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first attempt to support awkward arrays #647

Merged
merged 129 commits into from
Feb 7, 2023
Merged

first attempt to support awkward arrays #647

merged 129 commits into from
Feb 7, 2023

Commits on Nov 14, 2021

  1. first attempt to support awkward arrays

    @giovp
    giovp committed Nov 14, 2021
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  2. remove comments

    @giovp
    giovp committed Nov 14, 2021
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  3. better comment

    @giovp
    giovp committed Nov 14, 2021
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Commits on Nov 15, 2021

  1. add type to gen_adata

    @giovp
    giovp committed Nov 15, 2021
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  2. first attempt at concat

    @giovp
    giovp committed Nov 15, 2021
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  3. remove comment

    @giovp
    giovp committed Nov 15, 2021
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  4. add outer concat

    @giovp
    giovp committed Nov 15, 2021
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  5. add awkward to test dep

    @giovp
    giovp committed Nov 15, 2021
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  6. add awk arr to data gen

    @giovp
    giovp committed Nov 15, 2021
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Commits on Nov 16, 2021

  1. fix test base

    @giovp
    giovp committed Nov 16, 2021
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  2. init test for concat

    @giovp
    giovp committed Nov 16, 2021
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Commits on Nov 19, 2021

  1. fix concatenate tests

    @giovp
    giovp committed Nov 19, 2021
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Commits on Nov 25, 2021

  1. create mock class for awkward array

    @giovp
    giovp committed Nov 25, 2021
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  2. remove space

    @giovp
    giovp committed Nov 25, 2021
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Commits on Nov 28, 2021

  1. import ak when needed

    @giovp
    giovp committed Nov 28, 2021
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  2. relative import of awk array

    @giovp
    giovp committed Nov 28, 2021
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Commits on Nov 29, 2021

  1. fix optional dep import

    @giovp
    giovp committed Nov 29, 2021
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  2. resolve conflicts

    @giovp
    giovp committed Nov 29, 2021
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  3. Merge branch 'master' into val_shape

    @giovp
    giovp authored Nov 29, 2021
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Commits on Feb 10, 2022

  1. Merge branch 'master' into val_shape

    @giovp
    giovp authored Feb 10, 2022
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Commits on Mar 3, 2022

  1. merge and pre-commits

    @giovp
    giovp committed Mar 3, 2022
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  2. fix merge

    @giovp
    giovp committed Mar 3, 2022
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Commits on Mar 4, 2022

  1. draft IO for akward arrays

    @giovp
    giovp committed Mar 4, 2022
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  2. add awkward to docs and save form to attrs

    @giovp
    giovp committed Mar 4, 2022
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Commits on Jul 19, 2022

  1. Merge remote-tracking branch 'origin/master' into val_shape

    @grst
    grst committed Jul 19, 2022
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  2. Update dependencies

    @grst
    grst committed Jul 19, 2022
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  3. Update dim_len

    @grst
    grst committed Jul 19, 2022
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  4. ignore vscode directory

    @grst
    grst committed Jul 19, 2022
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  5. Validate that awkward arrays align to axes

    @grst
    grst committed Jul 19, 2022
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  6. Fix reindexing during merge

    @grst
    grst committed Jul 19, 2022
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  7. fix lint

    @grst
    grst committed Jul 19, 2022
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  8. remove duplicate import

    @grst
    grst committed Jul 19, 2022
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  9. Test different types of awkward arrays in different slots

    @grst
    grst committed Jul 19, 2022
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  10. Better function to generate awkward arrays

    @grst
    grst committed Jul 19, 2022
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  11. Better dim_len for awkward arrays

    @grst
    grst committed Jul 19, 2022
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  12. Working out how to best check the dim_len

    @grst
    grst committed Jul 19, 2022
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Commits on Jul 20, 2022

  1. Only accept awkward arrays that are "regular" in the aligned dimension 

    The conversion is left to the user. Explicit is better than implicit.
    @grst
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Commits on Aug 12, 2022

  1. Merge remote-tracking branch 'origin/master' into val_shape

    @grst
    grst committed Aug 12, 2022
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  2. Switch to v2 API

    @grst
    grst committed Aug 12, 2022
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  3. WIP rewrite awkward array generation

    @grst
    grst committed Aug 12, 2022
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  4. Improve awkward array generation and dim_len check

    @grst
    grst committed Aug 12, 2022
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  5. Switch to new awkward array generation in all tests

    @grst
    grst committed Aug 12, 2022
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  6. Fix test_transpose

    @grst
    grst committed Aug 12, 2022
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  7. Fix/workaround more tests

    @grst
    grst committed Aug 12, 2022
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Commits on Aug 13, 2022

  1. Add test for setting anndata slots to awkward arrays

    @grst
    grst committed Aug 13, 2022
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  2. enable tests for 3d ragged array in layers

    @grst
    grst committed Aug 13, 2022
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  3. Cleanup

    @grst
    grst committed Aug 13, 2022
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  4. Fix that X could not be set when creating AnnData object from scratch. 

