Code

Implement scverse datastucture#356

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grst merged 173 commits intomasterscverse/scirpy:masterfrom scverse_datastructurescverse/scirpy:scverse_datastructureCopy head branch name to clipboardApr 7, 2023

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Commits

Commits on Aug 13, 2022

• Create Awkward AnnData instead of putting everything in obs

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Commits on Aug 16, 2022

• add todo

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Commits on Aug 18, 2022

• Get chain indices for primary and secondary chains

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• WIP get module

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Commits on Aug 19, 2022

• Implement ir.get.airr

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• Clean up AirrCell

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• WIP restructure IO module

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• fix imports

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• Add helper function for unit tests

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• tl.chain_qc successfully runs on the new datastructure

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Commits on Oct 3, 2022

• Update convert anndata

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Commits on Oct 10, 2022

• Merge branch 'master' into scverse_datastructure

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Commits on Jan 4, 2023

• Merge branch 'master' into scverse_datastructure

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• switch to obsm-based data structure

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• update get module

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• Update anndata schema check and _make_adata util function.

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• fix _make_adata

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• update fixtures

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• Fix a couple of tests

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• Re-add to_airr_cells

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• Fix couple more tests

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Commits on Jan 5, 2023

• Fix more IO tests

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• More IO tests [skip ci]

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• Merge remote-tracking branch 'origin/master' into scverse_datastructure

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• Cleanup has_ir

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• WIP fix clonotype neighbors [skip ci]

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Commits on Jan 16, 2023

• WIP fix distance tests

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• WIP fix clonotype cluster tests

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• Fix spectratype functions [skip ci]

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Commits on Jan 17, 2023

• Fix more tests

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• Fix IR dist tests [skip ci]

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• Fix tests for ir dist

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• Fix spectratype test [skip ci]

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• Tests for new upgrade_schema function [skip ci]

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Commits on Jan 19, 2023

• Workaround for group_abundance plot without has_ir column

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• Cleanup has_ir

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• Clean multi_chain [skip ci]

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• stub new index_chains function

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• WIP index_chain function [skip ci]

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Commits on Jan 23, 2023

• Add stub test for index_chains

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• Stub second test for index_chains

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• Complete second test for index_chains [skip ci]

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Commits on Jan 26, 2023

• index_chains tests

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Commits on Jan 27, 2023

• Update target version to v0.13 [skip ci]

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• Merge branch 'master' into scverse_datastructure

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• Merge remote-tracking branch 'origin/master' into scverse_datastructure [skip ci]

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• add isort and autoflake

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• Fix circular import

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• Fix multichain handling (implement get._has_ir)

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• re-add fixtures

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• isort on tests [skip ci]

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• fix remaining IO tests

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• update todo flags [skip ci]

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Commits on Jan 29, 2023

• _is_na input sanitization already in AirrCell module [skip ci]

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• Fix issue with plotting; get rid of merge_with_ir [skip ci]

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• Remove test for merge_with_ir [skip ci]

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Commits on Feb 2, 2023

• Ensure consistent ordering or chains in merge_airr

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• Complete unit tests for merge_airr [skip ci]

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Commits on Feb 14, 2023

• Use pre-commit.ci for black formatting

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• Merge branch 'pre-commit' into scverse_datastructure

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• Bump minimum python version to 3.8

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• Bump minimum python version to 3.8

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• bump python version in CI tests

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• update imports of Literal

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• update pre-commit config [skip ci]

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• fix compat

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• WIP new chain_indices format

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• Fix get module

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• WIP fix tests

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• Fix tests [skip ci]

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• Fix dandelion tests

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Commits on Feb 15, 2023

• Update workflow tests

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• update min anndata version

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• Deprecate include_fields parameter and pass kwargs to from_airr_cells inIO

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• WIP update example datasets

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Commits on Feb 16, 2023

• update wu dataset generation

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Commits on Feb 17, 2023

• Update wu2020 dataset to mudata (preliminary)

