* 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>
* __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
The HistogramFooter needs to distinguish between an undefined
value and a value of 0. If the pvalAdj was 0, then the logFolChange
was previously not showing up.
#1888
* remove single val continous metadata from histogram, add to info drawer
* refactor to save singleContinuous values in state
* fix edge case, single continuous values reappeard in rsb when clipped
* refactor categorical controls state
* lint
* fix race condition in tests
* fix typo
* add missing update on subset
* remove obsolete code
* update jest and puppeteer major version; update all minors
* update when label changes
* remove lint from tests; increase timeouts in e2e tests
* initial refactoring to new async annomatrix
* refine error handling
* fix bad merge
* add continuous legend
* lint
* fix memoization in color table creators
* partial implementation of user defined annotations
* add new annotations action creator file
* first pass at user annotations
* additional user annotation bug fixes
* user annotation auto-save
* unit test cleanup
* lint
* refactor into multiple files
* cleanup
* add column GC
* fix several bugs in user annotations
* remove debug code
* no anonymous functions
* undo redo cleanup
* file cleanup
* scatterplot
* performance
* cleanup
* remove old code
* render in parallel with load
* fix race condition
* simply graph rendering
* render throttle DRY
* fix category label order
* fix typo in e2e test setup
* re-fix the e2e test setup
* be more tolerant of races
* anno matrix unit tests
* temp disable reembedding
* pilot port continuous histo to react-async
* name change
* lint
* fix repaint bug
* typo fix
* update snap to match new ids
* world/universe name cleanup
* move annoMatrix to src dir
* use private underscore naming convention
* fix corner case in all selected
* name cleanup
* add layout control
* init edge case
* lint
* port scatterplot
* fix label indexing bug and improve tests
* port category to react-async
* fix user annotation labelling while subset
* select all of prev layout on layout switch
* fix race with crossfilter update
* prettier lint
* fix misleading comment
* fix url composition in loader
* first pass at crossfilter tests
* lint
* lint
* fix typo
* improved error handling for network errors
* fix memoization bug
* add memo
* refactor for performnce
* add missing single-value handling in select exact parser
* small bugs discovered by tests
* lint
* additional crossfilter unit tests
* remove extraneous comment
* add support for automatic category determination
* lint
* fix render bug in category
* take advantage of schema categories guarantee
* lint
* do not clear history when resetting
* enhanced annomatrix gc
* lint
* finish renaming to follow conventions; fix clone race bug
* lint
* add priority based loading to improve initial data load UX
* crossfilter cache perf
* perf tuning
* remove timers
* documentation
* PR review changes
* PR review changes
* more PR review edits
* improve clarity of comment
* more PR review fixes
* port centroidLabels to use react-async
* remove dead code
* pr review updates
* oops, remove logging
* Refactor CSS layout and react logic for layout
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1022
* Menubar should wrap inside middle pane instead of overlapping left
sidebar when window is scrunched
* cellxgene should have a minimum width of 1240px
1. Replace absolute positioning and dimension calculation with css grid
2. Use flexbox for wrapping menubar buttons
* Middle pane (graph) can calculate its own size
* Removing components calculating their size/position relative to
eachother increases modularity, decreases use of global variables
* Improved some scrollbar behavior
* Removed responsive reducer, propagating window size to components
triggers unnecessary events and encourages breaking modularity; doing
this made some components state agnostic
Reference: https://css-tricks.com/snippets/css/complete-guide-grid/
* Reposition the continuous legend
* Small fixes
* Respond to feedback from @colinmegill
* Respond to feedback from @colinmegill
Add more documentation on the renderGraph method.
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1349
For more information see https://github.com/d3/d3-format
Note that does not _fully_ fix the issue described in #1349, but rather
makes the formatting issue far less likely. It is _still_ possible for
this to occur if the difference between two ticks in axes happes in the
a significant digit cropped by the scientific notation format
* Add color mapping to the bar chart.
* Change histogram color generation from Viridis to InterpolateCool.
* Coloring of Histrogram based up the x axis instead of y axis.
Coloring of Histrogram based up the x axis instead of y axis.
