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Author SHA1 Message Date
Bruce Martin a3df1a9f4a performance and correctness fixes to brushable histogram (#1390) 2020-04-13 20:03:46 -07:00
Bruce Martin 136093d583 add GET routes for expression data (#1387) 
* add GET routes for expression data

* fix comment typo
 2020-04-13 11:28:35 -07:00
Bruce Martin bff5745139 disable SSL cert verification (#1374) 2020-04-10 12:58:51 -07:00
Bruce Martin cfacdb15a8 fix typo (#1379) 2020-04-10 12:58:30 -07:00
Bruce Martin 2d2a7c2108 bump cache control max_age to one week (#1380) 2020-04-10 12:58:09 -07:00
Bruce Martin 61b330b9b0 fix non-finite condition in mean/var calculation (#1381) 2020-04-10 12:52:02 -07:00
Bruce Martin 0398249a20 CXG performance improvements (#1371) 
* initial kv cache

* add per-key locks

* comments

* memoize schema

* add missing initialization

* fix sever timing

* fetch only what is requested

* fix tests to not require strict ordering of columns

* clean up annotation request

* remove debugging print
 2020-04-09 10:19:26 -07:00
Bruce MartinandColin Megill e2a12ba9bb diffexp limit UI and configuration (#1336) 
* warning on maxCount for diffexp

* cleanup logging

* clarification

* make the limits configurable

* make diff exp limit work

* danger!

* remove debugging code

* fix merge with master

* fix unit tests

Co-authored-by: Colin Megill <colinmegill@gmail.com>
 2020-04-09 07:13:41 -07:00
Bruce Martin b466d952f9 add config and init for server timings (#1368) 
* add config and init for server timings

* add missing config error check
 2020-04-07 15:08:57 -07:00
Bruce Martin bcacb75296 load embeddings in parallel (#1352) 
* load embeddings in parallel

* correctly capture unclipped

* test

* another test

* add convenient copy assets target

* cleanup
 2020-04-07 09:48:07 -07:00
Bruce Martin 3b341a7191 add hcl dataset (#1366) 2020-04-07 07:51:32 -07:00
Bruce Martin 6193ae4997 Cleanup front-end build and python module contents (#1350) 
* cleanup build and module contents

* lint

* update chalk

* more cleanup

* fix unit test
 2020-04-06 19:04:06 -07:00
Bruce Martin ffa95b5a55 update s3fs requirements (#1348) 2020-04-05 09:22:32 -07:00
Bruce Martin 0d9f24115c cziscience landing page (#1347) 
* fix dead link in launch page

* first cut at landing page

* wording changes

* add additional refinements

* fixes from PR review
 2020-04-03 16:30:02 -07:00
Bruce Martin de8033e551 correctly handle categoricals that are not strings (#1346) 2020-04-03 15:50:02 -07:00
Bruce Martin 7c56041b11 categorical type handling fix (#1342) 
* fix numeric category conversion bug

* correctly compute categorical summaries

* lint

* remove debugging print
 2020-04-02 14:44:07 -07:00
Bruce Martin fa0164fdf6 use no-store cache control (#1337) 2020-04-02 09:20:35 -07:00
Bruce Martin c2a24ae0c6 add cache control headers (#1333) 
* add cache control headers

* add config param check
 2020-04-01 15:43:43 -07:00
Bruce Martin 33ce95ba09 work-around for column name encoding bug (#1324) 
* add attribute cleanup

* fix typo

* handle mappings

* logging

* fix regex

* remove debugging printfs

* update masked characters

* fix typo

* add missing incr
 2020-04-01 15:06:21 -07:00
Bruce Martin 708a5af039 Add fetch concurrency limit on obs annotation loading (#1318) 
* add fetch concurrency limit

* add tests for PromiseLimit
 2020-03-30 16:23:09 -07:00
Bruce Martin d4ec976aaa update locust routes to match new server URL structure (#1321) 2020-03-30 15:09:45 -07:00
Bruce MartinandColin Megill c8f98917c5 tos prompt (#1313) 
* tos toast

