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(feat): read_elem_as_dask method #1469

Merged
merged 160 commits into from
Jul 23, 2024
Merged

(feat): read_elem_as_dask method #1469

merged 160 commits into from
Jul 23, 2024

Commits on Apr 11, 2024

  1. (feat): read_elem_lazy method

    @ilan-gold
    ilan-gold committed Apr 11, 2024
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  2. (revert): error message

    @ilan-gold
    ilan-gold committed Apr 11, 2024
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  3. (refactor): declare is_csc reading elem directly in h5

    @ilan-gold
    ilan-gold committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. (chore): read_elem_lazy -> read_elem_as_dask

    @ilan-gold
    ilan-gold committed Apr 12, 2024
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  2. (chore): remove string handling

    @ilan-gold
    ilan-gold committed Apr 12, 2024
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  3. (refactor): use elem for h5 where posssble

    @ilan-gold
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Commits on Apr 17, 2024

  1. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
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  2. (chore): remove invlaud syntax

    @ilan-gold
    ilan-gold committed Apr 17, 2024
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  3. Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into i… 

    …g/read_dask_elem
    @ilan-gold
    ilan-gold committed Apr 17, 2024
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  4. (fix): put dask import inside function

    @ilan-gold
    ilan-gold committed Apr 17, 2024
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  5. (refactor): try maybe open?

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Commits on May 27, 2024

  1. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
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  2. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
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Commits on Jun 3, 2024

  1. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
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  2. (fix): revert encoding-version

    @ilan-gold
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  3. (chore): document create_sparse_store test function

    @ilan-gold
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  4. (chore): sort indices to prevent warning

    @ilan-gold
    ilan-gold committed Jun 3, 2024
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  5. (fix): remove utility function make_dask_array

    @ilan-gold
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  6. (chore): read_sparse_as_dask_h5 -> read_sparse_as_dask

    @ilan-gold
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  7. (feat): make params of h5_chunks and stride

    @ilan-gold
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  8. (chore): add distributed test

    @ilan-gold
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  9. (fix): TypeVar bind

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Commits on Jun 4, 2024

  1. (chore): release note

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Commits on Jun 5, 2024

  1. (chore): 0.10.8 -> 0.11.0

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Commits on Jun 26, 2024

  1. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
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  2. (fix): ruff for default pytest.fixture scope

    @ilan-gold
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Commits on Jul 1, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Philipp A. <[email protected]>
    @ilan-gold @flying-sheep
    ilan-gold and flying-sheep authored Jul 1, 2024
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  2. (fix): Any to DaskArray

    @ilan-gold
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  3. (fix): type make_index + fix undeclared

    @ilan-gold
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  4. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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  5. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
    ilan-gold authored Jul 1, 2024
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  6. fix rest

    @flying-sheep
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Commits on Jul 2, 2024

  1. (fix): use chunks kwarg

    @ilan-gold
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  2. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
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  3. (feat): expose chunks as an option to read_elem_as_dask via `data… 

    …set_kwargs`
    @ilan-gold
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  4. Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into i… 

    …g/read_dask_elem
    @ilan-gold
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  5. (fix): test_read_dispatched_null_case test

    @ilan-gold
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  6. (fix): disallowed spread syntax?

    @ilan-gold
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  7. (refactor): reuse compute_chunk_layout_for_axis_shape functionality

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Commits on Jul 3, 2024

  1. (fix): remove unneeded slice arguments

    @ilan-gold
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  2. (fix): revert message

    @ilan-gold
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  3. (refactor): make_index -> make_block_indexer

    @ilan-gold
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  4. (fix): export from experimental

    @ilan-gold
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  5. (fix): callback signature for `test_read_dispatched_null_case

    @ilan-gold
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  6. (chore): get_elem_name helper

    @ilan-gold
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  7. (chore): use H5Group consistently

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  8. (refactor): make chunks public facing API instead of dataset_kwargs

    @ilan-gold
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  9. (fix): regsiter for group not array

    @ilan-gold
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  10. (chore): add warning test

    @ilan-gold
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  11. (chore): make arg order consistent

    @ilan-gold
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Commits on Jul 5, 2024

  1. (feat): add callback typing for read_dispatched

    @ilan-gold
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  2. (chore): use npt.NDArray

    @ilan-gold
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  3. (fix): remove uneceesary union

    @ilan-gold
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  4. (chore): release note

    @ilan-gold
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  5. (fix); try protocol docs

    @ilan-gold
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  6. (feat): create InMemoryElem + DictElemType to remove Any

    @ilan-gold
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  7. (chore): refactor DictElemType -> InMemoryArrayOrScalarType for r… 

    …euse
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  8. (fix): use Union

    @ilan-gold
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  9. (fix): more Union

    @ilan-gold
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  10. (refactor): InMemoryElem -> InMemoryReadElem

    @ilan-gold
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  11. (chore): add needed types to public export + docs fix

    @ilan-gold
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Commits on Jul 8, 2024

  1. Merge branch 'main' into ig/read_dask_elem

    @flying-sheep
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  2. (chore): type write_elem functions

    @ilan-gold
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  3. (chore): create write_callback protocol

    @ilan-gold
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  4. Merge branch 'main' into ig/protocol_for_callback

    @ilan-gold
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  5. (chore): export + docs

    @ilan-gold
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  6. (fix): add string descriptions

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  7. (fix): try sphinx protocol doc

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  8. (fix): try ignoring exports

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  9. (fix): remap callback internal usages

    @ilan-gold
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  10. (fix): add docstring

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Commits on Jul 9, 2024

  1. Discard changes to pyproject.toml

    @flying-sheep
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  2. re-add dep

    @flying-sheep
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  3. Fix docs

    @flying-sheep
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  4. Almost works

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  5. works!

