deps: slim zarr dependencies

Author: jhamman

.pre-commit-config.yaml

@@ -28,18 +28,14 @@ repos:
         files: src|tests
         additional_dependencies:
           # Package dependencies
-          - asciitree
           - crc32c
           - donfig
-          - fasteners
           - numcodecs
           - numpy
           - typing_extensions
           - universal-pathlib
           # Tests
           - pytest
-          # Zarr v2
-          - types-redis
   - repo: https://github.com/scientific-python/cookie
     rev: 2024.08.19
     hooks:

pyproject.toml

@@ -23,12 +23,8 @@ maintainers = [
 requires-python = ">=3.11"
 # If you add a new dependency here, please also add it to .pre-commit-config.yml
 dependencies = [
-    'asciitree',
     'numpy>=1.25',
-    'fasteners',
-    'numcodecs>=0.10.2',
-    'fsspec>2024',
-    'crc32c',
+    'numcodecs>=0.12',
     'typing_extensions',
     'donfig',
 ]
@@ -52,17 +48,19 @@ license = {text = "MIT License"}
 keywords = ["Python", "compressed", "ndimensional-arrays", "zarr"]
 
 [project.optional-dependencies]
+remote = [
+    "fsspec",
+]
+sharding = [
+    "crc32c",
+]
 test = [
     "coverage",
     "pytest",
     "pytest-cov",
-    "msgpack",
-    "lmdb",
     "s3fs",
     "pytest-asyncio",
     "moto[s3]",
-    "flask-cors",
-    "flask",
     "requests",
     "mypy",
     "hypothesis",

src/zarr/codecs/crc32c_.py

@@ -5,7 +5,6 @@
 
 import numpy as np
 import typing_extensions
-from crc32c import crc32c
 
 from zarr.abc.codec import BytesBytesCodec
 from zarr.core.common import JSON, parse_named_configuration
@@ -35,6 +34,8 @@ async def _decode_single(
         chunk_bytes: Buffer,
         chunk_spec: ArraySpec,
     ) -> Buffer:
+        from crc32c import crc32c
+
         data = chunk_bytes.as_numpy_array()
         crc32_bytes = data[-4:]
         inner_bytes = data[:-4]
@@ -53,6 +54,8 @@ async def _encode_single(
         chunk_bytes: Buffer,
         chunk_spec: ArraySpec,
     ) -> Buffer | None:
+        from crc32c import crc32c
+
         data = chunk_bytes.as_numpy_array()
         # Calculate the checksum and "cast" it to a numpy array
         checksum = np.array([crc32c(cast(typing_extensions.Buffer, data))], dtype=np.uint32)

src/zarr/storage/remote.py

@@ -2,8 +2,6 @@
 
 from typing import TYPE_CHECKING, Any, Self
 
-import fsspec
-
 from zarr.abc.store import ByteRangeRequest, Store
 from zarr.storage.common import _dereference_path
 
@@ -130,6 +128,8 @@ def from_url(
         -------
         RemoteStore
         """
+        import fsspec
+
         fs, path = fsspec.url_to_fs(url, **storage_options)
         return cls(fs=fs, path=path, mode=mode, allowed_exceptions=allowed_exceptions)
 

tests/v3/test_buffer.py

@@ -97,6 +97,7 @@ async def test_async_array_gpu_prototype() -> None:
 
 @pytest.mark.asyncio
 async def test_codecs_use_of_prototype() -> None:
+    pytest.importorskip("crc32c")
     expect = np.zeros((10, 10), dtype="uint16", order="F")
     a = await AsyncArray.create(
         StorePath(StoreExpectingTestBuffer(mode="w")) / "test_codecs_use_of_prototype",
@@ -132,6 +133,7 @@ async def test_codecs_use_of_prototype() -> None:
 @gpu_test
 @pytest.mark.asyncio
 async def test_codecs_use_of_gpu_prototype() -> None:
+    pytest.importorskip("crc32c")
     expect = cp.zeros((10, 10), dtype="uint16", order="F")
     a = await AsyncArray.create(
         StorePath(MemoryStore(mode="w")) / "test_codecs_use_of_gpu_prototype",

tests/v3/test_codecs/test_codecs.py

@@ -73,6 +73,8 @@ async def test_order(
     runtime_read_order: MemoryOrder,
     with_sharding: bool,
 ) -> None:
+    if with_sharding:
+        pytest.importorskip("crc32c")
     data = np.arange(0, 256, dtype="uint16").reshape((32, 8), order=input_order)
     path = "order"
     spath = StorePath(store, path=path)
@@ -129,6 +131,8 @@ def test_order_implicit(
     runtime_read_order: MemoryOrder,
     with_sharding: bool,
 ) -> None:
+    if with_sharding:
+        pytest.importorskip("crc32c")
     data = np.arange(0, 256, dtype="uint16").reshape((16, 16), order=input_order)
     path = "order_implicit"
     spath = StorePath(store, path)

tests/v3/test_codecs/test_sharding.py

@@ -20,6 +20,8 @@
 from ..conftest import ArrayRequest
 from .test_codecs import _AsyncArrayProxy, order_from_dim
 
+pytest.importorskip("crc32c")
+
 
 @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"])
 @pytest.mark.parametrize("index_location", ["start", "end"])

tests/v3/test_codecs/test_transpose.py

@@ -27,6 +27,8 @@ async def test_transpose(
     runtime_read_order: MemoryOrder,
     with_sharding: bool,
 ) -> None:
+    if with_sharding:
+        pytest.importorskip("crc32c")
     data = np.arange(0, 256, dtype="uint16").reshape((1, 32, 8), order=input_order)
     spath = StorePath(store, path="transpose")
     codecs_: list[Codec] = (

tests/v3/test_config.py

@@ -215,6 +215,9 @@ def test_config_buffer_implementation() -> None:
     arr[:] = np.arange(100)
     assert np.array_equal(arr[:], data)
 
+
+def test_config_sharding_implementation() -> None:
+    pytest.importorskip("crc32c")
     data2d = np.arange(1000).reshape(100, 10)
     arr_sharding = zeros(
         shape=(100, 10),

tests/v3/test_store/test_core.py

@@ -39,7 +39,7 @@ async def test_make_store_path(tmpdir: str) -> None:
 
 
 async def test_make_store_path_fsspec(monkeypatch) -> None:
-    import fsspec.implementations.memory
+    fsspec = pytest.importorskip("fsspec")
 
     monkeypatch.setattr(fsspec.implementations.memory.MemoryFileSystem, "async_impl", True)
     store_path = await make_store_path("memory://")