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kaloster/various-fixes
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Author SHA1 Message Date
kaloster
5b48c7aecf debug 2024-09-12 21:43:38 -04:00
Ronen
ca8435de10 Merge branch 'main' into kaloster/various-fixes 2024-09-12 21:40:57 -04:00
kaloster
0bff55201a fix: update markdown images 2024-09-12 21:40:19 -04:00
Ronen
fd8b47b78e chore: Release 1.3.0 (#2700) 
* Bump version: 1.2.0 → 1.3.0-rc.0

* Bump version: 1.3.0-rc.0 → 1.3.0
1.3.0 		2024-09-12 16:05:14 -04:00
Ronen
487bd13ff8 chore: add support for python 3.12 (#2694) 2024-09-12 14:16:46 -04:00
Ronen
eb743efd9a fix: webpack upgrade (#2691) 2024-09-09 13:34:44 -04:00
Ronen
67d152e108 fix: mlflow critical upgrade (#2690) 2024-09-09 12:29:09 -04:00
Timmy Huang
c425d2e0b0 fix: underscore snakecase notation to hyphenated snakecase for diffexp-may-be-slow (#2687) 2024-09-05 10:09:13 -07:00
Timmy Huang
7bf5add6ef chore: Fix compatibility tests (#2685) 
* chore: Fix compatibility tests

* DEBUGGGG

* fix: update deps, fix unit tests

* fix: FE deps

* chore: update compatibility matrix

---------

Co-authored-by: kaloster <rkalo@contractor.chanzuckerberg.com>
 2024-09-05 09:26:40 -07:00
dependabot[bot]
4281a8f816 chore(deps-dev): bump follow-redirects from 1.15.1 to 1.15.6 in /client (#2661) 
Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.1 to 1.15.6.
- [Release notes](https://github.com/follow-redirects/follow-redirects/releases)
- [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.15.1...v1.15.6)

---
updated-dependencies:
- dependency-name: follow-redirects
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
 2024-04-18 14:54:49 +00:00
Emanuele Bezzi
53e9edfec1 docs: change link to the CZI science community Slack (#2662) 2024-03-19 10:19:28 -07:00
atarashansky
74fbec35fe chore: Release version 1.2.0 (#2652) 
* Bump version: 1.1.2 → 1.2.0-rc.0

* Bump version: 1.2.0-rc.0 → 1.2.0
v1.2.0 1.2.0 		2023-12-19 14:13:08 -08:00
atarashansky
5d4c782f3a chore: lower pinned requirements for backend server (#2651) 
* chore: lower pinned requirements for backend server

* update one requirement
 2023-12-19 13:39:47 -08:00
atarashansky
6505f6cbf5 chore: upgrade backend dependencies (#2641) 
chore: upgrade backend dependencies (#2641)
 2023-11-29 14:16:39 -08:00
Severiano Badajoz
4bb9a2b834 chore: update dependencies (#2636) 
* chore: update dependencies

* fix babel plugins and lint errors

* switch out obselete browser plugin

* add babel config for jest

* revert some babel/jest package bumps

* npm install

* tmp remove werkzeug pin

---------

Co-authored-by: Seve Badajoz <severiano.badajoz@chanzuckerberg.com>
 2023-10-20 21:08:09 -04:00
maniarathi
2d7aab3a9a fix: override default so that issues are not marked as stale (#2627) 2023-08-23 21:22:17 -04:00
maniarathi
f749733d54 feat: Add a Github Action that automatically closes stale PRs. (#2626) 2023-08-22 22:08:22 -04:00
atarashansky
ffcf6eb5d8 chore: Release version 1.1.2 (#2611) 
* Bump version: 1.1.1 → 1.1.2-rc.0

