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(feat): read_lazy for whole AnnData lazy-loading + xarray reading + read_elem_as_dask -> read_elem_lazy #1247

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(feat): read_lazy for whole AnnData lazy-loading + xarray reading + read_elem_as_dask -> read_elem_lazy #1247

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Commits on Jul 11, 2024

  1. unify names

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  2. claift ReadCallback signature

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

    @flying-sheep
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  4. (fix): clean up typing to use RWAble

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

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

    @ilan-gold
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  7. (fix): add qualname override

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

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

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

    @ilan-gold
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  11. (fix): use MutableMapping instead of dict due to broken docstring

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

    @ilan-gold
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  13. Add data docs

    @flying-sheep
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  14. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

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

    …ocstring"

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

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

    @flying-sheep
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  18. Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

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

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

    …g/read_dask_elem
    @ilan-gold
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  21. 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
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  3. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
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  4. (fix): remove _types.DaskArray from type checking block

    @ilan-gold
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Commits on Jul 15, 2024

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

    @ilan-gold
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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
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  4. (fix): don't set chunk sizes manually

    @ilan-gold
    ilan-gold committed Jul 15, 2024
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  5. (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
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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]>
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    ilan-gold and ivirshup authored Jul 18, 2024
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  4. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  5. (fix): correct self.callback check

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  6. Merge branch 'ig/read_dask_elem' into ig/xarray_compat

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

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

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

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

    @ilan-gold
    ilan-gold committed Jul 18, 2024
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  13. (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
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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
    flying-sheep committed Jul 22, 2024
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  15. simplify

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    flying-sheep committed Jul 22, 2024
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  16. rename

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

    @ilan-gold
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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

    @ilan-gold
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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

    @ilan-gold
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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

    @ilan-gold
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  2. (fix): release notes

    @ilan-gold
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  3. (fix): zarr doc in read_backed

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

    @ilan-gold
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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

    @ilan-gold
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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

    @ilan-gold
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  11. (refactor): use guard clause in __getitem__ better

    @ilan-gold
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  12. (chore): type get_index_dim

    @ilan-gold
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  13. (fix): shape return type

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  14. (refactor): _subset guard clause

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  15. (fix): use Counter

    @ilan-gold
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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

    @ilan-gold
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Commits on Aug 28, 2024

  1. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
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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

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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

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  5. (fix): remove read_elem_as_dask docs reference

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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

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  3. (fix): type of subset

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  4. (fix): MaskedArray `dtype

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  5. (fix): add index.setter

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  6. (chore): add concat compat for xarray

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  7. (fix): refactor concat for in-memory

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  8. (chore): add rest of test

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Commits on Sep 30, 2024

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

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  2. (refactor): own function for concat xarray

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  3. (fix): add basic off-axis mapping without reading in i.e just an index

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  4. (feat): add merge for alt annot

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  5. (fix): notebook

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  6. Merge branch 'main' into ig/xarray_compat

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  7. (fix): NaS in sparse dask

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  8. (chore): add X tracker

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  9. (chore): add more robust matrix type tests

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  10. (fix): ok now notebooks?

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Commits on Oct 1, 2024

  1. (feat): fix additional index load

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  2. (feat): no-load index

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  3. (fix): only use range indices for {obs,var}

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  4. (chore): add range index testing

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  5. (fix): ensure {obs,var}_names always exists on dataset

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  6. (fix): only use use_range_index on {obs,var}

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  7. (fix): don't check uniqueness to prevent index load + rename variable

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  8. (fix): check for presence of indexing key

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  9. always return index object

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  10. (fix): remove unnecessary check?

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  11. (chore): update notebook

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  12. (fix): docstring class

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  13. Merge branch 'main' into ig/xarray_compat

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  14. (fix): explicit 1d chunking for concat

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  15. (chore): change concat test name

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  16. (chore): rename test file

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  17. (chore): rename notebook

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  18. (chore): clarify load_annotation_index

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  19. (fix): allow concatenation along arbitrary index + indexing test

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  20. (fix): notebook path in docs

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  21. Merge branch 'main' into ig/xarray_compat

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Commits on Oct 2, 2024

  1. (fix): don't copy column in dataset concat

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  2. (fix): actually test h5

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  3. (feat): add h5ad concat support

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  4. (fix): add docsting example

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  5. Merge branch 'ig/xarray_compat' of github.com:scverse/anndata into ig… 

    …/xarray_compat
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  6. (fix): catch warnings

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  7. (fix): format

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  8. (fix): threaded tests annotation index

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  9. (fix): remove xarray test from minimum deps

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  10. (fix): skip experimental backed tests if xarray not installed

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  11. (chore): remove todo

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Commits on Oct 4, 2024

  1. (feat): add uns reading

    @ilan-gold
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  2. (feat): add Raw reading + tests

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  3. (chore): make test-full shorter

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  4. (fix): stricter type checking

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  5. (fix): dtype casting for concat

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  6. (chore): separate into two cleaner unit tests

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  7. (fix): typing of `make_xarray_extension_dtypes_dask

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  8. (chore): remove comment

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  9. (fix): clean up compat

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  10. (chore): xarray raises import error for read_lazy

