* embedding
* menu bottom left
* button
* change gutters to support lower toolbar
* fix scatterplot layout
* fix tests to match new layout
* fix smoke tests to match new layout
* better sentence, dataset.nObs to top
* scatterplot position
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
* 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
* 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>
* Decreased the scope of polygonToPath and distance variables. Added a
new variable for the lasso path color. Removed the color setting from
handleDragStart, since this is already set in handleDrag. Added a
closePathColor "#bb2f00" which is the complementary of lasso path color.
When a lasso can close, the color will change from blue to red.
* Fix some linter issues.
* Fixed some linter issues.
* Fixing some linter issues.
* Changed lasso open and closed to BLUE5 and GREEN5 respectively.
* add opacity change on selection state
* change overlay z-index to capture pointer
* https://www.youtube.com/watch?v=xrg-RgF5F8o
* render null if no coloring by continuous
* run lint on push + pr
* revert commit
wrong branch
* run eslint --fix
* camelcase
* camelCase config part 1
* part 2
* part 3 - removing subscripts
* fix "class-methods-use-this"
* fix "class-methods-use-this"
* fix eslint ignores
* add eslint ignore for set state in update
* reformat comments to appease eslint
* add a11y features
* sort-comp fix
* a11y fix
* add ignore for set state in update
* add a11y htmlFor
* remove unused toast
* remove unnecessary bind
* add ignore for set state in update
* add rel="noopener noreferrer"
Using target="_blank" without rel="noopener noreferrer" is a security risk: see https://mathiasbynens.github.io/rel-noopener
* use arrow function to bind
* remove unused definitions/declarations
* prettier
* remove unused state
* add comments to empty catch blocks remove curly brackets
* escape '
* use eqeqeq
* switch from default export
* remove ignore log
* remove static
* fix import
* revert subscripting config
* clean-up
* remove unnecessary subscript
* fix new errors from master
* change category click handler to a class property
* fix camelcase changes that slipped by
* unused import
* Fix newly introduced ESLint errors from addGenes
* 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.
* add test labels
* prettier + add clcik return to clickOn()
* prettier + begin test
* finish label counting test
* add util to get coordinates of element
* add test id to labels
* add test to check overlay transform
* remove logs
* rename to match master
* Remove unused variables and imports
* Simplify conditional
* Fix typo
* Do not overprune var data cache
There is a bug in how the universe and world gene sets are constructed
and passed to `ControlsHelpers.pruneVarDataCache` that causes the var
data cache to be over-pruned. This commit fixes the issue.
Consider the following example from the node console:
```
❯ node
Welcome to Node.js v13.5.0.
Type ".help" for more information.
> new Set([1], [2], [3])
Set(1) { 1 }
```
What we really want is the set `Set(3) { 1, 2, 3 }`, which can be
constructed as:
```
> new Set([].concat([1], [2], [3]))
Set(3) { 1, 2, 3 }
```
* add simple error message helper
* port all label name pickers to use the new LabelInput component
* use pure components where possible
* cleanup
* more cleanup
* lint
* change new label prompt
* check to see if display state has changed
* add display state
* create onDisplayChange
* check to see if displaying anything and add opacity drop
* pass callback down to children
* add middle truncation to labels
* remove unused import
* add a bit of documentation
* make prop addition more clear
* rename onDisplayChange -> overlayToggled for readability
* 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
* refactor reducer to no longer support hover state and hold many labels
* refactor to generate centroidCoordinates for all values of a category
* create hash for function and memoize export
* create button to display all labels for a category
* clear state
* create label for each thing
* calculate on each value
* change to in place modification of map
* switch to for loop with iterator instead of forEach
* use map from centroidLabel instead of creating copy
* adapt for map
* utilize tarrays
* begin documentation
* disable centroids if in zoom mode
* clean up
* persist uncalc coordinates
* document
* clean up and document
* cleanup and document
* fix
* fix undefined labels and document changes
* fix first element skip
* fix conditional recalc
* rename centroidLabel -> centroidLabels
* break out dilation on hover to new reducer
* numerous styling changes for readability
* change centroid icon
* remove colorAccessor from parameters
* recalc centroids on world change
* make label toggle undoable
* remove unused import
* highlight labels on hover
* remove special characters from svg id
* lighten backdrop
* only generate new centroids if they pre-exist
* fix issue with spaces in catagorical value name
* add label buttons to menubar
* change reducer to use colorAccessor and have single toggle
* fix check to see if svg should be rendered
* move svg overlays onto a single svg layer
* dilate on label hover
* remove logs
* allow centroid to update along side regl renders
* allow actions to pass through svg if in zoom mode
