Migrate from the deprecated codecov npm package and bash uploader to the
official codecov/codecov-action@v5. This fixes gcov errors on macOS runners
and provides better reliability for coverage uploads.
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
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
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.
* 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>
