html_url,issue_url,id,node_id,user,created_at,updated_at,author_association,body,reactions,performed_via_github_app,issue
https://github.com/pydata/xarray/issues/1809#issuecomment-486390856,https://api.github.com/repos/pydata/xarray/issues/1809,486390856,MDEyOklzc3VlQ29tbWVudDQ4NjM5MDg1Ng==,4133310,2019-04-24T19:22:52Z,2019-04-24T19:24:27Z,NONE,"I can't seem recreate this with a minimal example, `xarray` roundtrips a NetCDF file with a `coordinates` attribute correctly:
```python
from netCDF4 import Dataset
import xarray as xr
with Dataset('test.nc', format='NETCDF4', mode='w') as nc:
nc.createDimension('dim1', size=0)
var = nc.createVariable('var1', 'f8', dimensions=('dim1'))
var[:] = [1., 2., 3.]
var.setncattr('coordinates', 'dim1')
xr.open_dataset('test.nc').to_netcdf('test2.nc')
```
There is something peculiar about how WRF handles the `coordinates` attribute, but I can't see anything off about it yet.
Interestingly, I can workaround the WRF `coordinates` issue by setting `decode_coords=False` in `xarray.open_dataset()`, for example, this works:
```python
xr.open_dataset('wrfout_d01_2019-04-16_15_00_00', decode_coords=False).to_netcdf('test.nc')
```
while this doesn't:
```python
xr.open_dataset('wrfout_d01_2019-04-16_15_00_00').to_netcdf('test.nc')
```","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-485210441,https://api.github.com/repos/pydata/xarray/issues/1809,485210441,MDEyOklzc3VlQ29tbWVudDQ4NTIxMDQ0MQ==,4133310,2019-04-21T01:09:04Z,2019-04-24T19:24:02Z,NONE,"I ran into this issue trying to roundtrip a WRF output file. It looks like xarray raises an error for any NetCDF file that has variables with a `coordinates` attribute:
```python
# These coordinates are saved according to CF conventions
for var_name, coord_names in variable_coordinates.items():
attrs = variables[var_name].attrs
if 'coordinates' in attrs:
raise ValueError('cannot serialize coordinates because variable '
""%s already has an attribute 'coordinates'""
% var_name)
attrs['coordinates'] = ' '.join(map(str, coord_names))
```
~~Both this choice, and the proposed solution in this issue (delete all `coordinates` attributes), I don't understand.~~ Variables with a `coordinates` attribute are [CF conforming](http://cfconventions.org/Conformance/conformance.html), so xarray should be able to play along with this.
~~The solution that makes more sense to me is to raise a warning and overwrite or ignore the `coordinates` attribute, if the attribute is already present. Later step of the fix could even be a keyword argument to allow the user to choose whether to overwrite or ignore ""conflicting"" attributes.~~
Or perhaps I'm missing something obvious here... Let me know either way. I'd be happy to make a PR to patch this.
","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-445955599,https://api.github.com/repos/pydata/xarray/issues/1809,445955599,MDEyOklzc3VlQ29tbWVudDQ0NTk1NTU5OQ==,5695215,2018-12-10T20:11:32Z,2018-12-10T20:11:32Z,NONE,That's perfect. Thank you!,"{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-445921610,https://api.github.com/repos/pydata/xarray/issues/1809,445921610,MDEyOklzc3VlQ29tbWVudDQ0NTkyMTYxMA==,1217238,2018-12-10T18:31:31Z,2018-12-10T18:31:31Z,MEMBER,"@gbromley The best option is probably a loop, e.g.,
```python
def remove_problematic_attrs(ds):
for variable in ds.variables.values():
if 'coordinates' in variable.attrs:
del variable.attrs['coordinates']
```","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-445920567,https://api.github.com/repos/pydata/xarray/issues/1809,445920567,MDEyOklzc3VlQ29tbWVudDQ0NTkyMDU2Nw==,5695215,2018-12-10T18:28:28Z,2018-12-10T18:28:28Z,NONE,"Hello, I realized I never followed up with this but am again running into issues. The real problem for me is that deleting coordinates on 30+ variables isn't really feasible. Is it possible to delete the coordinates attribute for all variables?","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-391152491,https://api.github.com/repos/pydata/xarray/issues/1809,391152491,MDEyOklzc3VlQ29tbWVudDM5MTE1MjQ5MQ==,31113893,2018-05-22T21:51:13Z,2018-05-22T21:51:13Z,NONE,"Thanks for the solution (that was my SO post as well). Deleting the attrs.['coordinates'] was a clean workaround. Here's the requested WRF meta. It was concatenated with NCO, but meta should be consistent.
[WRF_meta.txt](https://github.com/pydata/xarray/files/2028696/WRF_meta.txt)
","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-391144127,https://api.github.com/repos/pydata/xarray/issues/1809,391144127,MDEyOklzc3VlQ29tbWVudDM5MTE0NDEyNw==,1217238,2018-05-22T21:18:41Z,2018-05-22T21:18:41Z,MEMBER,"See https://stackoverflow.com/questions/50475453/xarray-cannot-serialize-coordinates/50475925.
It seems like WRF may often produce netCDF files that lead to this issue. If the problem can be reproduced by simply opening and resaving a netCDF file then we may want to revisit our logic in xarray, because we always want `xarray.open_dataset(input_path).to_netcdf(output_path)` to work. If this is the case, it would be great if someone could share metadata for such a problematic netCDF file (e.g., from `ncdump -h`).","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-391103609,https://api.github.com/repos/pydata/xarray/issues/1809,391103609,MDEyOklzc3VlQ29tbWVudDM5MTEwMzYwOQ==,31113893,2018-05-22T18:58:40Z,2018-05-22T18:58:40Z,NONE,Did you ever find a solution to this?,"{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-355812453,https://api.github.com/repos/pydata/xarray/issues/1809,355812453,MDEyOklzc3VlQ29tbWVudDM1NTgxMjQ1Mw==,10050469,2018-01-07T10:19:13Z,2018-01-07T10:19:13Z,MEMBER,It looks like your variable has an attribute `coordinates`: try deleting it before writing the data.,"{""total_count"": 1, ""+1"": 1, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335
https://github.com/pydata/xarray/issues/1809#issuecomment-355793319,https://api.github.com/repos/pydata/xarray/issues/1809,355793319,MDEyOklzc3VlQ29tbWVudDM1NTc5MzMxOQ==,17162724,2018-01-07T02:05:18Z,2018-01-07T02:05:18Z,CONTRIBUTOR,Would you mind printing `md` first to show what it looks like?,"{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,286072335