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  6. (chore): use pascal-case

    @ilan-gold
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  7. (feat): type read/write funcs in callback

    @ilan-gold
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  8. (fix): use generic for Read as well.

    @ilan-gold
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  9. (fix): need more aliases

    @ilan-gold
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  10. Split table, format

    @flying-sheep
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  11. (refactor): move to _types file

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  12. Merge branch 'ig/protocol_for_callback' of github.com:scverse/anndata… 

    … into ig/protocol_for_callback
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  13. bump scanpydoc

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  14. Some basic syntax fixes

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  15. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

    @ilan-gold
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  16. (fix): change Read{Callback} type for kwargs

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  17. (chore): test chunks argument

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  18. (fix): type read_recarray

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  19. (fix): GroupyStorageType not StorageType

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  20. (fix): little type fixes

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  21. (fix): clarify H5File typing

    @ilan-gold
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  22. (fix): dask doc

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  23. (fix): dask docs

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  24. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

    @ilan-gold
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  25. (fix): typing

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  26. (fix): handle case when chunks is None

    @ilan-gold
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  27. (feat): add string-array reading

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  28. (fix): remove string-array because it is not tested

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Commits on Jul 10, 2024

  1. (refactor): clean up tests

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  2. (fix): overfetching problem

    @ilan-gold
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Commits on Jul 11, 2024

  1. Fix circular import

    @flying-sheep
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  2. add some typing

    @flying-sheep
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  3. fix mapping types

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  4. Fix Read/Write

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  5. Fix one more

    @flying-sheep
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  6. unify names

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  7. claift ReadCallback signature

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  8. Fix type aliases

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  9. (fix): clean up typing to use RWAble

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  10. Merge branch 'main' into ig/protocol_for_callback

    @ilan-gold
    ilan-gold authored Jul 11, 2024
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  11. (fix): use Union

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  12. (fix): add qualname override

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  13. (fix): ignore dask and masked array

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  14. (fix): ignore erroneous class warning

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  15. (fix): upgrade scanpydoc

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  16. (fix): use MutableMapping instead of dict due to broken docstring

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  17. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  18. Add data docs

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  19. Revert "(fix): use MutableMapping instead of dict due to broken d… 

    …ocstring"

This reverts commit 79d3fdc.
    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  20. (fix): add clarification

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  21. Simplify

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  22. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

    @ilan-gold
    ilan-gold authored Jul 11, 2024
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  23. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
    ilan-gold committed Jul 11, 2024
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  24. Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into i… 

    …g/read_dask_elem
    @ilan-gold
    ilan-gold committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
    ilan-gold authored Jul 12, 2024
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  2. (fix): remove double dask intersphinx

    @ilan-gold
    ilan-gold authored Jul 12, 2024
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  3. (fix): remove _types.DaskArray from type checking block

    @ilan-gold
    ilan-gold authored Jul 12, 2024
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Commits on Jul 15, 2024

  1. (refactor): use block_info for resolving fetch location

    @ilan-gold
    ilan-gold committed Jul 15, 2024
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  2. Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into i… 

    …g/read_dask_elem
    @ilan-gold
    ilan-gold committed Jul 15, 2024
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  3. (fix): dtype for reading

    @ilan-gold
    ilan-gold committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. (fix): ignore import cycle problem (why??)

    @ilan-gold
    ilan-gold committed Jul 16, 2024
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  2. (fix): add issue

    @ilan-gold
    ilan-gold committed Jul 16, 2024
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Commits on Jul 18, 2024

  1. (fix): subclass Reader to remove datasetkwargs

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  2. (fix): add message tp errpr

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  3. Update tests/test_io_elementwise.py 

    Co-authored-by: Isaac Virshup <[email protected]>
    @ilan-gold @ivirshup
    ilan-gold and ivirshup authored Jul 18, 2024
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  4. (fix): correct self.callback check

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  5. (fix): erroneous diffs

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  6. (fix): extra read_elem dataset_kwargs

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  7. (fix): remove more dataset_kwargs nonsense

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  8. (chore): add docs

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  9. (fix): use block_info for dense

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  10. (fix): more erroneous diffs

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  11. (fix): use context again

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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Commits on Jul 22, 2024

  1. (fix): change size by dimension in tests

    @ilan-gold
    ilan-gold committed Jul 22, 2024
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  2. (refactor): clean up get_elem_name

    @ilan-gold
    ilan-gold committed Jul 22, 2024
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  3. (fix): try new sphinx for error

    @ilan-gold
    ilan-gold committed Jul 22, 2024
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  4. (fix): return type

    @ilan-gold
    ilan-gold committed Jul 22, 2024
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  5. (fix): protocol for reading

    @ilan-gold
    ilan-gold committed Jul 22, 2024
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  6. (fix): bring back ignored warning

    @ilan-gold
    ilan-gold committed Jul 22, 2024
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  7. Fix docs

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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  8. almost fix typing

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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  9. add wrapper

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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  10. move into type checking

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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  11. (fix): small type fxes

    @ilan-gold
    ilan-gold committed Jul 22, 2024
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  12. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
    ilan-gold authored Jul 22, 2024
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  13. block info types

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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  14. simplify

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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  15. rename

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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  16. simplify more

    @flying-sheep
    flying-sheep committed Jul 22, 2024
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