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Author SHA1 Message Date
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
Bruce Martin
141f802824 differential expression improvements (#452) 
* add cutoff for low expression genes in topN selection

* remove debugging printfs

* change cli param name for diffexp cutoff

* change CLI param name

* second try at diffexp - using lfc sort with pval cutoff

* use lfc cutoff

* update comments to match code; cap p-value adjustment to max of 1

* lint

* explain diffexp in readme

* add link

* add diffexp-lfc-cutoff to test config

* update test to match revised diffexp spec

* fix latent bug in GET arg handling that was breaking tests

* lint

* comment cleanup

* fix variance overestimation so it is symmetric

* lint
 2018-11-16 14:44:56 -08:00
Charlotte Weaver
3475f3f12e Update release_process.md (#443) 
* Update release_process.md

* Clarified release process
 2018-11-16 14:36:43 -08:00
Jeremy Freeman
dff2526077 warm to cool (#454) 2018-11-16 14:33:32 -08:00
Marcus Kinsella
2b4aa92f67 Use externally-reachable image urls (#453) 
This is needed for the images to show up in pypi.
 2018-11-16 13:02:49 -08:00
Jeremy Freeman
3151306d7e readme updates (#436) 
lots of updates to the readme to: improve scientific and technical clarity, reflect all recent changes to the CLI (especially the addition of prepare), reflect all recent changes to our installation, improve explanation of how to handle a few different kinds of data, and expand instructions on contributing and developing
 2018-11-15 18:18:30 -08:00
Colin Megill
ef80c8df2a Change color scales to rainbow (#449) 
* rainbow

* eslint

* remove comments
 2018-11-15 18:17:55 -08:00
Charlotte Weaver
1a5f49239a Release 0.0.4 (#447) 
* 0.0.3 bump

* release 0.0.4
 2018-11-15 16:43:59 -08:00
Charlotte Weaver
dfc04d8de5 Add requirements to manifest (#445) 0.0.4 2018-11-15 11:56:22 -08:00
Marcus Kinsella
523048de43 Set long_description_content_type (#439) 
This _should_ make it look more attractive on pypi.
 2018-11-15 11:19:34 -08:00
Charlotte Weaver
07cda497d9 build bug fixes (#438) 
* Fixes compatibility conflict with numpy version and anndata version #434

* Forces description to be read as unicode

fixes #435
 2018-11-14 14:21:02 -08:00
Bruce Martin
00a68276a2 diffexp performance & UX improvements (#431) 
* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments
 2018-11-14 12:51:24 -08:00
Charlotte Weaver
bc0cecbd1c Release Test (#427) 
* bump-update

* Release Test!
 2018-11-14 11:03:52 -08:00