Commit Graph

29 Commits

Author SHA1 Message Date
kaloster
ea13d3e253 debug 2024-09-09 16:56:25 -04:00
kaloster
b43bce4321 debug 2024-09-09 16:53:52 -04:00
kaloster
8bde7c1c1f add setuptools 2024-09-09 16:51:10 -04:00
kaloster
b11b161dd3 add setuptools 2024-09-09 16:45:58 -04:00
kaloster
402b9b3f94 chore: python 3.12 2024-09-09 16:16:03 -04:00
Ronen
67d152e108 fix: mlflow critical upgrade (#2690) 2024-09-09 12:29:09 -04:00
atarashansky
6505f6cbf5 chore: upgrade backend dependencies (#2641)
chore: upgrade backend dependencies (#2641)
2023-11-29 14:16:39 -08:00
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
Rohan Agarwal
6c86216f6b Update actions/setup-python version (#2528) 2022-07-28 21:17:46 +00:00
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
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
Severiano Badajoz
0634160c0c Fix unit tests (#2428)
* only create toaster if we're on the browser

* drop/fix references to window

* add back fe unit tests
2021-09-15 00:43:59 +00:00
Madison Dunitz
f9c744327a Dunitz/2308-remove hosted (#2399)
* remove code for and references to czi-hosted

* revert client change
2021-09-02 13:18:35 -04:00
Severiano Badajoz
1998c0ad63 fix: don't run lint with --fix on push tests (#2273)
* fix: don't run lint with `--fix` on push tests

* npx

Co-authored-by: maniarathi <mani.arathi@gmail.com>
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
2021-07-27 16:43:01 +00:00
Madison Dunitz
78c9d24ed4 Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
2021-03-26 00:27:07 -05:00
Marcus Kinsella
fb61bd6e9c Split out the local backend (#2052)
This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
2021-02-18 12:58:22 -08:00
Madison Dunitz
998fa4762d run black formatter on repo (#1891)
* add black to lint make cmd

* add black dependency to installation to push test pipeline
2020-09-30 11:16:13 -05:00
Timmy Huang
dda530a67c add-GHActions-timeout-for-smoke-tests (#1743)
We need to explicitly set timeout for smoke tests, since GH Action's default is 360 mins (6 hours 😱 )

https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobsjob_idtimeout-minutes

Thank you!
2020-08-13 13:18:01 -07:00
Timmy Huang
2b0c4692ba e2e-add-more-logs (#1598) 2020-06-30 21:27:38 -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
Timmy Huang
83376627e8 1510-smoke-test (#1548)
* 1510-smoke-test

* config default

* update tests

* update test config

* fix linter errors

* more comments

* address comments

* use npm install in push_tests.yml

* use environment.default.json

* adding docs

* Take care of @mweiden's nits

* Save screenshots in the __tests__/screenshots/ directory

* typo

* docs

* Add chart tests (#1580)

* merge tests

* check if bin creation returned null before rendering charts (#1576)

* check if bin creation returned null before rendering charts

* refactor chart rendering into functions (#1577)

* little fixes from PR

* reintroduce fix to check for null values

* change getAllByClass to return element

* slice instead

* new stackedbar test

* feedback-1573-test (#1579)

* feedback-1573-test

* enable whole test set

* revert tests

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

* tweak test to actually render chart

* include snapshot

* remove async

* fix getAllHistograms

* properly grab id

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
2020-06-24 11:45:39 -07:00
Severiano Badajoz
271e7a1e76 Fix prettier related ESLint issues (#1493)
* add quotes

* add prettier dev-dep

* run prettier on src

* add eslint-prettier-plugin to install
2020-05-26 09:33:59 -07:00
Severiano Badajoz
889b582538 ESLint tooling and enforcement(#1492)
* add eslint-prettier

* add lint-staged

* ignore .eslintcache

* remove unused import

* attempt test change

* Revert "attempt test change"

This reverts commit 78d0e31d41.

* attempt to add error

* Revert "attempt to add error"

This reverts commit a5885c0942.

* add error

* create config

* add comment

* tweak glob

* Revert "add error"

This reverts commit 3187522396.

* add python error

* Revert "add python error"

This reverts commit d0b116ed15.

* lint on push + PR

* Revert "add comment"

This reverts commit efa4eb6676.

* add prettier rules to ESLint

* remove lint-diff targets
2020-05-21 14:27:49 -07:00
Severiano Badajoz
ce819383af re-enable front-end lint test (#1483)
* change lint to only src

* reenable lint all
2020-05-19 15:46:04 -07:00
Bruce Martin
5dc40158c4 disable eslint in github workflow (#1412) 2020-04-18 09:06:05 -07:00
Severiano Badajoz
e5dfd6e8fa Add eslint steps to lint job (#1335)
* add lint-client and lint-diff-client targets

* add lint-diff and lint targets

* prettier

* add lint-diff call to lint task

* temp

* tweak lint-diff

* add lint for PRs and lint for master

* remove temp

* remove incorrect branches syntax, use github_ref

* pull all branches

* format

* proper target and comment

* create separate steps with conditionals

* fix indentation

* refactor lint->lint-server, introduce lint to lint all

* trade diff-index for diff, do check against base instead of master

* remove fetching all branches

* Revert "remove fetching all branches"

This reverts commit 26ce7a0f05.

* tweak comparison

* use local eslint

* add eslint  dep install

* temp

* grab only base

* simplify fetch

* add pull_request type trigger

* specify pushes only to master

* change conditionals to be based on event name

* Revert "temp"

This reverts commit 3d59134cc0.

* "branch" => "branches"

* create separate installation step

* change command based on os
2020-04-15 09:41:45 -07:00
Matt Weiden
8b0adcdfcc Add codecov configuration (#1180)
* Add codecov configuration

* Modify workflow
2020-02-26 14:57:46 -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