dummy cached_property for py3.7; adopt future typing

Author: Mr-Milk

spatialtis/abc.py

@@ -1,7 +1,8 @@
+from __future__ import annotations
+
 import warnings
 from ast import literal_eval
 from collections import Counter
-from functools import cached_property
 from time import time
 from typing import Any, Dict, List, Optional, Union, Sequence
 
@@ -16,6 +17,16 @@
 from spatialtis.utils import df2adata_uns, doc, log_print, pretty_time, read_exp, read_shapes, default_args
 
 
+# cached_property is only for py3.8+
+# create a dummy one to be compatible with py3.7+
+# TODO: Remove after deprecation of py3.7
+try:
+    from functools import cached_property
+except ImportError:
+    def cached_property(obj):
+        return obj
+
+
 class NeighborsNotFoundError(Exception):
     pass
 
@@ -222,7 +233,7 @@ def _get_wkt_points(self, key):
                           "try `spatialtis.transform_points`")
         return points
 
-    def get_centroids(self) -> Union[object, list[list[float, float]]]:
+    def get_centroids(self) -> object | List:
         ckey = self.centroid_key
         # determine the type of centroid
         # by default, read 'spatial' from .obsm

spatialtis/preprocessing/read_10x.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import warnings
 from pathlib import Path
 from typing import List, Optional
@@ -8,8 +10,6 @@
 from scipy.io import mmread
 from scipy.sparse import csr_matrix
 
-from spatialtis.typing import File
-
 
 def read_10x_h5(h5file):
     with h5py.File(h5file) as h:
@@ -68,7 +68,7 @@ def read_10x_spatial(stlist):
 
 
 def read_visium(
-        paths: List[File],
+        paths: List[str | Path],
         read_filtered: bool = True,  # "filtered" or "raw"
         annotations: Optional[pd.DataFrame] = None,
 ) -> AnnData:

spatialtis/preprocessing/read_images.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import warnings
 from pathlib import Path
 from typing import List, Optional
@@ -8,12 +10,11 @@
 from scipy.sparse import csr_matrix
 from spatialtis_core import dumps_points_wkt, dumps_polygons_wkt, points_shapes
 
-from spatialtis.typing import File
 from spatialtis.utils import options_guard
 
 
-def stacked_channels(c_imgs: List[File],
-                     export: File = "stacked.tiff"
+def stacked_channels(c_imgs: List[str | Path],
+                     export: str | Path = "stacked.tiff"
                      ):
     """
     A helper functions to stack single channel images to multi-channels
@@ -85,8 +86,8 @@ def check_exists(files):
 
 
 def read_images(
-        images: List[File],
-        masks: List[File],
+        images: List[str | Path],
+        masks: List[str | Path],
         markers: Optional[pd.DataFrame] = None,
         annotations: Optional[pd.DataFrame] = None,
         image_axes: str = "cyx",

spatialtis/spatial/autocorr.py

@@ -15,7 +15,7 @@ def spatial_autocorr(
         method: str = "moran_i",
         pval: float = 0.05,
         two_tailed: bool = True,
-        layer_key: Optional[str] = None,
+        layer_key: str = None,
         export_key: str = "spatial_autocorr",
         **kwargs,
 ):

spatialtis/spatial/co_expression.py

@@ -8,7 +8,6 @@
 from spatialtis_core import fast_corr
 
 from spatialtis.abc import AnalysisBase, neighbors_pairs
-from spatialtis.typing import Number
 from spatialtis.utils import doc, pbar_iter, options_guard
 from spatialtis.utils.io import read_exp
 
@@ -19,9 +18,9 @@
 def spatial_coexp(data: AnnData,
                   method: str = "spearman",
                   use_cell_type: bool = False,
-                  selected_markers: Optional[List[str]] = None,
-                  layer_key: Optional[str] = None,
-                  corr_thresh: Optional[Number] = 0.5,
+                  selected_markers: List[str] = None,
+                  layer_key: str = None,
+                  corr_thresh: float = 0.5,
                   export_key: str = "spatial_coexp",
                   **kwargs, ):
     """Identifying spatial co-expression markers using correlation

spatialtis/spatial/distribution.py

@@ -1,11 +1,10 @@
-from typing import Optional
+from typing import Optional, Tuple
 
 import pandas as pd
 from anndata import AnnData
 from spatialtis_core import points_bbox, spatial_distribution_pattern
 
 from spatialtis.abc import AnalysisBase
-from spatialtis.typing import Number, Tuple
 from spatialtis.utils import doc, options_guard
 
