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(feat): read_lazy for xarray reading + read_elem_as_dask -> read_elem_lazy #1247

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(feat): read_lazy for xarray reading + read_elem_as_dask -> read_elem_lazy #1247

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Commits on Jul 3, 2024

  1. (fix): no xarray in min deps

    @ilan-gold
    ilan-gold committed Jul 3, 2024
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  2. (fix): elif for reqname

    @ilan-gold
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  3. (fix): import

    @ilan-gold
    ilan-gold committed Jul 3, 2024
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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
    ilan-gold committed Jul 5, 2024
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  3. (fix): remove uneceesary union

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  4. (chore): release note

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  5. (fix); try protocol docs

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  6. (feat): create InMemoryElem + DictElemType to remove Any

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  7. (chore): refactor DictElemType -> InMemoryArrayOrScalarType for r… 

    …euse
    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  8. (fix): use Union

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  9. (fix): more Union

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  10. (refactor): InMemoryElem -> InMemoryReadElem

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  11. (chore): add needed types to public export + docs fix

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  12. (fix): DataArray type

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  13. (fix): dims->sizes

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  14. (fix): move to _compat for ImportError stuff

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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  15. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Jul 5, 2024
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Commits on Jul 8, 2024

  1. Merge branch 'main' into ig/xarray_compat

    @flying-sheep
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  2. Merge branch 'main' into ig/read_dask_elem

    @flying-sheep
    flying-sheep committed Jul 8, 2024
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  3. (chore): type write_elem functions

    @ilan-gold
    ilan-gold committed Jul 8, 2024
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  4. (chore): create write_callback protocol

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

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

    @ilan-gold
    ilan-gold committed Jul 8, 2024
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  7. (fix): add string descriptions

    @ilan-gold
    ilan-gold committed Jul 8, 2024
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  8. (fix): try sphinx protocol doc

    @ilan-gold
    ilan-gold committed Jul 8, 2024
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  9. (fix): try ignoring exports

    @ilan-gold
    ilan-gold committed Jul 8, 2024
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  10. (fix): remap callback internal usages

    @ilan-gold
    ilan-gold committed Jul 8, 2024
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  11. (fix): add docstring

    @ilan-gold
    ilan-gold committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. Discard changes to pyproject.toml

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  2. re-add dep

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  3. Fix docs

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  4. Almost works

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  5. works!

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  6. (chore): use pascal-case

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  7. (feat): type read/write funcs in callback

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  8. (fix): use generic for Read as well.

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  9. (fix): need more aliases

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  10. Split table, format

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  11. (refactor): move to _types file

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  12. Merge branch 'ig/protocol_for_callback' of github.com:scverse/anndata… 

    … into ig/protocol_for_callback
    @ilan-gold
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  13. bump scanpydoc

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  14. Some basic syntax fixes

    @flying-sheep
    flying-sheep committed Jul 9, 2024
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  15. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  16. (fix): change Read{Callback} type for kwargs

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  17. (chore): test chunks argument

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  18. (fix): type read_recarray

    @ilan-gold
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  19. (fix): GroupyStorageType not StorageType

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  20. (fix): little type fixes

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  21. (fix): clarify H5File typing

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  22. (fix): dask doc

    @ilan-gold
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  23. (fix): dask docs

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  24. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

    @ilan-gold
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  25. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  26. (fix): typing

    @ilan-gold
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  27. (fix): handle case when chunks is None

    @ilan-gold
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  28. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  29. (feat): use read_elem_as_dask

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  30. (feat): add string-array reading

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  31. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  32. (fix): string array handling

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  33. (fix): remove string-array because it is not tested

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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  34. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
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  35. (fix): add back string-array for zarr

    @ilan-gold
    ilan-gold committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. (fix): add dataset_kwargs

    @ilan-gold
    ilan-gold committed Jul 10, 2024
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  2. (fix): compat zarr import

    @ilan-gold
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  3. (fix): zarr import

    @ilan-gold
    ilan-gold committed Jul 10, 2024
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  4. (refactor): clean up tests

    @ilan-gold
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  5. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Jul 10, 2024
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  6. (fix): overfetching problem

    @ilan-gold
    ilan-gold committed Jul 10, 2024
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  7. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
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  8. (fix): don't read in index multiple times

    @ilan-gold
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  9. (fix): don't overfetch

    @ilan-gold
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  10. Merge branch 'ig/xarray_compat' of github.com:scverse/anndata into ig… 

    …/xarray_compat
    @ilan-gold
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Commits on Jul 11, 2024

  1. Fix circular import

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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  2. add some typing

    @flying-sheep
    flying-sheep committed Jul 11, 2024
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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
    flying-sheep committed Jul 11, 2024
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  6. unify names

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    flying-sheep committed Jul 11, 2024
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  7. claift ReadCallback signature

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

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

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

    @ilan-gold
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  11. (fix): use Union

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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
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  15. (fix): upgrade scanpydoc

