…atic methods

* Create module for plugin JS

* Add docs

* Lint

* Ignore unused imports

* Cap `numpy` under v2

* bump patch version

* WIP: class to encapsulate widget logic

* Potentially working widget things

* Example of chat plugin

* Lint

* Update

* Update

* Spatial-Query plugin and example notebook

* Version

* Widget plugins module

* Update

* Linting

* Lint

* Update comments

* Update docs

* Update

…)) (#357)

* Unit test for anndata wrapper + to_dict

* linting

* Misc changes

* Bigtiff helper for rgb

* Remove unused import

* Lint

* Unused variables

* Update AnnDataWrapper to support h5ad files with ref spec json

* Lint

* Fix tests

* Update

* Fix binder issue

* bump version

* Added utility functions to update and remove a view

* Added tests for the utility functions

* Refactored to multiple functions

* Update exports for createPlugins

* Version

…stores (#371)

* Register artifacts in wrapper constructors

* Docs

* Add test

* Update

* Version bump

* Lint

* Update is_remote logic

* Update

* Try again

* Fix bugs

* Lint

* Update

* Omit

* Try again

* Fix bugs

* Lint

* Update

* Omit

* Add test

* JS version

* (refactor): separate out schema creation

* (feat): initial pass at spatial data

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

* (fix): try to get spots to appear

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

* Fix visium config

* (feat): firstt pass at `from_spatialdata_object`

* (refactor): refactor `from_spatialdata_object` and util funcs from static methods

* (feat): add url capability

* (temp): spatial data fixes

* (chore): change variable names

* (chore): fix notebooks

* (refactor): `path`->`elem`

* (chore): more clean ups and fixes

* (refactor): small name changes

* (refactor): revert public changes

* (fix): revert `.ipynb` files

* (chore): fix last final args

* (fix): name

* (fix): remove `request_init` completely and fix `setup.cfg`

* (fix): adapt to api

* (chore): remove erroneous notebook

* (fix): add type support

* (chore): add test

* (fix): automatic lint

* (fix): add default for `obsEmbedding`

* (fix): redefinition

* (fix): `path` and `embeddingType` swapped

* (fix): add annotattions to `utils.py`

* (chore): add `spatialdata` dep

* (fix): oops, comma for `toml`

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

* (fix): remove whitespace

* (api): small api cleanups

* (fix): args bug

* (fix): try spatialdata from master

* (chore): lint

* (chore): try `spatialdata` update

* (fix): `image_elem` usage + table key

* (chore): update SpatialData

* (fix): `shapes_elem`

* (fix): capitalize name of obs set

* (fix): use table for spots

* (fix): capitalization

* (fix): first letter only

* (fix): check `self._coordination_values`

* (chore): add `obsSets` check

* SpatialData changes into original SpatialData branch (#374)

* Try again

* Fix bugs

* Lint

* Update

* Omit

* Update pyproject.toml

* Keller mark/spatial data2 (#375)

* Try again

* Fix bugs

* Lint

* Update

* Omit

* Add test

* JS version

---------

Co-authored-by: ilan-gold <[email protected]>