Commit Graph

934 Commits

Author SHA1 Message Date
Sidney Bell
9bcafeb7c1 [WIP] Overhaul the documentation site (#1030)
Overhaul the whole documentation site
2019-11-22 14:54:20 -08:00
Bruce Martin
5713aa8792 category and label name validation updates (#1056)
* update label validation with new schema

* add new error messages for new label errors; general cleanup
2019-11-22 10:32:00 -08:00
Severiano Badajoz
9aaaad6709 tweak allotted width for value name + occupancy and tweak truncating (#1051) 2019-11-21 20:14:11 -08:00
Colin Megill
c2ededfc62 Anno editing label/category error states (#1048)
* anno error states

* label validation should not treat empty string as error

* disable Submit if no label or category entered

* edit category name error states

* flex start

* pr cleanup

* label name validation fixes

* PR comment responses
2019-11-21 19:08:29 -05:00
Bruce Martin
ee62dd355f [WIP] JS lint and dead code removal (#1053)
* lint and dead code removal

* fix regressions
2019-11-21 14:10:02 -08:00
Bruce Martin
9a540a4f0a fix erroneous state clearing (#1052) 2019-11-19 11:11:19 -08:00
Severiano Badajoz
5968da18b4 fix inconsistent sidebar value height(#1039) 2019-11-18 12:43:16 -08:00
Severiano Badajoz
bd5f816d58 fix dataset title clipping (#1040) 2019-11-18 12:42:55 -08:00
Severiano Badajoz
cf8f1a710d add padding to scatterplot shift (#1043) 2019-11-18 12:41:58 -08:00
Bruce Martin
2d0b646956 js dependency update (#1045) 2019-11-18 11:22:13 -08:00
Bruce Martin
b284e6f820 Improve CLI help (#1025)
* launch option changes

* more CLI help improvements

* change plot help

* additional changes requested

* change metavars for options and subcommand
2019-11-14 13:02:40 -08:00
Bruce Martin
5ea9ac8a9e Add provenance header to labels CSV file (#1041)
* add last mod time lookup to data locator

* store data locator in Driver

* save metadata header in labels csv

* lint

* fix tests

* change datetime format to second precision
2019-11-14 12:33:48 -08:00
Colin Megill
89d748b007 state (#1032) 2019-11-13 15:13:15 -05:00
Severiano Badajoz
68ad4b1228 bump @blueprintjs dependencies (#1038) 2019-11-13 11:56:48 -08:00
Bruce Martin
a52e86a69b improve category and label name validation (#1034) 2019-11-13 09:40:37 -08:00
Bruce Martin
04c83993d2 clear color-by mode when current category is deleted (#1033) 2019-11-12 15:31:06 -08:00
Bruce Martin
238b7420f7 update deprecated Pandas API (#1021)
* update use of deprecated API

* update pandas depencency
2019-11-08 09:49:52 -08:00
Colin Megill
cadf710bf8 remove duplicate handler (#1027) 2019-11-08 11:18:29 -05:00
Colin Megill
84900bad0e Warnings on anno textfields (#1023)
*  Warning for creating new label with an existing name

* category dup

* italics
2019-11-07 18:57:15 -05:00
Colin Megill
4c3d783fc8 Continuous data in right sidebar (#985)
* Create right sidebar files, move histos over

* restructure continuous legend + all padding

* right sidebar file

* proper graph positioning and resize

* new lasso values since right sidebar

* fix autosave position
2019-11-05 20:29:21 -05:00
Bruce Martin
461084eca1 Pin the 'unassigned' annotation value/label to bottom of list (#1018)
* pin unassigned label to bottom of category list

* pin unassigned label to bottom of category list
2019-11-05 09:22:39 -08:00
Bruce Martin
341d3015f0 fix typo (#1016) 2019-11-05 09:21:48 -08:00
Prete
6a95d956a9 Update Dockerfile (#1019)
Added python-requests package to the Dockerfile so cellxgene can use URLs as a data source.
2019-11-05 08:57:29 -08:00
Bruce Martin
7599af451f add context sensitivity to annotation "label" menu item (#1015)
* cache common results to reduce jank

* add util function in support of annotation labelling

* enable/disable annotation edit menus per issue 972; improve formatting

* PR review requests
2019-11-04 14:22:38 -08:00
Bruce Martin
823d819eee allow user to save an empty label dataframe (#1012) 2019-11-04 14:14:49 -08:00
Bruce Martin
a16c2e2747 crossfilter immutability error (#1009)
* add rename immutability test

* make rename immutable
2019-11-04 14:14:17 -08:00
Colin Megill
e50fd8b881 Animate list items on name change (#1008)
* animate list items

