clean up

docs/tutorials/api_usage.ipynb

@@ -604,7 +604,7 @@
     }
    ],
    "source": [
-    "sopa.io.write_xenium_explorer(\"tuto.explorer\", sdata)"
+    "sopa.io.explorer.write(\"tuto.explorer\", sdata)"
    ]
   },
   {

sopa/io/__init__.py

@@ -1,18 +1,4 @@
-from .explorer import (
-    write,
-    write_xenium_explorer,
-    align,
-    add_xenium_explorer_selection,
-    write_image,
-    write_transcripts,
-    write_cell_categories,
-    write_gene_counts,
-    write_polygons,
-    write_xenium_explorer_metadata,
-    str_cell_id,
-    int_cell_id,
-    save_column_csv,
-)
+from .explorer import write
 from .standardize import write_standardized
 from .reader.cosmx import cosmx
 from .reader.merscope import merscope
@@ -25,5 +11,5 @@
 from .reader.aics import aicsimageio
 from .reader.visium_hd import visium_hd
 from .report import write_report
-
 from ..utils.data import blobs, uniform, toy_dataset
+from . import explorer

sopa/io/explorer/__init__.py

@@ -2,5 +2,5 @@
 from .points import write_transcripts
 from .table import write_cell_categories, write_gene_counts, save_column_csv
 from .shapes import write_polygons
-from .converter import write, write_xenium_explorer, write_xenium_explorer_metadata
-from .utils import str_cell_id, int_cell_id, add_xenium_explorer_selection
+from .converter import write, write_metadata
+from .utils import str_cell_id, int_cell_id, add_explorer_selection

sopa/io/explorer/converter.py

@@ -2,7 +2,6 @@
 
 import json
 import logging
-import warnings
 from pathlib import Path
 
 import geopandas as gpd
@@ -47,14 +46,7 @@ def _should_save(mode: str | None, character: str):
     return character in mode if mode[0] == "+" else character not in mode
 
 
-def write(*args, **kwargs):
-    warnings.warn(
-        "sopa.io.write is deprecated, use sopa.io.write_xenium_explorer instead", DeprecationWarning, stacklevel=2
-    )
-    write_xenium_explorer(*args, **kwargs)
-
-
-def write_xenium_explorer(
+def write(
     path: str,
     sdata: SpatialData,
     image_key: str | None = None,
@@ -166,7 +158,7 @@ def write_xenium_explorer(
 
     ### Saving experiment.xenium file
     if _should_save(mode, "m"):
-        write_xenium_explorer_metadata(path, image_key, shapes_key, _get_n_obs(sdata, geo_df), pixel_size)
+        write_metadata(path, image_key, shapes_key, _get_n_obs(sdata, geo_df), pixel_size)
 
     if save_h5ad and SopaKeys.TABLE in sdata.tables:
         sdata.tables[SopaKeys.TABLE].write_h5ad(path / FileNames.H5AD)
@@ -181,7 +173,7 @@ def _get_n_obs(sdata: SpatialData, geo_df: gpd.GeoDataFrame) -> int:
     return len(geo_df) if geo_df is not None else 0
 
 
-def write_xenium_explorer_metadata(
+def write_metadata(
     path: str,
     image_key: str = "NA",
     shapes_key: str = "NA",

sopa/io/explorer/utils.py

@@ -55,7 +55,7 @@ def xenium_explorer_selection(path: str | Path, pixel_size: float = 0.2125, retu
     return [_selection_to_polygon(sub_df, pixel_size) for _, sub_df in df.groupby("Selection")]
 
 
-def add_xenium_explorer_selection(
+def add_explorer_selection(
     sdata: SpatialData,
     path: str,
     shapes_key: str,

sopa/io/standardize.py

@@ -17,7 +17,7 @@
 log = logging.getLogger(__name__)
 
 
-def sanity_check(sdata: SpatialData, delete_table: bool = False, warn: bool = False):
+def sanity_check(sdata: SpatialData, delete_table: bool = False):
     assert len(sdata.images) > 0, "The spatialdata object has no image. Sopa is not designed for this."
 
     image = get_spatial_image(sdata)
@@ -26,11 +26,6 @@ def sanity_check(sdata: SpatialData, delete_table: bool = False, warn: bool = Fa
     ), f"Image must have the following three dimensions: {VALID_DIMENSIONS}. Found {image.dims}"
     check_integer_dtype(image.dtype)
 
-    if len(sdata.points) > 1:
-        log.warning(
-            f"The spatialdata object has {len(sdata.points)} points objects. It's easier to have only one (corresponding to transcripts), since sopa will use it directly without providing a key argument"
-        )
-
     c_coords = get_channel_names(image)
     assert valid_c_coords(c_coords), f"Channel names must be strings, not {c_coords.dtype}"
 
@@ -42,9 +37,9 @@ def sanity_check(sdata: SpatialData, delete_table: bool = False, warn: bool = Fa
             del sdata.tables[SopaKeys.TABLE]
 
 
-def read_zarr_standardized(path: str, warn: bool = False) -> SpatialData:
+def read_zarr_standardized(path: str) -> SpatialData:
     sdata = spatialdata.read_zarr(path)
-    sanity_check(sdata, warn=warn)
+    sanity_check(sdata)
     return sdata