Commit Graph

623 Commits

Author SHA1 Message Date
Jeremy Freeman
75ca14e4aa add CLI tool for dataset preparation using scanpy (#364)
* add prepare cli

* fix handling of user path

* fixes for linter

* add flags and options for handling obs and var names

* add prepare cli

* fix handling of user path

* fixes for linter

* add flags and options for handling obs and var names

* address review requests
2018-10-26 16:44:41 -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
Charlotte Weaver
6c23a72e5f CLI renaming and phrasing (#385)
* Minor naming and phrasing changes from UX review

* category-selection-limit -> max-category-items
* Indicate load may taking a long time
* program -> command (for launch, prepare)
* debug -> verbose
* flask-debug -> debug

* Developer mode for debug

verbose on
open browser off

* move examples from epilogue to prefix
2018-10-26 15:59:34 -07:00
Charlotte Weaver
16b0741a6c Hide stack traces unless in debug mode (#384) 2018-10-26 13:36:53 -07:00
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
Charlotte Weaver
94f95d6565 CLI Launch (#366)
* Scanpy engine now required

Without the --engine param we need to error if scanpy engine cannot be imported rather than waiting for all engines

* CLI options and help matches proposal

(but not all options hooked up yet)

* Flesh out top level args

* Move computation args to engine

* CLI input file (#374)

* Fix test command

(tests still won't work)

* Input is file instead of directory
- also renamed example file

* Csweaver/debug (#376)

* Respect debug flag for logging flask calls

* Add loading messages

* max categories (#377)

* Add max categories

* Rename max_categories to category_selection_limit

* ensure whole numbers
2018-10-24 19:28:59 -07:00
Charlotte Weaver
02b2349807 Pin scikit-learn to fix imp error (#375) 2018-10-24 14:46:34 -07:00
Charlotte Weaver
9e5114a730 Ignore built media files (#372) 2018-10-24 13:02:17 -07:00
Charlotte Weaver
85f44ccabf Converts NaNs in pval to 1s (#365) 2018-10-24 10:57:29 -07:00
Colin Megill
7aa390b5a1 left sidebar improvements (#368)
* left sidebar improvements

* lint
2018-10-24 10:21:18 -04:00
Bruce Martin
3556bd11f5 fix lint (#369) 2018-10-24 07:12:51 -07:00
Charlotte Weaver
4ec938c166 Prefix client build (#367) 2018-10-23 15:56:57 -07:00
Bruce Martin
b74c9e15c6 build fixes (#362)
* add production web build to travis tests

* remove old builds before starting new build
2018-10-22 13:54:11 -07:00
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
Charlotte Weaver
efb55a6332 Renaming bind-all option to listen-all (#353)
See discussion here https://docs.google.com/document/d/1tcAvODhdlUUAOJPHoGQB3fWOPmnw3XjK7MVhDRwNUnk/edit#
2018-10-19 15:26:19 -07:00
Charlotte Weaver
2a3577f32b flask debug as hidden option (#352)
* Remove flask debug flag

* Add debug flag as a hidden option to keep reload on change for developers
2018-10-19 10:24:15 -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
Charlotte Weaver
06f402ab0a Do not calculate layout, used saved layout instead (#343)
* Do not calculate layout, used saved layout instead

See for rationale: https://docs.google.com/document/d/1HJFvbdDHxxgkCW0DZzdTZ9CUMgc2ef2rQFukATBQWvE/edit

* Error handling for when layout has not been precomputed

* Server error (500) not client error (400) for unprepared data
2018-10-18 11:51:38 -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
fionagriffin
f33a3cd1a3 Create Release_Validation_Recipe.md (#337) 2018-10-18 09:27:32 -07:00
Charlotte Weaver
7c8b89eba3 Launch browser to cellxgene (#325)
* Launch browser to cellxgene

Also added  --no-launch command line parameter

* Don't launch browser for tests

* rename no-launch to no-open

* Rejigger -no-open to positive destination

so later logic looks cleaner
2018-10-17 16:46:56 -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
Colin Megill
e7642e6a8f remove log 2018-10-15 11:20:52 -07:00
Colin Megill
8114d7565a dispose and delete 2018-10-15 11:20:52 -07:00
Colin Megill
8e08534d42 user defined gene 2018-10-15 11:20:52 -07:00
Colin Megill
2b77f8146b namespacing 2018-10-15 11:20:52 -07:00
Colin Megill
e1a437514e clean up log 2018-10-15 11:20:52 -07:00
Colin Megill
48fa221ad9 diffexp, regraph, brush 2018-10-15 11:20:52 -07:00
Colin Megill
fff331e1f0 stub additional validation for gene name 2018-10-15 11:20:52 -07:00
Colin Megill
8d07b400be adding and removing user defined genes 2018-10-15 11:20:52 -07:00
Colin Megill
5b2c07f105 clear differential reducer 2018-10-15 11:20:52 -07:00
Colin Megill
ca35ae0b40 cleanup in histogram 2018-10-15 11:20:52 -07:00
Colin Megill
1cf9fc76b0 break out differential genes from user defined 2018-10-15 11:20:52 -07:00
Colin Megill
a42f9f83f5 clear differential expression button interface 2018-10-15 11:20:52 -07:00
Colin Megill
9de44e6fd4 clear differential expression reducer 2018-10-15 11:20:52 -07:00
Colin Megill
ca37483447 remove old heatmap webgl code 2018-10-15 11:20:52 -07:00
Colin Megill
dd1b9229fc access varDataCache with kvCache.get 2018-10-15 11:20:52 -07:00
Colin Megill
73f55cb9f8 obs index to index 2018-10-15 11:20:52 -07:00
Colin Megill
8aa75458ed brushable histogram renders genes 2018-10-15 11:20:52 -07:00
Colin Megill
0c8f4ed824 rename to createVarDimension 2018-10-15 11:20:52 -07:00
Colin Megill
5165297e2a position tweak 2018-10-15 11:20:52 -07:00
Colin Megill
9c8e0e76ad remove export 2018-10-15 11:20:52 -07:00
Colin Megill
693dc7be12 switch to roboto condensed for space 2018-10-15 11:20:52 -07:00
Colin Megill
090bad040e worldIndex returns NaN 2018-10-15 11:20:52 -07:00