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174 Commits

Author SHA1 Message Date
Bruce Martin
20317fd08f Add URL data locators to launch sub-command (#920) 
* 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
 2019-09-15 09:01:53 -07:00
Bruce Martin
84c815cc04 pin h5py to 2.9.0 to temporarily work around regression (#916) 2019-09-11 13:20:15 -07:00
Charlotte Weaver
77de22d1ed merge louvain and prepare extra requires (#897) 2019-08-29 12:49:19 -07:00
Charlotte Weaver
28c4d28308 extract prepare from main install (#887) 
* extract prepare from main install

* add requirements-prepare to manifest
 2019-08-21 14:26:01 -07:00
Charlotte Weaver
b8c05763fe sparse tests (#894) 2019-08-21 14:09:36 -07:00
Charlotte Weaver
613f1a911f pin matplotlib dependency (#885) 
reordering packages does not work from dist install
 2019-08-14 14:21:07 -07:00
Charlotte Weaver
79a503e436 fix bad matplotlib library by installing scanpy first (#881) 2019-08-12 16:42:26 -07:00
Colin Megill
d16a69e158 bump version to 0.11.0 (#850) 
* bump version to 0.11.0

* manually fix version number
 2019-07-16 14:27:41 -04:00
Charlotte Weaver
3d98797d8c Installer (#840) 2019-07-12 12:29:22 -07:00
Charlotte Weaver
722a91f1d2 remove options widget + launch on file selection (#839) 
* remove options widget + launch on file selection

* extend drop area width
 2019-07-09 10:46:13 -07:00
Charlotte Weaver
8afb22a017 GUI UI Elements (#816) 2019-06-27 17:30:57 -07:00
Charlotte Weaver
5effe4bbbb removed --diffexp cli param (#826) 2019-06-26 14:46:58 -07:00
Charlotte Weaver
d5deb1579f [EASY] fix max-category-items (#813) 
* fix max-category-items

* match default for max category items

fe had 1000, be had 100
 2019-06-13 15:45:43 -07:00
Charlotte Weaver
afeddad343 windows fixes (#767) 2019-06-11 11:41:27 -07:00
Charlotte Weaver
0f17b84dc1 Add reload back in (#808) 2019-06-06 13:49:15 -07:00
Charlotte Weaver
3edb87d125 gui multiprocess - experimental feature (#780) 2019-06-06 10:52:05 -07:00
Bruce Martin
ca9a6796d8 release 0.10.1 (#797) 2019-05-30 13:44:42 -07:00
Bruce Martin
a6142bdf93 improve graph scale and centering (#796) 
* add gutter to embedding canvas

* improve layout scale and translate

* fix lint

* pin tables to version 3.5.1

* fix lasso coordinate smoke tests
 2019-05-30 13:31:41 -07:00
Bruce Martin
c6252825f3 release 0.10.0 (#794) 2019-05-29 16:55:43 -07:00
Bruce Martin
4b96b3a635 fix incompatibility of flask reload and port searching (#793) 
* WIP

* add --developer; fix incompatibility of --port and --debug

* put REST tests on separate ports

* PR review
 2019-05-29 16:38:57 -07:00
Bruce Martin
3dc45d6330 do not hard-wire column names in annotations (#785) 
* 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
 2019-05-24 21:00:54 -07:00
Bruce Martin
a8c2e408d1 update to latest anndata and remove restriction on scipy (#790) 2019-05-24 11:23:35 -07:00
Bruce Martin
2357d0c1b8 layout change UI (#776) 
* add layout to schema

* add layout choice action and reducer

* multi layout UI

* update unit tests

* add missing file

* update test schema

* fix duplicate test id

* fix tabs

* PR lint

* fix pytest
 2019-05-22 13:21:33 -07:00
Charlotte Weaver
ab4c74a321 remove psutil (#773) 2019-05-18 10:53:45 -07:00
Charlotte Weaver
e2ad28a510 exclude recent scipy versions (#770) 2019-05-17 15:13:22 -07:00
Bruce Martin
efa1709158 add multi-layout support to back-end (#766) 
* add multi-layout support to back-end

* remove obsolete code

* temporary code to apply heuristic choice of default layout

* fix tests

* update python tests

* more py lint

* PR review changes

* more PR lint

* PR lint
 2019-05-16 14:49:22 -07:00
Charlotte Weaver
d6040f687a port retry (#761) 
* 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
 2019-05-14 14:04:13 -07:00
Bruce Martin
b9a1e30652 large file size guardrails (#763) 
* large file guardrails

* fix lint

* PR review

* remove unused import

* use standard slice for CSR

* revert change
 2019-05-13 18:13:16 -07:00
Charlotte Weaver
8a94b1e086 fix #754 (#755) 2019-05-07 12:43:20 -07:00
Charlotte Weaver
c12cb2424a release bugfix (#749) 
* add __init__.py

