* 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"
* 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>
* type camera
* type reducer store
* type actionhelpers
* type catchErrorsWrap callsite
* missed camera member var
* type nameCreators
* type makeContinousDimensionName callsite
* type promise limit
* type quantile
* type range
* introduce TypedArray + NumericArray
* type range
* cleanup test
* fix call sites
* type plimit call site
* finish typing camera
* use our TypedArray
* type scientific and sigFig utils and callsites
* simple typings
* type catLabelSort
* type callsite
* type
* callsites
* type camera methods
* swap back to strings, set defaults accordingly
* partially type centroid
* explicit tuple and undefined check
* fix references to this
* call constructor with new and casting
* Revert "introduce TypedArray + NumericArray"
This reverts commit cf21538717.
* explicit tuple
* generics and import fixes
* add unsigned 8 clamped arrray
* back to literals
* use arraytypes
* fix return state
* type more actions
* Update client/src/util/actionHelpers.ts
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
* properly type dispatch
* properly type thunk
* use new dispatch
* remove nullish coallescer
* use AppDispatch
* generic jsonrequest
* use dispatch again
* lint
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
* disable formatting rules for eslint and add prettier in lint-staged
* update npm modules
* set plugin-proposal-private-methods to loose
* update snapshots due to popover package update
* add missing quotes
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
* 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
* __test: create geneset
* example dataset test geneset
* delete geneset test
* edit __test
* gene crud
* Update client/Makefile
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
* copy gene sets separately
* make fix
* ignore test files locally
* csv update
* updated csvs
* fix unit tests for gene set load routes
* add missing fix to czi_hosted unit test
* pin tiledb version, for czi_hosted backend, to <0.9
* Revert tiledb pin to be less than 0.9. Broken tests have been updated in main branch.
* newline, gitignore
* color by and subset
* diffexp sets equal
* add diff exp test class
* fix data class
* diffexp snapshot
* snapshot
* snap3
* snapshot parentInnerhtml
* remove snap
* updated anno snaps
* add test class to gene list div
* new snapshots
* kick off
* Revert "kick off"
This reverts commit 743f551d55.
* remove import
* eol
* revert changes to csv re: gene tests
* global name
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
Co-authored-by: Arathi Mani <arathi.mani@chanzuckerberg.com>
Co-authored-by: maniarathi <mani.arathi@gmail.com>
* feat: return two lists for diffexp (#2221)
* sp
* split out derive sort order, tests passing
* sp
* return diff exp results in two lists
* update
* copy implementation over to desktop
* add tests for two lists
* small fixes to complete backend implementation
* accept new diffexp response
* map diff exp response to genesets
* delete )
* name diffexp genesets with population names
* take constants out of state and allow width prop to override
* shorten mini-histo properly truncate and resize depending on expansion
* prepend new genesets
* rename data within diffexp action
* backend
* move diffexp ttest to common code module, update tests
* update for unit tests
* reference actual var
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
Co-authored-by: Madison Dunitz <dunitzm@gmail.com>
* update package lock
* allow falsey vals
* remove old diff exp handling
* save diff exp results as geneset
* delete test
* check for undefined or null
* use global geneset description for diffexp
* remove diffexp special code, no longer showing adjpval + logfoldchange
* remove differential map to state
* remove clear from FSM, since we no longer support those actions
* restore controlHelpers test with todo
* first cut at hosted gs routes
* lint
* update tests to match csv parser changes
* update tests to new API
* update gene set name validation rules to match requirements
* add path mapping from dataset to geneset
* add test cases for geneset GET route
* fix test assertion
* remove debugging code
* update gene set uri mapping function
* fix error message
* allow extra user-specified headers in gene set csv file
* clarify comment
