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 1087160635,I_kwDOAMm_X85AzME7,6103,reindex multidimensional fill_value skipping,1191149,closed,0,,,1,2021-12-22T20:14:00Z,2021-12-22T20:17:39Z,2021-12-22T20:17:38Z,CONTRIBUTOR,,,,"**What happened**: I started with a Dataframe that represented an identity matrix and used reindex with multiple dimensions and a fill_value. The goal was to produce a Dataset from a sparse dataframe and the identity matrix was the simplest example. The `fill_value` in reindex is defined as ""Value to use for newly missing values."" What I found was that fill_values were not applied at coordinates that were in the unique set of the any coord. For a pure identity matrix, that means fill_values were not applied anywhere (all rows are present, all cols are present). When I thin the identity matrix (skipping elements), the error is more obvious. On the rows and columns that have valid input data, the fill_value is not applied. **What you expected to happen**: I expected *all* new nan values to be filled with the fill value. **Minimal Complete Verifiable Example**: ``` import numpy as np import pandas as pd n = 10 thin = 2 df = pd.DataFrame.from_dict([ dict(ROW=v, COL=v, LAND=1) for v in np.arange(0, n, thin) ]).set_index(['ROW', 'COL']) ds = df.to_xarray() rds = ds.reindex(ROW=np.arange(n), COL=np.arange(n), fill_value=0) # p = rds.LAND.plot() # p.axes.set_facecolor('red') # p.axes.figure.savefig('test.png') print(rds.LAND[:]) print(rds.LAND[::thin, ::thin]) ``` Output: ``` array([[ 1., 0., nan, 0., nan, 0., nan, 0., nan, 0.], [ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [nan, 0., 1., 0., nan, 0., nan, 0., nan, 0.], [ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [nan, 0., nan, 0., 1., 0., nan, 0., nan, 0.], [ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [nan, 0., nan, 0., nan, 0., 1., 0., nan, 0.], [ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [nan, 0., nan, 0., nan, 0., nan, 0., 1., 0.], [ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]) Coordinates: * ROW (ROW) int64 0 1 2 3 4 5 6 7 8 9 * COL (COL) int64 0 1 2 3 4 5 6 7 8 9 array([[ 1., nan, nan, nan, nan], [nan, 1., nan, nan, nan], [nan, nan, 1., nan, nan], [nan, nan, nan, 1., nan], [nan, nan, nan, nan, 1.]]) Coordinates: * ROW (ROW) int64 0 2 4 6 8 * COL (COL) int64 0 2 4 6 8``` **Anything else we need to know?**: **Environment**:
Output of xr.show_versions() INSTALLED VERSIONS ------------------ commit: None python: 3.7.12 (default, Sep 10 2021, 00:21:48) [GCC 7.5.0] python-bits: 64 OS: Linux OS-release: 5.4.144+ machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.12.0 libnetcdf: 4.7.4 xarray: 0.18.2 pandas: 1.1.5 numpy: 1.19.5 scipy: 1.4.1 netCDF4: 1.5.8 pydap: None h5netcdf: None h5py: 3.1.0 Nio: None zarr: None cftime: 1.5.1.1 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: 1.3.2 dask: 2.12.0 distributed: 1.25.3 matplotlib: 3.2.2 cartopy: None seaborn: 0.11.2 numbagg: None pint: None setuptools: 57.4.0 pip: 21.1.3 conda: None pytest: 3.6.4 IPython: 5.5.0 sphinx: 1.8.6
","{""url"": ""https://api.github.com/repos/pydata/xarray/issues/6103/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,completed,13221727,issue 309592370,MDU6SXNzdWUzMDk1OTIzNzA=,2025,dask ImportWarning causes pytest failure,1191149,closed,0,,,2,2018-03-29T02:01:50Z,2018-03-30T03:44:55Z,2018-03-30T03:44:55Z,CONTRIBUTOR,,,,"#### Code Sample, a copy-pastable example if possible ```bash # Your code here pytest -v xarray/tests/test_backends.py::NetCDF4DataTest ``` #### Problem description Instead of passing all tests, this fails on the `test_88_character_filename_segmentation_fault` function. ``` E AssertionError: exception ImportWarning(""can't resolve package from __spec__ or __package__, falling back on __name__ and __path__"",) did not match pattern 'segmentation fault' ``` It oddly doesn't seem to be related to the 88 character issue. I traced this down to xarray/backends/common.py::get_scheduler where an ""ImportWarning"" is not being caught on line 49. #### Expected Output Passes all tests. Adding ImportWarning to the tuple of exceptions in get_scheduler fixes the problem. #### Output of ``xr.show_versions()``
# Paste the output here xr.show_versions() here >>> xr.show_versions() /Users/barronh/anaconda3/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters INSTALLED VERSIONS ------------------ commit: None python: 3.6.4.final.0 python-bits: 64 OS: Darwin OS-release: 17.4.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 xarray: 0.10.2 pandas: 0.22.0 numpy: 1.14.2 scipy: 1.0.0 netCDF4: 1.3.1 h5netcdf: None h5py: 2.7.1 Nio: None zarr: None bottleneck: 1.2.1 cyordereddict: None dask: 0.17.1 distributed: 1.21.3 matplotlib: 2.2.2 cartopy: None seaborn: 0.8.1 setuptools: 38.4.0 pip: 9.0.1 conda: 4.5.0 pytest: 3.4.2 IPython: 6.2.1 sphinx: 1.6.6
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