Code

(feat): read_elem_as_dask method#1469

Code

Merged

ilan-gold merged 160 commits intomainscverse/anndata:mainfrom ig/read_dask_elemscverse/anndata:ig/read_dask_elemCopy head branch name to clipboardJul 23, 2024

+459-69

Commits

Commits on Apr 11, 2024

• (feat): read_elem_lazy method

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  d111f04

• (revert): error message

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  00be7f0

• (refactor): declare is_csc reading elem directly in h5

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  fd635d7

Commits on Apr 12, 2024

• (chore): read_elem_lazy -> read_elem_as_dask

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  f5e7fda

• (chore): remove string handling

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  ae5396c

• (refactor): use elem for h5 where posssble

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Commits on Apr 17, 2024

• Merge branch 'main' into ig/read_dask_elem

  ilan-gold

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• (chore): remove invlaud syntax

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  52002b6

• Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into ig/read_dask_elem

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• (fix): put dask import inside function

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  aa1006e

• (refactor): try maybe open?

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Commits on May 27, 2024

• Merge branch 'main' into ig/read_dask_elem

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• Merge branch 'main' into ig/read_dask_elem

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Commits on Jun 3, 2024

• Merge branch 'main' into ig/read_dask_elem

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  97b8031

• (fix): revert encoding-version

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  1fc4cc3

• (chore): document create_sparse_store test function

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  5ca71ea

• (chore): sort indices to prevent warning

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  3672c18

• (fix): remove utility function make_dask_array

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  33c3599

• (chore): read_sparse_as_dask_h5 -> read_sparse_as_dask

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  157e710

• (feat): make params of h5_chunks and stride

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  375000d

• (chore): add distributed test

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• (fix): TypeVar bind

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Commits on Jun 4, 2024

• (chore): release note

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Commits on Jun 5, 2024

• (chore): 0.10.8 -> 0.11.0

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Commits on Jun 26, 2024

• Merge branch 'main' into ig/read_dask_elem

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  762d4c6

• (fix): ruff for default pytest.fixture scope

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  c935fe0

Commits on Jul 1, 2024

• Apply suggestions from code review

  Show description for 23e0ea2
  

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• (fix): Any to DaskArray

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  5b96c77

• (fix): type make_index + fix undeclared

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  0907a4e

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

  Show description for 20ced16
  pre-commit-ci[bot]

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• Merge branch 'main' into ig/read_dask_elem

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• fix rest

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Commits on Jul 2, 2024

• (fix): use chunks kwarg

  ilan-gold

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  419691b

• Merge branch 'main' into ig/read_dask_elem

  ilan-gold

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  a23df34

• (feat): expose chunks as an option to read_elem_as_dask via dataset_kwargs

  ilan-gold

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  fd2376a

• Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into ig/read_dask_elem

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• (fix): test_read_dispatched_null_case test

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  42b1093

• (fix): disallowed spread syntax?

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  78de057

• (refactor): reuse compute_chunk_layout_for_axis_shape functionality

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  717b997

Commits on Jul 3, 2024

• (fix): remove unneeded slice arguments

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  2b86293

• (fix): revert message

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• (refactor): make_index -> make_block_indexer

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  449fc1a

• (fix): export from experimental

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  1522de3

• (fix): callback signature for `test_read_dispatched_null_case

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  71c150d

• (chore): get_elem_name helper

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  b441366

• (chore): use H5Group consistently

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  0307a1d

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

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  ee075cd

• (fix): regsiter for group not array

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  89acec4

• (chore): add warning test

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• (chore): make arg order consistent

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Commits on Jul 5, 2024

• (feat): add callback typing for read_dispatched

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  cda8aa7

• (chore): use npt.NDArray

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  e8f62f4

• (fix): remove uneceesary union

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  f6e48ac

• (chore): release note

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  4de3246

• (fix); try protocol docs

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  ba817e0

• (feat): create InMemoryElem + DictElemType to remove Any

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  438d28d

• (chore): refactor DictElemType -> InMemoryArrayOrScalarType for reuse

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• (fix): use Union

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  cf13a57

• (fix): more Union

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• (refactor): InMemoryElem -> InMemoryReadElem

