336 lines
11 KiB
Python
336 lines
11 KiB
Python
"""Tests for rustyhdf5 Python bindings."""
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import os
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import tempfile
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import numpy as np
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import pytest
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import rustyhdf5
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@pytest.fixture
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def tmp_h5(tmp_path):
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"""Return a temporary HDF5 file path."""
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return str(tmp_path / "test.h5")
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@pytest.fixture
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def sample_read_file(tmp_h5):
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"""Create a sample HDF5 file for reading tests."""
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("temperatures", data=np.array([22.5, 23.1, 21.8]))
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f.create_dataset("counts", data=np.array([10, 20, 30], dtype=np.int32))
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f.attrs["version"] = 1
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f.attrs["description"] = "test file"
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return tmp_h5
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@pytest.fixture
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def grouped_read_file(tmp_h5):
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"""Create an HDF5 file with groups for reading tests."""
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("root_data", data=np.array([0.0, 1.0]))
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grp = f.create_group("sensors")
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grp.create_dataset("temperature", data=np.array([22.5, 23.1, 21.8]))
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grp.create_dataset("humidity", data=np.array([45, 50, 55], dtype=np.int32))
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grp.attrs["location"] = "lab"
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grp2 = f.create_group("metadata")
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grp2.create_dataset("timestamps", data=np.array([1000, 2000, 3000], dtype=np.int64))
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return tmp_h5
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# ---------------------------------------------------------------------------
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# Test: open and read datasets
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# ---------------------------------------------------------------------------
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def test_open_and_read_f64(sample_read_file):
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f = rustyhdf5.File(sample_read_file, "r")
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ds = f["temperatures"]
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data = ds[:]
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np.testing.assert_array_almost_equal(data, [22.5, 23.1, 21.8])
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f.close()
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def test_open_and_read_i32(sample_read_file):
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f = rustyhdf5.File(sample_read_file, "r")
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ds = f["counts"]
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data = ds[:]
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np.testing.assert_array_equal(data, [10, 20, 30])
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assert data.dtype == np.int32
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f.close()
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# ---------------------------------------------------------------------------
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# Test: dataset properties (shape, dtype)
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# ---------------------------------------------------------------------------
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def test_dataset_shape(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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ds = f["temperatures"]
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assert ds.shape == (3,)
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def test_dataset_dtype(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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assert f["temperatures"].dtype == "float64"
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assert f["counts"].dtype == "int32"
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# ---------------------------------------------------------------------------
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# Test: read attributes
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# ---------------------------------------------------------------------------
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def test_read_root_attrs(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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assert f.attrs["version"] == 1
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assert f.attrs["description"] == "test file"
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def test_attrs_len(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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assert len(f.attrs) >= 2
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def test_attrs_contains(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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assert "version" in f.attrs
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assert "nonexistent" not in f.attrs
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def test_attrs_keys(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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keys = f.attrs.keys()
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assert "version" in keys
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assert "description" in keys
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# ---------------------------------------------------------------------------
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# Test: read groups
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# ---------------------------------------------------------------------------
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def test_read_group_keys(grouped_read_file):
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with rustyhdf5.File(grouped_read_file, "r") as f:
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keys = f.keys()
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assert "sensors" in keys
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assert "metadata" in keys
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assert "root_data" in keys
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def test_read_group_dataset(grouped_read_file):
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with rustyhdf5.File(grouped_read_file, "r") as f:
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grp = f["sensors"]
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ds = grp["temperature"]
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data = ds[:]
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np.testing.assert_array_almost_equal(data, [22.5, 23.1, 21.8])
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def test_read_group_attrs(grouped_read_file):
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with rustyhdf5.File(grouped_read_file, "r") as f:
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grp = f["sensors"]
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assert grp.attrs["location"] == "lab"
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def test_nested_path_access(grouped_read_file):
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"""Test f['group/dataset'] path navigation."""
