* enforce column name uniqueness for obs and var
* parameterize the column name containing obs and var user-readable names
* use the new annotation index value from schema
* update f/e unit tests
* PR review suggestions
* lint
* 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
* 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
* create helper file for controls reducer
* 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
* lasso working
* break out invert into own function
* action
* add spatial dimension to crossfilter, in support of polygon lasso
* improve comments on new dimension API
* lasso vs zoom
* remove memoization
* update to flash 1.0.2; turn on threading
* stand-alone helper routines for array slicing
* fix issue #405
* reset diffexp state when world changes
* performance work in dimension creation; fix world slicing bug
* update tests to match new state mgmt api
* update flask
* do not make dimensions for useless annotations
* update test to match optimizations
Move to new REST v0.2 communication between front and back-end. This is a first cut implementation which is functional, but will need follow-up enhancements for performance, error checking, etc. Protocol spec is in docs directory.
* Add filtering via indexing
* Using new filter specs
Indexing working
* Added filtering by annotation value
* factor out common methods
* Documentation
* create enum for axis (obs/var)
* Better description for filter's return
* Add boolean to enumerated types
* Augmented enum for scanpy axis
* Create schema for annotations
Based on datatype within scanpy/anndata
+ tests
* remove obsolete schema parse script
* Update rest api to remove old routes and add schema route
* Separate development requirements
* Warning for unsupported datatypes
* include -r requirements.txt in dev
* Merged downcast warnings
* Fixed bug where names were NaNs
Needed to include the index too when creating the series
* Add config endpoint
* Generate app features from CLI selections
* Move features to driver
* Add tests for schema
* Clearer version wording
* python3 version of super
* version from engine to package level
* move features to driver
* Revise layout function to match the new spec
* GET for layout/obs
* PUT Layout (#211)
* PUT Layout
* Csweaver/annotations (#212)
* Update scanpy engine to support the rest v0.2 annotation requests
* GET endpoint for obs annotations + tests
* Documentation
* Test annotations in scanpy engine
* Description for annotation-keys param
* annotation->annotations
* clarified return for annotations
* Use URL query list for annotations fields
* parse_filter parses v0.2 GET filters (#215)
* parse_filter parses v0.2 GET filters
* Don't allow index filters from query params
* Better variable conversion
* Parse filter improvements
- uses default dict
- renamed filter -> query_filter
* Cleanup Tasks (#216)
* Add test_api back into travis build
* Do custom JSON encoding the correct way
* Run cellxgene server in test setup
* Cleanup new tests too
* Option to bind to all interfaces (#225)
app.run("0.0.0.0") instead of app.run("127.0.0.1") binds to all interfaces.
Note: There are comments on the internet that says that the flask server is not up to the task of production serving. I don't think that such scalability concerns apply here, but I was able to get cellxgene working with twistd relatively easily, and we could switch to that if there are scalability concerns.
Test plan: browsed to <ip>:5005/api/v0.2/config on a different host.
* Add filtering via indexing
* Using new filter specs
Indexing working
* Added filtering by annotation value
* factor out common methods
* Documentation
* create enum for axis (obs/var)
* Better description for filter's return
* Add boolean to enumerated types
* Augmented enum for scanpy axis
* Create schema for annotations
Based on datatype within scanpy/anndata
+ tests
* remove obsolete schema parse script
* Update rest api to remove old routes and add schema route
* Separate development requirements
* Warning for unsupported datatypes
* include -r requirements.txt in dev
* Merged downcast warnings
* Fixed bug where names were NaNs
Needed to include the index too when creating the series
* Add config endpoint
* Generate app features from CLI selections
* Move features to driver
* Add tests for schema
* Clearer version wording
* python3 version of super
* version from engine to package level
* move features to driver
* Revise layout function to match the new spec
* GET for layout/obs
* PUT Layout (#211)
* PUT Layout
* Csweaver/annotations (#212)
* Update scanpy engine to support the rest v0.2 annotation requests
* GET endpoint for obs annotations + tests
* Documentation
* Test annotations in scanpy engine
* Description for annotation-keys param
* annotation->annotations
* clarified return for annotations
* Use URL query list for annotations fields
* parse_filter parses v0.2 GET filters (#215)
* parse_filter parses v0.2 GET filters
* Don't allow index filters from query params
* Better variable conversion
* Parse filter improvements
- uses default dict
- renamed filter -> query_filter
* Cleanup Tasks (#216)
* Add test_api back into travis build
* Do custom JSON encoding the correct way
* Run cellxgene server in test setup
* Cleanup new tests too
* Option to bind to all interfaces (#225)
app.run("0.0.0.0") instead of app.run("127.0.0.1") binds to all interfaces.
