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Author SHA1 Message Date
Justin Kiggins
eb1dc8944f Update README.md (#2725)
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Trademark
 2025-05-14 12:03:19 -07:00
Ronen
487bd13ff8 chore: add support for python 3.12 (#2694) 2024-09-12 14:16:46 -04:00
Emanuele Bezzi
53e9edfec1 docs: change link to the CZI science community Slack (#2662) 2024-03-19 10:19:28 -07:00
ashin-czi
c0f4ad6dfa docs: updating readme and display version for rebranding (#2550) 
* docs: updating readme and display version for rebranding

- CELLxGENE -> CELLxGENE Annotate
- reverting __init__.py display_version back to "cellxgene"
- changing page titles to "CELLxGENE | Annotate"
 2022-08-25 15:41:26 +00:00
Emanuele Bezzi
15d2ce62b8 Migrate to the new documentation website (#2456) 2021-10-14 20:54:54 +00:00
signechambers1
56fcbae672 Remove safari from supported browsers (#2272) 
* Update README.md

* Update package.json

* Update obsoleteHTMLTemplate.html

* remove unneeded polyfills

* explicit deny safari

* remove from webpack and update lock

Co-authored-by: Seve Badajoz <sbadajoz@chanzuckerberg.com>
 2021-07-06 10:09:51 -10:00
Ambrose J Carr
e264724597 Add extension showcase to documentation (#1878) 2021-01-12 08:55:14 -05:00
Isaiah Norton
34742b9a94 Add link to dev_docs in Contributing section (#1957) 2020-11-09 21:57:00 -08:00
evanbiederstedt
1f9bba6f00 readme correction (#1896) 2020-10-01 22:44:59 -04:00
Ambrose J Carr
5781879da5 remove core team section (#1798) 2020-09-02 20:22:31 -04:00
Severiano Badajoz
8bbc183647 Explicit Browser Support (#1682) 
* add FastestSmallestTextEncoderDecoder polyfill

* remove nomodule from script import

* add browserslist

* add obsolete-webpack-plugin

* switch out modern-browser for preset-env

* add prompt on non target browser

* propagate prod changes to dev

* add core-js-3 and TextEncoder TextDecoder (#1671)

* add script to remove react, style html

* propagate changes to prod

* add script-ext-html-webpack-plugin for async

* more styling

* add eslint-plugin-compat

* extend compat plugin

* add existing polyfills

* add github fetch polyfill

* add AbortController polyfill

* change promptOnNonTargetBrowser to false

* propagate

* add browser links

* prettier

* add browser support to readme

* move polyfills to webpack

* remove CDN encoder polyfill

* Add no Explorer support

* fix incorrect package name

* propagate changes

* Update README.md

Co-authored-by: Ambrose J Carr <ambrosejcarr@users.noreply.github.com>

* add new deps

* create shared config

* swap out html-loader for filestream

* sanitize template

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
Co-authored-by: Ambrose J Carr <ambrosejcarr@users.noreply.github.com>
 2020-08-03 12:50:09 -07:00
Matt Weiden
152c07a28e Change default branch from 'master' to 'main' (#1589) 
The default branch has been changed. This PR cleans up references to
`master` and fixes links that would otherwise be broken.

For more background see the following references:
* https://www.independent.co.uk/life-style/gadgets-and-tech/news/github-master-slave-slavery-whitelist-language-inclusive-a9568576.html
* https://tools.ietf.org/id/draft-knodel-terminology-00.html
 2020-06-25 14:04:30 -07:00
Matt Weiden
d8231a9a3b Fixes to compatibility tests (#1205) 
* Unpin anndata ver in tests against anndata master

* Add branch config to work on push

* Add links to tests in GitHub Actions status badges

* Remove temporary branch name
 2020-03-10 08:19:36 -07:00
Matt Weiden
ded35c7252 Spelling fix in Compatibility Test workflow (#1178) 2020-02-26 11:12:16 -08:00
Matt Weiden
5c70cc5bcd Add codecov for code coverage of python and javascript (#1170) 
* Add codecov to Push Test workflow

* Empty commit

* Clear reports and tag each with flags

* Tag code reports by test

* Fix codecov tags

* One more fix
 2020-02-24 17:13:16 -08:00
Matt Weiden
c630be33df Simplify CI checks on git push, add nightly checks on cron (#1158) 
* Switch push tests to Github Actions

* Add nightly tests

* Add anndata check

* Add test status badges

* Add anndata 0.6.22.post1 workaround

* Rename Nightly tests to Compatibility Tests

* Fix to anndata fix

* Turn on cron schedule

* Fix badge mardown in README.md

* Fix cron schedule
 2020-02-18 11:57:19 -08:00
Sidney Bell
9c09ee6329 Update readme and other repo MD files (#1063) 
* Update readme

* Move roadmap to main docs site

* Avoid duplication by just putting a pointer to the actual docs
 2019-11-26 16:09:59 -08:00
Sidney Bell
9bcafeb7c1 [WIP] Overhaul the documentation site (#1030) 
Overhaul the whole documentation site
 2019-11-22 14:54:20 -08:00
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
Sidney Bell
f41f47cf1b Fix mistakenly removed badges (oops) (#955) 
* Fix mistakenly removed badges (oops)

* Update README.md

Co-Authored-By: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
 2019-09-30 16:00:29 -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
Justin Kiggins
57b1c3cbb4 put badges on one line in README (#862) 2019-07-31 16:01:09 -07:00
Marcio von Muhlen
40c533a45b Update README.md (#856) 
Full URLs for roadmap, contributor guide to fix 404s on Pypy.
 2019-07-26 13:35:46 -07:00
Severiano Badajoz
9eb8185e82 add badges to readme (#857) 
* prettier

* add pypi and commit badges

* formatting

* revert DOI badge

* Update README.md

Co-Authored-By: Justin Kiggins <justin.kiggins@chanzuckerberg.com>
 2019-07-25 16:52:38 -07:00
Sidney Bell
98b07b1284 Add code of conduct; move contributing guidelines to CONTRIBUTING.md (#842) 2019-07-11 10:09:35 -07:00
Justin Kiggins
9f9393a486 adds section on risks of hosted instances (#807) 
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com>
 2019-06-04 09:16:11 -07:00
Justin Kiggins
3152de4b7f fixes URL to getting started (#801) 2019-05-31 19:34:51 -07:00
Justin Kiggins
ffd7f0db49 adds zenodo badge (#795) 2019-05-30 10:23:49 -07:00
Charlotte Weaver
77a4495b28 Update README.md (#743) 
Fixes #702
 2019-05-02 16:54:39 -07:00
Justin Kiggins
1f735abe2b updates the roadmap & reorganizes the README (#712) 2019-04-18 13:10:03 -07:00
Sidney Bell
34e5a91dc6 Add calculate_qc_metrics to `prepare (#697) 
* Calculate QC metrics

* Add QC metrics to prepare section of readme

* Add pointer to scanpy qc metrics function

* Don't explicitly pass qc flag as arg

* Add explicit toggle for run-qc/skip-qc

* Move qc metrics calculation to separate step/function
 2019-04-09 08:56:07 -07:00
Charlotte Weaver
3167e38993 update docs to reflect python 3.7 support (#685) 2019-04-02 09:24:50 -07:00
Gökçen Eraslan
df46db965a bin/build-client.sh does not exist. (#671) 2019-03-25 10:26:27 -07:00
Sidney Bell
16f93397ae Support diffmap and phate layouts. Explicitly handle embeddings with >2 components. (#662) 
* Add diffmap and phate to supported embeddings

* Explicitly pull the first two components of any given layout
 2019-03-21 19:06:05 -07:00
Charlotte Weaver
68dfbcc2eb Add force graph to docs and example dataset (#630) 2019-03-05 20:59:54 -08:00
Sidney Bell
b6f946ec8a Add note about installing hdf5 to FAQ (#581) 2019-02-08 14:56:16 -08:00
Justin Kiggins
a6d2a2e119 updates link to scanpy recipe docs. fixes #564 (#565) 2019-01-28 10:00:29 -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
Justin Kiggins
aaa60bc303 new signup url (#516) 2018-12-14 16:32:41 -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
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
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
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
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
Marcus Kinsella
2b90c747f5 Fix readme images on PyPi (#467) 
But this time actually do that
 2018-11-26 15:27:05 -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
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