Zarr overwrites codec configuration when creating and opening Arrays #2800

import icechunk
import zarr

# Create icechunk repo
storage = icechunk.local_filesystem_storage("myrepo")
config = icechunk.RepositoryConfig.default()
config.set_virtual_chunk_container(
    icechunk.VirtualChunkContainer(
        "s3", "s3", icechunk.s3_store(region="us-east-1", anonymous=True)
    )
)

repo = icechunk.Repository.create(storage=storage, config=config)

# Create the array with the correct codecs
session = repo.writable_session("main")
root = zarr.group(session.store)
test_arr = root.create_array(
    "test",
    shape=(720, 1440),
    chunks=(720, 1440),
    dtype="float64",
    compressors=[
        {"name": "numcodecs.shuffle", "configuration": {"elementsize": 2}},
        {"name": "numcodecs.zlib", "configuration": {"level": 4}},
    ],
    filters=[
        {
            "name": "numcodecs.fixedscaleoffset",
            "configuration": {
                "scale": 100.0,
                "offset": 0.0,
                "dtype": "<f8",
                "astype": "<i2",
            },
        },
    ],
    fill_value=-9.99,
    dimension_names=["lat", "lon"],
)

session.store.set_virtual_ref(
    "test/c/0/0",
    "s3://noaa-oisst-v2/2024/01/01/oisst-avhrr-v02r01.19810101.nc",
    offset=58888,
    length=654174,
)

session.commit("Add virtual array")

# Check compressors
print(test_arr.compressors)

# (Shuffle(codec_name='numcodecs.shuffle', codec_config={'elementsize': 8}),
 # Zlib(codec_name='numcodecs.zlib', codec_config={'level': 4}))
# Shuffle is not correct!

# Check what was stored
session = repo.writable_session("main")
buff = await session.store.get("test/zarr.json", zarr.core.buffer.default_buffer_prototype())
buff.to_bytes()

# b'{"zarr_format":3,"node_type":"array","attributes":{},"shape":[720,1440],"data_type":"float64","chunk_grid":{"name":"regular","configuration":{"chunk_shape":[720,1440]}},"chunk_key_encoding":{"name":"default","configuration":{"separator":"/"}},"fill_value":-9.99,"codecs":[{"name":"numcodecs.fixedscaleoffset","configuration":{"astype":"<i2","id":"fixedscaleoffset","scale":100.0,"offset":0.0,"dtype":"float64"}},{"name":"bytes","configuration":{"endian":"little"}},{"name":"numcodecs.shuffle","configuration":{"id":"shuffle","elementsize":8}},{"name":"numcodecs.zlib","configuration":{"id":"zlib","level":4}}],"storage_transformers":[],"dimension_names":["lat","lon"]}'

# Manually overwrite the codec config
metadata = json.loads(buff.to_bytes().decode('utf-8'))
metadata["codecs"][2]["configuration"]["elementsize"] = 2
bytes = json.dumps(metadata).encode('utf-8')
await session.store.set("test/zarr.json", zarr.core.buffer.default_buffer_prototype().buffer.from_bytes(bytes))
session.commit("Update zarr.json")

# Read in the array again and check compressor config 
root = zarr.open_group(session.store, mode="r")
root["test"].compressors

# (Shuffle(codec_name='numcodecs.shuffle', codec_config={'elementsize': 8}),
#  Zlib(codec_name='numcodecs.zlib', codec_config={'level': 4}))
# Not what was set!!!