[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

README.md

@@ -51,36 +51,38 @@ ncols = 500  # Number of spots/cells
 counts = np.random.rand(nrows, ncols)
 
 # Create feature annotations
-row_data = BiocFrame({
-    "gene_ids": [f"gene_{i}" for i in range(nrows)],
-    "gene_names": [f"Gene_{i}" for i in range(nrows)]
-})
+row_data = BiocFrame(
+    {"gene_ids": [f"gene_{i}" for i in range(nrows)], "gene_names": [f"Gene_{i}" for i in range(nrows)]}
+)
 
 # Create spot/cell annotations
-col_data = BiocFrame({
-    "n_genes": [50, 200] * int(ncols / 2),
-    "condition": ["healthy", "tumor"] * int(ncols / 2),
-    "cell_id": [f"spot_{i}" for i in range(ncols)],
-    "sample_id": ["sample_1"] * int(ncols / 2) + ["sample_2"] * int(ncols / 2),
-})
+col_data = BiocFrame(
+    {
+        "n_genes": [50, 200] * int(ncols / 2),
+        "condition": ["healthy", "tumor"] * int(ncols / 2),
+        "cell_id": [f"spot_{i}" for i in range(ncols)],
+        "sample_id": ["sample_1"] * int(ncols / 2) + ["sample_2"] * int(ncols / 2),
+    }
+)
 
 # Generate spatial coordinates
-spatial_coords = BiocFrame({
-    "x": np.random.uniform(low=0.0, high=100.0, size=ncols),
-    "y": np.random.uniform(low=0.0, high=100.0, size=ncols)
-})
+spatial_coords = BiocFrame(
+    {"x": np.random.uniform(low=0.0, high=100.0, size=ncols), "y": np.random.uniform(low=0.0, high=100.0, size=ncols)}
+)
 
 # Create image data
-img_data = BiocFrame({
-    "sample_id": ["sample_1", "sample_1", "sample_2"],
-    "image_id": ["aurora", "dice", "desert"],
-    "data": [
-        construct_spatial_image_class("tests/images/sample_image1.jpg"),
-        construct_spatial_image_class("tests/images/sample_image2.png"),
-        construct_spatial_image_class("tests/images/sample_image3.jpg"),
-    ],
-    "scale_factor": [1, 1, 1],
-})
+img_data = BiocFrame(
+    {
+        "sample_id": ["sample_1", "sample_1", "sample_2"],
+        "image_id": ["aurora", "dice", "desert"],
+        "data": [
+            construct_spatial_image_class("tests/images/sample_image1.jpg"),
+            construct_spatial_image_class("tests/images/sample_image2.png"),
+            construct_spatial_image_class("tests/images/sample_image3.jpg"),
+        ],
+        "scale_factor": [1, 1, 1],
+    }
+)
 
 # Create SpatialExperiment object
 spe = SpatialExperiment(

setup.py

@@ -12,7 +12,7 @@
 if __name__ == "__main__":
     try:
         setup(use_scm_version={"version_scheme": "no-guess-dev"})
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "

src/spatialexperiment/__init__.py

@@ -26,11 +26,11 @@
 )
 
 __all__ = [
-    "read_tenx_visium",
-    "SpatialExperiment",
     "LoadedSpatialImage",
     "RemoteSpatialImage",
+    "SpatialExperiment",
     "StoredSpatialImage",
     "VirtualSpatialImage",
     "construct_spatial_image_class",
+    "read_tenx_visium",
 ]

src/spatialexperiment/_combineutils.py

@@ -1,15 +1,14 @@
 from __future__ import annotations
-from typing import List, Tuple
 
-from warnings import warn
-from copy import deepcopy
 import itertools
+from copy import deepcopy
+from warnings import warn
 
-from biocframe import BiocFrame
 import biocutils as ut
+from biocframe import BiocFrame
 
 
-def _append_indices_to_samples(bframes: List[BiocFrame]) -> List[BiocFrame]:
+def _append_indices_to_samples(bframes: list[BiocFrame]) -> list[BiocFrame]:
     """Append indices to sample IDs for a list of `BiocFrames`.
 
     For each `BiocFrame`, appends an index to all sample IDs to ensure uniqueness
@@ -29,7 +28,7 @@ def _append_indices_to_samples(bframes: List[BiocFrame]) -> List[BiocFrame]:
     return modified_bframes
 
 
-def merge_spatial_frames(x: List["SpatialExperiment"], relaxed: bool = False) -> Tuple[BiocFrame, BiocFrame]:
+def merge_spatial_frames(x: list[SpatialExperiment], relaxed: bool = False) -> tuple[BiocFrame, BiocFrame]:
     """Merge column data and image data from multiple ``SpatialExperiment`` objects.
 
