From ece4de440cdb0e09e5d770f3f740f48259b6e2ea Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pnanda@umich.edu>
Date: Fri, 24 May 2024 12:55:06 -0400
Subject: [PATCH] drop unmaintained pygeos for shapely 2.0 (#545)

* drop unmaintained pygeos for shapely 2.0

* removed unused pygeos env variable

---------

Co-authored-by: Luca Marconato <m.lucalmer@gmail.com>
---
 pyproject.toml              |  3 +--
 src/spatialdata/__init__.py |  7 -------
 src/spatialdata/_compat.py  | 27 ---------------------------
 tests/conftest.py           | 22 +++++++++-------------
 4 files changed, 10 insertions(+), 49 deletions(-)
 delete mode 100644 src/spatialdata/_compat.py

diff --git a/pyproject.toml b/pyproject.toml
index e6c187c1..860a2062 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
     "dask-image",
     "dask<=2024.2.1",
     "fsspec<=2023.6",
-    "geopandas",
+    "geopandas>=0.14",
     "multiscale_spatial_image==0.11.2",
     "networkx",
     "numpy",
@@ -35,7 +35,6 @@ dependencies = [
     "pandas",
     "pooch",
     "pyarrow",
-    "pygeos",
     "rich",
     "shapely>=2.0.1",
     "spatial_image==0.3.0",
diff --git a/src/spatialdata/__init__.py b/src/spatialdata/__init__.py
index 18eae0f8..3fd835d9 100644
--- a/src/spatialdata/__init__.py
+++ b/src/spatialdata/__init__.py
@@ -4,13 +4,6 @@
 
 __version__ = version("spatialdata")
 
-# Forcing usage of shapely 2.0 by geopandas
-# https://geopandas.org/en/stable/getting_started/install.html#using-the-optional-pygeos-dependency
-from ._compat import _check_geopandas_using_shapely
-
-_check_geopandas_using_shapely()
-
-
 __all__ = [
     "models",
     "transformations",
diff --git a/src/spatialdata/_compat.py b/src/spatialdata/_compat.py
deleted file mode 100644
index 3fb9b57a..00000000
--- a/src/spatialdata/_compat.py
+++ /dev/null
@@ -1,27 +0,0 @@
-def _check_geopandas_using_shapely() -> None:
-    """Check if geopandas is using shapely.
-
-    This is required until it becomes the default.
-    """
-    import warnings
-
-    with warnings.catch_warnings():
-        warnings.filterwarnings(
-            "ignore",
-            "Shapely 2.0 is installed, but because PyGEOS is also installed",
-            category=UserWarning,
-        )
-        import geopandas
-
-        if geopandas.options.use_pygeos is True:
-            geopandas.options.use_pygeos = False
-
-            warnings.warn(
-                (
-                    "Geopandas was set to use PyGEOS, changing to shapely 2.0 with:"
-                    "\n\n\tgeopandas.options.use_pygeos = True\n\n"
-                    "If you intended to use PyGEOS, set the option to False."
-                ),
-                UserWarning,
-                stacklevel=2,
-            )
diff --git a/tests/conftest.py b/tests/conftest.py
index 66f65e0c..f8a15a53 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,16 +1,11 @@
 from __future__ import annotations
 
-# isort: off
-import os
-from typing import Any
 from collections.abc import Sequence
-
-os.environ["USE_PYGEOS"] = "0"
-# isort:on
-
-from shapely import linearrings, polygons
 from pathlib import Path
-from spatialdata._types import ArrayLike
+from typing import Any
+
+import dask.dataframe as dd
+import geopandas as gpd
 import numpy as np
 import pandas as pd
 import pytest
@@ -19,9 +14,13 @@
 from geopandas import GeoDataFrame
 from multiscale_spatial_image import MultiscaleSpatialImage
 from numpy.random import default_rng
+from shapely import linearrings, polygons
 from shapely.geometry import MultiPolygon, Point, Polygon
 from spatial_image import SpatialImage
+from spatialdata._core._deepcopy import deepcopy as _deepcopy
 from spatialdata._core.spatialdata import SpatialData
+from spatialdata._types import ArrayLike
+from spatialdata.datasets import BlobsDataset
 from spatialdata.models import (
     Image2DModel,
     Image3DModel,
@@ -32,10 +31,6 @@
     TableModel,
 )
 from xarray import DataArray
-from spatialdata.datasets import BlobsDataset
-import geopandas as gpd
-import dask.dataframe as dd
-from spatialdata._core._deepcopy import deepcopy as _deepcopy
 
 RNG = default_rng(seed=0)
 
@@ -309,6 +304,7 @@ def labels_blobs() -> ArrayLike:
 def sdata_blobs() -> SpatialData:
     """Create a 2D labels."""
     from copy import deepcopy
+
     from spatialdata.datasets import blobs
 
     sdata = deepcopy(blobs(256, 300, 3))