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  • BorjaEst 4

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  • to_netcdf -> _fill_value without NaN · 4 ✖

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  • NONE · 4 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1063906458 https://github.com/pydata/xarray/issues/2037#issuecomment-1063906458 https://api.github.com/repos/pydata/xarray/issues/2037 IC_kwDOAMm_X84_aeya BorjaEst 47473455 2022-03-10T10:35:23Z 2022-03-10T10:59:17Z NONE

I see know why it did not had sense to push something. Basically cf requirements are in conflict with backend requirements. It would be needed to restructure tests and review which from backend have sense to apply. py ======================================================== short test summary info ======================================================== FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_write_store - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_write_store - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_ondisk_after_print - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_vectorized_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_isel_dataarray - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_roundtrip_test_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_roundtrip_timedelta_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_isel_dataarray - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_load - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_write_store - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_coordinate_variables_after_dataset_roundtrip - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_roundtrip_numpy_datetime_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_roundtrip_test_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_orthogonal_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_dataset_compute - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_roundtrip_timedelta_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_zero_dimensional_variable - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_dataset_compute - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_array_type_after_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_append_write - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_vectorized_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_coordinate_variables_after_dataset_roundtrip - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_isel_dataarray - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_append_overwrite_values - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_load - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_grid_mapping_and_bounds_are_coordinates_after_dataarray_roundtrip - Ke... FAILED xarray/tests/test_backends.py::TestGenericNetCDFData::test_cross_engine_read_write_netcdf3 - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_vectorized_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_grid_mapping_and_bounds_are_coordinates_after_dataarray_roundtrip - ... FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_append_overwrite_values - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_zero_dimensional_variable - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_ondisk_after_print - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_roundtrip_timedelta_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_append_with_invalid_dim_raises - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_orthogonal_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_array_type_after_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_orthogonal_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyInMemoryData::test_append_with_invalid_dim_raises - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_roundtrip_numpy_datetime_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_zero_dimensional_variable - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_roundtrip_test_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFileObject::test_append_write - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_ondisk_after_print - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_roundtrip_numpy_datetime_data - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_dataset_compute - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_append_write - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_load - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_array_type_after_indexing - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestGenericNetCDFData::test_engine - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_grid_mapping_and_bounds_are_coordinates_after_dataarray_roundtrip - KeyE... FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_coordinate_variables_after_dataset_roundtrip - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_append_with_invalid_dim_raises - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::TestScipyFilePath::test_append_overwrite_values - KeyError: ('O', 8) FAILED xarray/tests/test_backends.py::test_scipy_entrypoint - KeyError: ('O', 8)

However your snipet worked, but it is not applying to boundary variables, which is a cf requirement as well. Probably I would edit it to something like: py # remove _FillValue for coordinate variables as missing values are not permitted (issue #2037) # a coordinate variable is a one-dimensional variable with the same name as its dimension # see coordinate variable in http://cfconventions.org/cf-conventions/cf-conventions.html#terminology for var in new_vars.keys(): if new_vars[var].dims == (var,): new_vars[var].attrs["_FillValue"] = None if "bounds" in new_vars[var].attrs: bnds = new_vars[var].attrs['bounds'] new_vars[bnds].attrs["_FillValue"] = None I will create a PR with the hope a developer will take a look into this.

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  to_netcdf -> _fill_value without NaN 310833761
1063806501 https://github.com/pydata/xarray/issues/2037#issuecomment-1063806501 https://api.github.com/repos/pydata/xarray/issues/2037 IC_kwDOAMm_X84_aGYl BorjaEst 47473455 2022-03-10T08:44:15Z 2022-03-10T08:44:15Z NONE

@BorjaEst I haven't opened a PR for this slightly_smiling_face

@ellesmith88 is there a branch/fork where you implemented your trials or shall I start one and add your code?

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  to_netcdf -> _fill_value without NaN 310833761
1063707401 https://github.com/pydata/xarray/issues/2037#issuecomment-1063707401 https://api.github.com/repos/pydata/xarray/issues/2037 IC_kwDOAMm_X84_ZuMJ BorjaEst 47473455 2022-03-10T06:24:58Z 2022-03-10T06:25:12Z NONE

@ellesmith88 ellesmith88

but I couldn't quite get this to work, with some tests in test_backends.py failing. I could see that the fill value is being added in by maybe_default_fill_value in conventions.py so maybe it would be better to skip coordinate variable and bounds here. I can't really spend anymore time on this but putting it here in case its useful.

I see you are setting _FillValue to None but probably it should be set to False instead. See https://stackoverflow.com/questions/45693688/xarray-automatically-applying-fillvalue-to-coordinates-on-netcdf-output

I can give it a try. In which PR are you working on this?

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  to_netcdf -> _fill_value without NaN 310833761
1063705114 https://github.com/pydata/xarray/issues/2037#issuecomment-1063705114 https://api.github.com/repos/pydata/xarray/issues/2037 IC_kwDOAMm_X84_Ztoa BorjaEst 47473455 2022-03-10T06:20:40Z 2022-03-10T06:20:40Z NONE

I am posting here a temporal solution to this in case someone has the same issue. Based on https://stackoverflow.com/questions/45693688/xarray-automatically-applying-fillvalue-to-coordinates-on-netcdf-output py for var in ds.variables: if '_FillValue' not in ds[var].attrs: ds[var].attrs['_FillValue'] = False

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  to_netcdf -> _fill_value without NaN 310833761

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