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9089fc98f281bf50328973fbdeff941f3dc05a13
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86 Commits

Author SHA1 Message Date
Sidney Bell
9089fc98f2 annotations cli updates (#1190) 
* Switch logic from `--annotations` to `--disable-annotations

* Rename `--annotations-file` --> `--annotations-input-file` and remove `experimental`

* update docs

* update makefile

* update tests

* Disable annotations on standard client smoke test

* Update docs/posts/annotations.md

Co-Authored-By: Matt Weiden <538456+mweiden@users.noreply.github.com>

* Update docs/posts/annotations.md

* Renaming

* Docs

* Update tests

* Pesky typo -_-

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
 2020-03-11 11:57:52 -07:00
Severiano Badajoz
cc890fe391 fix url launching on Heroku deployments (#1196) 
* fix improper branch link

* set app to use dataset link

* temp repo change

* revert to master

* add options var

* tweak option order

* remove options config arg
 2020-03-04 13:05:11 -08:00
Sidney Bell
2832393f40 Make diffexp docs more specific (#1083) 
* Update diffexp docs w/ more explicit assumptions, etc.

* Minor edits

* Formatting and cross-checking with `diffexp.py`
 2020-01-16 15:44:10 -08:00
Sidney Bell
124254d5ed typo 2020-01-13 10:55:53 -08:00
Sidney Bell
ec79995be8 Reorganize annotations docs to emphasize hosted vs single-user modes (#1067) 2019-12-03 17:02:35 -08:00
Sidney Bell
517e0f3826 [docs] Fix annotations command 2019-12-02 09:26:07 -08:00
Sidney Bell
1ed68261d4 Add sceasy package to docs 2019-11-27 08:49:21 -08:00
Sidney Bell
bb3032ea2f Update getting started docs w/ direct url launch 2019-11-26 12:57:50 -08:00
Sidney Bell
5e471349e7 Cleanup docs files 2019-11-26 08:44:23 -08:00
Sidney Bell
0aee4b89e0 Fix docs font 2019-11-26 08:43:57 -08:00
Sidney Bell
575f71aaee Fix base url 2019-11-22 18:17:43 -08:00
Sidney Bell
298ded6e2d Add site files 2019-11-22 14:59:40 -08:00
Sidney Bell
85c1b6957e Final annotations notes 2019-11-22 14:53:35 -08:00
Sidney Bell
2f99b317a2 Update annotations docs 2019-11-22 13:57:50 -08:00
Sidney Bell
8535664e9c Typo 2019-11-22 11:26:55 -08:00
Sidney Bell
5ed9f5126b Switch demo datasets to launch directly from URL 2019-11-22 11:26:51 -08:00
Sidney Bell
621b88bff4 Simplify demo data download 2019-11-21 18:51:30 -08:00
Sidney Bell
ecedf666c7 Bold current page in nav 2019-11-21 18:51:13 -08:00
Sidney Bell
afff2ceec7 Update logo 2019-11-21 18:50:55 -08:00
Sidney Bell
be9a415a4a Typo 2019-11-21 17:02:59 -08:00
Sidney Bell
0295041972 Fix typos, etc in prepare 2019-11-21 17:02:50 -08:00
Sidney Bell
8fe7ee75e8 Minor text edits to launch 2019-11-21 17:02:30 -08:00
Sidney Bell
a3d96aae0a Minor text edits to hosted (i.e., typos) 2019-11-21 17:02:01 -08:00
Sidney Bell
d5d56d89d1 Change text color 2019-11-21 17:01:33 -08:00
Sidney Bell
a6a2841961 Update gifs in gallery (thank you @liaprins-czi !) 2019-11-21 17:01:24 -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
Severiano Badajoz
a5d343aaa4 add list of wild hosted cellxgene instances 2019-11-12 15:39:04 -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
Sidney Bell
9c8c28e1cb Overhaul the whole documentation site 2019-11-07 17:03:33 -08:00
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
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
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
Sidney Bell
69e69f4dae Add logo and favicon to docs (#880) 2019-08-12 16:03:41 -07:00
Sidney Bell
fcaa30d7cc readme updates (#878) 
* Add Lia to core team in readme

* Update readme

* Add logo to readme
 2019-08-12 12:56:26 -07:00
Sidney Bell
2df93d6d94 Add prepare example and update demo datasets (#810) 
* Update example datasets w/ pbmc3k and tabula muris

* Add `prepare` overview and example

* Add S3 data links

* Incorporate PR feedback & copyedits

* Switch to letter pointers

* unix line endings

* path
 2019-06-13 16:55:09 -07:00
Bruce Martin
efa1709158 add multi-layout support to back-end (#766) 
* add multi-layout support to back-end

* remove obsolete code

* temporary code to apply heuristic choice of default layout

* fix tests

* update python tests

* more py lint

* PR review changes

* more PR lint

* PR lint
 2019-05-16 14:49:22 -07:00
Bruce Martin
b521a17ffd improve column access speed for sparse matrices (#742) 
* improve column access speed for sparse matrices

* add FAQ entry about data format performance

* add note about using --sparse flag for prepare command

* clean up for PR review

* Update docs/faq.md

Co-Authored-By: bkmartinjr <bruce@chanzuckerberg.com>

* improvements to big data faq
 2019-05-01 15:44:01 -07:00
Justin Kiggins
1f735abe2b updates the roadmap & reorganizes the README (#712) 2019-04-18 13:10:03 -07:00
fionagriffin
07db2eb3ee Update data.md (#544) 2019-01-29 10:31:31 -08:00
Justin Kiggins
f87e4bfbd3 home page fix (#551) 
* explicit site.url in config

* infra for custom css

* moves home item to html layout

* adds baseurl to site config
 2019-01-28 09:13:09 -08:00
Charlotte Weaver
394da40bea Doc formatting improvements (#549) 2019-01-10 15:09:02 -08:00
Bruce Martin
5d60505407 remove --nan-to-num CLI parameter (#548) 
* remove --nan-to-num CLI parameter

* factor tests better

* lint - remove unused variables
 2019-01-10 15:03:03 -08:00
Colin Megill
f876a0091a Set theme jekyll-theme-cayman 2019-01-10 12:12:58 -05:00