import shutil from pathlib import Path from typing import Any, Callable, Optional, Tuple, Type, Union import h5py import numpy as np import pytest from pydantic import BaseModel, Field import zarr from numpydantic.interface.hdf5 import H5ArrayPath from numpydantic.interface.zarr import ZarrArrayPath from numpydantic import NDArray, Shape from numpydantic.maps import python_to_nptyping from numpydantic.dtype import Number @pytest.fixture(scope="session") def tmp_output_dir(request: pytest.FixtureRequest) -> Path: path = Path(__file__).parent.resolve() / "__tmp__" if path.exists(): shutil.rmtree(str(path)) path.mkdir() yield path if not request.config.getvalue("--with-output"): shutil.rmtree(str(path)) @pytest.fixture(scope="function") def tmp_output_dir_func(tmp_output_dir, request: pytest.FixtureRequest) -> Path: """ tmp output dir that gets cleared between every function cleans at the start rather than at cleanup in case the output is to be inspected """ subpath = tmp_output_dir / f"__tmpfunc_{request.node.name}__" if subpath.exists(): shutil.rmtree(str(subpath)) subpath.mkdir() return subpath @pytest.fixture(scope="module") def tmp_output_dir_mod(tmp_output_dir, request: pytest.FixtureRequest) -> Path: """ tmp output dir that gets cleared between every function cleans at the start rather than at cleanup in case the output is to be inspected """ subpath = tmp_output_dir / f"__tmpmod_{request.module}__" if subpath.exists(): shutil.rmtree(str(subpath)) subpath.mkdir() return subpath @pytest.fixture(scope="function") def array_model() -> ( Callable[[Tuple[int, ...], Union[Type, np.dtype]], Type[BaseModel]] ): def _model( shape: Tuple[int, ...] = (10, 10), dtype: Union[Type, np.dtype] = float ) -> Type[BaseModel]: shape_str = ", ".join([str(s) for s in shape]) class MyModel(BaseModel): array: NDArray[Shape[shape_str], python_to_nptyping[dtype]] return MyModel return _model @pytest.fixture(scope="session") def model_rgb() -> Type[BaseModel]: class RGB(BaseModel): array: Optional[ Union[ NDArray[Shape["* x, * y"], Number], NDArray[Shape["* x, * y, 3 r_g_b"], Number], NDArray[Shape["* x, * y, 3 r_g_b, 4 r_g_b_a"], Number], ] ] = Field(None) return RGB @pytest.fixture(scope="session") def model_blank() -> Type[BaseModel]: """A model with any shape and dtype""" class BlankModel(BaseModel): array: NDArray[Shape["*, ..."], Any] return BlankModel @pytest.fixture(scope="function") def hdf5_file(tmp_output_dir_func) -> h5py.File: h5f_file = tmp_output_dir_func / "h5f.h5" h5f = h5py.File(h5f_file, "w") yield h5f h5f.close() @pytest.fixture(scope="function") def hdf5_array( hdf5_file, request ) -> Callable[[Tuple[int, ...], Union[np.dtype, type]], H5ArrayPath]: def _hdf5_array( shape: Tuple[int, ...] = (10, 10), dtype: Union[np.dtype, type] = float ) -> H5ArrayPath: array_path = "/" + "_".join([str(s) for s in shape]) + "__" + dtype.__name__ data = np.random.random(shape).astype(dtype) _ = hdf5_file.create_dataset(array_path, data=data) return H5ArrayPath(Path(hdf5_file.filename), array_path) return _hdf5_array @pytest.fixture(scope="function") def zarr_nested_array(tmp_output_dir_func) -> ZarrArrayPath: """Zarr array within a nested array""" file = tmp_output_dir_func / "nested.zarr" path = "a/b/c" root = zarr.open(str(file), mode="w") array = root.zeros(path, shape=(100, 100), chunks=(10, 10)) return ZarrArrayPath(file=file, path=path) @pytest.fixture(scope="function") def zarr_array(tmp_output_dir_func) -> Path: file = tmp_output_dir_func / "array.zarr" array = zarr.open(str(file), mode="w", shape=(100, 100), chunks=(10, 10)) array[:] = 0 return file