fix: suppress 'not stored in most current format' UserWarning in old-format tests

Use `re.match`-compatible pattern (anchored at start) and add
`@pytest.mark.filterwarnings` to standalone parametrized tests outside
`TestReadWrite` that intentionally exercise the V01 container format.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: LucaMarconato

tests/io/test_attrs_io.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import tempfile
+import warnings
 from pathlib import Path
 
 import pytest
@@ -11,6 +12,7 @@
 from spatialdata._io.format import (
     SpatialDataContainerFormats,
     SpatialDataContainerFormatType,
+    CurrentSpatialDataContainerFormat,
 )
 
 FORMAT_V01 = SpatialDataContainerFormats["0.1"]
@@ -21,6 +23,17 @@
 class TestAttrsIO:
     """Test SpatialData.attrs read/write for all container formats."""
 
+    @pytest.fixture(autouse=True)
+    def _suppress_old_format_warning(self, sdata_container_format: SpatialDataContainerFormatType):
+        if isinstance(sdata_container_format, CurrentSpatialDataContainerFormat):
+            yield
+        else:
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "ignore", message="SpatialData is not stored in the most current format", category=UserWarning
+                )
+                yield
+
     def test_attrs_write_and_read(
         self,
         sdata_container_format: SpatialDataContainerFormatType,
@@ -111,7 +124,11 @@ def test_attrs_v1_to_v2() -> None:
         sdata.write(f_v1, sdata_formats=FORMAT_V01)
 
         # Read with V01
-        sdata_v1 = read_zarr(f_v1)
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore", message="SpatialData is not stored in the most current format", category=UserWarning
+            )
+            sdata_v1 = read_zarr(f_v1)
         assert sdata_v1.attrs == my_attrs
 
         # Write with V02

tests/io/test_format.py

@@ -2,6 +2,7 @@
 
 import json
 import tempfile
+import warnings
 from pathlib import Path
 from typing import Any
 
@@ -125,6 +126,14 @@ def test_format_raster_v1_v2_v3(self, images, rformat: type[SpatialDataFormatTyp
 class TestFormatConversions:
     """Test format conversions between older formats and newer."""
 
+    @pytest.fixture(autouse=True)
+    def _suppress_old_format_warning(self):
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore", message="SpatialData is not stored in the most current format", category=UserWarning
+            )
+            yield
+
     def test_shapes_v1_to_v2_to_v3(self, shapes):
         with tempfile.TemporaryDirectory() as tmpdir:
             f1 = Path(tmpdir) / "data1.zarr"

tests/io/test_partial_read.py

@@ -4,9 +4,10 @@
 import os
 import re
 import tempfile
+import warnings
 from collections.abc import Generator, Iterable
-from contextlib import contextmanager
-from dataclasses import dataclass
+from contextlib import contextmanager, nullcontext
+from dataclasses import dataclass, field
 from json import JSONDecodeError
 from pathlib import Path
 from typing import TYPE_CHECKING
@@ -69,6 +70,7 @@ class PartialReadTestCase:
     expected_elements: list[str]
     expected_exceptions: type[Exception] | tuple[type[Exception] | IOError, ...]
     warnings_patterns: list[str]
+    zarr_version: int = field(default=3)
 
 
 @pytest.fixture(scope="session")
@@ -103,6 +105,7 @@ def sdata_with_corrupted_elem_types_zgroup(session_tmp_path: Path) -> PartialRea
         expected_elements=not_corrupted,
         expected_exceptions=(JSONDecodeError, ZarrUserWarning),
         warnings_patterns=["labels: JSONDecodeError", "Object at"],
+        zarr_version=2,
     )
 
 
@@ -173,6 +176,7 @@ def sdata_with_corrupted_zattrs_elements(session_tmp_path: Path) -> PartialReadT
         expected_elements=not_corrupted,
         expected_exceptions=(OSError, JSONDecodeError),
         warnings_patterns=warnings_patterns,
+        zarr_version=2,
     )
 
 
@@ -216,6 +220,7 @@ def sdata_with_corrupted_image_chunks_zarrv2(session_tmp_path: Path) -> PartialR
         expected_elements=not_corrupted,
         expected_exceptions=(ArrayNotFoundError,),
         warnings_patterns=[rf"images/{corrupted}: ArrayNotFoundError"],
+        zarr_version=2,
     )
 
 
@@ -264,6 +269,7 @@ def sdata_with_corrupted_parquet_zarrv2(session_tmp_path: Path) -> PartialReadTe
         expected_elements=not_corrupted,
         expected_exceptions=ArrowInvalid,
         warnings_patterns=[rf"points/{corrupted}: ArrowInvalid"],
+        zarr_version=2,
     )
 
 
@@ -303,6 +309,7 @@ def sdata_with_missing_zattrs_element(session_tmp_path: Path) -> PartialReadTest
         expected_elements=not_corrupted,
         expected_exceptions=OSError,
         warnings_patterns=["OSError: Image location"],
+        zarr_version=2,
     )
 
 
@@ -349,6 +356,7 @@ def sdata_with_missing_image_chunks_zarrv2(
         expected_elements=not_corrupted,
         expected_exceptions=(ArrayNotFoundError,),
         warnings_patterns=[rf"images/{corrupted}: (ArrayNotFoundError|TypeError)"],
+        zarr_version=2,
     )
 
 
@@ -372,6 +380,7 @@ def sdata_with_invalid_zattrs_element_violating_spec(session_tmp_path: Path) ->
         expected_elements=not_corrupted,
         expected_exceptions=KeyError,
         warnings_patterns=[rf"images/{corrupted}: KeyError: coordinateTransformations"],
+        zarr_version=2,
     )
 
