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ecedf666c73260b600e8173e083f1edf63444418
Commit Graph

69 Commits

Author SHA1 Message Date
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
Colin Megill
528eb5d172 Set theme jekyll-theme-minimal 2019-01-10 12:10:11 -05:00
Justin Kiggins
eceab377f7 cleans up landing page (#541) 2019-01-04 14:20:23 -08:00
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
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
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
fionagriffin
6af7708d62 update index.md (#519) 
ready for features
 2018-12-18 11:10:29 -05:00
fionagriffin
7d40d89fd8 Update index.md (#507) 
Added content from readme
 2018-12-14 15:19:21 -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
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
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