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Author SHA1 Message Date
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
Colin Megill
b0daeb3a9b disable cell set buttons (#538) 2019-01-03 20:05:09 -05:00
fionagriffin
7499fca251 add datasets to data.md (#540) 
added links and general info for interesting example datasets to use with cellxgene
 2019-01-03 16:35:37 -08:00
GenevieveHaliburton
05a5a945bb Landing page faq comments (#536) 
* add to faq, clean up titles

* h4 headings for readibility

* Ordering, add section on errors
 2019-01-03 14:07:38 -08:00
Colin Megill
d3c96087b2 Add GIFs to docs (#537) 
* Add gif files

* rename gif for clarity

* add gifs

* reorder

* resize
 2019-01-03 15:24:33 -05:00
Bruce Martin
cfcf16aa69 [DO NOT MERGE] performance improvements in color-by feature (#535) 
performance improvements in color-by feature
 2018-12-27 14:05:49 -08:00
Justin Kiggins
bc59074300 new docs (#525) 
* new docs

* moves development docs to dev_docs
 2018-12-20 14:28:05 -08:00
Colin Megill
56f9bc543e Set theme jekyll-theme-minimal 2018-12-20 12:05:08 -05:00
James Taylor
f2eb2cad82 Use url_root from Flask rather than hardcoding hostname. (#520) 
Allows running in a container on a remote host, should also allow running
behind a proxy with a url prefix.
 2018-12-19 16:20:26 -08:00
Justin Kiggins
bd523280a4 improved quickstart (#523) 2018-12-19 13:38:30 -08:00
Justin Kiggins
fc45fb3899 creates FAQ page in docs (#522) 
* creates FAQ page

* revise index.md

* tweaks
 2018-12-19 13:18:16 -08:00
Charlotte Weaver
f0f7200f0b Move jsonification to engine level (#511) 2018-12-18 21:14:24 -08:00
fionagriffin
6af7708d62 update index.md (#519) 
ready for features
 2018-12-18 11:10:29 -05:00
Colin Megill
a297ea30e2 bump version (#518) 0.4.0 2018-12-17 14:30:34 -05:00
Colin Megill
0ef6c36f4c Cluster Occupancy (n dim cube) (#513) 
* create occupancy component

* occupancy working

* centering, width, flex spacing

* add is-number

* extend sort to cover string + int

* proof of concept sorted occupancy

* handle undefined occupancy entry, cleanup

* only render occupancy when colorby is cat

* cleanup unused vars

* cleanup
 2018-12-17 14:19:48 -05:00
Justin Kiggins
aaa60bc303 new signup url (#516) 2018-12-14 16:32:41 -08:00
fionagriffin
7d40d89fd8 Update index.md (#507) 
Added content from readme
 2018-12-14 15:19:21 -08:00
Charlotte Weaver
46ad346df1 Clarify that we do not support python 3.7 (#512) 
* Update setup.py

* Readme: no python 3.7

* specify 3.6 in venv

* clarify 3.7 error

we will support it eventually
 2018-12-13 15:15:56 -08:00
Charlotte Weaver
83154577e4 Black -- formatter for python (#508) 
* Add black

* use black to format code

* Black version
 2018-12-12 09:44:47 -08:00
Charlotte Weaver
a847951658 Update slack link (#506) 2018-12-11 10:20:22 -08:00
Charlotte Weaver
24af6efbcb Add Docker file (#505) 
* Add docker support

* Add readme

* minor fixes
 2018-12-11 10:18:10 -08:00
Colin Megill
126cac833a Rename README.md to index.md 2018-12-11 12:09:16 -05:00
Colin Megill
fc272dc42e github pages test 2018-12-11 12:05:14 -05:00
Colin Megill
d3a0d66139 Set theme jekyll-theme-architect 2018-12-10 18:16:40 -05:00
Charlotte Weaver
9604231a2a Add alternative to install [louvain] extra requires (#500) 
* louvain install by hand

* reworded
 2018-12-10 14:46:55 -08:00
Jeremy Freeman
6ea3b7f3cf use collapsable details to improve FAQ formatting (#503) 2018-12-07 21:07:57 +01:00
Charlotte Weaver
0d0a32f272 Added PR guidelines (#492) 
* Added PR guidelines

Added document to cover guidelines for creating, reviewing and merging PRs.

