add regression testing against v2.18

Author: d-v-b

tests/test_regression/__init__.py

@@ -0,0 +1,125 @@
+import subprocess
+from dataclasses import asdict, dataclass
+from itertools import product
+from pathlib import Path
+
+import numcodecs
+import numpy as np
+import pytest
+from numcodecs import LZ4, LZMA, Blosc, GZip, VLenUTF8, Zstd
+
+import zarr
+from zarr.core.array import Array
+from zarr.core.dtype.npy.string import VariableLengthString
+from zarr.core.metadata.v2 import ArrayV2Metadata
+from zarr.storage import LocalStore
+
+
+def runner_installed() -> bool:
+    try:
+        subprocess.check_output(["uv", "--version"])
+        return True
+    except FileNotFoundError:
+        return False
+
+
+def array_metadata_equals(a: ArrayV2Metadata, b: ArrayV2Metadata) -> bool:
+    dict_a, dict_b = asdict(a), asdict(b)
+    fill_value_a, fill_value_b = dict_a.pop("fill_value"), dict_b.pop("fill_value")
+    if (
+        isinstance(fill_value_a, float)
+        and isinstance(fill_value_b, float)
+        and np.isnan(fill_value_a)
+        and np.isnan(fill_value_b)
+    ):
+        return dict_a == dict_b
+    else:
+        return fill_value_a == fill_value_b and dict_a == dict_b
+
+
+@dataclass(kw_only=True)
+class ArrayParams:
+    values: np.ndarray[tuple[int], np.dtype[np.generic]]
+    fill_value: np.generic | str
+    compressor: numcodecs.abc.Codec
+
+
+basic_codecs = GZip(), Blosc(), LZ4(), LZMA(), Zstd()
+basic_dtypes = "|b", ">i2", ">i4", ">f4", ">f8", "<f4", "<f8", ">c8", "<c8", ">c16", "<c16"
+datetime_dtypes = "<M8[10ns]", ">M8[10us]", "<m8[2ms]", ">m8[4ps]"
+string_dtypes = ">S1", "<S4", "<U1", ">U4"
+
+basic_array_cases = [
+    ArrayParams(values=np.arange(4, dtype=dtype), fill_value=1, compressor=codec)
+    for codec, dtype in product(basic_codecs, basic_dtypes)
+]
+datetime_array_cases = [
+    ArrayParams(values=np.ones((4,), dtype=dtype), fill_value=1, compressor=codec)
+    for codec, dtype in product(basic_codecs, datetime_dtypes)
+]
+string_array_cases = [
+    ArrayParams(
+        values=np.array(["aaaa", "bbbb", "ccccc", "dddd"], dtype=dtype),
+        fill_value="foo",
+        compressor=codec,
+    )
+    for codec, dtype in product(basic_codecs, string_dtypes)
+]
+vlen_string_cases = [
+    ArrayParams(
+        values=np.array(["a", "bb", "ccc", "dddd"], dtype="O"),
+        fill_value="1",
+        compressor=VLenUTF8(),
+    )
+]
+array_cases = basic_array_cases + datetime_array_cases + string_array_cases + vlen_string_cases
+
+
+@pytest.fixture
+def source_array(tmp_path: Path, request: pytest.FixtureRequest) -> Array:
+    dest = tmp_path / "in"
+    store = LocalStore(dest)
+    array_params: ArrayParams = request.param
+    compressor = array_params.compressor
+    if array_params.values.dtype == np.dtype("|O"):
+        dtype = VariableLengthString()
+    else:
+        dtype = array_params.values.dtype
+    z = zarr.create_array(
+        store,
+        shape=array_params.values.shape,
+        dtype=dtype,
+        chunks=array_params.values.shape,
+        compressors=compressor,
+        fill_value=array_params.fill_value,
+        order="C",
+        filters=None,
+        chunk_key_encoding={"name": "v2", "configuration": {"separator": "/"}},
+        write_data=True,
+        zarr_format=2,
+    )
+    z[:] = array_params.values
+    return z
+
+
+@pytest.mark.skipif(not runner_installed(), reason="no python script runner installed")
+@pytest.mark.parametrize(
+    "source_array", array_cases, indirect=True, ids=tuple(map(str, array_cases))
+)
+def test_roundtrip(source_array: Array, tmp_path: Path) -> None:
+    out_path = tmp_path / "out"
+    copy_op = subprocess.run(
+        [
+            "uv",
+            "run",
+            Path(__file__).resolve().parent / "v2.18.py",
+            str(source_array.store).removeprefix("file://"),
+            str(out_path),
+        ],
+        capture_output=True,
+        text=True,
+    )
+    assert copy_op.returncode == 0
+    out_array = zarr.open_array(store=out_path, mode="r", zarr_format=2)
+    assert array_metadata_equals(source_array.metadata, out_array.metadata)
+    assert np.array_equal(source_array[:], out_array[:])

