7 Commits

Author	SHA1	Message	Date
Bruce Martin	5ea9ac8a9e	Add provenance header to labels CSV file (#1041) ... * add last mod time lookup to data locator * store data locator in Driver * save metadata header in labels csv * lint * fix tests * change datetime format to second precision	2019-11-14 12:33:48 -08:00
Bruce Martin	711f3b7048	Add support for anndata backed mode (#943) ... * 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) ... * 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) ... * 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) ... * 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) ... * 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