* finish ToS prompt

Co-authored-by: Colin Megill <colinmegill@gmail.com>
 2020-03-28 22:31:19 -07:00
Bruce Martin 8fac40b6ae various fixes for s3fs use (#1312) 
* various fixes for s3fs use

* lint
 2020-03-28 22:26:03 -07:00
Bruce Martin a398f85ccc turn off auto-reload in debug mode (#1301) 2020-03-26 13:34:56 -07:00
Bruce Martin 57938b487b remove static route redirects / bump static to top level (#1299) 
* add another favicon rule

* catch only top-level dataset names

* add config flag to disable redirects

* remove static redirect, point all links to top-level /static

* remove extraneous argument

* remove httpd redirect
 2020-03-26 10:45:10 -07:00
Bruce Martin 26605049a4 Various hardening to REST routes (#1293) 
* URL reweriting for static

* request size limits

* improve quotas, make tests work

* remove debugging code

* pass limits to front-end

* fix renaming boggle
 2020-03-25 16:14:52 -07:00
Bruce Martin 674f14f9bd harden dataset name handling (#1297) 2020-03-25 15:37:06 -07:00
Bruce Martin 752b9e4ab3 CORS and CSP headers (#1286) 
* do in-app compression only for CLI

* CORS and CSP headers

* lint

* add --debug to targets

* lint

* fix botched merge with master
 2020-03-24 08:05:37 -07:00
Bruce Martin d196cbc8f6 do in-app compression only for CLI (#1285) 2020-03-24 06:36:40 -07:00
Bruce Martin 96b092f0eb fix health root exception (#1283) 
* fix health root exception

* remove extraneous lambda
 2020-03-23 15:13:32 -07:00
Bruce MartinandMatt Weiden d99b84ba09 prepare - work around anndata bug (#1260) 
* work around anndata bug 344

* fix accidental cut and paste error

* Use modified make_index_unique function

Temporarily copy code from https://github.com/theislab/anndata/pull/345
until the issue is resolved and released.

* Add notes and test for make_index_unique

* Lint fix

* Format python

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
 2020-03-22 12:27:59 -07:00
Bruce Martin db7a485796 tighten up error reporting (#1269) 
* black reformat

* tighten up error reporting

* lint

* fine tuning

* additional improvements in exception handling

* lint

* include exception and traceback in log

* fix typo
 2020-03-22 09:55:47 -07:00
Bruce Martin 1351c8f724 restrict methods on all endpoints (#1271) 
* restrict methods on all endpoints

* lint
 2020-03-22 08:23:28 -07:00
Bruce Martin de006f8f91 initial implementation of a health check route (#1262) 
* initial implementation of a health check route

* remove debugging code

* lint
 2020-03-20 14:21:32 -07:00
Bruce Martin 040dbd3a95 refine load test (#1257) 2020-03-20 14:09:12 -07:00
Bruce Martin 8f09a4b1bc JS package fixes (#1248) 
* Remove accidental package install from build

* remove accidental package install
 2020-03-18 19:00:28 -07:00
Bruce Martin 38c4ecac8c locust load test script (#1244) 
* initial version of a locustfile driver

* README
 2020-03-18 11:27:07 -07:00
Bruce Martin 1e8d89f8f2 refinements for 0.15 (#1226) 2020-03-13 16:30:47 -07:00
Bruce Martin 9bc83fdd02 update contributor process recommendations (#1213) 
* update contrib process recommendations

* fix typos

* clarification

* fix build instructions

* updates suggested by Matt

* fix dead link
 2020-03-13 11:41:30 -07:00
Bruce Martin f28bd52d79 fix performance regression caused by excessive rendering (#1219) 2020-03-12 15:05:08 -07:00
Bruce Martin 63f1f38f7c use AnchorButton so the tooltip dismisses (#1217) 2020-03-12 08:36:36 -07:00
Bruce Martin 8beeb57c96 Use DataLocator consistently on backend (#1208) 
* allow DataLocator to accept another locator as init param

