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Author SHA1 Message Date
Charlotte Weaver 0f520f2fd4 [Merge on next release] Document how to install cellxgene prepare (#889) 
* Document how to install cellxgene prepare

after pr #887 merged

* formatting

* remove reference to cellxgene[louvain]
 2019-09-13 18:15:06 -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
Charlotte Weaver 6a86883c2d Remove stray quote (#854) 2019-07-19 12:40:54 -07:00
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 eac514e04d update favicon (#814) 2019-06-13 11:29:27 -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
Charlotte Weaver 1d6bb032a3 remove async from describe blocks (#805) 2019-06-03 14:59:16 -07:00
Charlotte Weaver 63af79d3f8 Add developer guidelines (#769) 
* Add developer guidelines

* minor formatting

* PR clarifications/lint

* more pr fixes

* link fix

* below->above

* pr suggestions
 2019-05-21 13:57:34 -07:00
Charlotte Weaver 2d4e827bea wait for element before getting text/html (#777) 2019-05-20 11:35:53 -07:00
Charlotte Weaver ab4c74a321 remove psutil (#773) 2019-05-18 10:53:45 -07:00
Charlotte Weaver 82d65addec always run smoke tests (#772) 2019-05-18 10:50:17 -07:00
Charlotte Weaver e2ad28a510 exclude recent scipy versions (#770) 2019-05-17 15:13:22 -07:00
Charlotte WeaverandTony Tung 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
Charlotte Weaver 2354731083 install from dist instead of build on travis (#760) 2019-05-09 15:32:06 -07:00
Charlotte Weaver d522cc8f91 Add clipping test to smoke tests (#757) 
* Add clipping test to smoke tests

* devtools on in debug
 2019-05-09 15:31:55 -07:00
Charlotte Weaver 86eb01eb2c improve release process (#752) 
* Add --no-cache-dir to make release-install target

Prevents installing from cache so you get the freshest release

* Testing releases is not optional

* Updated release documentation
 2019-05-08 09:36:00 -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
Charlotte Weaver 98b63fa9ea Moved to python threads (#745) 
So we could use daemon threads
 2019-05-03 14:48:48 -07:00
Charlotte Weaver 77a4495b28 Update README.md (#743) 
Fixes #702
 2019-05-02 16:54:39 -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 ad0a3c939c faster ci (#713) 
* parallelize docker build

* cache npm too

* testing skip install
 2019-04-15 16:34:40 -07:00
Charlotte Weaver d581a0d460 color by gene smoketest (#707) 
* add test for color by gene expression

gene expression and metadata color by are handled differently

* error on console.error

not just on thrown errors
 2019-04-11 17:06:36 -07:00
Charlotte Weaver 73852dd6f4 use flask's json (#703) 2019-04-09 12:59:09 -07:00
Charlotte Weaver c9a8e3ea42 Add manual UX tests (#699) 2019-04-08 13:23:17 -07:00
Charlotte Weaver 3167e38993 update docs to reflect python 3.7 support (#685) 2019-04-02 09:24:50 -07:00
Charlotte Weaver ce8326ddea bump version (#684) 2019-04-01 14:42:22 -07:00
Charlotte Weaver 5d4b11d287 Better smoke tests (#669) 2019-03-28 16:47:42 -07:00
Charlotte Weaver 096d477893 use Math.abs when calculating lasso area (#673) 2019-03-27 21:02:31 -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
Charlotte Weaver f96fd36ecb Update test ui names (#638) 
* Fixed changed testid

* Added debug mode for running tests
 2019-03-12 10:17:09 -07:00
Charlotte Weaver 68dfbcc2eb Add force graph to docs and example dataset (#630) 2019-03-05 20:59:54 -08:00
Charlotte Weaver 2583016693 Fix bug where prod would automatically run after release stage 2 (#625) 
* Fix bug where prod would automatically run after release stage 2

