(feat): SpatialData wrapper
#333
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* Create module for plugin JS * Add docs * Lint * Ignore unused imports
5 tasks
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@keller-mark Fixing notebook, apologies |
…)) (#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
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@keller-mark The only thing happening here is the |
* 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
Merged
* 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]>
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This is a first pass at a
SpatialDatawrapper.Complete #331 for
SpatialDatavia a static method (my preferred solution for 331).Some todos: