7 @@ class BaseFeatureStorage(ABC):
         )
 
     @abstractmethod
-    def store_metadata(self, meta_md5: str, element: Dict, meta: Dict) -> None:
+    def store_metadata(self, meta_md5: str, element: dict, meta: dict) -> None:
         """Store metadata.
 
         Parameters
@@ -229,7 +230,7 @@ class BaseFeatureStorage(ABC):
     def store_matrix(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,
@@ -271,8 +272,8 @@ class BaseFeatureStorage(ABC):
     def store_vector(
         self,
         meta_md5: str,
-        element: Dict,
-        data: Union[np.ndarray, List],
+        element: dict,
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
         """Store vector.
@@ -297,7 +298,7 @@ class BaseFeatureStorage(ABC):
     def store_timeseries(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
@@ -323,7 +324,7 @@ class BaseFeatureStorage(ABC):
     def store_scalar_table(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,

junifer/storage/hdf5.py

@@ -6,8 +6,9 @@
 
 
 from collections import defaultdict
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Optional, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -30,7 +31,7 @@ __all__ = ["HDF5FeatureStorage"]
 
 
 def _create_chunk(
-    chunk_data: List[np.ndarray],
+    chunk_data: list[np.ndarray],
     kind: str,
     element_count: int,
     chunk_size: int,
@@ -164,7 +165,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         self.force_float32 = force_float32
         self.chunk_size = chunk_size
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid storage types for input.
 
         Returns
@@ -176,7 +177,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         """
         return ["matrix", "vector", "timeseries", "scalar_table"]
 
-    def _fetch_correct_uri_for_io(self, element: Optional[Dict]) -> str:
+    def _fetch_correct_uri_for_io(self, element: Optional[dict]) -> str:
         """Return proper URI for I/O based on `element`.
 
         If `element` is None, will return `self.uri`.
@@ -210,8 +211,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         return f"{self.uri.parent}/{prefix}{self.uri.name}"  # type: ignore
 
     def _read_metadata(
-        self, element: Optional[Dict[str, str]] = None
-    ) -> Dict[str, Dict[str, Any]]:
+        self, element: Optional[dict[str, str]] = None
+    ) -> dict[str, dict[str, Any]]:
         """Read metadata (should not be called directly).
 
         Parameters
@@ -261,7 +262,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
 
         return metadata
 
-    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
@@ -281,8 +282,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         return metadata
 
     def _read_data(
-        self, md5: str, element: Optional[Dict[str, str]] = None
-    ) -> Dict[str, Any]:
+        self, md5: str, element: Optional[dict[str, str]] = None
+    ) -> dict[str, Any]:
         """Read data (should not be called directly).
 
         Parameters
@@ -338,8 +339,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         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.
 
@@ -562,7 +563,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         return df
 
     def _write_processed_data(
-        self, fname: str, processed_data: Dict[str, Any], title: str
+        self, fname: str, processed_data: dict[str, Any], title: str
     ) -> None:
         """Write processed data to HDF5 (should not be called directly).
 
@@ -594,8 +595,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_metadata(
         self,
         meta_md5: str,
-        element: Dict[str, str],
-        meta: Dict[str, Any],
+        element: dict[str, str],
+        meta: dict[str, Any],
     ) -> None:
         """Store metadata.
 
@@ -655,7 +656,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         self,
         kind: str,
         meta_md5: str,
-        element: List[Dict[str, str]],
+        element: list[dict[str, str]],
         data: np.ndarray,
         **kwargs: Any,
     ) -> None:
@@ -797,7 +798,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_matrix(
         self,
         meta_md5: str,
-        element: Dict[str, str],
+        element: dict[str, str],
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,
@@ -876,8 +877,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_vector(
         self,
         meta_md5: str,
-        element: Dict[str, str],
-        data: Union[np.ndarray, List],
+        element: dict[str, str],
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
         """Store vector.
@@ -919,7 +920,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_timeseries(
         self,
         meta_md5: str,
-        element: Dict[str, str],
+        element: dict[str, str],
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
@@ -949,7 +950,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_scalar_table(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,

junifer/storage/pandas_base.py

@@ -5,8 +5,9 @@
 # License: AGPL
 
 import json
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Dict, Iterable, List, Optional, Union
+from typing import Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -44,7 +45,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     ) -> None:
         super().__init__(uri=uri, single_output=single_output, **kwargs)
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid storage types for input.
 
         Returns
@@ -56,7 +57,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
         """
         return ["matrix", "vector", "timeseries"]
 
-    def _meta_row(self, meta: Dict, meta_md5: str) -> pd.DataFrame:
+    def _meta_row(self, meta: dict, meta_md5: str) -> pd.DataFrame:
         """Convert the metadata to a pandas DataFrame.
 
         Parameters
@@ -80,7 +81,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
 
     @staticmethod
     def element_to_index(
-        element: Dict, n_rows: int = 1, rows_col_name: Optional[str] = None
+        element: dict, n_rows: int = 1, rows_col_name: Optional[str] = None
     ) -> Union[pd.Index, pd.MultiIndex]:
         """Convert the element metadata to index.
 
@@ -101,7 +102,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
 
         """
         # Make mapping between element access keys and values
-        elem_idx: Dict[str, Iterable[str]] = {
+        elem_idx: dict[str, Iterable[str]] = {
             k: [v] * n_rows for k, v in element.items()
         }
 
@@ -129,7 +130,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
         return index
 
     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.
 
@@ -157,8 +158,8 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     def _store_2d(
         self,
         meta_md5: str,
-        element: Dict,
-        data: Union[np.ndarray, List],
+        element: dict,
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
         rows_col_name: Optional[str] = None,
     ) -> None:
@@ -194,8 +195,8 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     def store_vector(
         self,
         meta_md5: str,
-        element: Dict,
-        data: Union[np.ndarray, List],
+        element: dict,
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
         """Store vector.
@@ -232,7 +233,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     def store_timeseries(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
     ) -> None:

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.