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with rustyhdf5.File(grouped_read_file, "r") as f:
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ds = f["sensors/temperature"]
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data = ds[:]
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np.testing.assert_array_almost_equal(data, [22.5, 23.1, 21.8])
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# ---------------------------------------------------------------------------
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# Test: context manager
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# ---------------------------------------------------------------------------
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def test_context_manager(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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data = f["temperatures"][:]
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np.testing.assert_array_almost_equal(data, [22.5, 23.1, 21.8])
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# File should be closed after with block
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assert repr(f) == "<HDF5 File (closed)>"
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# ---------------------------------------------------------------------------
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# Test: create files / write mode
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# ---------------------------------------------------------------------------
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def test_write_simple(tmp_h5):
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("data", data=np.array([1.0, 2.0, 3.0]))
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# Verify by reading back
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with rustyhdf5.File(tmp_h5, "r") as f:
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data = f["data"][:]
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np.testing.assert_array_almost_equal(data, [1.0, 2.0, 3.0])
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def test_write_with_attrs(tmp_h5):
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("values", data=np.array([10, 20], dtype=np.int32))
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f.attrs["author"] = "test"
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f.attrs["count"] = 42
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with rustyhdf5.File(tmp_h5, "r") as f:
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assert f.attrs["author"] == "test"
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assert f.attrs["count"] == 42
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def test_write_with_group(tmp_h5):
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with rustyhdf5.File(tmp_h5, "w") as f:
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grp = f.create_group("experiment")
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grp.create_dataset("results", data=np.array([3.14, 2.72]))
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grp.attrs["version"] = 1
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with rustyhdf5.File(tmp_h5, "r") as f:
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ds = f["experiment/results"]
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np.testing.assert_array_almost_equal(ds[:], [3.14, 2.72])
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grp = f["experiment"]
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assert grp.attrs["version"] == 1
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# ---------------------------------------------------------------------------
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# Test: numpy array types round-trip
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# ---------------------------------------------------------------------------
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def test_roundtrip_float64(tmp_h5):
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original = np.array([1.1, 2.2, 3.3], dtype=np.float64)
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("data", data=original)
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with rustyhdf5.File(tmp_h5, "r") as f:
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result = f["data"][:]
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np.testing.assert_array_almost_equal(result, original)
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assert result.dtype == np.float64
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def test_roundtrip_float32(tmp_h5):
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original = np.array([1.5, 2.5, 3.5], dtype=np.float32)
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("data", data=original)
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with rustyhdf5.File(tmp_h5, "r") as f:
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result = f["data"][:]
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np.testing.assert_array_almost_equal(result, original)
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assert result.dtype == np.float32
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def test_roundtrip_int32(tmp_h5):
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original = np.array([-10, 0, 10, 100], dtype=np.int32)
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("data", data=original)
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with rustyhdf5.File(tmp_h5, "r") as f:
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result = f["data"][:]
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np.testing.assert_array_equal(result, original)
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assert result.dtype == np.int32
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def test_roundtrip_int64(tmp_h5):
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original = np.array([-1, 0, 1, 2**40], dtype=np.int64)
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("data", data=original)
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with rustyhdf5.File(tmp_h5, "r") as f:
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result = f["data"][:]
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np.testing.assert_array_equal(result, original)
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assert result.dtype == np.int64
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def test_roundtrip_uint8(tmp_h5):
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original = np.array([0, 127, 255], dtype=np.uint8)
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("data", data=original)
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with rustyhdf5.File(tmp_h5, "r") as f:
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result = f["data"][:]
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np.testing.assert_array_equal(result, original)
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assert result.dtype == np.uint8
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# ---------------------------------------------------------------------------
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# Test: chunked + compressed datasets
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# ---------------------------------------------------------------------------
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def test_chunked_gzip(tmp_h5):
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original = np.arange(100, dtype=np.float64)
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset(
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"compressed",
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data=original,
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chunks=(50,),
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compression="gzip",
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compression_opts=6,
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)
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with rustyhdf5.File(tmp_h5, "r") as f:
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result = f["compressed"][:]
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np.testing.assert_array_equal(result, original)
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# ---------------------------------------------------------------------------
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# Test: h5py interoperability
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# ---------------------------------------------------------------------------
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def test_h5py_can_read_our_file(tmp_h5):
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"""Verify that h5py can read files we create."""
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import h5py
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("values", data=np.array([1.0, 2.0, 3.0]))
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f.attrs["meta"] = "hello"
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with h5py.File(tmp_h5, "r") as f:
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np.testing.assert_array_equal(f["values"][:], [1.0, 2.0, 3.0])
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# h5py reads fixed-length strings as bytes
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assert f.attrs["meta"] == b"hello"
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def test_we_can_read_h5py_file(tmp_h5):
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"""Verify that we can read files created by h5py."""
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import h5py
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with h5py.File(tmp_h5, "w") as f:
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f.create_dataset("data", data=np.array([10.0, 20.0, 30.0]))
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f.attrs["version"] = 2
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with rustyhdf5.File(tmp_h5, "r") as f:
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data = f["data"][:]
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np.testing.assert_array_equal(data, [10.0, 20.0, 30.0])
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assert f.attrs["version"] == 2
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# ---------------------------------------------------------------------------
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# Test: 2D array shape
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# ---------------------------------------------------------------------------
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def test_2d_array_roundtrip(tmp_h5):
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original = np.array([[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]], dtype=np.float64)
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with rustyhdf5.File(tmp_h5, "w") as f:
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f.create_dataset("matrix", data=original)
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with rustyhdf5.File(tmp_h5, "r") as f:
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ds = f["matrix"]
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assert ds.shape == (2, 3)
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result = ds[:]
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np.testing.assert_array_almost_equal(result, original)
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# ---------------------------------------------------------------------------
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# Test: error handling
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# ---------------------------------------------------------------------------
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def test_open_nonexistent_file():
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with pytest.raises(OSError):
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rustyhdf5.File("/nonexistent/path.h5", "r")
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def test_invalid_mode(tmp_h5):
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with pytest.raises(ValueError):
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rustyhdf5.File(tmp_h5, "x")
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def test_key_error_on_missing_dataset(sample_read_file):
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with rustyhdf5.File(sample_read_file, "r") as f:
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with pytest.raises(KeyError):
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f["nonexistent"]
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