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/1638#issuecomment-341220444,https://api.github.com/repos/pydata/xarray/issues/1638,341220444,MDEyOklzc3VlQ29tbWVudDM0MTIyMDQ0NA==,806256,2017-11-01T19:51:55Z,2017-11-01T19:51:55Z,NONE,Posted the lost coordinate issue here: https://github.com/pydata/xarray/issues/1680,"{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,266320445
https://github.com/pydata/xarray/issues/1638#issuecomment-341198220,https://api.github.com/repos/pydata/xarray/issues/1638,341198220,MDEyOklzc3VlQ29tbWVudDM0MTE5ODIyMA==,806256,2017-11-01T18:33:24Z,2017-11-01T18:33:24Z,NONE,"Using v0.9.6 with `engine='h5netcdf'`
```
CPU times: user 1min, sys: 47.7 s, total: 1min 48s
Wall time: 2min 19s
```
Using #1648:
```
CPU times: user 1min 5s, sys: 54.9 s, total: 2min
Wall time: 2min 1s
```","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,266320445
https://github.com/pydata/xarray/issues/1638#issuecomment-339228857,https://api.github.com/repos/pydata/xarray/issues/1638,339228857,MDEyOklzc3VlQ29tbWVudDMzOTIyODg1Nw==,1217238,2017-10-25T06:32:35Z,2017-10-25T06:32:35Z,MEMBER,"Hmm. I'm not sure why h5netcdf was so much slower. I suspect the default engine you used might have been scipy, which we've noticed can be significantly faster in some cases. If you have time, I would be curious how well my branch in 1648 works using `engine='scipy'`.
Please file a separate issue if you can put together example code that reproduces the lost coordinate issue. I would like to dig into this.","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,266320445
https://github.com/pydata/xarray/issues/1638#issuecomment-339162189,https://api.github.com/repos/pydata/xarray/issues/1638,339162189,MDEyOklzc3VlQ29tbWVudDMzOTE2MjE4OQ==,806256,2017-10-24T23:02:34Z,2017-10-24T23:03:18Z,NONE,"Thank you for looking into this! I used the default engine to save, which looks like it was `netcdf4`. I did `pip install h5netcdf` and saved again. It took longer, ~2min instead of seconds. Loading was still 110ms and all the features are objects again! Though the coordinates --> variables thing is still happening.
```
Dimensions: (cell: 53760, gene: 23438)
Coordinates:
* cell (cell) object 'A17-B000126-3_39_F-1-1' ...
* gene (gene) object '0610005C13Rik' ...
Data variables:
Columns sorted (cell) float64 nan nan nan nan nan nan nan ...
Comments (cell) object 'nan' 'nan' 'nan' 'nan' ...
Double check (cell) float64 nan nan nan nan nan nan nan ...
EXP_ID (cell) object '170925_A00111_0066_AH3TKNDMXX' ...
Experiment ID (cell) object 'exp22' 'exp22' 'exp22' ...
FACS.instument (cell) object 'Sony SIM1' 'Sony SIM1' ...
FACS.selection (cell) object 'Multiple' 'Multiple' ...
Location (cell) object 'MACA20_3' 'MACA20_3' ...
Lysis Plate Batch (cell) object '20' '20' '20' '20' '20' ...
Number of input reads (cell) int64 1229254 730274 1075370 ...
Plate (cell) object '1' '1' '1' '1' '1' '1' '1' ...
TAXON (cell) object 'mus' 'mus' 'mus' 'mus' ...
Uniquely mapped reads number (cell) int64 1017682 634557 941828 1392029 ...
WELL_MAPPING (cell) object 'B000126' 'B000126' ...
counts (cell, gene) int64 0 0 0 0 442 0 0 0 0 0 0 ...
dNTP.batch (cell) object '457912' '457912' '457912' ...
date.prepared (cell) object '07-06-17' '07-06-17' ...
date.sorted (cell) object '170707' '170707' '170707' ...
log10 (cell, gene) float64 0.0 0.0 0.0 0.0 2.646 ...
log2 (cell, gene) float64 0.0 0.0 0.0 0.0 8.791 ...
mouse.age (cell) object '3' '3' '3' '3' '3' '3' '3' ...
mouse.id (cell) object '3_39_F' '3_39_F' '3_39_F' ...
mouse.number (cell) object '39' '39' '39' '39' '39' ...
mouse.sex (cell) object 'F' 'F' 'F' 'F' 'F' 'F' 'F' ...
nozzle.size (cell) object '100' '100' '100' '100' ...
oligodT.order.no (cell) object '6/23/17 12757296' ...
plate.type (cell) object 'Biorad HSP3901' ...
preparation.site (cell) object 'Biohub' 'Biohub' 'Biohub' ...
subtissue (cell) object 'nan' 'nan' 'nan' 'nan' ...
tissue (cell) object 'Skin' 'Skin' 'Skin' 'Skin' ...
```
Not sure if it matters, but one detail is that I created ~250 individual datasets (each sized at ~300 samples x 20,000 features) and then used `xr.concat(datasets, dim='cell')` to concatenate them because I couldn't read them all into memory at once.","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,266320445
https://github.com/pydata/xarray/issues/1638#issuecomment-338367929,https://api.github.com/repos/pydata/xarray/issues/1638,338367929,MDEyOklzc3VlQ29tbWVudDMzODM2NzkyOQ==,1217238,2017-10-21T06:27:57Z,2017-10-21T06:27:57Z,MEMBER,"Reading over Unidata/netcdf-c#402, it seems like we should probably copy the handling of _Encoding from netcdf4-python (Unidata/netcdf4-python#665) to our scipy interface. That would solve our problem of faithfully round-tripping data.","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,266320445
https://github.com/pydata/xarray/issues/1638#issuecomment-337426817,https://api.github.com/repos/pydata/xarray/issues/1638,337426817,MDEyOklzc3VlQ29tbWVudDMzNzQyNjgxNw==,1217238,2017-10-18T00:54:04Z,2017-10-18T00:54:04Z,MEMBER,"Which backend are you using to save the data? Try explicitly setting `engine` to either `netcdf4`, `h5netcdf` or `scipy`. I think h5netcdf may be your best bet but it's probably worth trying all of them. Sadly unicode strings in Python 3 / NumPy is still quite painful.
> Also, how did all the Coordinates somehow get moved into Data variables ?
This looks like a bug of some sort -- not sure how that happened!","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,266320445
https://github.com/pydata/xarray/issues/1638#issuecomment-337418537,https://api.github.com/repos/pydata/xarray/issues/1638,337418537,MDEyOklzc3VlQ29tbWVudDMzNzQxODUzNw==,806256,2017-10-18T00:17:25Z,2017-10-18T00:17:25Z,NONE,"Also, how did all the `Coordinates` somehow get moved into `Data variables` ?","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,266320445