     If duplicate sample IDs exist across objects, appends indices to make them unique.
@@ -70,7 +69,7 @@ def merge_spatial_frames(x: List["SpatialExperiment"], relaxed: bool = False) ->
     return _new_cols, _new_img_data
 
 
-def merge_spatial_coordinates(spatial_coords: List[BiocFrame], relaxed: bool = False) -> BiocFrame:
+def merge_spatial_coordinates(spatial_coords: list[BiocFrame], relaxed: bool = False) -> BiocFrame:
     """Merge spatial coordinates from multiple frames.
 
     Args:

src/spatialexperiment/_imgutils.py

@@ -1,12 +1,12 @@
-from typing import Union, List
-
 import os
 from io import BytesIO
 from pathlib import Path
 from urllib.parse import urlparse
+
 import numpy as np
-from PIL import Image
 from biocframe import BiocFrame
+from PIL import Image
+
 from .spatialimage import construct_spatial_image_class
 
 __author__ = "keviny2"
@@ -43,7 +43,7 @@ def read_image(input_image):
 
 
 def construct_img_data(
-    img: Union[str, os.PathLike], scale_factor: str, sample_id: str, image_id: str, load: bool = True
+    img: str | os.PathLike, scale_factor: str, sample_id: str, image_id: str, load: bool = True
 ) -> BiocFrame:
     """
     Construct an image data dataframe.
@@ -77,9 +77,9 @@ def construct_img_data(
 
 def get_img_idx(
     img_data: BiocFrame,
-    sample_id: Union[str, bool, None] = None,
-    image_id: Union[str, bool, None] = None,
-) -> List[int]:
+    sample_id: str | bool | None = None,
+    image_id: str | bool | None = None,
+) -> list[int]:
     """
     Retrieve the row index/indices of image(s) with matching 'sample_id' and 'image_id' from the 'img_data'.
 

src/spatialexperiment/_initutils.py

@@ -1,19 +1,19 @@
 from copy import deepcopy
-from typing import List, Tuple
 
 from biocframe import BiocFrame
 from PIL import Image
-from .spatialimage import construct_spatial_image_class
 from summarizedexperiment._frameutils import _sanitize_frame
 
+from .spatialimage import construct_spatial_image_class
+
 __author__ = "keviny2"
 __copyright__ = "keviny2"
 __license__ = "MIT"
 
 
 def construct_spatial_coords_from_names(
-    spatial_coords_names: List[str], column_data: BiocFrame
-) -> Tuple[BiocFrame, BiocFrame]:
+    spatial_coords_names: list[str], column_data: BiocFrame
+) -> tuple[BiocFrame, BiocFrame]:
     """Construct the `spatial_coords` dataframe from names.
 
     Args:
@@ -54,8 +54,8 @@ def construct_spatial_coords_from_names(
 def construct_img_data(
     sample_id: str,
     image_id: str,
-    image_sources: List[str],
-    scale_factors: List[float],
+    image_sources: list[str],
+    scale_factors: list[float],
     load_image: bool = False,
 ) -> BiocFrame:
     """Construct the image data for a `SpatialExperiment`.

src/spatialexperiment/_validators.py

@@ -1,7 +1,7 @@
 import warnings
 
-from biocframe import BiocFrame
 import biocutils as ut
+from biocframe import BiocFrame
 
 __author__ = "keviny2"
 __copyright__ = "keviny2"

src/spatialexperiment/io/tenx_visium.py

@@ -1,17 +1,17 @@
 """Creates a ``SpatialExperiment`` from the Space Ranger output directories for 10x Genomics Visium spatial gene expression data"""
 
-from typing import List, Union, Optional
-from warnings import warn
+import json
 import os
 import re
-import json
+from warnings import warn
 
-from biocframe import BiocFrame
 import biocutils as ut
+from biocframe import BiocFrame
 from singlecellexperiment import read_tenx_mtx
-from ..spatialexperiment import SpatialExperiment
+
 from .._imgutils import construct_img_data
 from .._initutils import construct_spatial_coords_from_names
+from ..spatialexperiment import SpatialExperiment
 
 
 def read_tissue_positions(tissue_positions_path) -> "pd.DataFrame":
@@ -46,8 +46,8 @@ def read_tissue_positions(tissue_positions_path) -> "pd.DataFrame":
 
 def read_img_data(
     path: str = ".",
-    sample_ids: Optional[List[str]] = None,
-    image_sources: Optional[List[str]] = None,
+    sample_ids: list[str] | None = None,
+    image_sources: list[str] | None = None,
     scale_factors: str = None,
     load: bool = True,
 ) -> BiocFrame:
@@ -118,11 +118,11 @@ def read_img_data(
 
 
 def read_tenx_visium(
-    samples: List[Union[str, os.PathLike]],
-    sample_ids: Optional[List[str]] = None,
+    samples: list[str | os.PathLike],
+    sample_ids: list[str] | None = None,
     type: str = "HDF5",
     data: str = "filtered",
-    images: List[str] = "lowres",
+    images: list[str] = "lowres",
     load: bool = True,
 ):
     """Create a ``SpatialExperiment`` from the Space Ranger output directories for 10x Genomics Visium spatial gene expression data.