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Author SHA1 Message Date
bkmartinjr
bf3bf58d6e improve launch docs 2019-11-09 13:03:47 -08:00
bkmartinjr
611c8b98b1 add --backed info to troubleshooting 2019-11-09 12:59:33 -08:00
bkmartinjr
d08506ae12 improve install docs 2019-11-09 12:49:22 -08:00
Sidney Bell
9c8c28e1cb Overhaul the whole documentation site 2019-11-07 17:03:33 -08:00
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
Bruce Martin
109c9e70ec Add obs index to label file (#928) 
* remove debug logging

* load and save obs/row index in label file

* lint

* update tests
 2019-09-19 09:16:01 -07:00
Colin Megill
197ea9214a fix italic (#935) 2019-09-18 19:36:49 -04:00
Colin Megill
81e57afe29 Anno fixes (easy) (#925) 
* change wording from value to label

* tooltip position

* Padding for text & code whitespace
 2019-09-18 19:22:51 -04:00
Bruce Martin
3660a6cc27 Experimental - manual annotations (#837) 
* icons, partway

* redux for values

* onChange

* cancel

* annotations lifecycle for category names

* copy categorical

* edit category

* add Dataframe.withColsFrom

* render user annotations; default add/delete annotation category

* add label name to actions

* category name edit

* error checking improvements

* change schema field isUserAnnotation to writable

* always have an unassigned label; implement delete label

* implement add new label and edit label name

* label current cell selection

* fix select exact bug in crossfilter

* clean up categorical reducer

* fix tests

* remove debugging printf

* implement subset/reset for user annotations

* undo redo support for user annotations

* remove duplicate button from categories

* add modal

* remove obsolete duplicate annotation reducers

* remove old debugging printf

* connect modal to annotation create and dup

* initial full-stack wiring

* finish up end-to-end wiring

* fix existing unit tests

* fix pytests to match new schema API

* remove debugging printfs

* add label file rotation

* remove obsolete comment

* add fbs encode/decode tests

* add tests for writable annotations

* simplify code

* fix hashing bug with FBS encoding

* lint

* fix smoke tests

* improve error checking in Dataframe.withColsFrom

* add unit test for Dataframe.withColsFrom

* add unit test for Dataframe.columns and Dataframe.renameCol

* fix bug in FBS encode, add better error checks, refactor

* add FBS encode/decode test

* add clarifying comment

* clean up action type names; fix state inconsistency in crossfilter update

* change autosave timer to 2.5sec

* sort categorical metadata render order so it remains consistent

* add temporary autogenerated label for add-new-label operation

* fix hover-over label menu interference with cell highlighting

* remove debugging code

* add missing reducer cases & fix typo

* make dataframe memoize more general purpose

* add dev mode for annos

* fix error on select duplicate

* handle zero occupancy categories

* correctly maintain unclipped AND clipped world

* correctly handle zero length FBS matrix and label files

* ensure all writable categorical schema contains an unassigned category

* handle case where building occupancy stack for category with no members

* dialog for creating label, disable button if duplicate or empty

* visually separate writeable

* edit category

* fix edit category name

* remove debugging code

* fix edit annotation label

* visually define unassigned, change options

* Pull in requirements.txt from `master`

* label currently selected cells

* duplicate label

* lint

* fix pytest merge issues

* rename --label-file to --experimental-label-file

* remove debugging console log

* spelling error fix; fix bug found in PR review.

* lint
 2019-09-18 07:33:41 -04:00
Bruce Martin
ab2c423006 JS package updates (#922) 2019-09-17 09:36:47 -07:00
Bruce Martin
922c375333 Rename "layout" to "embedding" in the UI (#921) 
* rename "layout" to "embedding" in the UI

* docs changes for layout

* fix typo in data docs

* new help text, per PR review
 2019-09-16 15:34:14 -07:00
Colin Megill
ec4da63408 Format histogram axes: 200,000 --> 200k (#913) 
* remove dead file

* tickformat
 2019-09-16 17:07:51 -04:00
Bruce Martin
20317fd08f Add URL data locators to launch sub-command (#920) 
* initial commit of URL support for launch

* lint

* modify tests to use new data locator

* add locator unit tests

* fix typo in faq

* more lint

* update faq per PR review
 2019-09-15 09:01:53 -07:00
Charlotte Weaver
0f520f2fd4 [Merge on next release] Document how to install cellxgene prepare (#889) 
* Document how to install cellxgene prepare

after pr #887 merged

* formatting

* remove reference to cellxgene[louvain]
 2019-09-13 18:15:06 -07:00
Bruce Martin
84c815cc04 pin h5py to 2.9.0 to temporarily work around regression (#916) 2019-09-11 13:20:15 -07:00
Charlotte Weaver
77de22d1ed merge louvain and prepare extra requires (#897) 2019-08-29 12:49:19 -07:00
Bruce Martin
c35f94fe6d add constraints on pan and zoom-over point (#904) 2019-08-28 17:56:46 -07:00
Bruce Martin
78a43402cb package dep update (#905) 2019-08-28 09:11:10 -07:00
Bruce Martin
b0562a11fd scale point size for graph and scatter plots (#903) 
* scale point size for graph and scatter plots

* improve comments
 2019-08-27 14:12:53 -07:00
Bruce Martin
b309367bb0 Add hover-over highlighting to the scatterplot (#900) 
* small perf improvement - do not recreate functions each time component is updated

* add hover-over highlighting to scatterplot
 2019-08-27 14:01:30 -07:00