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Create zarr_consolidate_metadata() - #184

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Bisaloo merged 11 commits into
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consolidated-metadata
May 24, 2026
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Create zarr_consolidate_metadata()#184
Bisaloo merged 11 commits into
develfrom
consolidated-metadata

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@Bisaloo Bisaloo commented May 22, 2026

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TODO:

Related to #116, HelenaLC/spatialdataR#198

Will also be useful for anndataR, as anndata python is moving towards using consolidated metadata for performance.

@Bisaloo Bisaloo linked an issue May 22, 2026 that may be closed by this pull request
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Bisaloo force-pushed the consolidated-metadata branch from 118b71a to 160ffe5 Compare May 24, 2026 12:39
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Bisaloo marked this pull request as ready for review May 24, 2026 12:39
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Bisaloo force-pushed the consolidated-metadata branch from 160ffe5 to 15ca4f4 Compare May 24, 2026 12:55
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This is how benchmark results would change (along with a 95% confidence interval in relative change) if 15ca4f4 is merged into devel:

  • ✔️pkg_load: 219ms -> 219ms [-0.98%, +0.94%]
  • ❗🐌read_blosc_lz4: 231ms -> 232ms [+0.08%, +0.82%]
  • ❗🐌read_boolean: 7.36ms -> 7.48ms [+0.19%, +3.02%]
  • ✔️read_c_order: 13.2ms -> 13.3ms [-0.14%, +0.94%]
  • ✔️read_double: 12.8ms -> 12.8ms [-0.5%, +0.47%]
  • ✔️read_empty: 7.74ms -> 7.76ms [-0.57%, +1.11%]
  • ✔️read_float16: 9.72ms -> 9.71ms [-1.25%, +1.12%]
  • ✔️read_float32: 9.72ms -> 9.65ms [-1.45%, +0.17%]
  • ✔️read_int16: 9.63ms -> 9.67ms [-0.48%, +1.21%]
  • ✔️read_int32: 12.7ms -> 12.7ms [-0.24%, +0.75%]
  • ✔️read_int64: 10.2ms -> 10.2ms [-0.95%, +0.52%]
  • ✔️read_int8: 9.57ms -> 9.68ms [0%, +2.16%]
  • ✔️read_lz4: 7.53ms -> 7.57ms [-0.29%, +1.34%]
  • ✔️read_string: 3.95ms -> 3.92ms [-2.15%, +0.78%]
  • ✔️read_uint32: 11.2ms -> 11.2ms [-0.35%, +1.04%]
  • ✔️read_uint64: 10.1ms -> 10.1ms [-1%, +1.02%]
  • ✔️read_unicode: 3.58ms -> 3.55ms [-3.34%, +1.93%]
  • ✔️read_vlen_utf8: 7.86ms -> 7.88ms [-0.6%, +1.19%]
  • ✔️read_zlib: 7.57ms -> 7.58ms [-0.72%, +0.95%]
  • ✔️read_zstd: 247ms -> 248ms [-0.35%, +1.14%]
  • ✔️write_blosc_lz4: 310ms -> 311ms [-1.76%, +2.48%]
  • ✔️write_bool: 11.4ms -> 11.4ms [-0.67%, +0.51%]
  • ❗🐌write_double: 28.2ms -> 28.6ms [+0.12%, +2.87%]
  • ✔️write_float32: 28.2ms -> 28.4ms [-1.65%, +2.54%]
  • ✔️write_int16: 28.3ms -> 28.6ms [-0.86%, +3.22%]
  • ✔️write_int32: 28.2ms -> 28.2ms [-1.71%, +1.66%]
  • ✔️write_int8: 28.2ms -> 28.6ms [-0.69%, +3.66%]
  • 🚀write_string: 11.1ms -> 11ms [-1.48%, -0.01%]
  • ❗🐌write_unicode: 10.2ms -> 10.3ms [+0.22%, +1.72%]
  • 🚀write_zstd: 762ms -> 754ms [-1.97%, -0.16%]
    Further explanation regarding interpretation and methodology can be found in the documentation.

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Bisaloo merged commit 7ac65fe into devel May 24, 2026
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Bisaloo deleted the consolidated-metadata branch May 24, 2026 13:52
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Add metadata consolidation feature

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