* initial cut at backed mode
* make flask multithreading conditional on debug flag
* update X access to support backed mode
* lint
* improve help message for backed mode
* fix tests
* add MatrixProxy to normalize supported matrix types
* add FAQ entry for --backed
* remove use of matrix.T
* clean up
* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user
* fix tests
* do not print diffexp speed warning if diffexp is disabled
* tweak wording of diffexp speed messages
* add FAQ entry on --disable-diffexp
* revise heuristic for warning about slow diffexp
* use quick tooltip delay on diffexp button
* add about arg
* add simple url validator
* attach about link to config api
* add links to configDefaults
* add conditional link in top left and menu item
* whitespace
* change to lower case
* move --about arg before click.command()
if this fixes it I have no idea why
* change link>URL
* be more descriptive about URL
* Make error more explicit
* refactor attach_data to accept about
* format
* change icon
* add trailing parenthesis
* whitespace
* initial commit of URL support for launch
* lint
* modify tests to use new data locator
* add locator unit tests
* fix typo in faq
* more lint
* update faq per PR review
* WIP
* import find_available_port method
* move method to utils
so I can add to eventually add to gui
* add fixed-port flag to tests
* Update server/utils/utils.py
Co-Authored-By: Tony Tung <tonytung@merly.org>
* pr review suggestions
* pr review suggestions
* fix outdated package.json
* update error message
* simplify find_available_port function
* Auto scan for ports unless port is specified.
* fix tests
* fix comment for find_available_port
* lint error
* differentiate port error from generic os error
* add errno to OSerror
* pr review fixes
* raise e -> raise
* oserror -> socket error
* move app creation to function
* create engine without load
* flake 8 fixes
* cleanup original scanpy test
* add default config
* handle missing data
* test data changes
* unify update
* load data isn't static anymore
* make app a class
* 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
* 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