* fixed typo

* another typo

* grammar

* Remove 5's title

The subheading is clearer as a top-level
 2018-12-06 13:43:10 -08:00
Bruce Martin
48e0ea542b clarifications to release recipe (#499) 
* clarifications to release recipe

* fix spelling errors
 2018-12-05 16:58:53 -08:00
Bruce Martin
95fd20b405 bump version to 0.3 (#498) 0.3.0 2018-12-05 14:35:17 -08:00
Charlotte Weaver
5c6cc597c8 Default warning in debug mode (#497) 2018-12-05 13:38:34 -08:00
Bruce Martin
3bfeadc2b9 improve handling of non-finite floating point values (#490) 
* improve HTTP error reporting

* generate standards-compatible JSON

* add --nan-to-num work-around for non-finite floating point values

* lint

* update tests

* correctly set Infinities to min/max

* REAMDE update for --nan-to-num

* define constant for repetitive warning message

* clarify where NaN errors will occure
 2018-12-04 14:56:16 -08:00
Bruce Martin
296ed752fa Improved summary counts of annotation values (#478) 
* convert annotation summary to a Map

* add 2d annotation count summary

* add memoization on 2D annotation counting

* add tests for annotation summarization

* fix import/exports

* rename WorldOps to WorldUtil

* rename WorldOps to WorldUtil

* add comment
 2018-12-03 09:15:03 -08:00
Charlotte Weaver
1e66ec2b89 Update scikit learn (#487) 
They finally fixed their cloud pickle issue
 2018-11-30 12:02:28 -08:00
Charlotte Weaver
4a50f0ed46 External host option (#481) 
* allow specifying host ip instead of listen all

* flask serving

* Limit to ip addresses only
 2018-11-29 17:01:49 -08:00
Bruce Martin
af0d1f6fb2 issue #480 workaround (#484) 
* only load annotation var names

* remove incorrect usage of var annotation data

* temporary workaround for issue #480

* lint

* issue warnings only once per item
 2018-11-29 16:33:21 -08:00
fionagriffin
a83ec60308 add FAQs to readme (#482) 
Added question and answer to FAQ; added link to scanpy documentation on scientific recipes.
 2018-11-29 13:59:10 -08:00
Charlotte Weaver
76c0cbf16b loose -> lose (#479) 2018-11-28 13:07:10 -08:00
Charlotte Weaver
455d987398 Add custom format for warnings (#477) 
[cellxgene] Warning: <message>
 2018-11-28 12:47:11 -08:00
Colin Megill
00b9a8fa72 Fuzzy search on genes (#473) 
* proof of concept blueprint typeahead

* poc with fuzzysearch lib

* typeahead adds gene on enter

* add gene on menu click

* typeahead clears correctly

* cleanup
 2018-11-28 09:50:02 -08:00
Charlotte Weaver
28f5263c88 bump version (#475) 0.2.3 2018-11-27 15:43:19 -08:00
Bruce Martin
933fac5fff Allow float64 to down-cast to float32 (#472) 
* warn if annotations will down-cast to float32

* correctly handle falsey data values
 2018-11-27 11:17:30 -08:00
Charlotte Weaver
0c26f227fe bump version (#470) 0.2.2 2018-11-26 15:38:47 -08:00
Marcus Kinsella
2b90c747f5 Fix readme images on PyPi (#467) 
But this time actually do that
 2018-11-26 15:27:05 -08:00
Charlotte Weaver
43a4e087ef Fix formatting issues (#468) 
- Fix step 8 bullets
- Appropriate capitalization
- Add link to release notes doc
 2018-11-26 13:52:00 -08:00
Charlotte Weaver
f2612707bb bumped version (#466) 0.2.1 2018-11-26 11:42:56 -08:00
Bruce Martin
138d30909a improve type handling for non-string annotation data (#465) 
* improve type handling for non-string annotation data

* improve clarity of code
 2018-11-26 10:32:29 -08:00
Charlotte Weaver
2b5094665f version 0.2.0 (#456) 0.2.0 2018-11-16 15:12:54 -08:00
Jeremy Freeman
a81258bc0d remove printing (#455) 2018-11-16 14:45:06 -08:00