tests/test_regression/test_regression.py

@@ -0,0 +1,81 @@
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#  "zarr==2.18",
+#  "numcodecs==0.15"
+# ]
+# ///
+
+import argparse
+
+import zarr
+from zarr._storage.store import BaseStore
+
+
+def copy_group(
+    *, node: zarr.hierarchy.Group, store: zarr.storage.BaseStore, path: str, overwrite: bool
+) -> zarr.hierarchy.Group:
+    result = zarr.group(store=store, path=path, overwrite=overwrite)
+    result.attrs.put(node.attrs.asdict())
+    for key, child in node.items():
+        child_path = f"{path}/{key}"
+        if isinstance(child, zarr.hierarchy.Group):
+            copy_group(node=child, store=store, path=child_path, overwrite=overwrite)
+        elif isinstance(child, zarr.core.Array):
+            copy_array(node=child, store=store, overwrite=overwrite, path=child_path)
+    return result
+
+
+def copy_array(
+    *, node: zarr.core.Array, store: BaseStore, path: str, overwrite: bool
+) -> zarr.core.Array:
+    result = zarr.create(
+        shape=node.shape,
+        dtype=node.dtype,
+        fill_value=node.fill_value,
+        chunks=node.chunks,
+        compressor=node.compressor,
+        filters=node.filters,
+        order=node.order,
+        dimension_separator=node._dimension_separator,
+        store=store,
+        path=path,
+        overwrite=overwrite,
+    )
+    result.attrs.put(node.attrs.asdict())
+    result[:] = node[:]
+    return result
+
+
+def copy_node(
+    node: zarr.hierarchy.Group | zarr.core.Array, store: BaseStore, path: str, overwrite: bool
+) -> zarr.hierarchy.Group | zarr.core.Array:
+    if isinstance(node, zarr.hierarchy.Group):
+        return copy_group(node=node, store=store, path=path, overwrite=overwrite)
+    elif isinstance(node, zarr.core.Array):
+        return copy_array(node=node, store=store, path=path, overwrite=overwrite)
+    else:
+        raise TypeError(f"Unexpected node type: {type(node)}")  # pragma: no cover
+
+
+def cli() -> None:
+    parser = argparse.ArgumentParser(
+        description="Copy a zarr hierarchy from one location to another"
+    )
+    parser.add_argument("source", type=str, help="Path to the source zarr hierarchy")
+    parser.add_argument("destination", type=str, help="Path to the destination zarr hierarchy")
+    args = parser.parse_args()
+
+    src, dst = args.source, args.destination
+    root_src = zarr.open(src, mode="r")
+    result = copy_node(node=root_src, store=zarr.NestedDirectoryStore(dst), path="", overwrite=True)
+
+    print(f"successfully created {result} at {dst}")
+
+
+def main() -> None:
+    cli()
+
+
+if __name__ == "__main__":
+    main()