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Author SHA1 Message Date
Bruce Martin 9420abfacc add Babel support for JS optioning chaining and nullish coallescing operators (#664) 2019-03-22 14:51:51 -07:00
Sidney Bell 16f93397ae Support diffmap and phate layouts. Explicitly handle embeddings with >2 components. (#662) 
* Add diffmap and phate to supported embeddings

* Explicitly pull the first two components of any given layout
 2019-03-21 19:06:05 -07:00
Colin Megill 016a4a422a Procedurally resize brush (#650) 
* add on brush end event

* brush snap move

* resize brush
 2019-03-20 14:46:20 -07:00
Bruce Martin 996b06cecc refactoring - immutable crossfilter (#647) 
* immutable crossfilter

* PR review changes
 2019-03-20 14:32:35 -07:00
Bruce Martin 571b7387e7 remove dead code from globals (#651) 2019-03-19 06:22:39 -07:00
Charlotte Weaver b6d468376a py37 fixes (#646) 
* add python version for nightly build

* update numpy version required

older versions interact poorly on anaconda + python 3.7
 2019-03-14 14:51:55 -07:00
Charlotte Weaver d8fc7e40a1 Support python3.7 (#645) 
* Support python3.7

* add 3.7 env to travis
 2019-03-14 12:08:46 -07:00
Charlotte Weaver e875ed739b More informative out-of-memory error (#644) 
* more informative error message: memory error

* flake fix
 2019-03-12 14:19:00 -07:00
Bruce Martin aa5ce4a2f1 correctly toggle group selection in categorical metadata (#640) 2019-03-12 10:49:29 -07:00
Bruce Martin 80969012c9 do not reset color scale when dismissing scatterplot (#637) 2019-03-12 10:49:01 -07:00
Bruce Martin caaee7e9bf do not reset color-by when subsetting world (#636) 
* do not reset colors when subsetting to world

* revert diffexp state change
 2019-03-12 10:48:35 -07:00
Charlotte Weaver f96fd36ecb Update test ui names (#638) 
* Fixed changed testid

* Added debug mode for running tests
 2019-03-12 10:17:09 -07:00
Bruce Martin 495dc55144 remove obsolete URL middleware (#639) 2019-03-11 16:03:33 -07:00
Colin Megill 8795f0f32c Add test ids and classes (#633) 
* data test ids and classes

* suggest
 2019-03-07 13:01:41 -08:00
Colin Megill a0f54b4871 Add menu (#631) 
* add menu

* Added library versions to config

and tests

* add template version number
 2019-03-06 11:56:46 -05:00
Charlotte Weaver 68dfbcc2eb Add force graph to docs and example dataset (#630) 2019-03-05 20:59:54 -08:00
Alex Wolf 82493d1019 Add forced directed graph drawing to allowed layout options (#626) 
* added forced directed graph drawing layout options

* added line breaks for 120 character limit
 2019-03-05 13:10:07 -08:00
Bruce Martin 3d6df0c044 implement improved disable/enable of Reset UI (#628) 2019-03-05 08:38:55 -08:00
Charlotte Weaver 2583016693 Fix bug where prod would automatically run after release stage 2 (#625) 
* Fix bug where prod would automatically run after release stage 2

* fixed make release-burned
 2019-03-01 20:20:16 -08:00
Bruce Martin d8e3721846 bumpversion to 0.7.0 (#623) 0.7.0 2019-03-01 12:25:30 -08:00
Bruce Martin a876740a3c create helper file for controls reducer (#615) 
* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions

* add Dataframe withCol/dropCol

* expression varData now stored in a dataframe

* dead code cleanup

* use dataframe.summarize()

* test cases for Dataframe.col.summarize

* update test cases for new dataframe summarize

* improve naming

* use new hasCol API

* add comments

* add more Dataframe.withCol tests

* add ability to specify row index in cut operation

* retire subsetVarData function

* correctly handle expression subsetting

* lint and improve comments

* rename cut to subset

* create helper file for controls reducer
 2019-02-28 09:21:19 -08:00
Bruce Martin e7ad6f5d1c [WIP DO NOT MERGE] correctly display graph legend for negative continuous metadata (#620) 
correctly display graph legend for negative continuous metadata
 2019-02-28 09:08:19 -08:00
Bruce Martin 2f1facaafb [WIP DO NOT MERGE] suppress display of continous annotation without a finite extent (#618) 
* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions

* add Dataframe withCol/dropCol

* expression varData now stored in a dataframe

* dead code cleanup

* use dataframe.summarize()