 
@@ -15,10 +14,10 @@ def cell_dispersion(
         method: str = "id",
         min_cells: int = 10,
         pval: float = 0.01,
-        r: Optional[Number] = None,
+        r: float = None,
         resample: int = 1000,
-        quad: Optional[Tuple[int, int]] = None,
-        rect_size: Optional[Number] = None,
+        quad: Tuple[int, int] = None,
+        rect_size: float = None,
         export_key: str = "cell_dispersion",
         **kwargs,
 ):

spatialtis/spatial/enrichment.py

@@ -1,21 +1,22 @@
+from __future__ import annotations
+
 import warnings
-from typing import Optional
+from typing import Optional, List
 
 import numpy as np
 import pandas as pd
 from anndata import AnnData
 from spatialtis_core import comb_bootstrap
 
 from spatialtis.abc import AnalysisBase
-from spatialtis.typing import Array
 from spatialtis.utils import doc
 
 
 @doc
 def spatial_enrichment(data: AnnData,
-                       threshold: Optional[float] = None,
-                       layer_key: Optional[str] = None,
-                       selected_markers: Optional[Array] = None,
+                       threshold: float = None,
+                       layer_key: str = None,
+                       selected_markers: List[str] | np.ndarray = None,
                        resample: int = 500,
                        pval: float = 0.01,
                        export_key: str = "spatial_enrichment",

spatialtis/spatial/heterogeneity.py

@@ -1,5 +1,4 @@
 import warnings
-from typing import Optional
 
 import pandas as pd
 from anndata import AnnData
@@ -13,7 +12,7 @@
 @doc
 def spatial_heterogeneity(data: AnnData,
                           method: str = "leibovici",
-                          d: Optional[int] = None,
+                          d: int = None,
                           cut: int = 3,
                           export_key: str = "heterogeneity",
                           **kwargs, ):

spatialtis/spatial/hotspot.py

@@ -1,17 +1,19 @@
-from typing import Optional, Tuple
+from __future__ import annotations
 
+from typing import Optional, Tuple, List
+
+import numpy as np
 import pandas as pd
 from anndata import AnnData
 from spatialtis_core import getis_ord, points_bbox
 
 from spatialtis.abc import AnalysisBase
-from spatialtis.typing import Array
 from spatialtis.utils import col2adata, doc
 
 
 @doc
 def hotspot(data: AnnData,
-            selected_types: Optional[Array] = None,
+            selected_types: List[str] | np.ndarray = None,
             search_level: int = 3,
             quad: Optional[Tuple[int, int]] = None,
             rect_side: Optional[Tuple[float, float]] = None,

spatialtis/spatial/ncd_markers.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 from ast import literal_eval
-from typing import Dict, Optional
+from typing import Dict, Optional, List
 
 import numpy as np
 import pandas as pd
@@ -9,18 +11,17 @@
 from spatialtis_core import neighbor_components
 
 from spatialtis.abc import AnalysisBase
-from spatialtis.typing import Number, Array
 from spatialtis.utils import doc, read_exp
 
 
 @doc
 def NCD_marker(data: AnnData,
-               selected_markers: Optional[Array] = None,
-               importance_cutoff: Number = 0.5,
-               layer_key: Optional[str] = None,
-               tree_kwargs: Optional[Dict] = None,
+               selected_markers: List[str] | np.ndarray = None,
+               importance_cutoff: float = 0.5,
+               layer_key: str = None,
+               tree_kwargs: Dict = None,
                test_method: str = "mannwhitneyu",
-               pval: Number = 0.01,
+               pval: float = 0.01,
                export_key: str = "ncd_marker",
                **kwargs, ):
     """Identify neighbor cells dependent marker