 
@@ -424,6 +433,7 @@ def _create_sdata_with_table_region_not_found(session_tmp_path: Path, zarr_versi
         warnings_patterns=[
             rf"The table is annotating '{re.escape(corrupted)}', which is not present in the SpatialData object"
         ],
+        zarr_version=zarr_version,
     )
 
 
@@ -460,11 +470,15 @@ def sdata_with_table_region_not_found_zarrv2(session_tmp_path: Path) -> PartialR
     indirect=True,
 )
 def test_read_zarr_with_error(test_case: PartialReadTestCase):
-    if test_case.expected_exceptions:
-        with pytest.raises(test_case.expected_exceptions):
+    ctx = warnings.catch_warnings() if test_case.zarr_version < 3 else nullcontext()
+    with ctx:
+        if test_case.zarr_version < 3:
+            warnings.filterwarnings("ignore", message="SpatialData is not stored in the most current format", category=UserWarning)
+        if test_case.expected_exceptions:
+            with pytest.raises(test_case.expected_exceptions):
+                read_zarr(test_case.path, on_bad_files="error")
+        else:
             read_zarr(test_case.path, on_bad_files="error")
-    else:
-        read_zarr(test_case.path, on_bad_files="error")
 
 
 @pytest.mark.parametrize(
@@ -490,8 +504,12 @@ def test_read_zarr_with_error(test_case: PartialReadTestCase):
     indirect=True,
 )
 def test_read_zarr_with_warnings(test_case: PartialReadTestCase):
-    with pytest_warns_multiple(UserWarning, matches=test_case.warnings_patterns):
-        actual: SpatialData = read_zarr(test_case.path, on_bad_files="warn")
+    ctx = warnings.catch_warnings() if test_case.zarr_version < 3 else nullcontext()
+    with ctx:
+        if test_case.zarr_version < 3:
+            warnings.filterwarnings("ignore", message="SpatialData is not stored in the most current format", category=UserWarning)
+        with pytest_warns_multiple(UserWarning, matches=test_case.warnings_patterns):
+            actual: SpatialData = read_zarr(test_case.path, on_bad_files="warn")
 
     actual_elements = {name for _, name, _ in actual.gen_elements()}
     assert set(test_case.expected_elements) == actual_elements

tests/io/test_readwrite.py

@@ -3,6 +3,7 @@
 import json
 import os
 import tempfile
+import warnings
 from collections.abc import Callable
 from pathlib import Path
 from typing import Any, Literal
@@ -57,6 +58,17 @@
 
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 class TestReadWrite:
+    @pytest.fixture(autouse=True)
+    def _suppress_old_format_warning(self, sdata_container_format: SpatialDataContainerFormatType):
+        if isinstance(sdata_container_format, CurrentSpatialDataContainerFormat):
+            yield
+        else:
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "ignore", message="SpatialData is not stored in the most current format", category=UserWarning
+                )
+                yield
+
     def test_images(
         self,
         tmp_path: str,
@@ -743,6 +755,7 @@ def test_single_scale_image_roundtrip_stays_dataarray(tmp_path: Path) -> None:
     assert list(image_group.keys()) == ["s0"]
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_self_contained(full_sdata: SpatialData, sdata_container_format: SpatialDataContainerFormatType) -> None:
     # data only in-memory, so the SpatialData object and all its elements are self-contained
@@ -804,6 +817,7 @@ def test_self_contained(full_sdata: SpatialData, sdata_container_format: Spatial
         assert all(description[element_name] for element_name in description if element_name != "combined")
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_symmetric_difference_with_zarr_store(
     full_sdata: SpatialData, sdata_container_format: SpatialDataContainerFormatType
@@ -846,6 +860,7 @@ def test_symmetric_difference_with_zarr_store(
         }
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_change_path_of_subset(full_sdata: SpatialData, sdata_container_format: SpatialDataContainerFormatType) -> None:
     """A subset SpatialData object has not Zarr path associated, show that we can reassign the path"""
@@ -917,6 +932,7 @@ def test_incremental_io_valid_name(full_sdata: SpatialData) -> None:
     _check_valid_name(full_sdata.write_transformations)
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_incremental_io_attrs(points: SpatialData, sdata_container_format: SpatialDataContainerFormatType) -> None:
     with tempfile.TemporaryDirectory() as tmpdir:
@@ -945,6 +961,7 @@ def test_incremental_io_attrs(points: SpatialData, sdata_container_format: Spati
 cached_sdata_blobs = blobs()
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("element_name", ["image2d", "labels2d", "points_0", "circles", "table"])
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_delete_element_from_disk(
@@ -996,6 +1013,7 @@ def test_delete_element_from_disk(
         assert element_path not in on_disk
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("element_name", ["image2d", "labels2d", "points_0", "circles", "table"])
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_element_already_on_disk_different_type(
@@ -1127,6 +1145,7 @@ def test_reading_invalid_name(tmp_path: Path):
     )
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_write_store_unconsolidated_and_read(full_sdata, sdata_container_format: SpatialDataContainerFormatType):
     with tempfile.TemporaryDirectory() as tmpdir:
@@ -1139,6 +1158,7 @@ def test_write_store_unconsolidated_and_read(full_sdata, sdata_container_format:
         assert_spatial_data_objects_are_identical(full_sdata, second_read)
 
 
+@pytest.mark.filterwarnings("ignore:SpatialData is not stored in the most current format:UserWarning")
 @pytest.mark.parametrize("sdata_container_format", SDATA_FORMATS)
 def test_can_read_sdata_with_reconsolidation(full_sdata, sdata_container_format: SpatialDataContainerFormatType):
     with tempfile.TemporaryDirectory() as tmpdir: