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Use zarrita rather than zarr.js #1680

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Use zarrita rather than zarr.js #1680

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keller-mark
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@keller-mark keller-mark commented Sep 11, 2023

Fixes #

Background

  • SpatialData examples contain arrays of <i8 integers. ZarrJS does not support these Support BigInt64Array gzuidhof/zarr.js#143
  • Zarr v3 is coming and zarrita supports this
  • ZarrJS has a large bundle size, in part due to support for writing, which we do not need. Zarrita is tree-shakeable.
  • Zarrita supports decoding string arrays stored as vlen-utf8, so we can get rid of that code here
  • ZarrJS does not support unicode string arrays with dtype like <U7
  • ZarrJS does not support zero-dimensional array access (e.g., scalar value stored as Zarr with shape [])

Change List

TODO

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github-actions bot commented Sep 11, 2023

Size Change: +874 kB (+8%) 🔍

Total Size: 12.5 MB

Filename Size Change
./packages/main/prod/dist/hglib-********.js 4.33 MB -2.76 kB (0%)
./packages/main/prod/dist/blosc-********.js 448 kB +448 kB (new file) 🆕
./packages/main/prod/dist/lz4-********.js 51.1 kB +51.1 kB (new file) 🆕
./packages/main/prod/dist/pako.esm-856454b6-********.js 69 kB +69 kB (new file) 🆕
./packages/main/prod/dist/zstd-********.js 308 kB +308 kB (new file) 🆕
ℹ️ View Unchanged
Filename Size Change
./packages/main/prod/dist/deflate-********.js 243 B 0 B
./packages/main/prod/dist/index-********.js 7.15 MB -352 B (0%)
./packages/main/prod/dist/index.min.js 726 B 0 B
./packages/main/prod/dist/jpeg-********.js 15.3 kB 0 B
./packages/main/prod/dist/lerc-********.js 47.2 kB -18 B (0%)
./packages/main/prod/dist/lzw-********.js 2.1 kB 0 B
./packages/main/prod/dist/packbits-********.js 576 B 0 B
./packages/main/prod/dist/pako.esm-********.js 68.6 kB 0 B
./packages/main/prod/dist/raw-********.js 168 B 0 B
./packages/main/prod/dist/webimage-********.js 836 B -36 B (-4%)
./packages/main/prod/dist/gzip-********.js 517 B +517 B (new file) 🆕
./packages/main/prod/dist/zlib-********.js 523 B +523 B (new file) 🆕

compressed-size-action

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github-actions bot commented Sep 11, 2023

Coverage Report

Status Category Percentage Covered / Total
🔵 Lines 75.58% 10356 / 13701
🔵 Statements 75.58% 10356 / 13701
🔵 Functions 62.6% 288 / 460
🔵 Branches 79.05% 951 / 1203
File Coverage
File Stmts % Branch % Funcs % Lines Uncovered Lines
Changed Files
packages/file-types/zarr/src/AnnDataSource.js 80.89% 77.77% 75% 80.89% 23-24, 38-41, 48-49, 51-52, 80-84, 100-104, 145-146, 157-158, 168-177
packages/file-types/zarr/src/ZarrDataSource.js 100% 50% 100% 100%
packages/file-types/zarr/src/anndata-loaders/ObsFeatureMatrixAnndataLoader.js 75.45% 84.21% 73.68% 75.45% 15-27, 49-50, 53, 68-72, 112-113, 138-139, 180-181, 214-215, 249-250, 273-296, 340-350, 353-366, 369-382
Generated in workflow #3220

@keller-mark keller-mark marked this pull request as ready for review September 12, 2023 00:08
@keller-mark keller-mark mentioned this pull request Sep 12, 2023
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@manzt
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manzt commented Sep 17, 2023

Cool! Want to chat this week about the zarrita TODOs? I can take a stab at improving these

@keller-mark keller-mark mentioned this pull request Sep 17, 2023
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@keller-mark keller-mark marked this pull request as draft September 17, 2023 16:00
@keller-mark
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@manzt yes! Will follow up on slack

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2 participants