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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
1773886549 I_kwDOAMm_X85pu1xV 7942 Numpy raises warning in `xarray.coding.times.cast_to_int_if_safe` mx-moth 132147 closed 0     2 2023-06-26T05:03:46Z 2023-09-17T08:15:27Z 2023-09-17T08:15:27Z CONTRIBUTOR      

What happened?

In recent versions of numpy, calling numpy.asarray(arr, dtype=numpy.int64) will raise a warning if the input array contains numpy.nan values. This line of code is used in xarray.coding.times.cast_to_int_if_safe(num):

python def cast_to_int_if_safe(num) -> np.ndarray: int_num = np.asarray(num, dtype=np.int64) if (num == int_num).all(): num = int_num return num

The function still returns the correct True/False values regardless of the warning.

What did you expect to happen?

No warning to be printed

Minimal Complete Verifiable Example

```Python import numpy import xarray

one_day = numpy.timedelta64(1, 'D') nat = numpy.timedelta64('nat')

timedelta_values = (numpy.arange(5) * one_day).astype('timedelta64[ns]') timedelta_values[2] = nat timedelta_values[4] = nat

dataset = xarray.Dataset(data_vars={ 'timedeltas': xarray.DataArray(data=timedelta_values, dims=['x']) }) dataset.to_netcdf('out.nc') ```

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.

Relevant log output

```Python $ python3 safe_cast.py /home/hea211/projects/emsarray/.conda/lib/python3.10/site-packages/xarray/coding/times.py:618: RuntimeWarning: invalid value encountered in cast int_num = np.asarray(num, dtype=np.int64)

$ ncdump out.nc netcdf out { dimensions: x = 5 ; variables: double timedeltas(x) ; timedeltas:_FillValue = NaN ; timedeltas:units = "days" ; data:

timedeltas = 0, 1, _, 3, _ ; } ```

Anything else we need to know?

I saw the numpy.can_cast function and tried to use that to solve the issue (see PR #7834), however this function did not do what I expected it to.

A search for other solutions to see whether an array of floating point values is representable as integers turned up Numpy: Check if float array contains whole numbers on Stack Overflow. There are a few solutions given in that question, although each has its drawbacks. The most complete solution appears to be is_integer_ufunc, which is a ufunc written in C. Unfortunately this is not installable via pip/conda, and is not included in numpy.

Environment

In [2]: import xarray as xr ...: xr.show_versions() /home/hea211/projects/emsarray/.conda/lib/python3.10/site-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils. warnings.warn("Setuptools is replacing distutils.") INSTALLED VERSIONS ------------------ commit: None python: 3.10.0 (default, Mar 3 2022, 09:58:08) [GCC 7.5.0] python-bits: 64 OS: Linux OS-release: 5.15.0-73-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_AU.UTF-8 LOCALE: ('en_AU', 'UTF-8') libhdf5: 1.12.2 libnetcdf: 4.9.1 xarray: 2023.4.2 pandas: 2.0.1 numpy: 1.24.3 scipy: None netCDF4: 1.6.3 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.6.2 nc_time_axis: None PseudoNetCDF: None iris: None bottleneck: 1.3.7 dask: 2023.4.1 distributed: 2023.4.1 matplotlib: 3.7.1 cartopy: 0.21.1 seaborn: None numbagg: None fsspec: 2023.5.0 cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 65.6.3 pip: 22.3.1 conda: None pytest: 7.3.1 mypy: 1.3.0 IPython: 8.12.0 sphinx: 4.3.2
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  completed xarray 13221727 issue

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