mirror of
https://github.com/p2p-ld/numpydantic.git
synced 2024-09-19 15:34:28 +00:00
153 lines
4.3 KiB
Python
153 lines
4.3 KiB
Python
import json
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import pytest
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import zarr
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from pydantic import BaseModel, ValidationError
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from numcodecs import Pickle
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from numpydantic.interface import ZarrInterface
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from numpydantic.interface.zarr import ZarrArrayPath
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from numpydantic.exceptions import DtypeError, ShapeError
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from tests.conftest import ValidationCase
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@pytest.fixture()
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def dir_array(tmp_output_dir_func) -> zarr.DirectoryStore:
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store = zarr.DirectoryStore(tmp_output_dir_func / "array.zarr")
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return store
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@pytest.fixture()
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def zip_array(tmp_output_dir_func) -> zarr.ZipStore:
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store = zarr.ZipStore(tmp_output_dir_func / "array.zip", mode="w")
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return store
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@pytest.fixture()
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def nested_dir_array(tmp_output_dir_func) -> zarr.NestedDirectoryStore:
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store = zarr.NestedDirectoryStore(tmp_output_dir_func / "nested")
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return store
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def _zarr_array(case: ValidationCase, store) -> zarr.core.Array:
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if issubclass(case.dtype, BaseModel):
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pytest.skip(
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f"Zarr can't handle objects properly at the moment, "
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"see https://github.com/zarr-developers/zarr-python/issues/2081"
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)
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# return zarr.full(
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# shape=case.shape,
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# fill_value=case.dtype(x=1),
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# dtype=object,
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# object_codec=Pickle(),
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# )
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else:
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return zarr.zeros(shape=case.shape, dtype=case.dtype, store=store)
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def _test_zarr_case(case: ValidationCase, store):
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array = _zarr_array(case, store)
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if case.passes:
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case.model(array=array)
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else:
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with pytest.raises((ValidationError, DtypeError, ShapeError)):
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case.model(array=array)
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@pytest.fixture(
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params=[
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None, # use the default store
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"dir_array",
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"zip_array",
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"nested_dir_array",
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],
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ids=["MutableMapping", "DirectoryStore", "ZipStore", "NestedDirectoryStore"],
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)
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def store(request):
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if isinstance(request.param, str):
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return request.getfixturevalue(request.param)
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else:
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return request.param
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def test_zarr_enabled():
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assert ZarrInterface.enabled()
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def test_zarr_check(interface_type):
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"""
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We should only use the zarr interface for zarr-like things
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"""
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if interface_type[1] is ZarrInterface:
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assert ZarrInterface.check(interface_type[0])
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else:
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assert not ZarrInterface.check(interface_type[0])
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def test_zarr_shape(store, shape_cases):
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_test_zarr_case(shape_cases, store)
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def test_zarr_dtype(dtype_cases, store):
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_test_zarr_case(dtype_cases, store)
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@pytest.mark.parametrize("array", ["zarr_nested_array", "zarr_array"])
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def test_zarr_from_tuple(array, model_blank, request):
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"""Should be able to do the same validation logic from tuples as an input"""
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array = request.getfixturevalue(array)
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if isinstance(array, ZarrArrayPath):
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instance = model_blank(array=(array.file, array.path))
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else:
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instance = model_blank(array=(array,))
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def test_zarr_from_path(zarr_array, model_blank):
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"""Should be able to just pass a path"""
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instance = model_blank(array=zarr_array)
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def test_zarr_array_path_from_iterable(zarr_array):
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"""Construct a zarr array path from some iterable!!!"""
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# from a single path
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apath = ZarrArrayPath.from_iterable((zarr_array,))
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assert apath.file == zarr_array
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assert apath.path is None
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inner_path = "/test/array"
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apath = ZarrArrayPath.from_iterable((zarr_array, inner_path))
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assert apath.file == zarr_array
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assert apath.path == inner_path
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def test_zarr_to_json(store, model_blank):
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expected_fields = (
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"Type",
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"Data type",
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"Shape",
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"Chunk shape",
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"Compressor",
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"Store type",
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"hexdigest",
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)
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lol_array = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
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array = zarr.array(lol_array, store=store)
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instance = model_blank(array=array)
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as_json = json.loads(instance.model_dump_json())["array"]
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assert "array" not in as_json
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for field in expected_fields:
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assert field in as_json
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assert len(as_json["hexdigest"]) == 40
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# dump the array itself too
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as_json = json.loads(instance.model_dump_json(context={"zarr_dump_array": True}))[
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"array"
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]
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for field in expected_fields:
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assert field in as_json
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assert len(as_json["hexdigest"]) == 40
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assert as_json["array"] == lol_array
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