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(feat): SpatialData wrapper#333

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ilan-gold wants to merge 63 commits intoig/anndata_api_cleanupvitessce/vitessce-python:ig/anndata_api_cleanupfrom ig/spatial_datavitessce/vitessce-python:ig/spatial_dataCopy head branch name to clipboard

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Commits

Commits on Apr 2, 2024

• (refactor): separate out schema creation

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• (feat): initial pass at spatial data

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• (feat): working notebook minus spots (maybe a vitessce bug?)

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Commits on Apr 3, 2024

• (fix): try to get spots to appear

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• (chore): comment out other stuff to make widget show more

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• Fix visium config

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Commits on Apr 4, 2024

• (feat): firstt pass at from_spatialdata_object

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Commits on Apr 16, 2024

• (refactor): refactor from_spatialdata_object and util funcs from static methods

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Commits on Apr 19, 2024

• (feat): add url capability

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Commits on May 6, 2024

• (temp): spatial data fixes

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Commits on May 7, 2024

• Merge branch 'ig/anndata_api_cleanup' into ig/spatial_data

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• (chore): more clean ups and fixes

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• Merge branch 'ig/anndata_api_cleanup' into ig/spatial_data

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Commits on May 15, 2024

• Create module for plugin JS (#337)

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Commits on May 16, 2024

• Merge branch 'ig/anndata_api_cleanup' into ig/spatial_data

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• (fix): adapt to api

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• (chore): remove erroneous notebook

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Commits on May 24, 2024

• (fix): add type support

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• (chore): add test

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• (fix): automatic lint

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• (fix): add default for obsEmbedding

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• (fix): redefinition

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• (fix): path and embeddingType swapped

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• (fix): add annotattions to utils.py

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• (chore): add spatialdata dep

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• (fix): oops, comma for toml

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• (fix): no more python3.8 bc of spatialdata

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• (fix): remove whitespace

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• (api): small api cleanups

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Commits on May 27, 2024

• (fix): args bug

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• (fix): try spatialdata from master

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• (chore): lint

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Commits on Jun 17, 2024

• NickAkhmetov/Cap numpy under v2 (#349)

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Commits on Jun 25, 2024

• (chore): try spatialdata update

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Commits on Jul 19, 2024

• NickAkhmetov/Copy requestInit when using from_dict (#352)

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Commits on Jul 24, 2024

• Plugin class (#350)

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Commits on Jul 29, 2024

• Update fill_template.py (#353)

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Commits on Aug 2, 2024

• Plugin for SpatialQuery (#354)

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Commits on Aug 31, 2024

• Unit test for to_dict output following .add_object(AnnDataWrapper(...)) (#357)

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• Misc: Spatial-query, kerchunk, and OME helper functions (#360)

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Commits on Sep 9, 2024

• Support for H5AD-based AnnData in AnnDataWrapper (#361)

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Commits on Sep 11, 2024

• Fix binder example (#363)

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Commits on Sep 19, 2024

• Fix bug (#367)

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Commits on Sep 24, 2024

• (fix): image_elem usage + table key

  ilan-gold

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• (chore): update SpatialData

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• (fix): shapes_elem

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• (fix): capitalize name of obs set

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• (fix): use table for spots

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• (fix): capitalization

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• (fix): first letter only

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• (fix): check self._coordination_values

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Commits on Oct 2, 2024

• Add notebook (#369)

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• Added utility functions to update and remove a view (#368)

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• Keller mark/more exports (#370)

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Commits on Oct 4, 2024

• (chore): add obsSets check

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• Allow passing artifacts as data in addition to paths, urls, and zarr stores (#371)

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• Merge

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Commits on Oct 7, 2024

• SpatialData changes into original SpatialData branch (#374)

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• Update pyproject.toml

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• Keller mark/spatial data2 (#375)

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Commits on Oct 15, 2024

• SpatialDataWrapper v2 (#373)

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• Fix spatialdata nb

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• Merge branch 'main' into ig/spatial_data

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