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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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1382661146 | I_kwDOAMm_X85Sabwa | 7068 | xr.where overrides coordinate attributes with global attributes | sfinkens 1991007 | closed | 0 | 1 | 2022-09-22T15:44:21Z | 2023-02-14T11:05:03Z | 2023-02-14T11:05:03Z | NONE | What happened?
What did you expect to happen?The coordinate attributes to remain unchanged. Minimal Complete Verifiable Example```Python import xarray as xr x_coord = xr.DataArray( [1, 2, 3], dims="x", attrs={"units": "m"} ) a = xr.DataArray( [1, 2, 3], dims="x", coords={"x": x_coord}, attrs={"units": "K"} ) res = xr.where(a > 1, a, 0, keep_attrs=True) assert res.coords["x"].attrs["units"] == "m" # Fails, overridden with "K" ``` MVCE confirmation
Relevant log outputNo response Anything else we need to know?Not sure if this is a duplicate of https://github.com/pydata/xarray/issues/2245. If so, feel free to close :) Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10)
[GCC 10.3.0]
python-bits: 64
OS: Linux
OS-release: 3.10.0-1160.53.1.el7.x86_64
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: de_DE.UTF-8
LOCALE: ('de_DE', 'UTF-8')
libhdf5: 1.10.6
libnetcdf: 4.7.4
xarray: 2022.6.0
pandas: 1.5.0
numpy: 1.23.3
scipy: 1.9.1
netCDF4: 1.5.6
pydap: None
h5netcdf: None
h5py: 3.3.0
Nio: None
zarr: 2.12.0
cftime: 1.6.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: 1.2.1
cfgrib: None
iris: None
bottleneck: None
dask: 2022.9.1
distributed: 2022.9.1
matplotlib: 3.6.0
cartopy: None
seaborn: None
numbagg: None
fsspec: 2022.8.2
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 65.3.0
pip: 22.2.2
conda: None
pytest: 7.1.3
IPython: None
sphinx: None
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648981227 | MDU6SXNzdWU2NDg5ODEyMjc= | 4190 | Polyfit fails with few non-NaN values | sfinkens 1991007 | closed | 0 | 1 | 2020-07-01T13:26:53Z | 2020-08-20T08:34:45Z | 2020-08-20T08:34:45Z | NONE | What happened:
A linear Traceback``` TypeError: only size-1 arrays can be converted to Python scalars The above exception was the direct cause of the following exception: Traceback (most recent call last): File "polyfit.py", line 6, in <module> out = arr.polyfit(dim='x', deg=1) File "/home/stephan/venv/variogram/lib/python3.8/site-packages/xarray/core/dataarray.py", line 3455, in polyfit return self._to_temp_dataset().polyfit( File "/home/stephan/venv/variogram/lib/python3.8/site-packages/xarray/core/dataset.py", line 5962, in polyfit coeffs, residuals = duck_array_ops.least_squares( File "/home/stephan/venv/variogram/lib/python3.8/site-packages/xarray/core/duck_array_ops.py", line 625, in least_squares return nputils.least_squares(lhs, rhs, rcond=rcond, skipna=skipna) File "/home/stephan/venv/variogram/lib/python3.8/site-packages/xarray/core/nputils.py", line 239, in least_squares out[:, nan_cols] = np.apply_along_axis( File "<__array_function__ internals>", line 5, in apply_along_axis File "/home/stephan/venv/variogram/lib/python3.8/site-packages/numpy/lib/shape_base.py", line 379, in apply_along_axis res = asanyarray(func1d(inarr_view[ind0], *args, **kwargs)) File "/home/stephan/venv/variogram/lib/python3.8/site-packages/xarray/core/nputils.py", line 227, in _nanpolyfit_1d out[:-1], out[-1], _, _ = np.linalg.lstsq(x[~mask, :], arr[~mask], rcond=rcond) ValueError: setting an array element with a sequence. ```I've played around with the degree a little bit and the error seems to occur as soon as What you expected to happen: The fit to succeed - I think two non-NaN values should be enough for a linear fit. I also noticed that there is no Minimal Complete Verifiable Example: ```python import xarray as xr import numpy as np arr = xr.DataArray([np.nan, 1, 2], dims='x', coords={'x': [0, 1, 2]}) arr.polyfit(dim='x', deg=1) ``` Anything else we need to know?: Environment: Output of <tt>xr.show_versions()</tt>INSTALLED VERSIONS ------------------ commit: None python: 3.8.2 (default, Apr 27 2020, 15:53:34) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 5.4.0-39-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.10.4 libnetcdf: 4.6.3 xarray: 0.15.2.dev112+g54b9450b pandas: 1.0.5 numpy: 1.19.0 scipy: 1.5.0 netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: None Nio: None zarr: 2.4.0 cftime: 1.1.3 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2.19.0 distributed: 2.19.0 matplotlib: 3.2.2 cartopy: None seaborn: None numbagg: None pint: None setuptools: 44.0.0 pip: 20.0.2 conda: None pytest: None IPython: 7.16.1 sphinx: None |