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  16. (fix): use MutableMapping instead of dict due to broken docstring

    @ilan-gold
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  17. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

    @ilan-gold
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  18. Add data docs

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  19. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
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  20. Revert "(fix): use MutableMapping instead of dict due to broken d… 

    …ocstring"

This reverts commit 79d3fdc.
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  21. (fix): add clarification

    @ilan-gold
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  22. Simplify

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

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

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

    …g/read_dask_elem
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  26. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
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Commits on Jul 12, 2024

  1. Merge branch 'main' into ig/read_dask_elem

    @ilan-gold
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  2. (fix): remove double dask intersphinx

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

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

    @ilan-gold
    ilan-gold committed 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
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  3. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Jul 15, 2024
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  4. (fix): don't set chunk sizes manually

    @ilan-gold
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  5. (fix): dtype for reading

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Commits on Jul 16, 2024

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

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  2. (fix): add issue

    @ilan-gold
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Commits on Jul 18, 2024

  1. (fix): subclass Reader to remove datasetkwargs

    @ilan-gold
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  2. (fix): add message tp errpr

    @ilan-gold
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  3. Update tests/test_io_elementwise.py 

    Co-authored-by: Isaac Virshup <[email protected]>
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  4. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

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  5. (fix): correct self.callback check

    @ilan-gold
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  6. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

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  7. (fix): erroneous diffs

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

    @ilan-gold
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  9. (fix): remove more dataset_kwargs nonsense

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  10. (chore): add docs

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  11. (fix): use block_info for dense

    @ilan-gold
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  12. (fix): more erroneous diffs

    @ilan-gold
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  13. (fix): use context again

    @ilan-gold
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Commits on Jul 22, 2024

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

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  2. (refactor): clean up get_elem_name

    @ilan-gold
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  3. (fix): try new sphinx for error

    @ilan-gold
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  4. (fix): return type

    @ilan-gold
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  5. (fix): protocol for reading

    @ilan-gold
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  6. (fix): bring back ignored warning

    @ilan-gold
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  7. Fix docs

    @flying-sheep
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  8. almost fix typing

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  9. add wrapper

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  10. move into type checking

    @flying-sheep
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  11. (fix): small type fxes

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

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  13. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
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  14. block info types

    @flying-sheep
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  15. simplify

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  16. rename

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  17. simplify more

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Commits on Jul 23, 2024

  1. (fix): migrate to use read_elem infrastructure

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

    @ilan-gold
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  3. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
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  4. (fix): no first access of categories

    @ilan-gold
    ilan-gold committed Jul 23, 2024
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  5. (fix): last small cleanups

    @ilan-gold
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  6. (fix): try not runnign xarray tests

    @ilan-gold
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  7. (fix): oops! forgot one test to mark!

    @ilan-gold
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Commits on Aug 5, 2024

  1. Merge branch 'main' into ig/xarray_compat

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Commits on Aug 6, 2024

  1. Update pyproject.toml 

    Co-authored-by: Philipp A. <[email protected]>
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  2. (fix): change unused category function from method to function

    @ilan-gold
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  3. Merge branch 'main' into ig/xarray_compat

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  4. (fix): actually track keys instead of relying on deafultdict behavior

    @ilan-gold
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  5. (chore): test unconsolidated warning

    @ilan-gold
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  6. Update pyproject.toml 

    Co-authored-by: Philipp A. <[email protected]>
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  7. (fix): use test-full/test

    @ilan-gold
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  8. (fix): typing for _gen_dataframe

    @ilan-gold
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  9. (chore): imrpoved comments for Dataset2D

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  10. (fix): iloc is an attr not a meth

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Commits on Aug 13, 2024

  1. Merge branch 'main' into ig/xarray_compat

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  2. (fix): release notes

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  3. (fix): zarr doc in read_backed

    @ilan-gold
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  4. (fix): docs string

    @ilan-gold
    ilan-gold committed Aug 13, 2024
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  5. (fix): wording in release note

    @ilan-gold
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Commits on Aug 26, 2024

  1. Merge branch 'main' into ig/xarray_compat

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Commits on Aug 27, 2024

  1. (chore): move _remove_unused_categories to static method

    @ilan-gold
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  2. (chore): use one isinstance call in coerce_arrays

    @ilan-gold
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  3. (chore): clean up read_dataframe

    @ilan-gold
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  4. (chore): handle case where chunks is not needed

    @ilan-gold
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  5. (chore): make reusable LazyDataStructures

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  6. (chore): use Path.suffix

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  7. (chore): msg for warnings

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  8. (chore): remove erroneous Union in TypeVar

    @ilan-gold
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  9. (fix): use cached_property for accessing dtype + test

    @ilan-gold
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  10. (refactor): use cached_property for categories

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  11. (refactor): use guard clause in __getitem__ better

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  12. (chore): type get_index_dim

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  13. (fix): shape return type

    @ilan-gold
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  14. (refactor): _subset guard clause