* fixed make release-burned
 2019-03-01 20:20:16 -08:00
Charlotte Weaver 2bae696986 Smoke tests (#604) 
smoke tests
 2019-02-27 15:46:58 -08:00
Charlotte Weaver 4e67c645f8 bumped version (#602) 
0.6.0 was burned on pypi
 2019-02-14 10:00:16 -08:00
Charlotte Weaver 8b28d51dfa bump version (#601) 2019-02-13 16:29:14 -08:00
Charlotte Weaver 40ad283107 create server testing doc (#592) 2019-02-13 15:35:45 -08:00
Charlotte Weaver 585a5808b9 check if accept type in content type string (#589) 2019-02-08 09:41:24 -08:00
Charlotte Weaver ad9be3cdd7 remove build-dev from .gitignore (#583) 2019-02-04 14:47:28 -08:00
Charlotte Weaver f737cc4ee4 Build improvements (#577) 2019-02-04 14:15:35 -08:00
Charlotte Weaver 1103272b95 De-dupe -d CLI option alias (#575) 
removed from debug, diffexp gets to keep it
 2019-01-30 16:11:21 -08:00
Charlotte Weaver d31c05c970 Add backed script to package.json (#566) 
* QOL script for FE devs to get & launch the backend

* ensure python3.6

* changed name to backend-dev
 2019-01-29 11:41:05 -08:00
Charlotte Weaver ecaa32cfb2 bump version (#563) 2019-01-17 17:14:44 -08:00
Charlotte Weaver 10693b08cc Add __init__ file so fbs can be imported (#562) 2019-01-17 17:11:31 -08:00
Charlotte Weaver b02361a6bf bump version (#560) 2019-01-17 16:54:25 -08:00
Charlotte Weaver 394da40bea Doc formatting improvements (#549) 2019-01-10 15:09:02 -08:00
Charlotte Weaver f0f7200f0b Move jsonification to engine level (#511) 2018-12-18 21:14:24 -08:00
Charlotte Weaver 46ad346df1 Clarify that we do not support python 3.7 (#512) 
* Update setup.py

* Readme: no python 3.7

* specify 3.6 in venv

* clarify 3.7 error

we will support it eventually
 2018-12-13 15:15:56 -08:00
Charlotte Weaver 83154577e4 Black -- formatter for python (#508) 
* Add black

* use black to format code

* Black version
 2018-12-12 09:44:47 -08:00
Charlotte Weaver a847951658 Update slack link (#506) 2018-12-11 10:20:22 -08:00
Charlotte Weaver 24af6efbcb Add Docker file (#505) 
* Add docker support

* Add readme

* minor fixes
 2018-12-11 10:18:10 -08:00
Charlotte Weaver 9604231a2a Add alternative to install [louvain] extra requires (#500) 
* louvain install by hand

* reworded
 2018-12-10 14:46:55 -08:00
Charlotte Weaver 0d0a32f272 Added PR guidelines (#492) 
* Added PR guidelines

Added document to cover guidelines for creating, reviewing and merging PRs.

* fixed typo

* another typo

* grammar

* Remove 5's title

The subheading is clearer as a top-level
 2018-12-06 13:43:10 -08:00
Charlotte Weaver 5c6cc597c8 Default warning in debug mode (#497) 2018-12-05 13:38:34 -08:00
Charlotte Weaver 1e66ec2b89 Update scikit learn (#487) 
They finally fixed their cloud pickle issue
 2018-11-30 12:02:28 -08:00
Charlotte Weaver 4a50f0ed46 External host option (#481) 
* allow specifying host ip instead of listen all

* flask serving

* Limit to ip addresses only
 2018-11-29 17:01:49 -08:00
Charlotte Weaver 76c0cbf16b loose -> lose (#479) 2018-11-28 13:07:10 -08:00
Charlotte Weaver 455d987398 Add custom format for warnings (#477) 
[cellxgene] Warning: <message>
 2018-11-28 12:47:11 -08:00
Charlotte Weaver 28f5263c88 bump version (#475) 2018-11-27 15:43:19 -08:00
Charlotte Weaver 0c26f227fe bump version (#470) 2018-11-26 15:38:47 -08:00
Charlotte Weaver 43a4e087ef Fix formatting issues (#468) 
- Fix step 8 bullets
- Appropriate capitalization
- Add link to release notes doc
 2018-11-26 13:52:00 -08:00
Charlotte Weaver f2612707bb bumped version (#466) 2018-11-26 11:42:56 -08:00
Charlotte Weaver 2b5094665f version 0.2.0 (#456) 2018-11-16 15:12:54 -08:00
Charlotte Weaver 3475f3f12e Update release_process.md (#443) 
* Update release_process.md