Note: There are comments on the internet that says that the flask server is not up to the task of production serving. I don't think that such scalability concerns apply here, but I was able to get cellxgene working with twistd relatively easily, and we could switch to that if there are scalability concerns.
Test plan: browsed to <ip>:5005/api/v0.2/config on a different host.
* Fix merge errors
- import warnings was improperly deleted
- scanpy engine tests were totally wrong
* Fix merge error with driver
* PUT /annotations (#235)
* Add query param for annotation name
* fix descriptions, eliminate else clause
* first cut at initial data load on rest 0.2 api
* Annotation var (#248)
* Fix bug strings are always objects in pandas
* Add axis to annotation method
* Add /annotation/var to REST api
* Csweaver/expressiondata (#242)
* Refactor expression method for REST v2
* Add message to QueryStringError
* Fix range filters
* Add GET route for /data
* /data PUT route
* rename expression to data_frame
* clarification of error
* Improve accept type handling
* support all schema types for 0.2 REST API
* remove REST 0.1 code; connect var annotations loading
* config reducer; use config to set data set title; remove obsolete templating code for data set title
* REST 0.2 expression conversion support
* partial port of expression to REST 0.2
* diffexp (#273)
* Add diffexp method to scanpy
and test
* Minor tweaks to diffexp
Get a minimal working version to unblock FE development
* Fixing things git deleted
* cleanup print statements
* Add index test
* additional, partial REST 0.2 bring up of diffexp
* Ignore unstructured annotations for data (#275)
This is a temp hack, need to figure out how to include data.uns if there is only one gene
* diffexp REST 0.2 port finish
* ignore unstructured annotaitons on all routes except layout
* correctly use varDataCache; maintain state during world rebuild
* correct varDataCache use
* temporarily disable all memoization
* refinements to expression data caching
* clear cell sets upon regraph/reset
* update version of REST to 0.2
* Travis build fixes
- comment out cache import
- fix duplicate test name
* Remove dependency from travis
* clarify semantics of config variables
* move generic action helpers into util
* mocks for redux refactor - for discussion
* more API design on redux refactor
* add new reuqired dependencies for build
* change babel target to use modern browser
* remove dead code
* remove dead code - joy plots
* checkpoint on redux refactoring
* checkpoint on redux refactoring
* fix mistaken rebase conflict resolution
* dead code removal; add name to dataframe backmap
* rename dataframe to universe
* update eslint config to more closely match prettier
* lint
* more eslint updates to match prettier
* additional config to make eslint match prettier
* add expression data to Universe/World
* remove obsolete reducers
* lint fixes
* more eslint cleanup
* lint
* lint
* fix but in countAllOnes when dimensions gt 1
* lint; do not display name metadata field
* lint; colors refactor
* lint; colors refactor
* update comments
* first cut at regraph and reset
* enable object-curly-braces consistent mode
* lint, handle regraph with no selection
* fix expression scatterplot bugs
* fix regression legend display
* add expression data cache
* remove console logging
* reset cell color on regraph/reset
* remove obsolete server URLs
* rename UniverseV01 to Universe_REST_API_v01
* add additional comments on the varDataCache
* merge universe reducer into controls reducer; simplify initialization-related actions
* use spread operator
* fix erroneous comment
* convert universe and world state to plain objects, and functionalize supporting code (remove ES6 classes)
* use spread operator
* lint
* improve variable names
* rename obsCrossfilter to crossfilter and obsDimensionMap to dimensionMap
* rename controls2 to controls
Bruce Martin