* 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
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
* Update dependencies
Flask to 2.0
Scipy etc. bumped to latest version not supporting 3.5
Others bumped to latest where possible
* py min v
* relax py version
* revert reqs changes
* revert all commits to before Typescript migration
* update compat workflow to match latest deps (#2335)
* update compat workflow to match latest deps
* attempt to debug
* attempt to debug
* remove debugging code
* typo
* update deps to match desktop (#2340)
* 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>
* rename X_approx_distribution to X_approximate_distribution (#2337)
* Correctly handle non-finite numbers in heuristic determination of X distribution (#2342)
* handle non-finites explicitly
* improve and test edge case handling for distribution estimation
* revert debugging changes
* code readability
* clean up type inferencing (#2332)
* unit tests for 64 bit conversion
* clean up type handling
* type inference tests
* more type inference fixes
* use schema to determine user intent for data typing
* stop using deprecated API
* fbs type encoding test
* add missing test
* add more tests
* correctly infer X type for CXG adaptor
* lint
* fix typo
* ts migration
* cleanup from PR review
* lint
* PR review changes
* remove unused packages from client (#2359)
* remove unused packages from client
* add missing peer dep
* fix: disable FE auth testing on compatibility tests (#2377)
* update: release process (#2277)
Co-authored-by: maniarathi <mani.arathi@gmail.com>
* fix: remove spaces in param setup (#2380)
* delete deploy workflow (#2396)
* undo reformatting which now does not pass lint
* fix snapshots which changed due to npm dep changes
* add missing quoting to snapshot
* another snapshot typo fix
* TS Revert (2) - replay PR #2347 and #2354 (#2403)
* replay edits from PR 2347
* TS Revert (3) - replay edits in PR #2327 (#2404)
* replay edits in PR 2327
* TS Revert (4) - replay PR #2355 (#2405)
* replay edits in PR 2355
* add additional babel config
* reformat with new prettier config
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Co-authored-by: maniarathi <mani.arathi@gmail.com>
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
