From 19675e4a7119a3d2015ef6aa3e47638cb97b3c7e Mon Sep 17 00:00:00 2001
From: Tom Nicholas <tom@earthmover.io>
Date: Mon, 24 Mar 2025 15:34:31 -0400
Subject: [PATCH 1/2] add test

---
 tests/test_metadata/test_v3.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py
index a47cbf43bb..afbab2a57c 100644
--- a/tests/test_metadata/test_v3.py
+++ b/tests/test_metadata/test_v3.py
@@ -411,3 +411,20 @@ def test_dtypes(dtype_str: str) -> None:
     else:
         # return type for vlen types may vary depending on numpy version
         assert dt.byte_count is None
+
+
+def test_metadata_comparison_with_nan_fill_value():
+    # regression test for https://github.com/zarr-developers/zarr-python/issues/2929
+    metadata_dict = {
+        "zarr_format": 3,
+        "node_type": "array",
+        "shape": (1,),
+        "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}},
+        "data_type": np.dtype("float32"),
+        "chunk_key_encoding": {"name": "default", "separator": "."},
+        "codecs": ({'name': 'bytes', 'configuration': {'endian': 'little'}},),
+        "fill_value": np.float32("nan"),
+    }
+    metadata1 = ArrayV3Metadata.from_dict(metadata_dict)
+    metadata2 = ArrayV3Metadata.from_dict(metadata_dict)
+    assert metadata1 == metadata2

From affa01ca1eef7bbb355474fb3ee8f0c0c7d16785 Mon Sep 17 00:00:00 2001
From: Tom Nicholas <tom@earthmover.io>
Date: Mon, 24 Mar 2025 15:37:08 -0400
Subject: [PATCH 2/2] override __eq__ method

---
 src/zarr/abc/metadata.py     | 24 +++++++++++++++++++++++-
 src/zarr/core/metadata/v3.py |  2 +-
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/zarr/abc/metadata.py b/src/zarr/abc/metadata.py
index a56f986645..55cc0bae56 100644
--- a/src/zarr/abc/metadata.py
+++ b/src/zarr/abc/metadata.py
@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 if TYPE_CHECKING:
     from typing import Self
@@ -10,6 +10,8 @@
 
 from dataclasses import dataclass, fields
 
+import numpy as np
+
 __all__ = ["Metadata"]
 
 
@@ -44,3 +46,23 @@ def from_dict(cls, data: dict[str, JSON]) -> Self:
         """
 
         return cls(**data)
+    
+    def __eq__(self, other: Any) -> bool:
+        """Checks metadata are identical, including special treatment for NaN fill_values."""
+        if not isinstance(other, type(self)):
+            return False
+        
+        metadata_dict1 = self.to_dict()
+        metadata_dict2 = other.to_dict()
+
+        # fill_value is a special case because numpy NaNs cannot be compared using __eq__, see https://stackoverflow.com/a/10059796
+        fill_value1 = metadata_dict1.pop("fill_value")
+        fill_value2 = metadata_dict2.pop("fill_value")
+        if np.isnan(fill_value1) and np.isnan(fill_value2):
+            fill_values_equal = fill_value1.dtype == fill_value2.dtype
+        else:
+            fill_values_equal = fill_value1 == fill_value2
+
+        # everything else in ArrayV3Metadata is a string, Enum, or Dataclass
+        return fill_values_equal and metadata_dict1 == metadata_dict2
+
diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py
index 9154762648..22606b1ae8 100644
--- a/src/zarr/core/metadata/v3.py
+++ b/src/zarr/core/metadata/v3.py
@@ -233,7 +233,7 @@ class ArrayV3MetadataDict(TypedDict):
     attributes: dict[str, JSON]
 
 
-@dataclass(frozen=True, kw_only=True)
+@dataclass(frozen=True, kw_only=True, eq=False)
 class ArrayV3Metadata(Metadata):
     shape: ChunkCoords
     data_type: DataType