* remove artifact from circle
* remove comment
* remove disabling of centroid button
* fix conditional map to screen
* make styling label conditions stricter
* prettier
* refactor onto master
* refactor computePointFlags() to use pointDilation store
* notify when viewport changes
* move svg attributes out of lasso setup and prevent rerenders/writes
* begin playing with transform matrix
* first solution for camera interaction
* create transform using nested groups
* semi-working method using nested groups with transforms
* inversely scale text
* properly do final transform
* cleanup dead / test code
* reinstate original functionality
* breakout centroid labels labels into separate component
* default toggle on for testing
* separate lasso and centroid layers
* remove unnecessary attributes, working hover
* dilation on label hover
* fix dilation on scatterplot
* add dilation on label hover
* break overlay into separate component
* make overlay agnostic to children
* move label mouse actions to centroidlabels component, add overlay state
* remove lasso on switch to camera
* disallow user selection
* fix reducer
* fix subset with continuous color error
* reset labels on color by continuous
* revert centroids on by default
* refactor for nested restructuring
* remove update checking
* remove unused method
* readd deleted hover delay
* remove old centroid setup
* remove centroid from undoable
* cleanup dead code
* remove dead code
* rollback unnecessary changes
* begin adding annotation functionality
* add annotation functionality
* add reset and undo functionality
* change centroids on layout change
* don't create label for unassigned
* add comment pointing out POI for performance
* touch up matrix transform comment
* add comment explaining coordinate space and children's assumed space
* remove dead code
* switch to pure component
* connect centroidLabels to redux
* clean up camera check and null result
* tool tip change
* rename centroid toggle and the like
* fix the misalignment of buttons, also make blueprint use consistent
* fix comment spelling mistakes
* introduce variable for cleaner logic expressions and state assignment
* alter tooltip text to back color by interaction
* remove manual iterator manipulation for forEach()
* remove debounce
* nit fix
* tooltip wording fix
* lint
* Create right sidebar files, move histos over
* restructure continuous legend + all padding
* right sidebar file
* proper graph positioning and resize
* new lasso values since right sidebar
* fix autosave position
* freeze objects
* component rendering perf work
* use PureComponent where safe
* remove obsolete WorldUtil code
* make brushable histogram a pure component
* many graph/scatterplot fixes: 722, 882, 758, 886
* fix e2e test breakage caused by graph transform work
* convert webgl point shaders to use flags rather than explicit point size
* remove unused packages from dependencies
* fix typo in regl prop name
* factor common code into util helper file
* legibility tweaks
* enable centroid
* introduce new sizing
* scale point size based off hovered category
* add styling
* fix margins
* disable centroid labels
* remove unused code and add detail to comment
* remove cell dilation on selection toggle
* move hover to name label
* hover on value except for checkbox
* add border radius to value
* Connect mouse over events to reducer actions
* Change Styling on hover
* Rename reducer actions to be more descriptive
* Reorder reducer in cascade
* Create centroid calculation util
* Whitespace
* Typo fix, use correct action
* Create centroid calc util
* Create centroid svg setup
* Refactor existing svg layer to toolSVG
* Change calcCentroid signature and centroidXY to match mapPointToScreen
* Add id and styling
* Run prettier
* Set z-index to 999
* Draw the label
* Introduce the centroid SVG, refactor code to allow both SVG layers
* Add text label and compute radius based on population
* Implement optional chaining
* Update font family
* Optimize calcMeanCentroid()
* Create and utilize calcMedianCentroid()
* Remove mass circle from label
* Remove styling change on hover
* Remove reducer action logs
* Prettier
* Swap out binds for arrow functions
* Style text
* switch from selectAll() to select()
* Reflect centroid container's purpose in id
* Remove mass from the output
* Swap to obj
* Add finite check
* Don't draw centroid if no finite values
* Fix finite check
* Remove log
* Toggle label coloring based on colorBy state
* Pass cursor events through centroid svg
* menubar 1
* zoom switching
* centering, pixel perfect canvas
* remove dead args and code
* clipping
* remove log
* if
* connect props
* lint
* undo
* logo left, componetize
* graph back to full height
* shadow to top
* do not prematurely call event handlers during render
* change test to deal with async histogram creation
* left section padding
* lint
* adjust graph to account for top bar,
* lasso tests
* refine histogram tests
* remove testing (onlys)
* change pan speed to 1 per issue #722
* correct handle scaling of graph when aspect ratio less than one
* add package lock
* add invert to our scale functions
* correctly transform to/from gl coordinates
* remove unused import
* fix naming of import
* update smoke tests
* 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
Bruce Martin