* Respond to feedback from @colinmegill
* Only color histograms that are selected for colorby
* Add some small refactors to BrushableHistogram's componentDidUpdate
* Fix histogram coloring and binning
* Reuse binning functions from util/dataframe/histogram.js; this fixes
an issue with there being near-zero width bins
* Fix color mapping so that it matches the scale in the legend
* Do not attempt to plot bins if the calculated binWidth is zero; this
can happen if all values are the same
* Refactor the function that draws the histogram a bit
* Respond to feedback from @bkmartinjr
Co-authored-by: Donald Paul Herman <Donaldpherman@hotmail.com>
* load annotations individually
* fix type check to be more general
* update node CI version from 10 to 12
* node 11
* debug print node version
* travis node version to latest
* try nvm
* remove extraneous node_js statement
* remove node version debugging printf
* incrementally load all annotations and layout
* process annotations and layout as they are loaded
* fix tests
* sort categories incrementally
* incrementally build category view summary; add category loading spinner
* add spinner to continuous metadata
* configure undoable reducer
* incremental crossfilter creation
* improve busy layout
* more layout cleanup
* correctly reconcile categories in schema
* refine layout of lsb spinners
* more spinner layout work
* more spinner layout
* always load layout before obs annotations
* freeze objects
* component rendering perf work
* use PureComponent where safe
* remove obsolete WorldUtil code
* make brushable histogram a pure component
* Add numeric inputs for percentiles
* Define initial values for percentile cutoffs in world reducer
* add percentil to crossfilter dimensions
* worldEqUniverse now handles cloned worlds
* add Dataframe.mapColumns
* Wire up handlers for percentile inputs
* World reducer and stateManager know about continuousPercentileMin/Max
* Create world as universe clone (not pointer) to avoid clobbering vals
* Define basic actions for setting continuousPercentileMin/Max
* Under the hood, deal with percentiles between 0 and 1
* Move percentile inputs to visualization settings menu
* Fix padding for undo/redo buttons
* Trigger world rebuild from percentile actions
* BROKEN - pseudocode for clamping dataframe by percentiles upon world rebuild
* fix error handling on clip quantiles; start world clipping implementation
* more unclipped reorg
* rename crossfilter.percentile to quantile
* simplify schema access
* update continuous legend when scale changes
* update color cache when clip changes
* clip obs annotations and var data when clip quantile changes
* use own fromEntries
* fix tests
* stable non-finite float sort/search
* clarify comments
* fix syntax typo
* use new stand-alone clip
* clip expresssion data
* add select tests for non-finite scalars
* basic styles
* clip UI now requires explicit commit
* reset enable/disable accounts for clip percentiles
* better error messages
* fix bug in undo interaction with programatic min brush selection
* small refactoring
* support clipping of int data
* do not perform unnecessary summarizations
* improve caching of dataframe compiled columns
* add percentile precompute to Dataframe.summarize
* use Dataframe.summarize for clip percentiles
* remove obsolete quantile code from corssfilter
* histogram scale and label Y axis, add unclipped X range labels
* layout tweaks
* scatterplot now updates when clip changes
* improve comments
* remove debugging comment
* rework clip number entry validation for usability
* ui tweaks to histogram colors and layout
* enable undo/redo for clip user action
* refine UI on clip value entry
* api cleanup
* update confusing comment
* clarify purpose of isValidDigitKeyEvent
* fix misleading comment
* apply appropriate button-group classes; do not mix span and div
* variable name and comment changes suggested in PR review
* rename sort to sortArray; remove unused and dead code path
* naming changes suggested in PR review
* code review improvements for clarity
* more small changes from PR review
* lint fixes for PR review
* fix spelling error
* clarify that function performs in-place modification of world
* add comment to clarify intent of range operation
* fix bad indents in comments
* clean up __columnsAccessor comments and code
* improve comments around clipPredicate
* field name consistency
* improve comment on quantiles params
* save graph selection in redux state
* fix old graph brush select regressions
* refactor graph brush selection to work with undo/redo
* update tests to match new crossfilter spatial select API
* graph selection state now in redux
* remove dead code
* sync graph selection with redux state; improvements to undoable machinery
* fix regression in undoable
* differentiate graph selection cancel from deselect action
* simplify calculation