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• First attempt to make tutorial work with mudata

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• fix issue with slicing awkward array when slice mask is empty

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• Change clonotype calling behavior for missing cdr3 sequences

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• fix awkward type conversion in index_chains

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• Get rid of tqdm workaround which is not needed anymore

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Commits on Feb 25, 2023

• Update API in tutorial to what it *should* look like in the future

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• Stub parameter validation [skip ci]

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Commits on Feb 26, 2023

• implement params check class

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• update API docs

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• Apply new params check to first function

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• document params check

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• Remove anndata version check decorators

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• Restructure to fix cirular import [skip ci]

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• Unit tests for parms check

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• Fix notebook pairing

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• Params check in index_chains

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• update ir_dist with paramscheck [skip ci]

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• Merge remote-tracking branch 'origin/master' into scverse_datastructure

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Commits on Mar 5, 2023

• Refactor ParamsCheck class

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• Refactor chain_qc

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Commits on Mar 7, 2023

• WIP implement param checks

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• Update type hints

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• Improve _ParamsCheck class [skip ci]

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Commits on Mar 8, 2023

• Fix typing in a couple of files.

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• Iterate on tutorial [skip ci]

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• Iterate on tutorial

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• Rename _ParamsCheck to DataHandler

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• Implement get_obs in DataHandler

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• WIP fix clonotype_network

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• Fix clonotype_network plot [skip ci]

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Commits on Mar 9, 2023

• Update clonal_expansion

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• Fix alpha diversity

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• Fix repertoire overlap and spectratype

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• Fix clonotype modularity

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• Fix ir_query [skip ci]

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• Fix clonotype convergence

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• Fix clonotype imbalance

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• Fix clonotype imbalance

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• Update processing scripts for Wu2020

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• Update maynard loading script

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• Merge branch 'scverse_datastructure' of github.com:icbi-lab/scirpy into scverse_datastructure

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• disable check for same fields in AirrCell [skip ci]

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Commits on Mar 10, 2023

• Update maynard processing script

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Commits on Mar 12, 2023

• WIP tests with mudata

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• Update example datasets [skip ci]

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Commits on Mar 13, 2023

• Fix test for clonotype convergence

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Commits on Mar 15, 2023

• Experimental: use wrapper class for fixture

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Commits on Mar 16, 2023

• Remove outdated TODO statements

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• Revert "Experimental: use wrapper class for fixture"

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• Implement inplace logic in DataHandler

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• Parametrize fixtures to represent both AnnData and MuData [skip ci]

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• Use DataHandler to write results to obs.

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Commits on Mar 20, 2023

• WIP fix tests

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• Fix _get_colors [skip ci]

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• Fix tests

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• Fix test_get_color

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Commits on Mar 21, 2023

• Implement context managers in get module

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• Fix clustermap

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• Fix normalize in spectratype

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• Tutorial again complete 🎉

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• Fix some open TODOs

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• Add tests for get context managers

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Commits on Mar 23, 2023

• update datasets module

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• Remove function cdr_convergence, which was never publicly documented anyway

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• Update some docstrings

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• remove erroneous import [skip ci]

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Commits on Mar 24, 2023

• WIP update docs

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• Update usage principles and data structure

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Commits on Mar 25, 2023

• Update MuData section [skip ci]

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Commits on Mar 28, 2023

• WIP update IO tutorial

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• Update IO tutorial

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• Update datastructure section with info about single AnnData object

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Commits on Mar 29, 2023

• Update main tutorial

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• Update API docs page

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• Fix docstrings

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• Fix TODOs

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• Fix sphinx warnings

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• update isort

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Commits on Apr 6, 2023

• constrain pandas

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• Pandas workarounds

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• Revert "Pandas workarounds"

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• pandas version

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• Fix problem with color by gene in clonotype_network

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• fix missing import in datasets

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Commits on Apr 7, 2023

• Merge remote-tracking branch 'origin/master' into scverse_datastructure

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• Update dependencies

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