fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-24 02:18:11 +08:00
Code Issues Packages Projects Releases Wiki Activity
919 Commits 22 Branches 50 Tags
bf3bf58d6e8f48dc92afcd0e02bdf3e8189b28fc
Commit Graph
4 Commits
Author SHA1 Message Date
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
Charlotte Weaver 10693b08cc Add __init__ file so fbs can be imported (#562) 2019-01-17 17:11:31 -08:00
Bruce Martin b90447c387 binary wire format with flatbuffers (#509) 
* first flatbuffer schema

* do not lint auto-generated files

* add flatbuffers package

* add flatbuffer module

* wire up /data/X/T route

* use flatbuffers for matrix data fetc

* clarity and comments

* add flatbuffer layout route

* clean up obsolete code

* fix tests

* move flake8 config to setup.cfg

* add comments

* lint

* rework layout routes for fbs

* add more type support to fbs

* lint

* add flatbuffer support for annotations

* function name improvements

* fix botched merge with master

* remove unused import

* route cleanup for flatbuffers

* rename function for clarity

* add missing globals to Jest tests

* fix client JS tests

* fix routes for Python tests

* comments for clarity

* non-finite floating point hardening

* more non-finite number handling

* lint

* fix tests for summarizeAnnotations

* harden diffexp calculation against FP errors

* cleanup unused code

* lint

* add encoding tests for flatbuffers

* application type specified as strings

* fix spelling error

* improve variable names

* add note about documentation gap

* rename FBS DataFrame to Matrix
 2019-01-09 14:26:05 -08:00