* test cases for Dataframe.col.summarize

* update test cases for new dataframe summarize

* improve naming

* use new hasCol API

* add comments

* add more Dataframe.withCol tests

* add ability to specify row index in cut operation

* retire subsetVarData function

* correctly handle expression subsetting

* lint and improve comments

* rename cut to subset

* suppress display of continous annotation withont a finite extent

* fix botched merge

* more fix of botched merged
 2019-02-28 09:05:48 -08:00
Bruce Martin ffd6273419 Dataframe, part deux - add varData and summarize() (#608) 
* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions

* add Dataframe withCol/dropCol

* expression varData now stored in a dataframe

* dead code cleanup

* use dataframe.summarize()

* test cases for Dataframe.col.summarize

* update test cases for new dataframe summarize

* improve naming

* use new hasCol API

* add comments

* add more Dataframe.withCol tests

* add ability to specify row index in cut operation

* retire subsetVarData function

* correctly handle expression subsetting

* lint and improve comments

* rename cut to subset

* changes based on PR review
 2019-02-28 08:34:22 -08:00
Charlotte Weaver 2bae696986 Smoke tests (#604) 
smoke tests
 2019-02-27 15:46:58 -08:00
Bruce Martin 6b33315cbe Dataframe (#576) 
* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions
 2019-02-22 11:31:34 -08:00
Bruce Martin 57c4e9ff33 Flatbuffer cleanup (#598) 
* dead code and route removal

* more dead code cleanup

* fix scanpy_engine tests

* lint

* add missing catch in filter parsing

* update scanpy NaN tests

* more fbs tests and dead test removal

* remove forced default for content type negotiation

* bit of cleanup

* more fbs test cleanup

* lint

* remove swagger

* swagger cleanup

* lint

* correctly handle lack of templates

* more dead code removal

* remove unused files

* fix dev build

* lint
 2019-02-19 08:50:29 -08:00
Charlotte Weaver 4e67c645f8 bumped version (#602) 
0.6.0 was burned on pypi
0.6.1 		2019-02-14 10:00:16 -08:00
Charlotte Weaver 8b28d51dfa bump version (#601) 0.6.0 2019-02-13 16:29:14 -08:00
Charlotte Weaver 40ad283107 create server testing doc (#592) 2019-02-13 15:35:45 -08:00
Isaac Virshup 0f8d7a55de Set API path based on access address (#568) 
* Make api paths relative

* Remove request import

* Set publicPath to be relative
 2019-02-11 09:01:37 -08:00
Sidney Bell b6f946ec8a Add note about installing hdf5 to FAQ (#581) 2019-02-08 14:56:16 -08:00
Colin Megill dbb3a309a9 Lasso (#586) 
* lasso working

* break out invert into own function

* action

* add spatial dimension to crossfilter, in support of polygon lasso

* improve comments on new dimension API

* lasso vs zoom
 2019-02-08 11:48:51 -08:00
Bruce Martin 2e9525741f doc divergence warning (#591) 2019-02-08 11:00:51 -08:00
Charlotte Weaver 585a5808b9 check if accept type in content type string (#589) 2019-02-08 09:41:24 -08:00
Bruce Martin 6f464f4f92 package dependency updates (#585) 
* lint

* update dev-related package dependencies
 2019-02-06 12:57:09 -08:00
Colin Megill 08ea7d5137 Better input validation (#580) 2019-02-05 10:44:59 -05:00
Charlotte Weaver ad9be3cdd7 remove build-dev from .gitignore (#583) 2019-02-04 14:47:28 -08:00
Charlotte Weaver f737cc4ee4 Build improvements (#577) 2019-02-04 14:15:35 -08:00
Charlotte Weaver 1103272b95 De-dupe -d CLI option alias (#575) 
removed from debug, diffexp gets to keep it
 2019-01-30 16:11:21 -08:00
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
fionagriffin 07db2eb3ee Update data.md (#544) 2019-01-29 10:31:31 -08:00
Justin Kiggins a6d2a2e119 updates link to scanpy recipe docs. fixes #564 (#565) 2019-01-28 10:00:29 -08:00
Justin Kiggins f87e4bfbd3 home page fix (#551) 
* explicit site.url in config

* infra for custom css

* moves home item to html layout

* adds baseurl to site config
 2019-01-28 09:13:09 -08:00
Charlotte Weaver ecaa32cfb2 bump version (#563) 0.5.1 2019-01-17 17:14:44 -08:00
Charlotte Weaver 10693b08cc Add __init__ file so fbs can be imported (#562) 2019-01-17 17:11:31 -08:00
Charlotte Weaver b02361a6bf bump version (#560) 0.5.0 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