Commit Graph

149 Commits

Author SHA1 Message Date
Colin Megill
2df7161cd8 Bulk add genes (#567)
* bulk add

* cleanup
2019-01-29 16:26:09 -05:00
Charlotte Weaver
d31c05c970 Add backed script to package.json (#566)
* QOL script for FE devs to get & launch the backend

* ensure python3.6

* changed name to backend-dev
2019-01-29 11:41:05 -08:00
Charlotte Weaver
ecaa32cfb2 bump version (#563) 2019-01-17 17:14:44 -08:00
Charlotte Weaver
b02361a6bf bump version (#560) 2019-01-17 16:54:25 -08:00
Colin Megill
3fa888c6d4 user defined gene sets scatterplot, remove works (#556) 2019-01-16 03:37:08 -05:00
Colin Megill
a42c9aca1c resetting interface spinner but locked interface (#555) 2019-01-16 03:36:35 -05:00
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
Colin Megill
42e25a1a1f Async on long running operations (#543)
* compute differential button

* add user gene loading state to reducer

* create input group, consume usergeneloading

* add loading state
2019-01-07 16:45:47 -05:00
Colin Megill
b0daeb3a9b disable cell set buttons (#538) 2019-01-03 20:05:09 -05:00
Bruce Martin
cfcf16aa69 [DO NOT MERGE] performance improvements in color-by feature (#535)
performance improvements in color-by feature
2018-12-27 14:05:49 -08:00
Colin Megill
a297ea30e2 bump version (#518) 2018-12-17 14:30:34 -05:00
Colin Megill
0ef6c36f4c Cluster Occupancy (n dim cube) (#513)
* create occupancy component

* occupancy working

* centering, width, flex spacing

* add is-number

* extend sort to cover string + int

* proof of concept sorted occupancy

* handle undefined occupancy entry, cleanup

* only render occupancy when colorby is cat

* cleanup unused vars

* cleanup
2018-12-17 14:19:48 -05:00
Bruce Martin
95fd20b405 bump version to 0.3 (#498) 2018-12-05 14:35:17 -08:00
Bruce Martin
3bfeadc2b9 improve handling of non-finite floating point values (#490)
* improve HTTP error reporting

* generate standards-compatible JSON

* add --nan-to-num work-around for non-finite floating point values

* lint

* update tests

* correctly set Infinities to min/max

* REAMDE update for --nan-to-num

* define constant for repetitive warning message

* clarify where NaN errors will occure
2018-12-04 14:56:16 -08:00
Bruce Martin
296ed752fa Improved summary counts of annotation values (#478)
* convert annotation summary to a Map

* add 2d annotation count summary

* add memoization on 2D annotation counting

* add tests for annotation summarization

* fix import/exports

* rename WorldOps to WorldUtil

* rename WorldOps to WorldUtil

* add comment
2018-12-03 09:15:03 -08:00
Bruce Martin
af0d1f6fb2 issue #480 workaround (#484)
* only load annotation var names

* remove incorrect usage of var annotation data

* temporary workaround for issue #480

* lint

* issue warnings only once per item
2018-11-29 16:33:21 -08:00
Colin Megill
00b9a8fa72 Fuzzy search on genes (#473)
* proof of concept blueprint typeahead

* poc with fuzzysearch lib

* typeahead adds gene on enter

* add gene on menu click

* typeahead clears correctly

* cleanup
2018-11-28 09:50:02 -08:00
Charlotte Weaver
28f5263c88 bump version (#475) 2018-11-27 15:43:19 -08:00
Bruce Martin
933fac5fff Allow float64 to down-cast to float32 (#472)
* warn if annotations will down-cast to float32

* correctly handle falsey data values
2018-11-27 11:17:30 -08:00
Charlotte Weaver
0c26f227fe bump version (#470) 2018-11-26 15:38:47 -08:00
Charlotte Weaver
f2612707bb bumped version (#466) 2018-11-26 11:42:56 -08:00
Bruce Martin
138d30909a improve type handling for non-string annotation data (#465)
* improve type handling for non-string annotation data

* improve clarity of code
2018-11-26 10:32:29 -08:00
Charlotte Weaver
2b5094665f version 0.2.0 (#456) 2018-11-16 15:12:54 -08:00
Jeremy Freeman
dff2526077 warm to cool (#454) 2018-11-16 14:33:32 -08:00
Colin Megill
ef80c8df2a Change color scales to rainbow (#449)
* rainbow

* eslint

* remove comments
2018-11-15 18:17:55 -08:00
Charlotte Weaver
1a5f49239a Release 0.0.4 (#447)
* 0.0.3 bump

* release 0.0.4
2018-11-15 16:43:59 -08:00
Bruce Martin
00a68276a2 diffexp performance & UX improvements (#431)
* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments
2018-11-14 12:51:24 -08:00
Charlotte Weaver
bc0cecbd1c Release Test (#427)
* bump-update