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  6970a97

• (chore): add needed types to public export + docs fix

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Commits on Jul 8, 2024

• Merge branch 'main' into ig/read_dask_elem

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• (chore): type write_elem functions

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• (chore): create write_callback protocol

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• Merge branch 'main' into ig/protocol_for_callback

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• (chore): export + docs

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• (fix): add string descriptions

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  fbe44f0

• (fix): try sphinx protocol doc

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• (fix): try ignoring exports

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• (fix): remap callback internal usages

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• (fix): add docstring

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Commits on Jul 9, 2024

• Discard changes to pyproject.toml

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• re-add dep

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• Fix docs

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• Almost works

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• works!

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• (chore): use pascal-case

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• (feat): type read/write funcs in callback

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• (fix): use generic for Read as well.

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• (fix): need more aliases

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• Split table, format

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• (refactor): move to _types file

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• Merge branch 'ig/protocol_for_callback' of github.com:scverse/anndata into ig/protocol_for_callback

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• bump scanpydoc

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• Some basic syntax fixes

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• Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

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• (fix): change Read{Callback} type for kwargs

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• (chore): test chunks argument

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• (fix): type read_recarray

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• (fix): GroupyStorageType not StorageType

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• (fix): little type fixes

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  e5ea2b0

• (fix): clarify H5File typing

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• (fix): dask doc

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• (fix): dask docs

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• Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

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• (fix): typing

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• (fix): handle case when chunks is None

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  eabaf35

• (feat): add string-array reading

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

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Commits on Jul 10, 2024

• (refactor): clean up tests

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  33aebb2

• (fix): overfetching problem

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Commits on Jul 11, 2024

• Fix circular import

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• add some typing

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  0e22449

• fix mapping types

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  ec546f4

• Fix Read/Write

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• Fix one more

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• unify names

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• claift ReadCallback signature

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• Fix type aliases

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• (fix): clean up typing to use RWAble

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• Merge branch 'main' into ig/protocol_for_callback

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• (fix): use Union

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• (fix): add qualname override

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• (fix): ignore dask and masked array

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• (fix): ignore erroneous class warning

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• (fix): upgrade scanpydoc

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

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• Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

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• Add data docs

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• Revert "(fix): use MutableMapping instead of dict due to broken docstring"

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• (fix): add clarification

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• Simplify

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• Merge branch 'ig/protocol_for_callback' into ig/read_dask_elem

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• Merge branch 'main' into ig/read_dask_elem

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• Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into ig/read_dask_elem

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Commits on Jul 12, 2024

• Merge branch 'main' into ig/read_dask_elem

  ilan-gold

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• (fix): remove double dask intersphinx

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• (fix): remove _types.DaskArray from type checking block

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Commits on Jul 15, 2024

• (refactor): use block_info for resolving fetch location

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• Merge branch 'ig/read_dask_elem' of github.com:scverse/anndata into ig/read_dask_elem

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• (fix): dtype for reading

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Commits on Jul 16, 2024

• (fix): ignore import cycle problem (why??)

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• (fix): add issue

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Commits on Jul 18, 2024

• (fix): subclass Reader to remove datasetkwargs

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• (fix): add message tp errpr

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• Update tests/test_io_elementwise.py

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• (fix): correct self.callback check

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• (fix): erroneous diffs

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• (fix): extra read_elem dataset_kwargs

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• (fix): remove more dataset_kwargs nonsense

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• (chore): add docs

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• (fix): use block_info for dense

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• (fix): more erroneous diffs

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• (fix): use context again

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Commits on Jul 22, 2024

• (fix): change size by dimension in tests

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• (refactor): clean up get_elem_name

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• (fix): try new sphinx for error

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• (fix): return type

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• (fix): protocol for reading

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• (fix): bring back ignored warning

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• Fix docs

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• almost fix typing

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• add wrapper

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• move into type checking

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• (fix): small type fxes

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• Merge branch 'main' into ig/read_dask_elem

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• block info types

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• simplify

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• rename

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• simplify more

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