* remove debugging code
* fix responsive repaint bug in graph selection tool
* undoable debugging and code cleanliness
* undoable action filter state now merges, rather than replaces
* improve comments
* add debounce to undoable action filter; improve comments and debug sanity check code
* comments
* fix undoable bug with clear scatterplot actions
* disable undoable debug flag
* cleanup API and comments around statemachine
* add test id attribute to lasso
* add better error handling for gene fetch requests
* immutable crossfilter
* first cut at reducer refactor with cascade model
* add initial redo/undo implementation
* small optimization
* integrate expression with history
* add tests for new reducers and fix a couple of small initialization bugs
* treat tiny lasso selections as a clear
* better function name for clarity
* fix undo for differential expression
* remove logging
* fix regression due to bad merge
* cleanup and comments for clarity
* improve undoable configuration for flexibility
* fix stale comments
* remove debugging code from production build
* rename categoricalSelectionState
* rename file
* improve comments
* initial dataframe commit
* initial dataframe port of core app
* rename variables for clarity
* remove unused import
* comment out unused code
* fix array handling bug in crossfilter dimension creation
* allow creation of empty dataframes
* handle non-existent columns
* handle non-existent columns
* revise tests for new dataframe
* comments for clarity
* comments for clarity
* generate bulk add placeholder with real gene names
* fix bug in gene name adding
* more dataframe unit tests
* fix bug - subset from current world, not universe
* put cut and pasted code into a single function
* improve caching of crossfilter
* remove cascading update bug from graph
* more performance work
* improve state handling for scatterplot
* performance optimization of critical path
* add column summarization
* dataframe utils
* add callOnceLazy
* fix tests
* minor updates found during review
* fix misspelling
* remove RESTv02 from function names
* comment cleanup
* cut/icut col parameter defaults to null
* break up large test
* improve tests and comments on dataframe at/has functions
* add Dataframe withCol/dropCol
* expression varData now stored in a dataframe
* dead code cleanup
* use dataframe.summarize()
* test cases for Dataframe.col.summarize
* update test cases for new dataframe summarize
* improve naming
* use new hasCol API
* add comments
* add more Dataframe.withCol tests
* add ability to specify row index in cut operation
* retire subsetVarData function
* correctly handle expression subsetting
* lint and improve comments
* rename cut to subset
* changes based on PR review
* initial dataframe commit
* initial dataframe port of core app
* rename variables for clarity
* remove unused import
* comment out unused code
* fix array handling bug in crossfilter dimension creation
* allow creation of empty dataframes
* handle non-existent columns
* handle non-existent columns
* revise tests for new dataframe
* comments for clarity
* comments for clarity
* generate bulk add placeholder with real gene names
* fix bug in gene name adding
* more dataframe unit tests
* fix bug - subset from current world, not universe
* put cut and pasted code into a single function
* improve caching of crossfilter
* remove cascading update bug from graph
* more performance work
* improve state handling for scatterplot
* performance optimization of critical path
* add column summarization
* dataframe utils
* add callOnceLazy
* fix tests
* minor updates found during review
* fix misspelling
* remove RESTv02 from function names
* comment cleanup
* cut/icut col parameter defaults to null
* break up large test
* improve tests and comments on dataframe at/has functions
* first flatbuffer schema
* do not lint auto-generated files
* add flatbuffers package
* add flatbuffer module
* wire up /data/X/T route
* use flatbuffers for matrix data fetc
* clarity and comments
* add flatbuffer layout route
* clean up obsolete code
* fix tests
* move flake8 config to setup.cfg
* add comments
* lint
* rework layout routes for fbs
* add more type support to fbs
* lint
* add flatbuffer support for annotations
* function name improvements
* fix botched merge with master
* remove unused import
* route cleanup for flatbuffers
* rename function for clarity
* add missing globals to Jest tests
* fix client JS tests
* fix routes for Python tests
* comments for clarity
* non-finite floating point hardening
* more non-finite number handling
* lint
* fix tests for summarizeAnnotations
* harden diffexp calculation against FP errors
* cleanup unused code
* lint
* add encoding tests for flatbuffers
* application type specified as strings
* fix spelling error
* improve variable names
* add note about documentation gap
* rename FBS DataFrame to Matrix