* bump version
 2019-05-06 10:16:36 -07:00
Bruce Martin
1471d6b214 release 0.9.0 (#746) 2019-05-04 08:41:56 -07:00
Charlotte Weaver
98b63fa9ea Moved to python threads (#745) 
So we could use daemon threads
 2019-05-03 14:48:48 -07:00
Bruce Martin
b521a17ffd improve column access speed for sparse matrices (#742) 
* improve column access speed for sparse matrices

* add FAQ entry about data format performance

* add note about using --sparse flag for prepare command

* clean up for PR review

* Update docs/faq.md

Co-Authored-By: bkmartinjr <bruce@chanzuckerberg.com>

* improvements to big data faq
 2019-05-01 15:44:01 -07:00
Charlotte Weaver
8a72010768 PyQt5 -> PySide2 (#738) 2019-05-01 09:03:16 -07:00
Charlotte Weaver
9f10d8095a GUI app (experimental) (#730) 
* add default config

* first pass

* flake8

* cleanup

* first pass at using qthreads

* cleanup

* WIP

* better error handling

* improved UI

* bugfix

* fix merge bugs

* import order

* cleanup

* make gui requirements optional

* pr review requested changes

* Update server/gui/main.py

Co-Authored-By: csweaver <charlottesweaver@gmail.com>

* pr review request

* qt child class methods -> camelCase

* whitespace
 2019-04-30 12:52:15 -07:00
Charlotte Weaver
ea187f48e0 add scripts from cli (#680) 
* add scripts from cli

* add warning when including scripts

* flake8 fixes

* confirm scripts injection
 2019-04-22 12:30:57 -07:00
Charlotte Weaver
9c6273eb94 core library (#711) 
* 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
 2019-04-22 12:24:07 -07:00
Charlotte Weaver
73852dd6f4 use flask's json (#703) 2019-04-09 12:59:09 -07:00
Sidney Bell
34e5a91dc6 Add calculate_qc_metrics to `prepare (#697) 
* Calculate QC metrics

* Add QC metrics to prepare section of readme

* Add pointer to scanpy qc metrics function

* Don't explicitly pass qc flag as arg

* Add explicit toggle for run-qc/skip-qc

* Move qc metrics calculation to separate step/function
 2019-04-09 08:56:07 -07:00
Sidney Bell
c9a56fa73a Update scanpy version (#688) 
Update to version 1.3.7
 2019-04-04 12:16:30 -07:00
Charlotte Weaver
ce8326ddea bump version (#684) 2019-04-01 14:42:22 -07:00
Sidney Bell
16f93397ae Support diffmap and phate layouts. Explicitly handle embeddings with >2 components. (#662) 
* Add diffmap and phate to supported embeddings

* Explicitly pull the first two components of any given layout
 2019-03-21 19:06:05 -07:00
Charlotte Weaver
b6d468376a py37 fixes (#646) 
* add python version for nightly build

* update numpy version required

older versions interact poorly on anaconda + python 3.7
 2019-03-14 14:51:55 -07:00
Charlotte Weaver
d8fc7e40a1 Support python3.7 (#645) 
* Support python3.7

* add 3.7 env to travis
 2019-03-14 12:08:46 -07:00
Charlotte Weaver
e875ed739b More informative out-of-memory error (#644) 
* more informative error message: memory error

* flake fix
 2019-03-12 14:19:00 -07:00
Colin Megill
a0f54b4871 Add menu (#631) 
* add menu

* Added library versions to config

and tests

* add template version number
 2019-03-06 11:56:46 -05:00
Alex Wolf
82493d1019 Add forced directed graph drawing to allowed layout options (#626) 
* added forced directed graph drawing layout options

* added line breaks for 120 character limit
 2019-03-05 13:10:07 -08:00
Bruce Martin
d8e3721846 bumpversion to 0.7.0 (#623) 2019-03-01 12:25:30 -08:00
Bruce Martin
57c4e9ff33 Flatbuffer cleanup (#598) 
* dead code and route removal

* more dead code cleanup

* fix scanpy_engine tests

* lint

* add missing catch in filter parsing

* update scanpy NaN tests

* more fbs tests and dead test removal

* remove forced default for content type negotiation

* bit of cleanup

* more fbs test cleanup

* lint

* remove swagger

* swagger cleanup

* lint

* correctly handle lack of templates

* more dead code removal

* remove unused files

* fix dev build

* lint
 2019-02-19 08:50:29 -08:00
Charlotte Weaver
4e67c645f8 bumped version (#602) 
0.6.0 was burned on pypi
 2019-02-14 10:00:16 -08:00