* migrate to DataLocator

* migrate to DataLocator

* lint

* migrate to DataLocator

* add check for erroroneous use of remote path and annotations

* lint

* revert default data location - now back go CWD

* remove unused import
 2020-03-10 19:12:49 -07:00
Bruce Martin 28ddb60b2f update JS deps (#1203) 2020-03-10 10:59:12 -07:00
Bruce Martin ffdcc24a40 remove pinned tables dependency (#1202) 2020-03-10 07:47:54 -07:00
Bruce Martin 144b19c449 experimental re-embedding (#1186) 
* first cut at re-embedding route and back-end support

* update and expand config route tests

* add scanpy_umap

* add reembedding to config route parameters

* front-end support for reembedding fetch and UI

* remove unused imports

* add loading state

* save reembedding in reducer state

* improve withColsFrom

* transmit reembed schema to client; pick unique embedding names

* display embeddings

* format

* lint

* spaces, tab size 2

* lint

* test hack for smoke-test race

* back out hack sleep

* add check for backed mode

* add unit test for reembedding

* lint

* hide re-embedding CLI param from help
 2020-03-09 16:53:30 -07:00
Bruce Martin bf7d7342d5 Improve label picking (#1179) 
* add simple error message helper

* port all label name pickers to use the new LabelInput component

* use pure components where possible

* cleanup

* more cleanup

* lint

* change new label prompt
 2020-02-28 15:46:40 -07:00
Bruce Martin 7bc58bba2b undo/redo cleanup (#1165) 
* fix refactoring error which disabled annotation file clearing

* fix undo behavior on add category label

* fix various undo/redo bugs

* remove logging

* further refinement of annotation undo/redo and actions

* address PR comment
 2020-02-24 18:51:26 -07:00
Bruce Martin fb1f0c6469 fix latent crossfilter bug (#1162) 2020-02-21 14:14:41 -07:00
Bruce Martin d2bae0c4f6 CXG creator and dataset parameters (#1163) 
* remove redundant call to make_response (lint)

* initial commit of H5AD to CXG converter

* lint

* PR review suggested comments

* cxg adaptor now understands group metadata

* lint
 2020-02-21 12:49:45 -07:00
Bruce Martin 349c413d8b anndata X indexing & version compatibility improvements (#1157) 
* revert MatrixProxy; replace with correct use of adata slicing

* work around 0.6 adata slicing bug

* fix incorrect var slice

* simplify slicing of X

* add warning about performance impact of anndata<=0.7

* lint and remove unused code

* improve comment

* lint

* correctly parse versions

* temp files should preserve file suffix if possible - anndata 0.7 compat

* update anndata dependency to 0.6.20

* resolve PR review comments
 2020-02-19 09:57:51 -07:00
Bruce Martin e770db1e2c load annotations incrementally (#1107) 
* load annotations individually

* fix type check to be more general

* update node CI version from 10 to 12

* node 11

* debug print node version

* travis node version to latest

* try nvm

* remove extraneous node_js statement

* remove node version debugging printf

* incrementally load all annotations and layout

* process annotations and layout as they are loaded

* fix tests

* sort categories incrementally

* incrementally build category view summary; add category loading spinner

* add spinner to continuous metadata

* configure undoable reducer

* incremental crossfilter creation

* improve busy layout

* more layout cleanup

* correctly reconcile categories in schema

* refine layout of lsb spinners

* more spinner layout work

* more spinner layout

* always load layout before obs annotations
 2020-02-10 11:22:27 -08:00
Bruce Martin 1c9b9f6a08 js package dep update (#1145) 
* js package dep update

