feat: rewrite the CosMx reader (stitching, multimodal, co-registration)

pyproject.toml

@@ -37,6 +37,10 @@ dependencies = [
     "tifffile>=2023.8.12",
     "ome-types",
     "xmltodict",
+    # CosMx reader
+    "polars",
+    "dask",
+    "zarr>=3",
 ]
 
 [project.optional-dependencies]
@@ -188,6 +192,7 @@ lint.ignore = [
 ]
 [tool.ruff.lint.per-file-ignores]
 "src/spatialdata_io/__init__.py" = ["I001"]
+"tests/*" = ["D"]
 
 [tool.jupytext]
 formats = "ipynb,md"

src/spatialdata_io/readers/cosmx/__init__.py

@@ -0,0 +1,7 @@
+"""NanoString CosMx reader."""
+
+from __future__ import annotations
+
+from ._reader import cosmx
+
+__all__ = ["cosmx"]