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Generalize handling of chunked array types #7019

Merged
merged 189 commits into from
May 18, 2023
Merged

Generalize handling of chunked array types #7019

merged 189 commits into from
May 18, 2023

Commits on Sep 10, 2022

  1. generalise chunk methods to allow cubed

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  3. fic typing typo

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  4. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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Commits on Sep 11, 2022

  1. fixed circular import

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  2. fix some mypy errors

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  3. added cubed to mypy ignore list

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  4. Merge branch 'main' into cubed_integration

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Commits on Sep 12, 2022

  1. simplify __array_ufunc__ check

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  2. Revert "simplify __array_ufunc__ check" as I pushed to wrong branch 

    This reverts commit cdcb3fb.
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Commits on Sep 20, 2022

  1. update cubed array type

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  2. Merge branch 'main' into cubed_integration

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  3. fix missed conflict

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  4. sketch for ChunkManager adapter class

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Commits on Sep 23, 2022

  1. Remove erroneous docstring about usage of map_blocks 

    Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
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  2. apply_ufunc -> apply_gufunc 

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  3. chunk -> from_array 

    Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
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  4. remove staticmethods

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  5. attempt to type methods of ABC

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  6. from_array

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  7. attempt to specify types

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Commits on Sep 26, 2022

  1. method for checking array type

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Commits on Oct 27, 2022

  1. Merge branch 'main' into pr/7019

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  2. Update pyproject.toml

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Commits on Jan 21, 2023

  1. Merge branch 'main' into cubed_integration

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Commits on Jan 22, 2023

  1. fixed import errors

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  2. generalize .chunk method kwargs

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  3. used dask functions in dask chunkmanager

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  4. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  5. define signatures for apply_gufunc, blockwise, map_blocks

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  6. prototype function to detect which parallel backend to use

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Commits on Mar 6, 2023

  1. Merge branch 'main' into cubed_integration

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  2. add cubed.apply_gufunc

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  3. ruffify

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  4. add rechunk and compute methods for cubed

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  5. xr.apply_ufunc now dispatches to chunkmanager.apply_gufunc

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  6. CubedManager.chunks

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  7. attempt to keep dask and cubed imports lazy

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  8. generalize idxmax

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  9. move unify_chunks import to ChunkManager

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  10. generalize Dataset.load()

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  11. check explicitly for chunks attribute instead of hard-coding cubed

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  12. better function names

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  13. add cubed version of unify_chunks

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  14. recognize wrapped duck dask arrays (e.g. pint wrapping dask)

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Commits on Mar 7, 2023

  1. add some tests for fetching ChunkManagers

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Commits on Mar 9, 2023

  1. add from_array_kwargs to open_dataset

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  2. add from_array_kwargs to open_zarr

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  3. pipe constructors through chunkmanager

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Commits on Mar 10, 2023

  1. generalize map_blocks inside coding

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Commits on Mar 13, 2023

  1. Merge branch 'main' into cubed_integration

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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  3. fixed full_like

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  4. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  5. add from_array_kwargs to open_zarr

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Commits on Mar 14, 2023

  1. don't import dask.tokenize

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  2. fix bugs with passing from_array_kwargs down

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  3. generalise reductions by adding to chunkmanager

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  4. moved nanfirst/nanlast to duck_array_ops from dask_array_ops

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  5. generalize interp

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  6. generalized chunk_hint function inside indexing

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  7. DaskIndexingAdapter->ChunkedIndexingAdapter

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  8. Merge branch 'main' into cubed_integration

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  9. Revert "DaskIndexingAdapter->ChunkedIndexingAdapter" 

    This reverts commit 4ca044b.
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  10. pass cubed-related kwargs down through to_zarr by adding .store to Ch… 

    …unkManager
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  11. fix typing_extensions on py3.9

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  12. fix ImportError with cubed array type

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  13. give up trying to import TypeAlias in CI

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  14. fix import of T_Chunks

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  15. fix no_implicit_optional warnings

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  16. don't define CubedManager if cubed can't be imported

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  17. fix local mypy errors

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Commits on Mar 15, 2023

  1. don't explicitly pass enforce_ndim into dask.array.map_blocks

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  2. fix drop_axis default

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Commits on Mar 16, 2023

  1. Merge branch 'main' into cubed_integration

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  2. use indexing adapter on cubed arrays too

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  3. use array API-compatible version of astype function

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  4. whatsnew

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  5. document new kwargs

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Commits on Mar 21, 2023

  1. add chunkmanager entrypoint

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  2. move CubedManager to a separate package

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  3. guess chunkmanager based on whats available

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Commits on Mar 22, 2023

  1. Merge branch 'main' into cubed_integration

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  2. fix bug with tokenizing

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  3. adapt tests to emulate existence of entrypoint

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  4. use fixture to setup/teardown dummy entrypoint

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  5. refactor to make DaskManager unavailable if dask not installed

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  6. typing

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  7. Merge branch 'main' into cubed_integration

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  8. move whatsnew to latest xarray version

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  9. remove superfluous lines from whatsnew

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Commits on Mar 23, 2023

  1. fix bug where zarr backend attempted to use dask when not installed

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  2. Remove rogue print statement 

    Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
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  3. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  4. Clarify what's new 

    Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
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  5. use monkeypatch to mock registering of dummy chunkmanager

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  6. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  7. more tests for guessing chunkmanager correctly

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  8. raise TypeError if no chunkmanager found for array types

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  9. Correct is_chunked_array check 

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Commits on Mar 24, 2023

  1. vendor dask.array.core.normalize_chunks

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  2. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  3. add default implementation of rechunk in ABC

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  4. remove cubed-specific type check in daskmanager

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  5. nanfirst->chunked_nanfirst

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  6. revert adding cubed to NON_NUMPY_SUPPORTED_ARRAY_TYPES

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  7. licensing to vendor functions from dask

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  8. fix bug

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  9. ignore mypy error

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Commits on Mar 29, 2023

  1. separate chunk_manager kwarg from from_array_kwargs dict

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  2. rename kwarg to chunked_array_type

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Commits on Mar 30, 2023

  1. Merge branch 'main' into cubed_integration

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Commits on Apr 5, 2023

  1. refactor from_array_kwargs in .chunk ready for deprecation

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  2. print statements in test so I can comment on them

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  3. remove print statements now I've commented on them in PR

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  4. should fix dask naming tests

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  5. Merge branch 'main' into cubed_integration

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  6. make dask-specific kwargs explicit in from_array

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Commits on Apr 6, 2023

  1. debugging print statements

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  2. Revert "debugging print statements" 

    This reverts commit 7dc6581.
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  3. fix gnarly bug with auto-determining chunksizes caused by not referri… 

    …ng to dask.config
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  4. hopefully fix broken docstring

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  5. Revert "make dask-specific kwargs explicit in from_array" 

    This reverts commit 53d6094.
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  6. Merge branch 'main' into cubed_integration

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  7. show chunksize limit used in failing tests

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  8. move lazy indexing adapter up out of chunkmanager code

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  9. try upgrading minimum version of dask

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Commits on Apr 11, 2023

  1. Revert "try upgrading minimum version of dask" 

    This reverts commit 796a577.
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  2. un-vendor dask.array.core.normalize_chunks

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  3. Merge branch 'main' into cubed_integration

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Commits on Apr 12, 2023

  1. refactored to all passing ChunkManagerEntrypoint objects directly

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Commits on Apr 17, 2023

  1. Remove redundant Nones from types 

    Co-authored-by: Illviljan <14371165+Illviljan@users.noreply.github.com>
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  2. From future import annotations 

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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

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  4. From functools import annotations 

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  6. From future import annotations 

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  7. Merge branch 'main' into cubed_integration

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Commits on May 1, 2023

  1. defined type for NormalizedChunks

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  2. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  4. standardized capitalization of ChunkManagerEntrypoint

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  5. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  6. Merge branch 'main' into cubed_integration

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  7. ensure ruff doesn't remove import

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Commits on May 2, 2023

  1. ignore remaining typing errors stemming from unclear dask typing for … 

    …chunks arguments
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  2. Merge branch 'main' into cubed_integration

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  3. rename store_kwargs->chunkmanager_store_kwargs

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  4. missed return value

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Commits on May 4, 2023

  1. array API fixes for astype

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  2. Revert "array API fixes for astype" 

    This reverts commit 9cd9078.
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Commits on May 10, 2023

  1. Merge branch 'main' into cubed_integration

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Commits on May 12, 2023

  1. Apply suggestions from code review

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  2. Update xarray/tests/test_parallelcompat.py

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  4. overridden -> subclassed 

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  5. from_array_kwargs is optional 

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  6. ensured all compute calls go through chunkmanager

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  7. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  8. Raise if multiple chunkmanagers recognize array type 

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Commits on May 13, 2023

  1. from_array_kwargs is optional 

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  2. from_array_kwargs is optional 

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  3. from_array_kwargs is optional 

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  4. from_array_kwargs is optional 

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  5. from_array_kwargs is optional 

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  6. fixes for chunk methods

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  7. Merge branch 'main' into cubed_integration

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  8. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

    …rray into cubed_integration
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  9. correct readme to reflect fact we aren't vendoring dask in this PR an… 

    …y more
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  10. update whatsnew

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  11. more docstring corrections

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  12. remove comment

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Commits on May 16, 2023

  1. Raise NotImplementedErrors in all abstract methods 

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  2. type hints for every arg in ChunkManagerEntryPOint methods

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  3. more explicit typing + fixes for mypy errors revealed

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  4. Keyword-only arguments in full_like etc. 

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  6. None as default instead of {}

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  7. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

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  8. fix bug apparently introduced by changing default type of drop_axis k… 

    …warg to map_blocks
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  9. Removed hopefully-unnecessary mypy ignore 

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  11. removed unnecessary mypy ignores

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  12. Merge branch 'cubed_integration' of https://github.com/TomNicholas/xa… 

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Commits on May 18, 2023

  1. change default value of drop_axis kwarg in map_blocks and catch when … 

    …dask version < 2022.9.1
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  2. fix checking of dask version in map_blocks

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