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(feat): SpatialData wrapper #333

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(feat): SpatialData wrapper #333

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Commits on Apr 2, 2024

  1. (refactor): separate out schema creation

    @ilan-gold
    ilan-gold committed Apr 2, 2024
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  2. (feat): initial pass at spatial data

    @ilan-gold
    ilan-gold committed Apr 2, 2024
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  3. (feat): working notebook minus spots (maybe a vitessce bug?)

    @ilan-gold
    ilan-gold committed Apr 2, 2024
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Commits on Apr 3, 2024

  1. (fix): try to get spots to appear

    @ilan-gold
    ilan-gold committed Apr 3, 2024
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  2. (chore): comment out other stuff to make widget show more

    @ilan-gold
    ilan-gold committed Apr 3, 2024
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  3. Fix visium config

    @keller-mark
    keller-mark committed Apr 3, 2024
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Commits on Apr 4, 2024

  1. (feat): firstt pass at from_spatialdata_object

    @ilan-gold
    ilan-gold committed Apr 4, 2024
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Commits on Apr 16, 2024

  1. (refactor): refactor from_spatialdata_object and util funcs from st… 

    …atic methods
    @ilan-gold
    ilan-gold committed Apr 16, 2024
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Commits on Apr 19, 2024

  1. (feat): add url capability

    @ilan-gold
    ilan-gold committed Apr 19, 2024
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Commits on May 6, 2024

  1. (temp): spatial data fixes

    @ilan-gold
    ilan-gold committed May 6, 2024
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Commits on May 7, 2024

  1. Merge branch 'ig/anndata_api_cleanup' into ig/spatial_data

    @ilan-gold
    ilan-gold committed May 7, 2024
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  2. (chore): more clean ups and fixes

    @ilan-gold
    ilan-gold committed May 7, 2024
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  3. Merge branch 'ig/anndata_api_cleanup' into ig/spatial_data

    @ilan-gold
    ilan-gold committed May 7, 2024
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Commits on May 15, 2024

  1. Create module for plugin JS (#337) 

    * Create module for plugin JS

* Add docs

* Lint

* Ignore unused imports
    @keller-mark
    keller-mark authored May 15, 2024
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Commits on May 16, 2024

  1. Merge branch 'ig/anndata_api_cleanup' into ig/spatial_data

    @ilan-gold
    ilan-gold committed May 16, 2024
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  2. (fix): adapt to api

    @ilan-gold
    ilan-gold committed May 16, 2024
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  3. (chore): remove erroneous notebook

    @ilan-gold
    ilan-gold committed May 16, 2024
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Commits on May 24, 2024

  1. (fix): add type support

    @ilan-gold
    ilan-gold committed May 24, 2024
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  2. (chore): add test

    @ilan-gold
    ilan-gold committed May 24, 2024
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  3. (fix): automatic lint

    @ilan-gold
    ilan-gold committed May 24, 2024
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  4. (fix): add default for obsEmbedding

    @ilan-gold
    ilan-gold committed May 24, 2024
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  5. (fix): redefinition

    @ilan-gold
    ilan-gold committed May 24, 2024
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  6. (fix): path and embeddingType swapped

    @ilan-gold
    ilan-gold committed May 24, 2024
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  7. (fix): add annotattions to utils.py

    @ilan-gold
    ilan-gold committed May 24, 2024
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  8. (chore): add spatialdata dep

    @ilan-gold
    ilan-gold committed May 24, 2024
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  9. (fix): oops, comma for toml

    @ilan-gold
    ilan-gold committed May 24, 2024
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  10. (fix): no more python3.8 bc of spatialdata

    @ilan-gold
    ilan-gold committed May 24, 2024
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  11. (fix): remove whitespace

    @ilan-gold
    ilan-gold committed May 24, 2024
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  12. (api): small api cleanups

    @ilan-gold
    ilan-gold committed May 24, 2024
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Commits on May 27, 2024

  1. (fix): args bug

    @ilan-gold
    ilan-gold committed May 27, 2024
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  2. (fix): try spatialdata from master

    @ilan-gold
    ilan-gold committed May 27, 2024
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  3. (chore): lint

    @ilan-gold
    ilan-gold committed May 27, 2024
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Commits on Jun 17, 2024

