* only load annotation var names
* remove incorrect usage of var annotation data
* temporary workaround for issue #480
* lint
* issue warnings only once per item
* add cutoff for low expression genes in topN selection
* remove debugging printfs
* change cli param name for diffexp cutoff
* change CLI param name
* second try at diffexp - using lfc sort with pval cutoff
* use lfc cutoff
* update comments to match code; cap p-value adjustment to max of 1
* lint
* explain diffexp in readme
* add link
* add diffexp-lfc-cutoff to test config
* update test to match revised diffexp spec
* fix latent bug in GET arg handling that was breaking tests
* lint
* comment cleanup
* fix variance overestimation so it is symmetric
* lint
* new diffexp REST API spec
* new diffexp REST API; faster diffexp and dataframe slicing
* first draft of fast diffexp
* convert variance calculation to two-pass method
* lint
* update front-end use of API
* fix typo in spec
* disable content compression
* catch index filter format errors
* clean up of dead code
* resolve PR review comments
* fix anaconda build
* Added link for TKAgg
* Add matplotlib to requirements
We are pulling it in through scanpy, but since we are importing it directly we should include it explicitly
* 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
* refactor cli to improve ux and enable easy incorporation of prepare as a subcommand
* switches to use click, which removes some boilerplate and gets us some improved ux for free
* changes the entry point for the cli
* changes the name of the browser option to --open and makes the default false
* add --obs-names and --var-names CLI params
* fix lint
* performance improvements in scanpy engine
* fix lint
* fix typo
* correctly handle sparse formats in diffexp
* fix diffexp and 1d slicing
* diffexp uses t-stat, not pval; clean up arg handling
* make _slice a static method
* revise scanpy tests to match new API
* add prepare cli
* fix handling of user path
* fixes for linter
* add flags and options for handling obs and var names
* add prepare cli
* fix handling of user path
* fixes for linter
* add flags and options for handling obs and var names
* address review requests
* Minor naming and phrasing changes from UX review
* category-selection-limit -> max-category-items
* Indicate load may taking a long time
* program -> command (for launch, prepare)
* debug -> verbose
* flask-debug -> debug
* Developer mode for debug
verbose on
open browser off
* move examples from epilogue to prefix
* Scanpy engine now required
Without the --engine param we need to error if scanpy engine cannot be imported rather than waiting for all engines
* CLI options and help matches proposal
(but not all options hooked up yet)
* Flesh out top level args
* Move computation args to engine
* CLI input file (#374)
* Fix test command
(tests still won't work)
* Input is file instead of directory
- also renamed example file
* Csweaver/debug (#376)
* Respect debug flag for logging flask calls
* Add loading messages
* max categories (#377)
* Add max categories
* Rename max_categories to category_selection_limit
* ensure whole numbers
* Launch browser to cellxgene
Also added --no-launch command line parameter
* Don't launch browser for tests
* rename no-launch to no-open
* Rejigger -no-open to positive destination
so later logic looks cleaner
* range encode filter range lists
* speed up data load
* add comment on scanpy read params
* update to latest scanpy/anndata
* performance improvments in data loading
* fix typo
* work around scanpy bug
* remove debugging print statements
