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https://github.com/pydata/xarray/issues/2215#issuecomment-394753520 https://api.github.com/repos/pydata/xarray/issues/2215 394753520 MDEyOklzc3VlQ29tbWVudDM5NDc1MzUyMA== 1217238 2018-06-05T15:28:45Z 2018-06-05T15:28:45Z MEMBER

Are you sure the indexes along the aligned dimensions match exactly? Small differences in floats are the most common source of this issue.

Try using second.reindex_like(first, method='nearest') instead of xarray.align(first, second).

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