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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 |
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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
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
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 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 | ||||||
1705163672 | PR_kwDOAMm_X85QQiiY | 7834 | Use `numpy.can_cast` instead of casting and checking | mx-moth 132147 | closed | 0 | 5 | 2023-05-11T06:36:06Z | 2023-06-26T05:06:30Z | 2023-06-26T05:06:29Z | CONTRIBUTOR | 1 | pydata/xarray/pulls/7834 | In numpy >= 1.24 unsafe casting raises a RuntimeWarning for an operation that xarray does often to check if casting is safe.
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xarray 13221727 | pull | |||||
1071806607 | PR_kwDOAMm_X84va6lN | 6049 | Attempt datetime coding using cftime when pandas fails | mx-moth 132147 | closed | 0 | 2 | 2021-12-06T07:12:35Z | 2022-01-04T00:28:15Z | 2021-12-24T11:48:22Z | CONTRIBUTOR | 0 | pydata/xarray/pulls/6049 | A netCDF4 dataset we use has a time variable defined as:
Note the xarray can successfully open this dataset and parse the time units, making a time variable with the expeced values. However, attempting to save this dataset (e.g. after slicing some geographic bounds or selecting a subset of variables), xarray would raise an error trying to reformat the time This fix applies the same logic used in the decoding step to the encoding step - specifically, attempt to use
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xarray 13221727 | pull |
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