mirror of
https://github.com/p2p-ld/numpydantic.git
synced 2024-09-19 23:44:28 +00:00
144 lines
4.2 KiB
Python
144 lines
4.2 KiB
Python
import shutil
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from pathlib import Path
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from typing import Any, Callable, Optional, Tuple, Type, Union
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from warnings import warn
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import h5py
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import numpy as np
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import pytest
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from pydantic import BaseModel, Field
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import zarr
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from numpydantic.interface.hdf5 import H5ArrayPath
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from numpydantic.interface.zarr import ZarrArrayPath
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from numpydantic import NDArray, Shape
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from numpydantic.maps import python_to_nptyping
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from numpydantic.dtype import Number
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@pytest.fixture(scope="session")
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def tmp_output_dir(request: pytest.FixtureRequest) -> Path:
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path = Path(__file__).parent.resolve() / "__tmp__"
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if path.exists():
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shutil.rmtree(str(path))
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path.mkdir()
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yield path
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if not request.config.getvalue("--with-output"):
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try:
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shutil.rmtree(str(path))
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except PermissionError as e:
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# sporadic error on windows machines...
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warn(
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f"Temporary directory could not be removed due to a permissions error: \n{str(e)}"
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)
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@pytest.fixture(scope="function")
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def tmp_output_dir_func(tmp_output_dir, request: pytest.FixtureRequest) -> Path:
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"""
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tmp output dir that gets cleared between every function
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cleans at the start rather than at cleanup in case the output is to be inspected
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"""
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subpath = tmp_output_dir / f"__tmpfunc_{request.node.name}__"
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if subpath.exists():
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shutil.rmtree(str(subpath))
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subpath.mkdir()
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return subpath
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@pytest.fixture(scope="module")
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def tmp_output_dir_mod(tmp_output_dir, request: pytest.FixtureRequest) -> Path:
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"""
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tmp output dir that gets cleared between every function
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cleans at the start rather than at cleanup in case the output is to be inspected
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"""
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subpath = tmp_output_dir / f"__tmpmod_{request.module}__"
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if subpath.exists():
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shutil.rmtree(str(subpath))
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subpath.mkdir()
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return subpath
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@pytest.fixture(scope="function")
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def array_model() -> (
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Callable[[Tuple[int, ...], Union[Type, np.dtype]], Type[BaseModel]]
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):
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def _model(
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shape: Tuple[int, ...] = (10, 10), dtype: Union[Type, np.dtype] = float
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) -> Type[BaseModel]:
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shape_str = ", ".join([str(s) for s in shape])
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class MyModel(BaseModel):
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array: NDArray[Shape[shape_str], dtype]
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return MyModel
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return _model
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@pytest.fixture(scope="session")
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def model_rgb() -> Type[BaseModel]:
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class RGB(BaseModel):
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array: Optional[
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Union[
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NDArray[Shape["* x, * y"], Number],
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NDArray[Shape["* x, * y, 3 r_g_b"], Number],
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NDArray[Shape["* x, * y, 3 r_g_b, 4 r_g_b_a"], Number],
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]
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] = Field(None)
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return RGB
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@pytest.fixture(scope="session")
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def model_blank() -> Type[BaseModel]:
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"""A model with any shape and dtype"""
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class BlankModel(BaseModel):
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array: NDArray[Shape["*, ..."], Any]
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return BlankModel
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@pytest.fixture(scope="function")
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def hdf5_file(tmp_output_dir_func) -> h5py.File:
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h5f_file = tmp_output_dir_func / "h5f.h5"
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h5f = h5py.File(h5f_file, "w")
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yield h5f
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h5f.close()
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@pytest.fixture(scope="function")
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def hdf5_array(
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hdf5_file, request
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) -> Callable[[Tuple[int, ...], Union[np.dtype, type]], H5ArrayPath]:
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def _hdf5_array(
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shape: Tuple[int, ...] = (10, 10), dtype: Union[np.dtype, type] = float
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) -> H5ArrayPath:
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array_path = "/" + "_".join([str(s) for s in shape]) + "__" + dtype.__name__
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data = np.random.random(shape).astype(dtype)
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_ = hdf5_file.create_dataset(array_path, data=data)
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return H5ArrayPath(Path(hdf5_file.filename), array_path)
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return _hdf5_array
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@pytest.fixture(scope="function")
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def zarr_nested_array(tmp_output_dir_func) -> ZarrArrayPath:
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"""Zarr array within a nested array"""
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file = tmp_output_dir_func / "nested.zarr"
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path = "a/b/c"
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root = zarr.open(str(file), mode="w")
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array = root.zeros(path, shape=(100, 100), chunks=(10, 10))
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return ZarrArrayPath(file=file, path=path)
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@pytest.fixture(scope="function")
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def zarr_array(tmp_output_dir_func) -> Path:
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file = tmp_output_dir_func / "array.zarr"
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array = zarr.open(str(file), mode="w", shape=(100, 100), chunks=(10, 10))
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array[:] = 0
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return file
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