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id node_id number title user state locked assignee milestone comments created_at updated_at ▲ closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
2163608564 I_kwDOAMm_X86A9gv0 8802 Error when using `apply_ufunc` with `datetime64` as output dtype gcaria 44147817 open 0     4 2024-03-01T15:09:57Z 2024-05-03T12:19:14Z   CONTRIBUTOR      

What happened?

When using apply_ufunc with datetime64[ns] as output dtype, code throws error about converting from specific units to generic datetime units.

What did you expect to happen?

No response

Minimal Complete Verifiable Example

```Python import xarray as xr import numpy as np

def _fn(arr: np.ndarray, time: np.ndarray) -> np.ndarray: return time[:10]

def fn(da: xr.DataArray) -> xr.DataArray: dim_out = "time_cp"

return xr.apply_ufunc(
    _fn,
    da,
    da.time,
    input_core_dims=[["time"], ["time"]],
    output_core_dims=[[dim_out]],
    vectorize=True,
    dask="parallelized",
    output_dtypes=["datetime64[ns]"],
    dask_gufunc_kwargs={"allow_rechunk": True, 
                        "output_sizes": {dim_out: 10},},
    exclude_dims=set(("time",)),
)

da_fake = xr.DataArray(np.random.rand(5,5,5), coords=dict(x=range(5), y=range(5), time=np.array(['2024-01-01', '2024-01-02', '2024-01-03', '2024-01-04', '2024-01-05'], dtype='datetime64[ns]') )).chunk(dict(x=2,y=2))

fn(da_fake.compute()).compute() # ValueError: Cannot convert from specific units to generic units in NumPy datetimes or timedeltas

fn(da_fake).compute() # same errors as above ```

MVCE confirmation

  • [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [X] Complete example — the example is self-contained, including all data and the text of any traceback.
  • [X] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • [X] New issue — a search of GitHub Issues suggests this is not a duplicate.
  • [X] Recent environment — the issue occurs with the latest version of xarray and its dependencies.

Relevant log output

```Python

ValueError Traceback (most recent call last) Cell In[211], line 1 ----> 1 fn(da_fake).compute()

File /srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/core/dataarray.py:1163, in DataArray.compute(self, kwargs) 1144 """Manually trigger loading of this array's data from disk or a 1145 remote source into memory and return a new array. The original is 1146 left unaltered. (...) 1160 dask.compute 1161 """ 1162 new = self.copy(deep=False) -> 1163 return new.load(kwargs)

File /srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/core/dataarray.py:1137, in DataArray.load(self, kwargs) 1119 def load(self, kwargs) -> Self: 1120 """Manually trigger loading of this array's data from disk or a 1121 remote source into memory and return this array. 1122 (...) 1135 dask.compute 1136 """ -> 1137 ds = self._to_temp_dataset().load(**kwargs) 1138 new = self._from_temp_dataset(ds) 1139 self._variable = new._variable

File /srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/core/dataset.py:853, in Dataset.load(self, kwargs) 850 chunkmanager = get_chunked_array_type(lazy_data.values()) 852 # evaluate all the chunked arrays simultaneously --> 853 evaluated_data = chunkmanager.compute(lazy_data.values(), kwargs) 855 for k, data in zip(lazy_data, evaluated_data): 856 self.variables[k].data = data

File /srv/conda/envs/notebook/lib/python3.10/site-packages/xarray/core/daskmanager.py:70, in DaskManager.compute(self, data, kwargs) 67 def compute(self, data: DaskArray, kwargs) -> tuple[np.ndarray, ...]: 68 from dask.array import compute ---> 70 return compute(*data, kwargs)

File /srv/conda/envs/notebook/lib/python3.10/site-packages/dask/base.py:628, in compute(traverse, optimize_graph, scheduler, get, args, kwargs) 625 postcomputes.append(x.dask_postcompute()) 627 with shorten_traceback(): --> 628 results = schedule(dsk, keys, kwargs) 630 return repack([f(r, a) for r, (f, a) in zip(results, postcomputes)])

File /srv/conda/envs/notebook/lib/python3.10/site-packages/numpy/lib/function_base.py:2372, in vectorize.call(self, args, kwargs) 2369 self._init_stage_2(args, kwargs) 2370 return self -> 2372 return self._call_as_normal(*args, kwargs)

File /srv/conda/envs/notebook/lib/python3.10/site-packages/numpy/lib/function_base.py:2365, in vectorize._call_as_normal(self, args, *kwargs) 2362 vargs = [args[_i] for _i in inds] 2363 vargs.extend([kwargs[_n] for _n in names]) -> 2365 return self._vectorize_call(func=func, args=vargs)

File /srv/conda/envs/notebook/lib/python3.10/site-packages/numpy/lib/function_base.py:2446, in vectorize._vectorize_call(self, func, args) 2444 """Vectorized call to func over positional args.""" 2445 if self.signature is not None: -> 2446 res = self._vectorize_call_with_signature(func, args) 2447 elif not args: 2448 res = func()

File /srv/conda/envs/notebook/lib/python3.10/site-packages/numpy/lib/function_base.py:2506, in vectorize._vectorize_call_with_signature(self, func, args) 2502 outputs = _create_arrays(broadcast_shape, dim_sizes, 2503 output_core_dims, otypes, results) 2505 for output, result in zip(outputs, results): -> 2506 output[index] = result 2508 if outputs is None: 2509 # did not call the function even once 2510 if otypes is None:

ValueError: Cannot convert from specific units to generic units in NumPy datetimes or timedeltas ```

Anything else we need to know?

No response

Environment

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    xarray 13221727 issue
963006707 MDExOlB1bGxSZXF1ZXN0NzA1NzEzMTc1 5680 ENH: Add default fill values for decode_cf gcaria 44147817 open 0     8 2021-08-06T19:54:05Z 2022-06-09T14:50:16Z   CONTRIBUTOR   0 pydata/xarray/pulls/5680
  • [x] Closes #2374
  • [x] Tests added
  • [x] Passes pre-commit run --all-files
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst

This is a work in progress, mostly so that I can ask some clarifying questions.

I see that netCDF4 is an optional dependency for xarray, so probably import netCDF4 can't be used. Should xarray simply hard-code default fill values ?

From the issue's conversation, it wasn't clear to me whether an argument should control the use of the default fill value. Since some tests fail now I guess the answer is yes.

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    xarray 13221727 pull
1178365524 I_kwDOAMm_X85GPG5U 6405 Docstring of `open_zarr` fails to mention that `decode_coords` could be a string too gcaria 44147817 open 0     0 2022-03-23T16:30:11Z 2022-03-23T16:49:14Z   CONTRIBUTOR      

What is your issue?

The docstring of open_zarr fails to mention that decode_coords could be a string too (and what the accepted string values mean)

https://github.com/pydata/xarray/blob/fed852073eee883c0ed1e13e28e508ff0cf9d5c1/xarray/backends/zarr.py#L687-L689

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    xarray 13221727 issue

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