* Release Test!
2018-11-14 11:03:52 -08:00
Colin Megill
dbff824854 Viewport fills entire screen (#430)
* full pane webgl and svg

* fixes for full pane selection and centering

* force graph remount, clear brush state
2018-11-13 11:45:38 -05:00
Colin Megill
9decf134e0 fixed scatterplot infinite render (#429)
* add more to state from componentDidMount

* always brush

* destructure

* move render to function

* fixed scatterplot infinite render

* remove logging
2018-11-09 20:28:22 -05:00
Bruce Martin
6916aec6c3 update package dependencies (#417) 2018-11-07 13:58:21 -08:00
Bruce Martin
9f7e1f1cb0 use quicksort instead of default system sort (#413) 2018-11-07 13:35:00 -08:00
Bruce Martin
2d5bc9d0c9 Performance work, plus fix #405 (#406)
* remove memoization

* update to flash 1.0.2; turn on threading

* stand-alone helper routines for array slicing

* fix issue #405

* reset diffexp state when world changes

* performance work in dimension creation; fix world slicing bug

* update tests to match new state mgmt api

* update flask

* do not make dimensions for useless annotations

* update test to match optimizations
2018-11-05 13:57:58 -08:00
Colin Megill
0dcc17d6d5 rerender axes on regraph (#403)
* remove cells loading now that we have toast

* rerender histogram axes

* remove logging
2018-11-05 09:29:49 -05:00
Bruce Martin
6e46a65c32 fix add gene action format bug (#398) 2018-11-01 14:24:49 -07:00
Bruce Martin
9d7754e31e Improve front-end HTTP error handling (#397)
* UI for HTTP error handing in diffexp route

* HTTP error handling for other routes

* clean up toasters
2018-10-30 19:02:11 -07:00
Bruce Martin
bc15e9229f update config params to match REST API spec (#393) 2018-10-30 11:03:40 -07:00
Colin Megill
ed66ae6e4a tooltips, copy, scatterplot tray (#383)
* tooltips, copy, scatterplot tray

* reset interface

* copy
2018-10-26 19:21:39 -04:00
Colin Megill
d221d76be6 test for world, graph border, legend label (#378)
* test for world, graph border, legend label

* typo
2018-10-25 12:16:55 -04:00
Colin Megill
7aa390b5a1 left sidebar improvements (#368)
* left sidebar improvements

* lint
2018-10-24 10:21:18 -04:00
Colin Megill
96675f806c hotfix duplicate globals declaration 2018-10-22 16:39:41 -04:00
Colin Megill
df671192be Begin integrating blueprint (#359)
* toast test

* modify webpack build to allow for global CSS; use CSS modules to scope component styling

* remove heatmap

* add label to index resets

* swapping out buttons for blueprint

* adding constants to globals

* swapping out blueprint buttons

* title position, sidebar improvements

* sidebar styles

* adding toasts for validation errors

* zebra section trial

* integrating blueprint, switching buttons over, breaking out scatter

* clean up console
2018-10-22 15:46:37 -04:00
Bruce Martin
0c271bc815 categorical metadata performance work (#356)
* do not create unecessary option state for categories we will not display

* performance improvements for categorical metadata handling
2018-10-22 09:56:41 -07:00
Bruce Martin
5dea303bcd handle case of excessively large number of options in categorical met… (#350)
* handle case of excessively large number of options in categorical metadata
* move max category options count into globals
2018-10-18 18:07:39 -07:00
Bruce Martin
2616b5c185 finish tests for world (#340)
* Create Release_Validation_Recipe.md

* nameCreators test and better error handling

* add test for createObsDimensionMap

* add last set of tests for world module
2018-10-18 09:54:57 -07:00
Bruce Martin
f9f43c42c0 more lint - components (#336)
* more lint

* fix typo introduced in delinting

* more lint

* remove dead code

* lint fixes

* lint
2018-10-17 07:17:51 -07:00
Colin Megill
952578680a Remove heatmap, add diffexp info to histograms (#339)
* Create Release_Validation_Recipe.md

* compose middle ware for redux devtools

* update package.json and lock

* remove heatmap, add to left side bar

* redux devtools extension
2018-10-16 16:29:20 -07:00
Bruce Martin
76ec29734a Performance work (#334)
* range encode filter range lists

* speed up data load

* add comment on scanpy read params

* update to latest scanpy/anndata

* performance improvments in data loading

* fix typo

* work around scanpy bug

* remove debugging print statements
2018-10-16 15:49:40 -07:00
Bruce Martin
6b0aafd27c package dependency cleanup (#330)
* update npm packages.  babel 7, redux 4, etc

* remove obsolete babel config file

* use correct icons
2018-10-15 17:36:13 -07:00
Colin Megill
65f5244ff7 add name getter to world test 2018-10-15 11:20:52 -07:00