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Zarr support#190

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keller-mark wants to merge 31 commits intoscverse:mainscverse/anndataR:mainfrom keller-mark:keller-mark/zarrkeller-mark/anndataR:keller-mark/zarrCopy head branch name to clipboard

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Commits on May 6, 2024

• WIP

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  19698c3

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• More tests passing

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• Fix df read bug

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Commits on May 7, 2024

• More tests passing after fixing zero-dimensional get bug in pizzarr

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• WIP: writing

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• Fix more tests

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• Zarr df writing

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• WIP: ZarrAnnData class

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• Tests passing

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Commits on May 8, 2024

• Tests that compare h5ad to zarr

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Commits on May 17, 2024

• Use Rarr to read full numeric arrays

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Commits on Jun 18, 2024

• Fix bugs. Add test for from_SingleCellExperiment with Zarr

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Commits on Jun 20, 2024

• Add a to_dense param to ZarrAnnData constructor. Add overwrite params internally.

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• Update

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• Backwards dense/sparse

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Commits on Nov 1, 2024

• Merge branch 'keller-mark/zarr' of https://github.com/keller-mark/anndataR into keller-mark/zarr

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• Merge branch 'keller-mark/zarr' into zarr

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• Simplify how obs and var names handled in ZarrAnnData (similar to scverse#171)

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• update extdata and documentation

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Commits on Nov 2, 2024

• fix set/get zarr _index, update text example.zarr and update tests similar to HDF5AnnData

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Commits on Nov 5, 2024

• Merge pull request #5 from Artur-man/zarr

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• Merge

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• Fix test

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• Revert unnecessary changes

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• Formatting

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• Merge pull request #6 from keller-mark/keller-mark/zarr-2

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• Add comments

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• Merge pull request #7 from keller-mark/keller-mark/comments

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Commits on Nov 6, 2024

• remove unnecessary example zarr store

  Artur-man

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• lintr and R check for zarr related utilities and functions, updated some documentation

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• add pizzarr to Suggests and README

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