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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1316423844 | I_kwDOAMm_X85Odwik | 6822 | RuntimeError when formatting sparse-backed DataArray in f-string | khaeru 1634164 | closed | 0 | 2 | 2022-07-25T07:58:11Z | 2022-08-09T09:17:39Z | 2022-08-08T15:11:35Z | NONE | What happened?On upgrading from xarray 2022.3.0 to 2022.6.0, f-string formatting of sparse-backed DataArray raises an exception. What did you expect to happen?
Minimal Complete Verifiable Example```Python import pandas as pd import xarray as xr s = pd.Series( range(4), index=pd.MultiIndex.from_product([list("ab"), list("cd")]), ) da = xr.DataArray.from_series(s, sparse=True) print(f"{da}") ``` MVCE confirmation
Relevant log output```Python xarray 2022.3.0:<xarray.DataArray (level_0: 2, level_1: 2)>
<COO: shape=(2, 2), dtype=float64, nnz=4, fill_value=nan> xarray 2022.6.0:Traceback (most recent call last): Anything else we need to know?Along with the versions below, I have confirmed the error occurs with both sparse 0.12 and sparse 0.13. Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.10.4 (main, Jun 29 2022, 12:14:53) [GCC 11.2.0]
python-bits: 64
OS: Linux
OS-release: 5.15.0-41-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_CA.UTF-8
LOCALE: ('en_CA', 'UTF-8')
libhdf5: 1.10.7
libnetcdf: 4.8.1
xarray: 2022.6.0
pandas: 1.4.2
numpy: 1.22.4
scipy: 1.8.0
netCDF4: 1.5.8
pydap: None
h5netcdf: 0.12.0
h5py: 3.6.0
Nio: None
zarr: None
cftime: 1.5.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: 1.3.2
dask: 2022.01.0+dfsg
distributed: 2022.01.0+ds.1
matplotlib: 3.5.1
cartopy: 0.20.2
seaborn: 0.11.2
numbagg: None
fsspec: 2022.01.0
cupy: None
pint: 0.18
sparse: 0.13.0
flox: None
numpy_groupies: None
setuptools: 62.1.0
pip: 22.0.2
conda: None
pytest: 6.2.5
IPython: 7.31.1
sphinx: 4.5.0
|
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completed | xarray 13221727 | issue | ||||||
| 503711327 | MDU6SXNzdWU1MDM3MTEzMjc= | 3381 | concat() fails when args have sparse.COO data and different fill values | khaeru 1634164 | open | 0 | 4 | 2019-10-07T21:54:06Z | 2021-07-08T17:43:57Z | NONE | MCVE Code Sample```python import numpy as np import pandas as pd import sparse import xarray as xr Indices and raw datafoo = [f'foo{i}' for i in range(6)] bar = [f'bar{i}' for i in range(6)] raw = np.random.rand(len(foo) // 2, len(bar)) DataArraya = xr.DataArray( data=sparse.COO.from_numpy(raw), coords=[foo[:3], bar], dims=['foo', 'bar']) print(a.data.fill_value) # 0.0 Created from a pd.Seriesb_series = pd.DataFrame(raw, index=foo[3:], columns=bar) \ .stack() \ .rename_axis(index=['foo', 'bar']) b = xr.DataArray.from_series(b_series, sparse=True) print(b.data.fill_value) # nan Works despite inconsistent fill-valuesa + b a * b Fails: complains about inconsistent fill-valuesxr.concat([a, b], dim='foo') # ***The fill_value argument doesn't helpxr.concat([a, b], dim='foo', fill_value=np.nan)def fill_value(da): """Try to coerce one argument to a consistent fill-value.""" return xr.DataArray( data=sparse.as_coo(da.data, fill_value=np.nan), coords=da.coords, dims=da.dims, name=da.name, attrs=da.attrs, ) Fails: "Cannot provide a fill-value in combination with something thatalready has a fill-value"print(xr.concat([a.pipe(fill_value), b], dim='foo'))If we cheat by recreating 'a' from scratch, copying the fill value of theintended other argument, it works again:a = xr.DataArray( data=sparse.COO.from_numpy(raw, fill_value=b.data.fill_value), coords=[foo[:3], bar], dims=['foo', 'bar']) c = xr.concat([a, b], dim='foo') print(c.data.fill_value) # nan But simple operations again create objects with potentially incompatiblefill-valuesd = c.sum(dim='bar') print(d.data.fill_value) # 0.0 ``` Expected
Problem DescriptionSome basic xarray manipulations don't work on xarray should automatically coerce objects into a compatible state, or at least provide users with methods to do so. Behaviour should also be documented, e.g. in this instance, which operations (here, Output of
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xarray 13221727 | issue | ||||||||
| 143764621 | MDU6SXNzdWUxNDM3NjQ2MjE= | 805 | pd.Period can't be used as a 1-element coord | khaeru 1634164 | closed | 0 | 5 | 2016-03-27T00:45:52Z | 2016-12-24T00:09:48Z | 2016-12-24T00:09:48Z | NONE | With xarray 0.7.2, following this basic example from the docs, but with a modification in the last line to use ``` python import numpy as np import xarray as xr temp = 15 + 8 * np.random.randn(2, 2, 3) precip = 10 * np.random.rand(2, 2, 3) lon = [[-99.83, -99.32], [-99.79, -99.23]] lat = [[42.25, 42.21], [42.63, 42.59]] ds = xr.Dataset({'temperature': (['x', 'y', 'time'], temp), 'precipitation': (['x', 'y', 'time'], precip)}, coords={'lon': (['x', 'y'], lon), 'lat': (['x', 'y'], lat), 'time': pd.date_range('2014-09-06', periods=3), 'reference_time': pd.Period('2014')}) ``` This raises:
I noticed (#645) that there are other issues stemming from pandas' PeriodIndex & company, so if this is not a straightforward fix I will understand! |
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completed | xarray 13221727 | issue |
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