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  • xarray · 3 ✖
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
874331538 MDExOlB1bGxSZXF1ZXN0NjI4OTE0NDQz 5252 Add mode="r+" for to_zarr and use consolidated writes/reads by default shoyer 1217238 closed 0     14 2021-05-03T07:57:16Z 2021-06-22T06:51:35Z 2021-06-17T17:19:26Z MEMBER   0 pydata/xarray/pulls/5252

mode="r+" only allows for modifying pre-existing array values in a Zarr store. This makes it a safer default mode when doing a limited region write. It also offers a nice performance bonus when using consolidated metadata, because the store to modify can be opened in "consolidated" mode -- rather than painfully slow non-consolidated mode.

This PR includes several related changes to to_zarr():

  1. It adds support for the new mode="r+".
  2. consolidated=True in to_zarr() now means "open in consolidated mode" if using using mode="r+", instead of "write in consolidated mode" (which would not make sense for r+).
  3. It allows setting consolidated=True when using region, mostly for the sake of fast store opening with r+.
  4. Validation in to_zarr() has been reorganized to always use the existing Zarr group, rather than re-opening zar stores from scratch, which could require additional network requests.
  5. Incidentally, I've renamed the ZarrStore.ds attribute to ZarrStore.zarr_group, which is a much more descriptive name.

These changes gave me a ~5x boost in write performance in a large parallel job making use of to_zarr with region.

  • [x] Tests added
  • [x] Passes pre-commit run --all-files
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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     xarray 13221727 pull
29136905 MDU6SXNzdWUyOTEzNjkwNQ== 60 Implement DataArray.idxmax() shoyer 1217238 closed 0   1.0 741199 14 2014-03-10T22:03:06Z 2020-03-29T01:54:25Z 2020-03-29T01:54:25Z MEMBER       
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   completed xarray 13221727 issue
188113943 MDU6SXNzdWUxODgxMTM5NDM= 1097 Better support for subclasses: tests, docs and API shoyer 1217238 open 0     14 2016-11-08T21:54:00Z 2019-08-22T13:07:44Z   MEMBER      

Given that people do currently subclass xarray objects, it's worth considering making a subclass API like pandas: http://pandas.pydata.org/pandas-docs/stable/internals.html#subclassing-pandas-data-structures

At the very least, it would be nice to have docs that describe how/when it's safe to subclass, and tests that verify our support for such subclasses.

 
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     xarray 13221727 issue

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