Bruce Martin
711f3b7048
Add support for anndata backed mode ( #943 )
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* initial cut at backed mode
* make flask multithreading conditional on debug flag
* update X access to support backed mode
* lint
* improve help message for backed mode
* fix tests
* add MatrixProxy to normalize supported matrix types
* add FAQ entry for --backed
* remove use of matrix.T
* clean up
* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user
* fix tests
* do not print diffexp speed warning if diffexp is disabled
* tweak wording of diffexp speed messages
* add FAQ entry on --disable-diffexp
* revise heuristic for warning about slow diffexp
* use quick tooltip delay on diffexp button
2019-10-08 11:16:07 -07:00
Bruce Martin
3660a6cc27
Experimental - manual annotations ( #837 )
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* icons, partway
* redux for values
* onChange
* cancel
* annotations lifecycle for category names
* copy categorical
* edit category
* add Dataframe.withColsFrom
* render user annotations; default add/delete annotation category
* add label name to actions
* category name edit
* error checking improvements
* change schema field isUserAnnotation to writable
* always have an unassigned label; implement delete label
* implement add new label and edit label name
* label current cell selection
* fix select exact bug in crossfilter
* clean up categorical reducer
* fix tests
* remove debugging printf
* implement subset/reset for user annotations
* undo redo support for user annotations
* remove duplicate button from categories
* add modal
* remove obsolete duplicate annotation reducers
* remove old debugging printf
* connect modal to annotation create and dup
* initial full-stack wiring
* finish up end-to-end wiring
* fix existing unit tests
* fix pytests to match new schema API
* remove debugging printfs
* add label file rotation
* remove obsolete comment
* add fbs encode/decode tests
* add tests for writable annotations
* simplify code
* fix hashing bug with FBS encoding
* lint
* fix smoke tests
* improve error checking in Dataframe.withColsFrom
* add unit test for Dataframe.withColsFrom
* add unit test for Dataframe.columns and Dataframe.renameCol
* fix bug in FBS encode, add better error checks, refactor
* add FBS encode/decode test
* add clarifying comment
* clean up action type names; fix state inconsistency in crossfilter update
* change autosave timer to 2.5sec
* sort categorical metadata render order so it remains consistent
* add temporary autogenerated label for add-new-label operation
* fix hover-over label menu interference with cell highlighting
* remove debugging code
* add missing reducer cases & fix typo
* make dataframe memoize more general purpose
* add dev mode for annos
* fix error on select duplicate
* handle zero occupancy categories
* correctly maintain unclipped AND clipped world
* correctly handle zero length FBS matrix and label files
* ensure all writable categorical schema contains an unassigned category
* handle case where building occupancy stack for category with no members
* dialog for creating label, disable button if duplicate or empty
* visually separate writeable
* edit category
* fix edit category name
* remove debugging code
* fix edit annotation label
* visually define unassigned, change options
* Pull in requirements.txt from `master`
* label currently selected cells
* duplicate label
* lint
* fix pytest merge issues
* rename --label-file to --experimental-label-file
* remove debugging console log
* spelling error fix; fix bug found in PR review.
* lint
2019-09-18 07:33:41 -04:00
Bruce Martin
20317fd08f
Add URL data locators to launch sub-command ( #920 )
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* initial commit of URL support for launch
* lint
* modify tests to use new data locator
* add locator unit tests
* fix typo in faq
* more lint
* update faq per PR review
2019-09-15 09:01:53 -07:00
Charlotte Weaver
5effe4bbbb
removed --diffexp cli param ( #826 )
2019-06-26 14:46:58 -07:00
Bruce Martin
efa1709158
add multi-layout support to back-end ( #766 )
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* add multi-layout support to back-end
* remove obsolete code
* temporary code to apply heuristic choice of default layout
* fix tests
* update python tests
* more py lint
* PR review changes
* more PR lint
* PR lint
2019-05-16 14:49:22 -07:00
Charlotte Weaver
9c6273eb94
core library ( #711 )
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* move app creation to function
* create engine without load
* flake 8 fixes
* cleanup original scanpy test
* add default config
* handle missing data
* test data changes
* unify update
* load data isn't static anymore
* make app a class
2019-04-22 12:24:07 -07:00
