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(feat): experimental read_backed method for zarr + hdf5 via read_dispatched #947

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wants to merge 147 commits into from
Closed

(feat): experimental read_backed method for zarr + hdf5 via read_dispatched #947

wants to merge 147 commits into from

Commits on Apr 29, 2022

  1. Start backed sparse support for zarr

    @ivirshup
    ivirshup committed Apr 29, 2022
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Commits on Oct 31, 2022

  1. Merge branch 'master' into zarr-sparse-array

    @ivirshup
    ivirshup committed Oct 31, 2022
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Commits on Nov 8, 2022

  1. Merge branch 'master' into zarr-sparse-array

    @ivirshup
    ivirshup committed Nov 8, 2022
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  2. Fix sparse_to_dense

    @ivirshup
    ivirshup committed Nov 8, 2022
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Commits on Feb 8, 2023

  1. Merge branch 'master' into zarr-sparse-array

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

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Commits on Mar 3, 2023

  1. Start write_dispatched

    @ivirshup @ilan-gold
    ivirshup authored and ilan-gold committed Mar 3, 2023
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  2. (wip): remote reading via new AxisArrays and AnnData object

    @ilan-gold
    ilan-gold committed Mar 3, 2023
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  3. (chore): rename

    @ilan-gold
    ilan-gold committed Mar 3, 2023
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  4. (chore): venv to .gitignore

    @ilan-gold
    ilan-gold committed Mar 3, 2023
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  5. (fix): concatenation test

    @ilan-gold
    ilan-gold committed Mar 3, 2023
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  6. Revert changes to some backwards compat tests

    @ivirshup @ilan-gold
    ivirshup authored and ilan-gold committed Mar 3, 2023
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  7. Start fixing error reporting 

    To fix error reporting, I've put the attempt to catch an error during IO on top of the `read_elem` method.
Since the decorator is sometimes used on functions, I modified it to be able to handle the signature of both a method and a function.

What's weird is that sometimes the decorator is being passed the arguments of a method, that has a name like a method, but is a function.
So that still needs to be fixed.
    @ivirshup @ilan-gold
    ivirshup authored and ilan-gold committed Mar 3, 2023
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  8. Fixes after merge

    @ivirshup @ilan-gold
    ivirshup authored and ilan-gold committed Mar 3, 2023
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  9. Clean up error reporting + remove commented out code

    @ivirshup @ilan-gold
    ivirshup authored and ilan-gold committed Mar 3, 2023
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  10. (wip): semi-working demo?

    @ilan-gold
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  11. (chore): compat for old index key

    @ilan-gold
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  12. (chore): only use backed

    @ilan-gold
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  13. (feat): add custom to_df method

    @ilan-gold
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  14. (feat): get dataframe access working properly

    @ilan-gold
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  15. (chore): remove TODO

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  16. (chore): write up to-do's

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  17. (chore): add head method

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  18. (chore): add better check for to_df

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  19. (feat): categorical zarr array.

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

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  21. (feat): add categorical array to the read_remote

    @ilan-gold
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  22. (chore): remove todo

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  23. (chore): remove commented out parts

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  24. (chore): remove more unused methods

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  25. (chore): more cleanup

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  26. (chore): remove unused imports from utils

    @ilan-gold
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  27. (chore): refactor to use cached_property

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  28. (chore): more rebase cleanup

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  29. (fix): correct imports

    @ilan-gold
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  30. (feat): begin base AnnData class

    @ilan-gold
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Commits on Mar 7, 2023

  1. (feat): being in-place view mechanism

    @ilan-gold
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  2. (chore): remove from to-do list, at least for now

    @ilan-gold
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  3. (feat): abstract _init_as_actual

    @ilan-gold
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  4. (feat): begin reorganizing anndata initialization

    @ilan-gold
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Commits on Mar 8, 2023

  1. (fix): fix args + checks so that tests run

    @ilan-gold
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  2. (fix): check _X for backed

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  3. (fix): ensure x_indices exists

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  4. (feat): refactor _init_as_actual on remote anndata

    @ilan-gold
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  5. (fix): revert sparse changes.

    @ilan-gold
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Commits on Mar 9, 2023

  1. (chore): revert erroneous comment change

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  2. Merge branch 'main' into ig/read_remote_dispatched

    @ilan-gold
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  3. (feat): consolidate metadata by default

    @ilan-gold
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  4. (feat): begin unit tests

    @ilan-gold
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  5. (fix): fix index on obs.to_df()

    @ilan-gold
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Commits on Mar 16, 2023

  1. (feat): swap out zarr categorical array for xarray (#946) 

    * (feat): swap out `zarr` categorical array for `xarray`

* (chore): siimplify `to_df`

* (chore): add xarray dep

* (fix): don't add `index` to df twice

* (chore): add `LazyCategoricalArray` test

* (feat): add full array `__eq__`

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

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* (chore): split tests

* (chore): fully remove unused variables

* (chore): remove auto-generated typing

* (chore): return reading in categories at __init__

* (fix): use `any` not `some`

* (feat): add cache workaround

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    @ilan-gold @pre-commit-ci
    ilan-gold and pre-commit-ci[bot] authored Mar 16, 2023
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  2. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

    @ilan-gold
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Commits on Mar 20, 2023

  1. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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Commits on Mar 21, 2023

  1. (fix): implement __ne__

    @ilan-gold
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  2. (feat): try not reading in index

    @ilan-gold
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  3. (fix): string_array -> string-array

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  5. (chore): remove large comment