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547373923 | MDU6SXNzdWU1NDczNzM5MjM= | 3675 | Dataset.expand_dims expands dimensions on coordinate bounds | sfinkens 1991007 | closed | 0 | 2 | 2020-01-09T10:03:08Z | 2020-01-09T11:03:22Z | 2020-01-09T11:03:22Z | NONE | MCVE Code Sample```python import xarray as xr ds = xr.Dataset({'data': ('x', [1, 2]), 'x': ('x', [1, 2]), 'x_bnds': (('x', 'bnds'), [[0.5, 1.5], [1.5, 2.5]])}) ds['x'].attrs['bounds'] = 'x_bnds' ds = ds.expand_dims({'time': [0]}) ``` Output:
Expected Output
Problem Description
Output of
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446016536 | MDU6SXNzdWU0NDYwMTY1MzY= | 2974 | Problems reading grouped netCDF file generated with h5netcdf engine | sfinkens 1991007 | closed | 0 | 3 | 2019-05-20T09:35:54Z | 2019-05-21T07:13:01Z | 2019-05-21T03:08:11Z | NONE | Code Sample, a copy-pastable example if possible```python import xarray as xr data1 = [[1, 2], [3, 4]] y1 = [1, 2] x1 = [1, 2] data2 = [[1, 2, 3], [4, 5, 6], [7, 8, 9]] y2 = [1, 2, 3] x2 = [1, 2, 3] dataset1 = xr.Dataset({'data1': xr.DataArray(data1, dims=('y', 'x'), coords={'y': y1, 'x': x1})}) dataset2 = xr.Dataset({'data2': xr.DataArray(data2, dims=('y', 'x'), coords={'y': y2, 'x': x2})}) dataset1.to_netcdf('test.nc', mode='w', group='grp1', engine='h5netcdf') dataset2.to_netcdf('test.nc', mode='a', group='grp2', engine='h5netcdf') xr.open_dataset('test.nc', group='grp1', engine='h5netcdf') # works xr.open_dataset('test.nc', group='grp1', engine='netcdf4') # fails ``` Traceback:
```
Traceback (most recent call last):
File "test_xr.py", line 21, in <module>
print(xr.open_dataset('test.nc', group='grp1', engine='netcdf4'))
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/backends/api.py", line 394, in open_dataset
ds = maybe_decode_store(store)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/backends/api.py", line 324, in maybe_decode_store
drop_variables=drop_variables, use_cftime=use_cftime)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/conventions.py", line 480, in decode_cf
ds = Dataset(vars, attrs=attrs)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/dataset.py", line 383, in __init__
self._set_init_vars_and_dims(data_vars, coords, compat)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/dataset.py", line 405, in _set_init_vars_and_dims
data_vars, coords, compat=compat)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/merge.py", line 377, in merge_data_and_coords
indexes=indexes)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/merge.py", line 446, in merge_core
expanded = expand_variable_dicts(aligned)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/merge.py", line 222, in expand_variable_dicts
var = as_variable(var, name=name)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/variable.py", line 117, in as_variable
obj = obj.to_index_variable()
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/variable.py", line 408, in to_index_variable
encoding=self._encoding, fastpath=True)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/variable.py", line 1825, in __init__
self._data = PandasIndexAdapter(self._data)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/indexing.py", line 1219, in __init__
self.array = utils.safe_cast_to_index(array)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/utils.py", line 78, in safe_cast_to_index
index = pd.Index(np.asarray(array), **kwargs)
File "/cmsaf/nfshome/routcm/Modules_CentOS/python/3.7.2/lib/python3.7/site-packages/numpy/core/numeric.py", line 501, in asarray
return array(a, dtype, copy=False, order=order)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/indexing.py", line 510, in __array__
return np.asarray(array[self.key], dtype=None)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/backends/netCDF4_.py", line 64, in __getitem__
self._getitem)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/core/indexing.py", line 778, in explicit_indexing_adapter
result = raw_indexing_method(raw_key.tuple)
File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/h5netcdf/lib/python3.7/site-packages/xarray/backends/netCDF4_.py", line 75, in _getitem
array = getitem(original_array, key)
File "netCDF4/_netCDF4.pyx", line 4317, in netCDF4._netCDF4.Variable.__getitem__
File "netCDF4/_netCDF4.pyx", line 5249, in netCDF4._netCDF4.Variable._get
File "netCDF4/_netCDF4.pyx", line 1842, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: Start+count exceeds dimension bound
```
Output of group: grp1 { dimensions: y = 3 ; x = 3 ; variables: int64 data1(y, x) ; int64 x(x) ; int64 y(y) ; data: data1 = NetCDF: Start+count exceeds dimension bound Location: file vardata.c; line 478 ``` Problem descriptionIf datasets with different coordinates have been written to different netCDF groups using the If the file is generated using the Expected OutputSince the file is readable by the Output of
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completed | xarray 13221727 | issue |
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