  1. NickAkhmetov/Cap numpy under v2 (#349) 

    * Cap `numpy` under v2

* bump patch version
    @NickAkhmetov
    NickAkhmetov authored Jun 17, 2024
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Commits on Jun 25, 2024

  1. (chore): try spatialdata update

    @ilan-gold
    ilan-gold committed Jun 25, 2024
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Commits on Jul 19, 2024

  1. NickAkhmetov/Copy requestInit when using from_dict (#352)

    @NickAkhmetov
    NickAkhmetov authored Jul 19, 2024
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Commits on Jul 24, 2024

  1. Plugin class (#350) 

    * WIP: class to encapsulate widget logic

* Potentially working widget things

* Example of chat plugin

* Lint

* Update

* Update
    @keller-mark
    keller-mark authored Jul 24, 2024
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Commits on Jul 29, 2024

  1. Update fill_template.py (#353)

    @keller-mark
    keller-mark authored Jul 29, 2024
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Commits on Aug 2, 2024

  1. Plugin for SpatialQuery (#354) 

    * Spatial-Query plugin and example notebook

* Version

* Widget plugins module

* Update

* Linting

* Lint

* Update comments

* Update docs

* Update
    @keller-mark
    keller-mark authored Aug 2, 2024
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Commits on Aug 31, 2024

  1. Unit test for to_dict output following .add_object(AnnDataWrapper(...… 

    …)) (#357)

* Unit test for anndata wrapper + to_dict

* linting
    @keller-mark
    keller-mark authored Aug 31, 2024
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  2. Misc: Spatial-query, kerchunk, and OME helper functions (#360) 

    * Misc changes

* Bigtiff helper for rgb

* Remove unused import

* Lint

* Unused variables
    @keller-mark
    keller-mark authored Aug 31, 2024
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Commits on Sep 9, 2024

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

    * Update AnnDataWrapper to support h5ad files with ref spec json

* Lint

* Fix tests

* Update
    @keller-mark
    keller-mark authored Sep 9, 2024
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Commits on Sep 11, 2024

  1. Fix binder example (#363) 

    * Fix binder issue

* bump version
    @keller-mark
    keller-mark authored Sep 11, 2024
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Commits on Sep 19, 2024

  1. Fix bug (#367)

    @keller-mark
    keller-mark authored Sep 19, 2024
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Commits on Sep 24, 2024

  1. (fix): image_elem usage + table key

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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  2. (chore): update SpatialData

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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  3. (fix): shapes_elem

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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  4. (fix): capitalize name of obs set

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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  5. (fix): use table for spots

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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  6. (fix): capitalization

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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  7. (fix): first letter only

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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  8. (fix): check self._coordination_values

    @ilan-gold
    ilan-gold committed Sep 24, 2024
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Commits on Oct 2, 2024

  1. Add notebook (#369)

    @keller-mark
    keller-mark authored Oct 2, 2024
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  2. Added utility functions to update and remove a view (#368) 

    * Added utility functions to update and remove a view

* Added tests for the utility functions

* Refactored to multiple functions
    @tkakar
    tkakar authored Oct 2, 2024
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  3. Keller mark/more exports (#370) 

    * Update exports for createPlugins

* Version
    @keller-mark
    keller-mark authored Oct 2, 2024
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Commits on Oct 4, 2024

  1. (chore): add obsSets check

    @ilan-gold
    ilan-gold committed Oct 4, 2024
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  2. Allow passing artifacts as data in addition to paths, urls, and zarr … 

    …stores (#371)

* Register artifacts in wrapper constructors

* Docs

* Add test

* Update

* Version bump

* Lint

* Update is_remote logic

* Update
    @keller-mark
    keller-mark authored Oct 4, 2024
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  3. Merge

    @keller-mark
    keller-mark committed Oct 4, 2024
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Commits on Oct 7, 2024

  1. SpatialData changes into original SpatialData branch (#374) 

    * Try again

* Fix bugs

* Lint

* Update

* Omit
    @keller-mark
    keller-mark authored Oct 7, 2024
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  2. Update pyproject.toml

    @keller-mark
    keller-mark authored Oct 7, 2024
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  3. Keller mark/spatial data2 (#375) 

    * Try again

* Fix bugs

* Lint

* Update

* Omit

* Add test

* JS version
    @keller-mark
    keller-mark authored Oct 7, 2024
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