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  6. (style): _to_backed -> to_backed

    @ilan-gold
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  7. (fix): revert backed test

    @ilan-gold
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  8. Merge branch 'main' into zarr-sparse-array

    @ilan-gold
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  9. (fix): add basic zarr backed reading for test

    @ilan-gold
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Commits on Mar 23, 2023

  1. (feat): add support for non-consolidated stores

    @ilan-gold
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Commits on Mar 28, 2023

  1. (feat): first stage of base class refactor

    @ilan-gold
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Commits on Mar 29, 2023

  1. (feat): add categorical array view functionality

    @ilan-gold
    ilan-gold committed Mar 29, 2023
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  2. (feat): allow indexing into a view

    @ilan-gold
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Commits on Mar 30, 2023

  1. (chore): remove print statement

    @ilan-gold
    ilan-gold committed Mar 30, 2023
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  2. (style): batch is_view checks

    @ilan-gold
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  3. Merge branch 'zarr-sparse-array' into ig/read_remote_dispatched

    @ilan-gold
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  4. (fix): use sparse_dataset in remote

    @ilan-gold
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  5. (feat): add support for general index columns

    @ilan-gold
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  6. (feat): add support for raw

    @ilan-gold
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  7. (fix): ensure file is always present

    @ilan-gold
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  8. (feat): add some checks.

    @ilan-gold
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  10. (feat): add indptr caching

    @ilan-gold
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  11. Merge branch 'ig/read_remote_dispatched' of github.com:scverse/anndat… 

    …a into ig/read_remote_dispatched
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Commits on Apr 19, 2023

  1. (fix): don't use .X in __init__

    @ilan-gold
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  2. (feat): use dask for raw arrays

    @ilan-gold
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  3. (fix): clean categories

    @ilan-gold
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  4. (fix): 1d axis array view \to_df\

    @ilan-gold
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  5. (chore): tests

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Commits on May 4, 2023

  1. (feat): lazy subset mechanism for lazy cat array

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  2. (feat): finish all dtypes

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Commits on May 5, 2023

  1. (fix): use base compressed class directly

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  2. Merge branch 'ig/read_remote_dispatched' of github.com:scverse/anndat… 

    …a into ig/read_remote_dispatched
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Commits on May 8, 2023

  1. (chore): read_remote -> read_backed

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  2. (chore); add nullable bool/int tests

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Commits on May 9, 2023

  1. (feat): reorganize dirs

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  2. (chore): add access tracking test

    @ilan-gold
    ilan-gold committed May 9, 2023
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  3. (feat): add more array tests

    @ilan-gold
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  4. (fix): repr in jupyter setting + refactor

    @ilan-gold
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  5. (fix): fix layers support

    @ilan-gold
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  6. (fix): add columns attr + cleanup

    @ilan-gold
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Commits on May 10, 2023

  1. (fix): dont deepcopy the lazy array

    @ilan-gold
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  2. (feat): to_memory for AnnData object

    @ilan-gold
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  3. (feat): add to_memory test + corresponding fixes

    @ilan-gold
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  4. Merge branch 'ig/read_remote_dispatched' of github.com:scverse/anndat… 

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Commits on May 16, 2023

  1. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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Commits on May 19, 2023

  1. (fix): resolve tuple ambiguity

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  2. (fix): copy using backing categories array, not values

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  3. (feat): sparse arrays as dask

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  4. (chore): add access checks on X, `layers

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Commits on May 24, 2023

  1. (fix): ensure return type of dask array

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Commits on May 25, 2023

  1. (feat): subset_idx on backed class

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  2. Merge branch 'ig/read_remote_dispatched' of github.com:scverse/anndat… 

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Commits on May 26, 2023

  1. (fix): ensure old tests pass

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Commits on May 31, 2023

  1. (fix): name variable accurately

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Commits on Jun 1, 2023

  1. (fix): use correct access pattern for to_memory

    @ilan-gold
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  2. (feat): add exclude feature for to_memory

    @ilan-gold
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  3. (fix): efficient reading in of matrices by splitting up reading over … 

    …different axes
    @ilan-gold
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  4. (fix): legacy backed mode

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Commits on Jun 6, 2023

  1. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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  2. (fix): remove all

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Commits on Jun 14, 2023

  1. (chore): add docstrings

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  3. (fix): h5py support

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Commits on Jul 17, 2023

  1. (feat): migrate Dask to DataArray

    @ilan-gold
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  2. (feat): catgoricals now using DataArray as well.

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Commits on Jul 19, 2023

  1. (feat): xarray Dataset for obs/var

    @ilan-gold
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  2. (fix): refactor view mechanism

    @ilan-gold
    ilan-gold committed Jul 19, 2023
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  3. (fix): fix column handling for to_memory

    @ilan-gold
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Commits on Jul 30, 2023

  1. (feat): obsm/varm xr.Dataset

    @ilan-gold
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  2. (chore): refactor ZarrArray subset function

    @ilan-gold
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  3. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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  4. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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Commits on Aug 1, 2023

  1. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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  2. (fix): backed for experimental merge.py

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  3. (fix): pyproject.toml missing comma

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Commits on Aug 8, 2023

  1. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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  3. (chore): remove pre-commit deps

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  5. (fix): don't let ruff change == for DataFrame to is

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  6. (chore): move xarray to test deps

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  7. (style): change folder structure

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Commits on Oct 10, 2023

  1. Merge branch 'ig/refactor_base_class' into ig/read_remote_dispatched

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