Keller mark/spatial data2 #375
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keller-mark
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Oct 15, 2024
* (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 <ilanbassgold@gmail.com>
keller-mark
added a commit
that referenced
this pull request
Oct 15, 2024
* (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 * Fix spatialdata nb --------- Co-authored-by: ilan-gold <ilanbassgold@gmail.com>
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