* fix: release candidate 1.1.2

* Bump version: 1.1.2-rc.0 → 1.1.2

* promote

---------

Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net>
1.1.2 		2023-04-26 15:01:57 -04:00
atarashansky
c209a9bca7 fix: pin flask requirement to be less than 2.3 (#2609) 
Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net>
 2023-04-26 13:58:40 -04:00
Kuni Katsuya
85319d45a4 chore: tech issue template 2023-02-06 15:46:54 -08:00
Andrew Tolopko
514f1627ea Update license copyright year (#2600) 2023-02-03 16:01:53 -05:00
Severiano Badajoz
127de34a20 feat: Add PR Linting (#2560) 2022-10-24 18:08:25 +00:00
Andrew Tolopko
54ab9d79b6 docs: fix test pypi install command (#2515) 
fix test pypi install command in release_process.md
 2022-09-29 19:30:11 +00:00
Andrew Tolopko
f48d06fb90 Bump version: 1.1.0 → 1.1.1 (#2572) 1.1.1 2022-09-21 15:33:28 -04:00
Severiano Badajoz
84563291a0 fix: fix static file serving in webpack (#2574) 
Co-authored-by: Seve Badajoz <severiano.badajoz@chanzuckerberg.com>
 2022-09-21 18:03:03 +00:00
Andrew Tolopko
ddb601c103 feat: annotate command improvements (#2568) 
* Replace --input-h5ad-file with a positional argument, for consistency with other CLI commands
* Replace --update-h5ad-file with --overwrite, for consistency with `prepare` command.
* Fix/clarify various help descriptions
* Fix final output message when input file is overwritten
* Fix annotate top-level help description
 2022-09-15 11:55:58 -04:00
ashin-czi
450261f109 chore: updating Annotate favicon and logo icon (#2556) 
* chore: replacing html icon with png icon and updating favicon
 2022-08-25 16:01:03 +00:00
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
atarashansky
ff5da77372 fix unit tests (#2562) 
Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.local>
 2022-08-25 08:02:58 -07:00
Andrew Tolopko
a9044b01df release version 1.1.0 (#2548) 
* Bump version: 1.0.1 → 1.1.0-rc.0

* bump version to v1.1.0

* Bump version: 1.1.0-rc.0 → 1.1.0-rc.1

* bump version to v1.1.0 rc1

rc0 was previously used by an aborted release attempt

* Bump version: 1.1.0-rc.1 → 1.1.0

Co-authored-by: Seve Badajoz <severiano.badajoz@chanzuckerberg.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
 2022-08-23 10:02:23 -07:00
ashin-czi
11b948369f fix: reverting back to old icon 2022-08-18 14:49:59 -04:00
ashin-czi
a2dc0c25b1 chore: updating Annotate favicon 2022-08-11 13:30:19 -04:00
Andrew Tolopko
a9ef01a6f9 fix test (#2549) 
address issues building mlflow model in GHA test env
1.1.0 v1.1.0 		2022-07-29 11:17:04 -04:00
Andrew Tolopko
03d9e8e6aa fix unit test 
avoid performing pip installs for mlflow-based tests
 2022-07-29 09:57:55 -04:00
Andrew Tolopko
30e19e47c6 feat: add cli annotation subcommand (#2539) 
add `cellxgene annotate` subcommand for invoking MLflow model to generate new `obs` annotations, initially intended for cell type annotations.
 2022-07-29 05:15:54 -07:00
Emanuele Bezzi
d2b20129f7 use fsspec.download for S3 artifacts + additional logging (#2536) 2022-07-29 11:05:36 +00:00
Rohan Agarwal
6c86216f6b Update actions/setup-python version (#2528) 2022-07-28 21:17:46 +00:00
Andrew Tolopko
4df50a7677 fix: s3 user annotations (#2541) 
do _not_ attempt to create the user annotations directory if an s3 location is specified
 2022-07-28 20:00:15 +00:00
Andrew Tolopko
69a6d52240 fix embedding selection (#2543) 
reverted code to previous implementation that was presumably changed due to a "destructuring assignment" lint error; explicitly ignoring error now
 2022-07-28 15:49:33 -04:00
Andrew Tolopko
06da05eb9f skip failing tests to unblock adding of new features (#2545) 
skipped tests will be reinstated in future issues
 2022-07-28 15:11:36 -04:00
Severiano Badajoz
d753441acc chore(webpack): remove script-ext-html-webpack-plugin (#2534) 
Co-authored-by: Seve Badajoz <severiano.badajoz@chanzuckerberg.com>
 2022-07-12 13:42:20 -04:00
Rohan Agarwal
8b4c1e418e chore: replace optimize-css-assets-webpack-plugin with css-minimizer-webpack-plugin (#2525) 
* Replace optimize-css-assets-webpack-plugin with css-minimizer-webpack-plugin

