issues: 511498714

This data as json

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
511498714 MDU6SXNzdWU1MTE0OTg3MTQ= 3438 Re-indexing causes coordinates to be dropped 1200058 closed 0     2 2019-10-23T18:31:18Z 2020-01-09T01:46:46Z 2020-01-09T01:46:46Z NONE      

Hi, I encounter a problem with the index being dropped when I rename a dimension and stack it afterwards:

MCVE Code Sample

```python ds = xr.Dataset({ "test": xr.DataArray( [[[1,2],[3,4]], [[1,2],[3,4]]], dims=("genes", "observations", "subtissues"), coords={ "observations": xr.DataArray(["x-1", "y-1"], dims=("observations",)), "individuals": xr.DataArray(["x", "y"], dims=("observations",)), "genes": xr.DataArray(["a", "b"], dims=("genes",)), "subtissues": xr.DataArray(["c", "d"], dims=("subtissues",)), } ) })

`individuals` is set here:python3 print(ds.rename_dims(observations="individuals")) <xarray.Dataset> Dimensions: (genes: 2, individuals: 2, subtissues: 2) Coordinates: observations (individuals) <U3 'x-1' 'y-1' * individuals (individuals) <U1 'x' 'y' * genes (genes) <U1 'a' 'b' * subtissues (subtissues) <U1 'c' 'd' Data variables: test (genes, individuals, subtissues) int64 1 2 3 4 1 2 3 4 Stacking caused `individuals` to disappear and be replaced with integers:python3 print(ds.rename_dims(observations="individuals").stack(observations=["individuals", "genes"])) <xarray.Dataset> Dimensions: (observations: 4, subtissues: 2) Coordinates: * observations (observations) MultiIndex - individuals (observations) int64 0 0 1 1 - genes (observations) object 'a' 'b' 'a' 'b' * subtissues (subtissues) <U1 'c' 'd' Data variables: test (subtissues, observations) int64 1 1 3 3 2 2 4 4 Explicitly setting `individuals` keeps them correctly after stacking:python3 print(ds.rename_dims(observations="individuals").set_index({"individuals": "individuals"}).set_coords("individuals").stack(observations=["individuals", "genes"])) <xarray.Dataset> Dimensions: (observations: 4, subtissues: 2) Coordinates: * observations (observations) MultiIndex - individuals (observations) object 'x' 'x' 'y' 'y' - genes (observations) object 'a' 'b' 'a' 'b' * subtissues (subtissues) <U1 'c' 'd' Data variables: test (subtissues, observations) int64 1 1 3 3 2 2 4 4 ```

Is this by intention?

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.7.4 (default, Aug 13 2019, 20:35:49) [GCC 7.3.0] python-bits: 64 OS: Linux OS-release: 3.10.0-957.10.1.el7.x86_64 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: 4.6.1 xarray: 0.14.0 pandas: 0.25.1 numpy: 1.17.2 scipy: 1.3.1 netCDF4: 1.4.2 pydap: None h5netcdf: 0.7.4 h5py: 2.9.0 Nio: None zarr: 2.3.2 cftime: 1.0.3.4 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2.5.2 distributed: 2.5.2 matplotlib: 3.1.1 cartopy: None seaborn: 0.9.0 numbagg: None setuptools: 41.4.0 pip: 19.2.3 conda: None pytest: 5.0.1 IPython: 7.8.0 sphinx: None 
{
    "url": "https://api.github.com/repos/pydata/xarray/issues/3438/reactions",
    "total_count": 0,
    "+1": 0,
    "-1": 0,
    "laugh": 0,
    "hooray": 0,
    "confused": 0,
    "heart": 0,
    "rocket": 0,
    "eyes": 0
}
   completed 13221727 issue

Links from other tables