* Clarified release process
 2018-11-16 14:36:43 -08:00
Charlotte Weaver 1a5f49239a Release 0.0.4 (#447) 
* 0.0.3 bump

* release 0.0.4
 2018-11-15 16:43:59 -08:00
Charlotte Weaver dfc04d8de5 Add requirements to manifest (#445) 2018-11-15 11:56:22 -08:00
Charlotte Weaver 07cda497d9 build bug fixes (#438) 
* Fixes compatibility conflict with numpy version and anndata version #434

* Forces description to be read as unicode

fixes #435
 2018-11-14 14:21:02 -08:00
Charlotte Weaver bc0cecbd1c Release Test (#427) 
* bump-update

* Release Test!
 2018-11-14 11:03:52 -08:00
Charlotte Weaver 47ce0cfc49 Update release_process.md (#428) 2018-11-09 16:58:01 -08:00
Charlotte Weaver 018e3ae5c4 bump-update (#426) 2018-11-09 14:17:07 -08:00
Charlotte Weaver aa29c91470 Prepare fixes (#416) 
* Error on overwrite=false but no output file

* Add prepare requirements to requirements.txt

* no saved output error -> warning

* Catch clustering import error

* lint fixes

* Fix missing output message
 2018-11-09 13:51:30 -08:00
Charlotte Weaver dd56d0937c fix anaconda build (#421) 
* 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
 2018-11-09 13:22:45 -08:00
Charlotte Weaver dfcef6075e add updating the cli version (#420) 
* add updating the cli version

* remove bdist_wheel -- no platform specific needs
 2018-11-09 12:52:10 -08:00
Charlotte Weaver b4edd56735 Requirements updates (#422) 
* Unpin requirements that do not need to be fixed

* add twine to dev requirements

* Add versions to dev too
 2018-11-09 12:50:15 -08:00
Charlotte Weaver 1dc80145dc Add bumpversion (#423) 
* Add bumpversion

* Update readme for bumpversion
 2018-11-09 10:01:02 -08:00
Charlotte Weaver 7d5c054b90 Launch validation (#414) 
* WIP

* Cleanup

* Validation

* typo

* Max category limit 100 -> 500
 2018-11-07 13:01:13 -08:00
Charlotte Weaver 26d222cd75 Move computation options to app (#386) 
no need to import scanpy engine for CLI help so speeds up time response
 2018-10-26 17:07:21 -07:00
Charlotte Weaver 6c23a72e5f CLI renaming and phrasing (#385) 
* 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
 2018-10-26 15:59:34 -07:00
Charlotte Weaver 16b0741a6c Hide stack traces unless in debug mode (#384) 2018-10-26 13:36:53 -07:00
Charlotte Weaver 94f95d6565 CLI Launch (#366) 
* 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
 2018-10-24 19:28:59 -07:00
Charlotte Weaver 02b2349807 Pin scikit-learn to fix imp error (#375) 2018-10-24 14:46:34 -07:00
Charlotte Weaver 9e5114a730 Ignore built media files (#372) 2018-10-24 13:02:17 -07:00
Charlotte Weaver 85f44ccabf Converts NaNs in pval to 1s (#365) 2018-10-24 10:57:29 -07:00
Charlotte Weaver 4ec938c166 Prefix client build (#367) 2018-10-23 15:56:57 -07:00
Charlotte Weaver efb55a6332 Renaming bind-all option to listen-all (#353) 
See discussion here https://docs.google.com/document/d/1tcAvODhdlUUAOJPHoGQB3fWOPmnw3XjK7MVhDRwNUnk/edit#
 2018-10-19 15:26:19 -07:00