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  • Feature/pickle rasterio · 13 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
395647556 https://github.com/pydata/xarray/pull/2131#issuecomment-395647556 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NTY0NzU1Ng== shoyer 1217238 2018-06-08T05:00:59Z 2018-06-08T05:00:59Z MEMBER

v0.10.7 is out

 
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   Feature/pickle rasterio 323017930
395535173 https://github.com/pydata/xarray/pull/2131#issuecomment-395535173 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NTUzNTE3Mw== rsignell-usgs 1872600 2018-06-07T19:20:24Z 2018-06-07T19:20:24Z NONE

Sounds good. Thanks @shoyer!

 
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   Feature/pickle rasterio 323017930
395534752 https://github.com/pydata/xarray/pull/2131#issuecomment-395534752 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NTUzNDc1Mg== shoyer 1217238 2018-06-07T19:18:55Z 2018-06-07T19:18:55Z MEMBER

@rsignell-usgs Sure, though interp() (https://github.com/pydata/xarray/pull/2104) is almost ready, too, so we might wait for that.

 
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   Feature/pickle rasterio 323017930
395524953 https://github.com/pydata/xarray/pull/2131#issuecomment-395524953 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NTUyNDk1Mw== rsignell-usgs 1872600 2018-06-07T18:45:42Z 2018-06-07T18:45:42Z NONE

Might this PR warrant a new minor release?

 
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   Feature/pickle rasterio 323017930
395476675 https://github.com/pydata/xarray/pull/2131#issuecomment-395476675 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NTQ3NjY3NQ== rsignell-usgs 1872600 2018-06-07T16:07:14Z 2018-06-07T16:11:08Z NONE

@jhamman woohoo! Cell [20] completes nicely now: https://gist.github.com/rsignell-usgs/90f15e2da918e3c6ba6ee5bb6095d594 I'm getting some errors in Cell [20], but I think those are unrelated and didn't affect the successful completion of the tasks, right? (this is on an HPC system)

 
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   Feature/pickle rasterio 323017930
395447613 https://github.com/pydata/xarray/pull/2131#issuecomment-395447613 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NTQ0NzYxMw== rsignell-usgs 1872600 2018-06-07T14:46:21Z 2018-06-07T14:47:07Z NONE

@jhamman , although I'm getting distributed workers to compute the mean from a bunch of images, I'm getting a "Failed to Serialize" error in cell [23] of this notebook: https://gist.github.com/rsignell-usgs/90f15e2da918e3c6ba6ee5bb6095d594 If this is a bug, I think it was there before the recent updates.

You should be able to run this notebook without modification. 

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   Feature/pickle rasterio 323017930
395413795 https://github.com/pydata/xarray/pull/2131#issuecomment-395413795 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NTQxMzc5NQ== jhamman 2443309 2018-06-07T13:08:10Z 2018-06-07T13:08:10Z MEMBER

All the tests are passing here. Its been a while so perhaps it would be good to get another review from @pydata/xarray.

@rsignell-usgs - can you give this another whirl on your use case? 

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   Feature/pickle rasterio 323017930
394887291 https://github.com/pydata/xarray/pull/2131#issuecomment-394887291 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM5NDg4NzI5MQ== rsignell-usgs 1872600 2018-06-05T23:00:51Z 2018-06-05T23:13:08Z NONE

@jhamman , still very much interested in this -- could the existing functionality be merged and enhanced later?

 
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   Feature/pickle rasterio 323017930
389331934 https://github.com/pydata/xarray/pull/2131#issuecomment-389331934 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM4OTMzMTkzNA== jhamman 2443309 2018-05-15T22:20:21Z 2018-05-15T22:20:21Z MEMBER

@shoyer - I like the idea of a wrapper object that achieves both of these tasks. I'm incrementally working that way and have just updated the Pickle Wrapper for now. 

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   Feature/pickle rasterio 323017930
389330810 https://github.com/pydata/xarray/pull/2131#issuecomment-389330810 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM4OTMzMDgxMA== rsignell-usgs 1872600 2018-05-15T22:15:22Z 2018-05-15T22:15:22Z NONE 
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   Feature/pickle rasterio 323017930
389298331 https://github.com/pydata/xarray/pull/2131#issuecomment-389298331 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM4OTI5ODMzMQ== shoyer 1217238 2018-05-15T20:14:06Z 2018-05-15T20:14:06Z MEMBER

Thinking about this a little more, maybe we should consolidate pickling with autoclosing into a single, composable wrapper class. Usage would look something like: ```python wrapper = FileWrapper(netCDF4.Dataset, path, mode='r', autoclose=False, kwargs=kwargs) with wrapper: # will close/open wrapped file with wrapper.acquire() as ds: # context manager is dummy, simply returning the open file object ... # do stuff with ds, a netCDF4.Dataset instance

or could write wrapper.close() instead of using the context manager

wrapper = FileWrapper(netCDF4.Dataset, path, mode='r', autoclose=True, kwargs=kwargs) with wrapper: # explicit opening/closing the wrapper is a no-op if autoclose=True with wrapper.acquire() as ds: # context manager opens/closes file # if file is already open, it's a no-op ... # do stuff with ds, a netCDF4.Dataset instance ```

We could then expose xarray.backends.FileWrapper as part of our external API for backend authors (without coupling it into the Datastore class directly).

Eventually, we might even change the default for autoclose to automatically use LRU caching (but that obviously would come later).

 
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   Feature/pickle rasterio 323017930
389278261 https://github.com/pydata/xarray/pull/2131#issuecomment-389278261 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM4OTI3ODI2MQ== jhamman 2443309 2018-05-15T19:04:18Z 2018-05-15T19:04:18Z MEMBER

@rsignell-usgs - I think this should work in its current form. I'm writing some additional tests now and have some cleanup tasks as indicated in the reviews but I do not expect the behavior to change.

 
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   Feature/pickle rasterio 323017930
389277628 https://github.com/pydata/xarray/pull/2131#issuecomment-389277628 https://api.github.com/repos/pydata/xarray/issues/2131 MDEyOklzc3VlQ29tbWVudDM4OTI3NzYyOA== rsignell-usgs 1872600 2018-05-15T19:02:06Z 2018-05-15T19:02:06Z NONE

@jhamman should I test this out on my original workflow or wait a bit?

 
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   Feature/pickle rasterio 323017930

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