* Fix lint issues in JS

* remove favicons

* update snapshots

* update annotations snapshots

Co-authored-by: Trent Smith <1429913+Bento007@users.noreply.github.com>
Co-authored-by: Seve Badajoz <sbadajoz@chanzuckerberg.com>
 2022-06-07 13:13:17 -07:00
Madison Dunitz
f2bd6ebce1 remove unnecessary postgres req (#2524) 2022-05-27 12:15:17 -07:00
Bruce Martin
de44739f8b add fsspec support to gene set and cell annotations (#2512) 2022-04-20 18:18:47 -07:00
Severiano Badajoz
002c9a5c7f release version 1.0.1 (#2497) 
* Bump version: 1.0.0 → 1.0.1-rc.0

* Bump version: 1.0.1-rc.0 → 1.0.1
1.0.1 		2022-02-28 15:18:21 -08:00
dependabot[bot]
e6a0351079 chore(deps): bump nanoid from 3.1.25 to 3.3.1 in /client (#2488) 
Bumps [nanoid](https://github.com/ai/nanoid) from 3.1.25 to 3.3.1.
- [Release notes](https://github.com/ai/nanoid/releases)
- [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md)
- [Commits](https://github.com/ai/nanoid/compare/3.1.25...3.3.1)

---
updated-dependencies:
- dependency-name: nanoid
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-02-25 09:57:22 -08:00
dependabot[bot]
38fdc649f5 chore(deps): bump axios from 0.21.1 to 0.21.4 in /client (#2491) 
Bumps [axios](https://github.com/axios/axios) from 0.21.1 to 0.21.4.
- [Release notes](https://github.com/axios/axios/releases)
- [Changelog](https://github.com/axios/axios/blob/master/CHANGELOG.md)
- [Commits](https://github.com/axios/axios/compare/v0.21.1...v0.21.4)

---
updated-dependencies:
- dependency-name: axios
  dependency-type: indirect
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-02-24 14:20:17 -08:00
dependabot[bot]
69a5d5e837 chore(deps): bump tmpl from 1.0.4 to 1.0.5 in /client (#2490) 
Bumps [tmpl](https://github.com/daaku/nodejs-tmpl) from 1.0.4 to 1.0.5.
- [Release notes](https://github.com/daaku/nodejs-tmpl/releases)
- [Commits](https://github.com/daaku/nodejs-tmpl/commits/v1.0.5)

---
updated-dependencies:
- dependency-name: tmpl
  dependency-type: indirect
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-02-24 14:05:26 -08:00
dependabot[bot]
b854c58eea chore(deps): bump simple-get from 3.1.0 to 3.1.1 in /client (#2489) 
Bumps [simple-get](https://github.com/feross/simple-get) from 3.1.0 to 3.1.1.
- [Release notes](https://github.com/feross/simple-get/releases)
- [Commits](https://github.com/feross/simple-get/compare/v3.1.0...v3.1.1)

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- dependency-name: simple-get
  dependency-type: indirect
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-02-24 13:46:07 -08:00
dependabot[bot]
2d650ba50d chore(deps): bump follow-redirects from 1.14.2 to 1.14.8 in /client (#2484) 
Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.2 to 1.14.8.
- [Release notes](https://github.com/follow-redirects/follow-redirects/releases)
- [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.14.2...v1.14.8)

---
updated-dependencies:
- dependency-name: follow-redirects
  dependency-type: indirect
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-02-24 11:57:08 -08:00