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Commits on Oct 14, 2024

  1. (fix) ignore some uncovered lines

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  2. use existing warn import

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Commits on Oct 16, 2024

  1. merge

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  2. (chore): add awkward nitpick_ignore comment

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  3. (refactor): use generator for new datasets

    @ilan-gold
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  4. (chore): docs + types in merge.py

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  5. (recactor): use set for index_name in merge.py

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  6. (refactor): comprehension for {alt_}annotations_in_memory

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  7. (chore): types in lazy_methods.py

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  8. (chore): lazy_methods.py index handling made clearer

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  9. (chore): move comment

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  10. (chore): dedupe read_params usage

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  11. (chore): **kwargs usage doesn't affect call when empty

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  12. (fix): clean up _lazy_arrays.py typing

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  13. (fix): no assert, raise ValueError

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  14. (fix): use get instead of membership check + no in-place

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  15. (chore): pytest mark to beginning + diskfmt -> diskfmt + thread s… 

    …afety using `worker_id`
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  16. (fix): remove resetting key trackers

    @ilan-gold
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  17. (fix): adata only has 4 cchunks in test, udpate comment

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  18. (chore): better use arrange-act-assert

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  19. (chore): ids for boolean params

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  20. (chore): contextlib + better assert objects

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  21. (chore): refactor concatenation for arrange-act-assert

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  22. merge again?

    @ilan-gold
    ilan-gold committed Oct 16, 2024
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  23. (fix): notebook submodule

    @ilan-gold
    ilan-gold committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. (fix): use find_spec pattern

    @ilan-gold
    ilan-gold committed Oct 17, 2024
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  2. (chore): re-insert types for AccessTrackingStore

    @ilan-gold
    ilan-gold committed Oct 17, 2024
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  3. (chore): dedent docstrings

    @ilan-gold
    ilan-gold committed Oct 17, 2024
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  4. (chore): raise error if slots have changed on ZarrOrHDF5Wrapper

    @ilan-gold
    ilan-gold committed Oct 17, 2024
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  5. (fix): add slots to please xarray

    @ilan-gold
    ilan-gold committed Oct 17, 2024
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  6. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
    ilan-gold authored Oct 17, 2024
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  7. Merge branch 'main' into ig/xarray_compat

    @flying-sheep
    flying-sheep authored Oct 17, 2024
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  8. (chore): remove redefinition

    @ilan-gold
    ilan-gold committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. (refactor): reuse join type

    @ilan-gold
    ilan-gold committed Oct 18, 2024
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  2. (fix): mixed type dataframe merging

    @ilan-gold
    ilan-gold committed Oct 18, 2024
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Commits on Oct 21, 2024

  1. (fix): condition for going to memory in mixed typing

    @ilan-gold
    ilan-gold committed Oct 21, 2024
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  2. (refactor): mixed type helper function

    @ilan-gold
    ilan-gold committed Oct 21, 2024
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  3. (fix): try linking to dask/awkward in docs build

    @ilan-gold
    ilan-gold committed Oct 21, 2024
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  4. (fix): awkward array docs

    @ilan-gold
    ilan-gold committed Oct 21, 2024
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Commits on Oct 25, 2024

  1. (chore): ValueError -> AssertionError

    @ilan-gold
    ilan-gold committed Oct 25, 2024
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  2. (fix): clean up _lazy_arrays.py

    @ilan-gold
    ilan-gold committed Oct 25, 2024
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  3. (fix): ValueError->KeyError for store

    @ilan-gold
    ilan-gold committed Oct 25, 2024
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  4. (chore): add note about unify_extension_dtypes

    @ilan-gold
    ilan-gold committed Oct 25, 2024
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  5. (chore): add ids

    @ilan-gold
    ilan-gold committed Oct 25, 2024
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Commits on Oct 31, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Philipp A. <[email protected]>
    @ilan-gold @flying-sheep
    ilan-gold and flying-sheep authored Oct 31, 2024
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  2. (fix): move all changes form anndata_elem

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  3. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  4. (fix): read_elem_as_dask->read_elem_lazy

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  5. (chore): refactor test_read_lazy fixtures

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  6. Update tests/test_read_lazy.py 

    Co-authored-by: Philipp A. <[email protected]>
    @ilan-gold @flying-sheep
    ilan-gold and flying-sheep authored Oct 31, 2024
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  7. Merge branch 'ig/xarray_compat' of github.com:scverse/anndata into ig… 

    …/xarray_compat
    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  8. (chore): restore types

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  9. (fix): do randint

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  10. (chore): ermove slots check

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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  11. (fix): return read_lazy

    @ilan-gold
    ilan-gold committed Oct 31, 2024
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Commits on Nov 6, 2024

  1. (fix): concating with hdf5 and cluster obviates need for locks works … 

    …with normal pytest
    @ilan-gold
    ilan-gold committed Nov 6, 2024
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Commits on Nov 7, 2024

  1. (fix): add warning catch

    @ilan-gold
    ilan-gold committed Nov 7, 2024
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  2. Merge branch 'main' into ig/xarray_compat

    @ilan-gold
    ilan-gold authored Nov 7, 2024
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