From c5097e2eba942a07f8d29fa2f962cfe1995b0b45 Mon Sep 17 00:00:00 2001
From: Dante Rigo <dhillrigo@gmail.com>
Date: Fri, 28 Aug 2026 10:53:48 -0700
Subject: [PATCH] Fix ZarrAvgMerger under zarr 3.3: map chunks=True to
 auto-chunking

zarr 3.3 removed boolean chunk arguments, so ZarrAvgMerger's documented
default chunks=True raised ValueError on every construction. Map True to
None (zarr 3.3's spelling of auto-chunking) when zarr >= 3.3.0; the
substitution is version-gated because on zarr 3.0 None means a single
whole-shape chunk, not auto-chunking. chunks=False and explicit shapes
still work on every version and pass through unchanged.

zarr 3.3 also requires the bytes codec to specify endianness for
multi-byte dtypes, so the test fixtures' {"name": "bytes",
"configuration": {}} configs now set endian little; this form is
accepted from zarr 3.0 on.

Adds a regression test asserting the default produces auto-chunking
rather than one whole-shape chunk.

Verified with the full test_zarr_avg_merger suite on zarr 3.0.0, 3.2.0
and 3.3.0. The zarr 2 paths are untouched: the mapping is gated on the
zarr version, and the fixture change only affects v3-selected configs.

Signed-off-by: Dante Rigo <dhillrigo@gmail.com>
---
 monai/inferers/merger.py               |  8 ++++++-
 tests/inferers/test_zarr_avg_merger.py | 30 +++++++++++++++++++++-----
 2 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/monai/inferers/merger.py b/monai/inferers/merger.py
index 3d07925e457..e55b18402a1 100644
--- a/monai/inferers/merger.py
+++ b/monai/inferers/merger.py
@@ -307,7 +307,13 @@ def __init__(
             self.value_store = zarr.storage.TempStore() if value_store is None else value_store  # type: ignore
             self.count_store = zarr.storage.TempStore() if count_store is None else count_store  # type: ignore
 
-        self.chunks = chunks
+        # zarr 3.3 rejects boolean chunk arguments; `None` there means auto-chunking,
+        # which is what `chunks=True` meant before. On zarr < 3.3 `None` instead means
+        # a single whole-shape chunk, so the substitution must not be applied there.
+        if chunks is True and version_geq(get_package_version("zarr"), "3.3.0"):
+            self.chunks: Sequence[int] | bool | None = None
+        else:
+            self.chunks = chunks
 
         # Initialize codecs/compressor attributes with proper types
         self.codecs: list | None = None
diff --git a/tests/inferers/test_zarr_avg_merger.py b/tests/inferers/test_zarr_avg_merger.py
index b4e26d6bebd..e8aff312836 100644
--- a/tests/inferers/test_zarr_avg_merger.py
+++ b/tests/inferers/test_zarr_avg_merger.py
@@ -195,11 +195,20 @@
 ]
 
 # Define zarr v3 codec configurations with proper bytes codec
-ZARR_V3_LZ4_CODECS = [{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "lz4"}}]
+ZARR_V3_LZ4_CODECS = [
+    {"name": "bytes", "configuration": {"endian": "little"}},
+    {"name": "blosc", "configuration": {"cname": "lz4"}},
+]
 
-ZARR_V3_PICKLE_CODECS = [{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zstd"}}]
+ZARR_V3_PICKLE_CODECS = [
+    {"name": "bytes", "configuration": {"endian": "little"}},
+    {"name": "blosc", "configuration": {"cname": "zstd"}},
+]
 
-ZARR_V3_LZMA_CODECS = [{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zlib"}}]
+ZARR_V3_LZMA_CODECS = [
+    {"name": "bytes", "configuration": {"endian": "little"}},
+    {"name": "blosc", "configuration": {"cname": "zlib"}},
+]
 
 # test for LZ4 compressor (zarr v2) or codecs (zarr v3)
 TEST_CASE_13_COMPRESSOR_LZ4 = [
@@ -289,7 +298,10 @@
 TEST_CASE_19_VALUE_CODECS = [
     dict(
         merged_shape=TENSOR_4x4.shape,
-        value_codecs=[{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zstd"}}],
+        value_codecs=[
+            {"name": "bytes", "configuration": {"endian": "little"}},
+            {"name": "blosc", "configuration": {"cname": "zstd"}},
+        ],
     ),
     [
         (TENSOR_4x4[..., :2, :2], (0, 0)),
@@ -304,7 +316,10 @@
 TEST_CASE_20_COUNT_CODECS = [
     dict(
         merged_shape=TENSOR_4x4.shape,
-        count_codecs=[{"name": "bytes", "configuration": {}}, {"name": "blosc", "configuration": {"cname": "zlib"}}],
+        count_codecs=[
+            {"name": "bytes", "configuration": {"endian": "little"}},
+            {"name": "blosc", "configuration": {"cname": "zlib"}},
+        ],
     ),
     [
         (TENSOR_4x4[..., :2, :2], (0, 0)),
@@ -449,6 +464,11 @@ def test_zarr_avg_merge_none_merged_shape_error(self):
         with self.assertRaises(ValueError):
             ZarrAvgMerger(merged_shape=None, store=self.merged_name)
 
+    def test_zarr_avg_merger_default_chunks_auto(self):
+        """chunks=True must mean auto-chunking, not one whole-shape chunk (zarr 3.3 removed boolean chunks)."""
+        merger = ZarrAvgMerger(merged_shape=(4096, 4096), store=self.merged_name)
+        self.assertNotEqual(merger.output.chunks, (4096, 4096))
+
 
 if __name__ == "__main__":
     unittest.main()