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Author SHA1 Message Date
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
...

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

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
...

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

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)

---
updated-dependencies:
- dependency-name: simple-get
  dependency-type: indirect
...

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

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

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-02-24 11:57:08 -08:00
Ben MR
8bac98f25c Fix float16 support [#2379] (#2483) 
* Fix float16 support [#2379]

Convert to float32 on startup unless backed, in which case error. scipy does not support complex slicing from float16 data so this is the easiest fix for now.

* minor msg change
 2022-02-10 15:20:47 -08:00
maniarathi
ceb0cc6f27 Update license to 2022. (#2478) 2022-01-14 14:07:35 -05:00
Severiano Badajoz
853976b716 release version 1.0.0 (#2466) 
* Bump version: 0.19.0 → 1.0.0-rc.0

* Bump version: 1.0.0-rc.0 → 1.0.0
1.0.0 		2021-11-02 14:53:26 -07:00
Emanuele Bezzi
a344f292a9 Restore logo and favicon in docs/ (#2464) 2021-10-14 21:13:04 +00:00
Emanuele Bezzi
15d2ce62b8 Migrate to the new documentation website (#2456) 2021-10-14 20:54:54 +00:00
Colin Megill
8e011314e9 Remove log (#2463) 2021-10-14 18:02:54 +00:00
Ben MR
c81731d32c [FE: fix #2371] fix for when labels are null (#2462) 
Categoricals can have nulls
 2021-10-05 12:17:34 -07:00
Colin Megill
3b091d888d Update diffexpButtons.js (#2461) 2021-10-04 15:35:55 -07:00
Timmy Huang
79aeedc6c3 refactor: 2235 remove cookie banner (#2459) 2021-10-04 11:26:01 -07:00
Colin Megill
e6bacf043b typo fix (#2460) 2021-10-01 18:28:47 -07:00
Colin Megill
be020deaa6 Update infoMenu.js (#2455) 
Fixes #2452
 2021-09-29 13:00:55 -07:00
Emanuele Bezzi
4034256d9c Create CNAME file to point docs to the new website (#2453) 
Add a CNAME file that will redirect the current github pages (hosted at https://chanzuckerberg.github.io/cellxgene/) to the new website.
 2021-09-29 13:28:49 -04:00
Ben MR
5163e35e1f fix #2446 update release docs and commands (#2448) 
* update release docs and commands

* update doc on release-test install
 2021-09-29 15:06:35 +00:00
Ben MR
f4986c9c7d Release version 0.19.0 (#2444) 
* Bump version: 0.18.0 → 0.19.0-rc.0

* release can 0.19.0

* Bump version: 0.19.0-rc.0 → 0.19.0-rc.1

* bump rc

* Bump version: 0.19.0-rc.1 → 0.19.0

* release final
0.19.0 		2021-09-28 11:10:24 -07:00
Colin Megill
a0011b0872 cursor pointer on mit license and version (#2447) 2021-09-27 09:47:34 -07:00
Colin Megill
77fff0bd9c Remove pointer on gene (#2445) 
* Remove grab

Fixes #2438

* snapshot

* pointer

* snapshot
 2021-09-24 12:21:32 -07:00
Ben MR
6a4884d97c Re-add bumpversion to makefile (#2443) 2021-09-23 22:08:00 +00:00
Colin Megill
15714e9924 Remove grab (#2439) 
* Remove grab

Fixes #2438

* snapshot
 2021-09-23 10:30:55 -07:00
Severiano Badajoz
5eb0ecc997 chore: update frontend packages (#2442) 
* run audit

* migrate husky
 2021-09-22 10:22:44 -07:00
Andrew Tolopko
e2772d1da9 #2410 reenable scheduled compatibility test (#2440) 
re-enable scheduled compat matrix tests on main branch; was temporarily commented out for testing on branch
 2021-09-21 17:27:45 -04:00
Colin Megill
7f068cd576 Reverse gene list order (#2432) 
Fixes #2420
 2021-09-21 11:53:50 -07:00
jacobrheath
e4961a579e feat: removing sastisfaction gh action for gh app (#2441) 2021-09-21 10:09:30 -07:00
Andrew Tolopko
c0263f6ce5 #2410 update compatibility test matrix (#2431) 
Github Actions Workflow updates compatibility matrix:
- Added MacOS Catalina and Big Sur to test compat matrix
- Added Python 3.9 to test compat matrix, but avoid running 3.9 for matrix jobs that do not have `tables` pypi build available for the given env
- Maintains running tests on both cellxgene main branch and latest pypi release.
- Add explicit matrix exclusions for matrix combinations that will never pass (see comments).
- Numerous refactorings to the workflow config to simplify matrix. Basically a rewrite.
- The anndata pkg is now tested at a pinned release and at latest release, but no longer using `master` branch version. To limit cross-product explosion of matrix jobs, the pinned anndata version is only tested on py3.8 and cellxgene latest release.
- Run unit and smoke tests in a single job, to improve speed, reduce workflow complexity and the number of jobs. Also fixes the redundant testing of unit tests. Within each job, the unit and smoke tests are run in separate steps for ease of troubleshooting. 
- Fixed termination of backend server to allow both smoke tests to run within a single job (both attempt to use 5005 port, sequentially, but first server was not being terminated).
- Replaced `continue-on-error: true` with `fail-fast: false`, which allows all matrix jobs to run independently, while also ensuring the that entire workflow is flagged as failed if any matrix job fails
-  The `smoke-test-annotations` fail intermittently and have been disabled. Fix will be addressed in story: https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2433
 2021-09-21 08:32:19 -04:00
Madison Dunitz
3ebbb0ccbf move common code into server, update tests and makefile (#2425) 
* move common code into server, update tests and makefile

remove backend directory, refactor

update smoke tests
 2021-09-20 18:50:06 -07:00