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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

+2,805-6

Commits

Commits on May 6, 2024

• WIP

  keller-mark

  committed
  19698c3

• More tests passing

  keller-mark

  committed
  5100a40

• Fix df read bug

  keller-mark

  committed
  4c9d01f

Commits on May 7, 2024

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

  keller-mark

  committed
  eb8b69c

• WIP: writing

  keller-mark

  committed
  58f5ce4

• Fix more tests

  keller-mark

  committed
  a15513a

• Zarr df writing

  keller-mark

  committed
  1ef1be6

• WIP: ZarrAnnData class

  keller-mark

  committed
  77a7ee2

• Tests passing

  keller-mark

  committed
  27ce6c1

Commits on May 8, 2024

• Tests that compare h5ad to zarr

  keller-mark

  committed
  8790715

Commits on May 17, 2024

• Use Rarr to read full numeric arrays

  keller-mark

  committed
  bb0c6c7

Commits on Jun 18, 2024

• Fix bugs. Add test for from_SingleCellExperiment with Zarr

  keller-mark

  committed
  0456ecd

Commits on Jun 20, 2024

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

  keller-mark

  committed
  acac772

• Update

  keller-mark

  committed
  30316ed

• Backwards dense/sparse

  keller-mark

  committed
  c6b4d89

Commits on Nov 1, 2024

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

  Artur-man

  committed
  9cadc26

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

  Artur-man

  committed
  a40a618

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

  Artur-man

  committed
  1afd6eb

• update extdata and documentation

  Artur-man

  committed
  7f53049

Commits on Nov 2, 2024

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

  Artur-man

  committed
  3800f38

Commits on Nov 5, 2024

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

  Show description for 4a7d4c2
  keller-mark

  authored
  4a7d4c2

• Merge

  keller-mark

  committed
  c881bb9

• Fix test

  keller-mark

  committed
  4a1bbde

• Revert unnecessary changes

  keller-mark

  committed
  15dfbde

• Formatting

  keller-mark

  committed
  438809a

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

  Show description for 2215402
  keller-mark

  authored
  2215402

• Add comments

  keller-mark

  committed
  087ffb7

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

  Show description for 37d1ae5
  keller-mark

  authored
  37d1ae5

Commits on Nov 6, 2024

• remove unnecessary example zarr store

  Artur-man

  committed
  357a8d7

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

  Artur-man

  committed
  d192e68

• add pizzarr to Suggests and README

  Artur-man

  committed
  1e0e868