* fix comment
2019-11-04 14:09:16 -05:00
Charlotte Weaver
3e61bb807d e2e testing documentation (#1000) 2019-11-03 10:56:28 -08:00
dependabot[bot]
345e2c344b Bump lodash.template from 4.4.0 to 4.5.0 in /client (#1002)
Bumps [lodash.template](https://github.com/lodash/lodash) from 4.4.0 to 4.5.0.
- [Release notes](https://github.com/lodash/lodash/releases)
- [Commits](https://github.com/lodash/lodash/compare/4.4.0...4.5.0)

Signed-off-by: dependabot[bot] <support@github.com>
2019-11-03 10:56:04 -08:00
Colin Megill
3f0567c59f disable editing if already editing (#999) 2019-10-31 13:46:59 -04:00
Colin Megill
934f61f2a1 categoryAddingNewLabel (#995) 2019-10-24 22:02:38 -04:00
Bruce Martin
60a23b681c QOL documentation: csweaver contributions from PR #912 (#977)
* csweaver changes from PR #912

* fix formatting error
2019-10-24 08:44:36 -07:00
Bruce Martin
e581dec8f5 release 0.12.0 (#981) 0.12.0 2019-10-08 12:34:21 -07:00
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
Colin Megill
1467357db5 re-label (#973) 2019-10-07 16:02:09 -04:00
Bruce Martin
de6721b682 fix broken link (#978) 2019-10-07 11:08:18 -07:00
Colin Megill
296352b620 remove modal for inline edit category name, and autofocus (#962)
* remove modal for inline edit category name, and autofocus

* remove comment, rename to categorybeingedited
2019-10-04 13:41:05 -04:00
Bruce Martin
3f2811d9da rendering performance improvements (#968)
* freeze objects

* component rendering perf work

* use PureComponent where safe

* remove obsolete WorldUtil code

* make brushable histogram a pure component
2019-10-04 07:59:22 -07:00
Bruce Martin
700c871e6d reduce dot scaling upon zoom (#963)
* remove obsolete code

* change point scaling with zoom distance
2019-10-04 07:58:38 -07:00
Severiano Badajoz
f865187a5d fix long values in sidebar (#911)
* tweak overflow and add truncation

* remove log

* alter char limit to evenly space around occupancy

* use global hover delay

* create constants for truncation lengths and fix truncation on self color

* create globals for short and long sidebar value length

* fix alignment

* create quick delay global
2019-10-02 11:01:22 -07:00
Bruce Martin
ad290b3630 scale scatterplot point rendering size with overall app size, not scatterplot canvas size (#956) 2019-10-01 12:25:21 -07:00
Bruce Martin
21218f1c59 update contact and core team metadata (#947)
* update contact and core team metadata

* fix spelling error
2019-10-01 10:26:38 -07:00
Sidney Bell
f41f47cf1b Fix mistakenly removed badges (oops) (#955)
* Fix mistakenly removed badges (oops)

* Update README.md

Co-Authored-By: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
2019-09-30 16:00:29 -07:00
Severiano Badajoz
d94508d534 fix bulk add failing on first gene in world (#954) 2019-09-30 15:21:21 -07:00
Severiano Badajoz
44cb276cdf Add configurable about this dataset links (#907)
* add about arg

* add simple url validator

* attach about link to config api

* add links to configDefaults

* add conditional link in top left and menu item

* whitespace

* change to lower case

* move --about arg before click.command()

if this fixes it I have no idea why

* change link>URL

* be more descriptive about URL

* Make error more explicit

* refactor attach_data to accept about

* format

* change icon

* add trailing parenthesis

* whitespace
2019-09-25 19:23:49 -07:00
Colin Megill
e64f4f06fb enter submits modals (#945) 2019-09-25 15:18:33 -07:00
Severiano Badajoz
32feb36172 better handle long dataset titles (#909)
* truncate middle of long title names

* remove width

* In the case of VERY long titles, hide overflow

* align bottom of title with cellxgene

* add character length global and shrink length
2019-09-23 16:31:54 -07:00
Severiano Badajoz
c983e878e9 fix incorrect gene add error on empty query (#910)
* fix add gene button

* make bulk add case insensitive

* increase performance, incl memoizing

* change which lists are memoized

* improve hash to use ID from dataframe column

* Add requested fixes, and actually make bulk add work

* add default result to empty gene query

* replace with unicode ellipses

* change empty message
2019-09-23 16:31:07 -07:00
Severiano Badajoz
077541c762 fix bugs surrounding gene adding (#919)
* fix add gene button

* make bulk add case insensitive

* increase performance, incl memoizing

* change which lists are memoized

* improve hash to use ID from dataframe column

* Add requested fixes, and actually make bulk add work
2019-09-23 16:30:53 -07:00
Bruce Martin
3d15db7c5e parameterize pbmc3k scanpy engine test (#939) 2019-09-20 17:41:32 -07:00