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  • A read-only TileDB backend · 14 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
796925819 https://github.com/pydata/xarray/issues/4987#issuecomment-796925819 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5NjkyNTgxOQ== max-sixty 5635139 2021-03-11T17:55:28Z 2021-03-11T17:55:28Z MEMBER

Not at this point. We just released 0.17 so I would think we're at least a week or two away from 0.18.

Just to set expectations — I hadn't thought we were releasing so soon — though I'd be happy to, and it's getting easier & easier to do releases.

 
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796919656 https://github.com/pydata/xarray/issues/4987#issuecomment-796919656 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5NjkxOTY1Ng== jhamman 2443309 2021-03-11T17:46:18Z 2021-03-11T17:46:18Z MEMBER

Not at this point. We just released 0.17 so I would think we're at least a week or two away from 0.18. 

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   A read-only TileDB backend 820480606
796873186 https://github.com/pydata/xarray/issues/4987#issuecomment-796873186 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5Njg3MzE4Ng== jp-dark 24235303 2021-03-11T16:39:27Z 2021-03-11T16:39:27Z CONTRIBUTOR

@jhamman Is there a planned date for releasing the backend updates to PyPI?

 
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   A read-only TileDB backend 820480606
794029445 https://github.com/pydata/xarray/issues/4987#issuecomment-794029445 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5NDAyOTQ0NQ== jp-dark 24235303 2021-03-09T15:14:34Z 2021-03-09T15:14:34Z CONTRIBUTOR

I was able to use this backend from an external code base with the entry point procedure as described in the new docs, and it was completely painless. Great job with the backend refactor!

 
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791681130 https://github.com/pydata/xarray/issues/4987#issuecomment-791681130 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MTY4MTEzMA== jhamman 2443309 2021-03-05T20:52:06Z 2021-03-05T20:52:06Z MEMBER

4989 includes the full refactor. The plan is to merge this to xarray/master on Monday.

 
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791639282 https://github.com/pydata/xarray/issues/4987#issuecomment-791639282 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MTYzOTI4Mg== jp-dark 24235303 2021-03-05T19:43:10Z 2021-03-05T19:43:10Z CONTRIBUTOR

Is there a branch of xarray that currently supports loading backend engines from third-party libraries?

 
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790860834 https://github.com/pydata/xarray/issues/4987#issuecomment-790860834 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MDg2MDgzNA== jp-dark 24235303 2021-03-04T19:13:07Z 2021-03-04T19:18:57Z CONTRIBUTOR

See PR #4998 for the example

edit: This example should be able to read a NetCDF dataset using the protocol engine: xr.open_dataset("example.nc", engine="protocol")

 
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   A read-only TileDB backend 820480606
790851791 https://github.com/pydata/xarray/issues/4987#issuecomment-790851791 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MDg1MTc5MQ== jp-dark 24235303 2021-03-04T19:00:38Z 2021-03-04T19:00:38Z CONTRIBUTOR

@alexamici @shoyer To be clear, my short term plan is absolutely to move the TileDB backend from my draft pull request here to a small plugin in library (thanks for linking the cfgrib @alexamici!).

I only bring up the protocol thing because the backend is really close to a place where a lot of the boilerplate for the lazy loading, etc. could be provided on the xarray side with a simple API requirement on the third-party library side. I'll push up a small proof-of-concept with a read-only netCDF4 example shortly.

 
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   A read-only TileDB backend 820480606
790782639 https://github.com/pydata/xarray/issues/4987#issuecomment-790782639 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MDc4MjYzOQ== alexamici 226037 2021-03-04T17:16:48Z 2021-03-04T17:22:31Z MEMBER

@jp-dark it is in fact possible to write an xarray backend without explicitly depending on xarray in your setup.py if you put all your backend glue code in a separate module not imported by the main __init__.py.

We use the setuptools entrypoints infrastructure that triggers a module load only from within xarray itself.

This is still work in progress, but we are implementing this strategy in cfgrib with success. You can get inspiration from the following PR by @aurghs:

https://github.com/ecmwf/cfgrib/pull/203

 
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   A read-only TileDB backend 820480606
790140398 https://github.com/pydata/xarray/issues/4987#issuecomment-790140398 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MDE0MDM5OA== shoyer 1217238 2021-03-03T23:12:37Z 2021-03-03T23:12:37Z MEMBER

@jp-dark How would you feel about writing another small library, e.g., "xarray-tiledb" that can explicitly depend on both xarray and tiledb?

We can potentially do some of xarray's backend stuff with protocols, but there are some aspects (especially for more advanced features like lazy loading) that will likely need the hard xarray dependency.

 
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   A read-only TileDB backend 820480606
790109209 https://github.com/pydata/xarray/issues/4987#issuecomment-790109209 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MDEwOTIwOQ== jp-dark 24235303 2021-03-03T22:10:46Z 2021-03-03T22:10:46Z CONTRIBUTOR

As a provider of a third-party backend, I would love to be able to integrate with xarray without including xarray as a dependency in my library, and xarray is actually really close to a place where that would be possible.

The main development effort on the xarray side would be creating a generic LazyLoadingBackendStore that accepts duck-typed backends (xarray can define them using Protocols for mypy goodness).

If there is interest in pursuing this, I can help with developing a prototype to test feasibility.

 
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   A read-only TileDB backend 820480606
790024577 https://github.com/pydata/xarray/issues/4987#issuecomment-790024577 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MDAyNDU3Nw== jhamman 2443309 2021-03-03T20:13:44Z 2021-03-03T20:13:44Z MEMBER

This is a great spot @jp-dark! Looking forward to seeing your progress.

 
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   A read-only TileDB backend 820480606
790023571 https://github.com/pydata/xarray/issues/4987#issuecomment-790023571 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc5MDAyMzU3MQ== jp-dark 24235303 2021-03-03T20:12:02Z 2021-03-03T20:12:02Z CONTRIBUTOR

@jhamman - thanks for the quick response! As I work through bumps would it be best to comment here or on one of the other currently open issues for the backend refactor?

 
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   A read-only TileDB backend 820480606
789933725 https://github.com/pydata/xarray/issues/4987#issuecomment-789933725 https://api.github.com/repos/pydata/xarray/issues/4987 MDEyOklzc3VlQ29tbWVudDc4OTkzMzcyNQ== jhamman 2443309 2021-03-03T17:52:36Z 2021-03-03T17:54:38Z MEMBER

Hi @jp-dark! Thanks for opening this issue and the draft pull request in #4988. As you probably know, we're in the process of completing a major refactor of our storage backends system (see #4989 and #4810 for the current state of that work). One of the main feature additions in this work is the new entrypoints functionality which will allow backends (like TileDB) to declare backend support without including the code in the Xarray itself.

In light of this new functionality, we'd like to see if we can put the TileDB backend in TileDB itself (or in an another adjacent package). The end user functionality would be the same as the entrypoint would be registered at install time. We'd be happy to document the TileDB in the Xarray documentation as well.

This is the development pattern we are headed to with most of our backends, including some of the current backends. We'd be happy to help work with you to sort out the details as I'm sure there will be one or two early adopter bumps to work through.

cc @alexamici @aurghs @shoyer 

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   A read-only TileDB backend 820480606

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