    Apparently the checks are quite different than when adding a Layer.
    @grst
    grst committed Aug 13, 2022
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Commits on Aug 19, 2022

  1. Remove code to make awkward array regular after merge. 

    This is now done by the awkward array library.
    @grst
    grst committed Aug 19, 2022
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Commits on Aug 29, 2022

  1. Do not explicitly copy awkward arrays

    @grst
    grst committed Aug 29, 2022
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  2. Merge branch 'master' into val_shape

    @grst
    grst authored Aug 29, 2022
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  3. Implement transposing awkward arrays

    @grst
    grst committed Aug 29, 2022
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  4. Add docs stub and update type hints

    @grst
    grst committed Aug 29, 2022
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  5. Fix: dtype not available during merge if both X are awkward

    @grst
    grst committed Aug 29, 2022
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  6. Fix IO

    @ivirshup
    ivirshup authored Aug 29, 2022
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Commits on Aug 30, 2022

  1. Request pre-release version of awkward

    @grst
    grst committed Aug 30, 2022
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  2. Exclude awkward layer in loom tests

    @grst
    grst committed Aug 30, 2022
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  3. Merge branch 'master' into val_shape

    @grst
    grst authored Aug 30, 2022
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  4. Pull in only changes relevant to obsm/varm

    @grst
    grst committed Aug 30, 2022
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  5. Merge branch 'val_shape' of github.com:scverse/anndata into val_shape

    @grst
    grst committed Aug 30, 2022
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  6. Update tests

    @grst
    grst committed Aug 30, 2022
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  7. Fix type hints

    @grst
    grst committed Aug 30, 2022
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Commits on Aug 31, 2022

  1. Update error message in algined mapping

    @grst
    grst committed Aug 31, 2022
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  2. Use compat module to support both awkward v1.9rc and 2.x

    @grst
    grst committed Aug 31, 2022
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  3. Merge branch 'master' into val_shape

    @grst
    grst authored Aug 31, 2022
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  4. restructure tests

    @grst
    grst committed Aug 31, 2022
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  5. Add tests for copies and view

    @grst
    grst committed Aug 31, 2022
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  6. Remove unused imoport

    @grst
    grst committed Aug 31, 2022
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Commits on Sep 2, 2022

  1. Fix how actual shape is computed in aligned mapping

    @grst
    grst committed Sep 2, 2022
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  2. Attempt to support views with ak.behavior

    @grst
    grst committed Sep 2, 2022
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  3. Use shallow copy

    @grst
    grst committed Sep 2, 2022
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Commits on Sep 3, 2022

  1. Add dim_len_awkward function including tests

    @grst
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  2. Test that assigning an awkward v1 arrays fails

    @grst
    grst committed Sep 3, 2022
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  3. Add stub for element-wise IO tests

    @grst
    grst committed Sep 3, 2022
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Commits on Sep 4, 2022

  1. Restructur dim_len_awkward

    @grst
    grst committed Sep 4, 2022
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  2. Add more test cases for awkward IO

    @grst
    grst committed Sep 4, 2022
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  3. WIP add tests for concatenating AwkArrays with missing values

    @grst
    grst committed Sep 4, 2022
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  4. Fix AwkwardArrayView

    @grst
    grst committed Sep 4, 2022
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  5. Simplify awkward array view code

    @grst
    grst committed Sep 4, 2022
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Commits on Sep 5, 2022

  1. Use None to remove name from awkward array

    @grst
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  2. Mark test_no_awkward_v1 as xfail for uns

    @grst
    grst committed Sep 5, 2022
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Commits on Sep 6, 2022

  1. Add test for categorical arrays

    @grst
    grst committed Sep 6, 2022
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  2. Update docs/fileformat-prose.rst 

    Co-authored-by: Isaac Virshup <[email protected]>
    @grst @ivirshup
    grst and ivirshup authored Sep 6, 2022
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  3. Update anndata/_core/aligned_mapping.py 

    Co-authored-by: Isaac Virshup <[email protected]>
    @grst @ivirshup
    grst and ivirshup authored Sep 6, 2022
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  4. Update anndata/tests/helpers.py 

    Co-authored-by: Isaac Virshup <[email protected]>
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    grst and ivirshup authored Sep 6, 2022
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  5. Update awkward tests to use assert_equal with exact=True

    @grst
    grst committed Sep 6, 2022
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Commits on Sep 8, 2022

  1. Bump required version

    @ivirshup
    ivirshup authored Sep 8, 2022
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  2. Update categorical syntax, add new categorical test

    @ivirshup
    ivirshup authored Sep 8, 2022
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Commits on Sep 13, 2022