* roll back start-server-and-test
 2020-02-05 13:11:05 -08:00
Bruce Martin 3afc03b95b fix state prop bug with camera transform (#1138) 2020-01-31 12:13:35 -08:00
Bruce Martin 69c639b14d pin anndata to 0.6.22post1 (#1122) 2020-01-22 13:23:05 -08:00
Bruce Martin 431c8bdabc disable magic nan parsing in read_csv (#1115) 2020-01-17 09:26:15 -08:00
Bruce Martin 8b329630f8 fix for issue 1112 - all user annotation category names must be unique across all obs annotatoins (#1114) 2020-01-16 09:28:29 -08:00
Bruce Martin 30f3ce49e4 update JS dependencies (#1106) 2020-01-15 17:11:51 -08:00
Bruce Martin 677433bbf5 Fix label sorting bugs (#1102) 
* move category label sort to utils

* refactor cat label sort

* fix category label sort and color assignment

* convert whitespace from tabs to spaces
 2020-01-09 13:34:25 -08:00
Bruce Martin 2d39cb3b30 sort the embedding names for the UI (#1098) 2020-01-09 06:33:14 -08:00
Bruce Martin 18177b108f fix 1090 - add unassigned label to the new category, not the source category (#1094) 2020-01-09 06:32:38 -08:00
Bruce Martin dfaf0d0603 allow hyphen in annotation file name (#1074) 
* remove old detritus

* allow hyphen in label file name
 2020-01-02 15:44:40 -08:00
Bruce Martin 6370025caf update all JS package deps (#1076) 
* update dependencies - minor revisions

* update min node_js version to 10

* major npm package dep updates

* a few more updates
 2020-01-02 09:14:09 -08:00
Bruce Martin c9b6044c4f release 0.13.0 (#1064) 2019-11-26 15:45:13 -08:00
Bruce Martin fa89a5a375 create annotations output dir if it does not exist (#1062) 
* create annotations output dir if it doees not exist

* lint
 2019-11-26 13:35:20 -08:00
Bruce Martin f8cef71eed help text changes (#1061) 
* requested CLI help changes for launch sub-command

* update file name prose

* more wording changes

* more PR requests
 2019-11-26 13:35:01 -08:00
Bruce Martin d2171b9a2f fix perf regression introduced by user anno changes (#1060) 2019-11-25 18:16:49 -08:00
Bruce Martin a593e95ab3 annotations CLI and file UX rework (#1049) 
* rename config param label-file

* annotations rework - CLI params, file naming and backups

* lint

* improve cli option error checks

* enable session cookies

* enable session cookies

* add session id

* name annotations file in multi-dataset and multi-user safe manner

* pass data user hash to front-end

* add annotation collection name support to front-end

* add constant for annotation data collection name

* parameterize annotation collection name; make it sticky in the session

* clarify comments

* hard wire a temporary data collection name for testing

* prettier

* test comment

* package command

* set annotations  filename dialog

* name  and hash are visible

* wire up data collection capture
 2019-11-25 15:28:28 -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
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
bkmartinjr 0415c30f0b add security notice to readme 2019-11-20 10:42:27 -08:00
bkmartinjr 79e534e397 additional caveats/warnings for hosting 2019-11-20 10:40:00 -08:00
bkmartinjr f4919340e9 merge 2019-11-20 10:33:17 -08:00
bkmartinjr 976f9d9ff8 add hosting notes 2019-11-20 10:28:40 -08:00
Bruce Martin 9a540a4f0a fix erroneous state clearing (#1052) 2019-11-19 11:11:19 -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
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
bkmartinjr 54d144bb75 add build dependencies for igraph and louvain 2019-11-12 07:56:03 -08:00
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
Bruce Martin 238b7420f7 update deprecated Pandas API (#1021) 
* update use of deprecated API

* update pandas depencency
 2019-11-08 09:49:52 -08:00
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
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
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) 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
Bruce Martin de6721b682 fix broken link (#978) 2019-10-07 11:08:18 -07:00
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
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
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
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