Commit Graph

758 Commits

Author SHA1 Message Date
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
Charlotte Weaver
394da40bea Doc formatting improvements (#549) 2019-01-10 15:09:02 -08:00
Bruce Martin
5d60505407 remove --nan-to-num CLI parameter (#548)
* remove --nan-to-num CLI parameter

* factor tests better

* lint - remove unused variables
2019-01-10 15:03:03 -08:00
Colin Megill
f876a0091a Set theme jekyll-theme-cayman 2019-01-10 12:12:58 -05:00
Colin Megill
528eb5d172 Set theme jekyll-theme-minimal 2019-01-10 12:10:11 -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
Justin Kiggins
eceab377f7 cleans up landing page (#541) 2019-01-04 14:20:23 -08:00