  1. Start concat tests for awkward

    @ivirshup
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  2. Merge branch 'master' into val_shape

    @ivirshup
    ivirshup committed Sep 13, 2022
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Commits on Sep 26, 2022

  1. Add release notes

    @grst
    grst committed Sep 26, 2022
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  2. Add testcases for dim_len with awkward arrays of strings

    @grst
    grst committed Sep 26, 2022
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  3. Fix dim_len for arrays of strings

    @grst
    grst committed Sep 26, 2022
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Commits on Dec 14, 2022

  1. Merge branch 'master' into val_shape

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

    for more information, see https://pre-commit.ci
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Commits on Jan 2, 2023

  1. Merge branch 'master' into val_shape

    @grst
    grst authored Jan 2, 2023
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  2. Awkward v2 fixes 

    Several functions changed until the stable awkward v2 version was released.
    @grst
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  3. Exclude awkward arrays from fill_value concat test

    @grst
    grst committed Jan 2, 2023
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  4. fix flake8

    @grst
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Commits on Jan 23, 2023

  1. Merge branch 'master' into val_shape

    @ivirshup
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Commits on Jan 27, 2023

  1. Add IO testcase for AIRR data

    @grst
    grst committed Jan 27, 2023
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Commits on Jan 30, 2023

  1. Merge branch 'master' into val_shape

    @ivirshup
    ivirshup committed Jan 30, 2023
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  2. Fix link

    @ivirshup
    ivirshup committed Jan 30, 2023
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  3. Get inner join working for concatenation

    @ivirshup
    ivirshup committed Jan 30, 2023
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  4. Merge branch 'master' into val_shape

    @ivirshup
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Commits on Jan 31, 2023

  1. Bump some concatenation cases to a later PR

    @ivirshup
    ivirshup committed Jan 31, 2023
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Commits on Feb 1, 2023

  1. Generate empty arrays for outer join

    @ivirshup
    ivirshup committed Feb 1, 2023
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  2. Raise NotImplementedError when creating a view of an awkward array wi… 

    …th custom behavior
    @grst
    grst committed Feb 1, 2023
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  3. Add warning when setting awkward array in aligned mapping

    @grst
    grst committed Feb 1, 2023
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  4. Merge branch 'master' into val_shape

    @grst
    grst authored Feb 1, 2023
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  5. Get much more of concatenation 'working'

    @ivirshup
    ivirshup committed Feb 1, 2023
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  6. Merge branch 'master' into val_shape

    @ivirshup
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  7. Use warning instead of logging

    @ivirshup
    ivirshup committed Feb 1, 2023
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Commits on Feb 2, 2023

  1. extend todo comment about views

    @grst
    grst committed Feb 2, 2023
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  2. Fix IO, and to_memory for views of awkward arrays

    @ivirshup
    ivirshup committed Feb 2, 2023
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  3. Removed a number of test cases that we're not targeting 

    This fixed a number of tests because we had a 1d awkward array being generated, and we currently don't support 1d arrays in obsm well. Tracked in #652.
    @ivirshup
    ivirshup committed Feb 2, 2023
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  4. Implement outer indexing on axis 0 of an awkward array

    @ivirshup
    ivirshup committed Feb 2, 2023
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  5. Fix gen_awkward when one of the dimensions has size 0

    @ivirshup
    ivirshup committed Feb 2, 2023
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  6. Fix equality function for awkward arrays. Was throwing an error when … 

    …the arrays weren't broadcastable.
    @ivirshup
    ivirshup committed Feb 2, 2023
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  7. Modify outer concatenation test to accept current behaviour of awkwar… 

    …d array
    @ivirshup
    ivirshup committed Feb 2, 2023
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  8. Merge branch 'master' into val_shape

    @ivirshup
    ivirshup committed Feb 2, 2023
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  9. Add tests for mixed type concatenation with awkward arrays

    @ivirshup
    ivirshup committed Feb 2, 2023
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Commits on Feb 3, 2023

  1. Add warning about outer joins

    @ivirshup
    ivirshup committed Feb 3, 2023
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  2. Call ak._util.arrays_approx_equal instead of rolling our own

    @ivirshup
    ivirshup committed Feb 3, 2023
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Commits on Feb 6, 2023

  1. update awkward to 2.0.7 (unfortunately: errors)

    @ivirshup
    ivirshup committed Feb 6, 2023
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  2. remove unnecessary checks from AwkwardArrayView

    @grst
    grst committed Feb 6, 2023
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Commits on Feb 7, 2023

  1. Workaround scikit-hep/awkward#2209

    @ivirshup
    ivirshup committed Feb 7, 2023
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Feb 7, 2023
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  3. Removed extra layer of nesting from on-disk format for awkward arrays

    @ivirshup
    ivirshup committed Feb 7, 2023
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