Fix fill value round trip [xarray?] bug #294
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mosegontar
reviewed
Oct 23, 2025
| ds = xr.open_zarr(store_factory.primary_store()) | ||
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| result = validation.check_for_expected_shards(primary_store, ds) | ||
| assert result.passed, result.message |
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With write_empty_chunks=False, we get:
FAILED tests/common/region_job_test.py::test_region_job_empty_chunk_writing[nan] - AssertionError: ['var0', 'var1', 'var2', 'var3'] are missing expected shards: {"var0": ["1/0/0"], "var1": ["1/0/0"], "var2": ["1/0/0"], "var3": [...
FAILED tests/common/region_job_test.py::test_region_job_empty_chunk_writing[0.0] - AssertionError: ['var0', 'var1', 'var2', 'var3'] are missing expected shards: {"var0": ["1/0/0"], "var1": ["1/0/0"], "var2": ["1/0/0"], "var3": [...
Results (15.59s):
10 passed
2 failed
- tests/common/region_job_test.py:175 test_region_job_empty_chunk_writing[nan]
- tests/common/region_job_test.py:175 test_region_job_empty_chunk_writing[0.0]
aldenks
commented
Oct 23, 2025
tests/common/region_job_test.py
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| @pytest.mark.filterwarnings( | ||
| "ignore:This process .* is multi-threaded, use of fork.* may lead to deadlocks in the child" | ||
| ) |
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We can remove this now. we use spawn
tests/common/template_config_test.py
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| all changes to the dataset's TemplateConfig are reflected in the on-disk Zarr template. | ||
| Also ensure that the get_template() -> write_metadata() round trip produces exactly | ||
| the same zarr.json as already exists on disk. |
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And finally check that the fill value we get in the case of a missing shard matches the template
tests/common/template_config_test.py
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| # 2. Ensure that get_template() -> write_metadata() round trips without any changes | ||
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| # Compute an end_time to pass to get_template() | ||
| dim_coords = template_config.dimension_coordinates() | ||
| append_dim_coords = dim_coords[template_config.append_dim] | ||
| end_time = append_dim_coords[-1] + pd.Timedelta(milliseconds=1) | ||
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| template_ds = template_config.get_template(end_time) | ||
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| test_write_metadata_path = tmp_path / "write_metadata_test.zarr" | ||
| template_utils.write_metadata( | ||
| template_ds, | ||
| test_write_metadata_path, | ||
| ) | ||
| with open(test_write_metadata_path / "zarr.json") as f: | ||
| written_template = json.load(f) | ||
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| assert existing_template == written_template | ||
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| # 3. Ensure that the value we get when reading from an area that has not been written | ||
| # to matches the fill value in template_config encodings | ||
| # Coords are written by write_metadata() so we do expect them to be filled and don't test that here | ||
| ds = xr.open_zarr(test_write_metadata_path, chunks=None) | ||
| for var in template_config.data_vars: | ||
| var_da = ds[var.name] | ||
| np.testing.assert_array_equal( | ||
| var_da.isel(dict.fromkeys(var_da.dims, 0)).values, var.encoding.fill_value | ||
| ) |
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lets break this test into 3 separate tests
mosegontar
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Ensure fill_value present in encoding and set write_empty_chunks to True. Update fill value for NDVI and SWANN to 0.0
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The array encoding fill_value is not properly read back when opening a zarr.