    @ilan-gold
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  15. (fix): use Counter

    @ilan-gold
    ilan-gold committed Aug 27, 2024
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  16. (refactor): fix_known_differences usage of as_type

    @ilan-gold
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  17. Merge branch 'main' into ig/xarray_compat

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Commits on Aug 28, 2024

  1. Merge branch 'main' into ig/xarray_compat

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  2. (chore): fragment

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  3. (chore): fix the generic problem

    @ilan-gold
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  4. (chore): clean up tests

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Commits on Aug 30, 2024

  1. Merge branch 'main' into ig/xarray_compat

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  2. Update tests/test_read_backed_experimental.py 

    Co-authored-by: Philipp A. <[email protected]>
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  3. Merge branch 'main' into ig/xarray_compat

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Commits on Sep 2, 2024

  1. (fix): should -> shall

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  2. Apply suggestions from code review 

    Co-authored-by: Philipp A. <[email protected]>
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  3. (fix): _gen_xarray_dict_iterator_from_elems -> `_gen_xarray_dict_it… 

    …erator_from_elems`
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  4. (feat): indexing with DataArray

    @ilan-gold
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  5. Merge branch 'main' into ig/xarray_compat

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Commits on Sep 4, 2024

  1. (fix): check h5 store

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  2. Merge branch 'main' into ig/xarray_compat

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  3. (fix):check DataArray closer

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  4. (fix): clean up api.md from merge

    @ilan-gold
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  5. (fix): remove read_elem_as_dask docs reference

    @ilan-gold
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  6. (chore): add notebooks/read_backed_experimental

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  7. (chore): update notebooks

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Commits on Sep 18, 2024

  1. (refactor): set pytestmark at the top

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  2. (chore): clarify comment

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  3. (refactor): add assert_access_count method for AccessTrackingStore

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  4. (refactor): read_backed->read_lazy

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  5. (fix): actually read_backed -> read_lazy

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  6. (chore): time to require aiohttp fsspec and zarr and requests

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  7. Merge branch 'main' into ig/xarray_compat

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  8. (chore): update notebook

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  9. Merge branch 'main' into ig/xarray_compat

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Commits on Sep 20, 2024

  1. (fix): actually only read index once

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Commits on Sep 23, 2024

  1. (chore): add concat test

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  2. (feat): add columns compat

    @ilan-gold
    ilan-gold committed Sep 23, 2024
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  3. (fix): type of subset

    @ilan-gold
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  4. (fix): MaskedArray `dtype

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  5. (fix): add index.setter

    @ilan-gold
    ilan-gold committed Sep 23, 2024
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  6. (chore): add concat compat for xarray

    @ilan-gold
    ilan-gold committed Sep 23, 2024
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  7. (fix): refactor concat for in-memory

    @ilan-gold
    ilan-gold committed Sep 23, 2024
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  8. (chore): add rest of test

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    ilan-gold committed Sep 23, 2024
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Commits on Sep 30, 2024

  1. (feat): allow for concat with masked type using dask

    @ilan-gold
    ilan-gold committed Sep 30, 2024
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  2. (refactor): own function for concat xarray

    @ilan-gold
    ilan-gold committed Sep 30, 2024
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  3. (fix): add basic off-axis mapping without reading in i.e just an index

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    ilan-gold committed Sep 30, 2024
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  4. (feat): add merge for alt annot

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    ilan-gold committed Sep 30, 2024
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  5. (fix): notebook

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    ilan-gold committed Sep 30, 2024
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  6. Merge branch 'main' into ig/xarray_compat

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    ilan-gold committed Sep 30, 2024
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  7. (fix): NaS in sparse dask

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    ilan-gold committed Sep 30, 2024
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  8. (chore): add X tracker

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    ilan-gold committed Sep 30, 2024
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  9. (chore): add more robust matrix type tests

    @ilan-gold
    ilan-gold committed Sep 30, 2024
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  10. (fix): ok now notebooks?

    @ilan-gold
    ilan-gold committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. (feat): fix additional index load

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  2. (feat): no-load index

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  3. (fix): only use range indices for {obs,var}

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  4. (chore): add range index testing

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  5. (fix): ensure {obs,var}_names always exists on dataset

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  6. (fix): only use use_range_index on {obs,var}

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  7. (fix): don't check uniqueness to prevent index load + rename variable

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  8. (fix): check for presence of indexing key

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  9. always return index object

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  10. (fix): remove unnecessary check?

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    ilan-gold committed Oct 1, 2024
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  11. (chore): update notebook

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  12. (fix): docstring class

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  13. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  14. (fix): explicit 1d chunking for concat

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  15. (chore): change concat test name

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  16. (chore): rename test file

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  17. (chore): rename notebook

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  18. (chore): clarify load_annotation_index

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  19. (fix): allow concatenation along arbitrary index + indexing test

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  20. (fix): notebook path in docs

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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  21. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Oct 1, 2024
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