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Author SHA1 Message Date
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
Charlotte Weaver 2a3577f32b flask debug as hidden option (#352) 
* Remove flask debug flag

* Add debug flag as a hidden option to keep reload on change for developers
 2018-10-19 10:24:15 -07:00
Charlotte Weaver 06f402ab0a Do not calculate layout, used saved layout instead (#343) 
* Do not calculate layout, used saved layout instead

See for rationale: https://docs.google.com/document/d/1HJFvbdDHxxgkCW0DZzdTZ9CUMgc2ef2rQFukATBQWvE/edit

* Error handling for when layout has not been precomputed

* Server error (500) not client error (400) for unprepared data
 2018-10-18 11:51:38 -07:00
Charlotte Weaver 7c8b89eba3 Launch browser to cellxgene (#325) 
* 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
 2018-10-17 16:46:56 -07:00
Charlotte Weaver 2e9d576890 Correct capitalization in swagger template (#320) 2018-10-11 16:43:26 -07:00
Charlotte Weaver 3229babd14 Add caching back in (#312) 
* Add caching back in

Works now against filter instead of dataframe view

* Layout cache and move post->put

* Fix tests
 2018-10-11 16:29:46 -07:00
Charlotte Weaver b90292ce4c Bump interactive limits (#319) 2018-10-11 15:56:58 -07:00
Charlotte Weaver 210787cb5d Filter in engine (#307) 
* Add empty filter case

* Filtering dataframes moved to engine instead of rest

* minor changes from PR review

* Minor fixes from PR review

Pass {} instead of none if no filter
chain exceptions
typos
 2018-10-11 15:23:31 -07:00
Charlotte Weaver eb3b3fc59a Reorganize order of methods in engine and rest (#305) 2018-10-10 16:44:05 -07:00
Charlotte Weaver dce778f658 Config file is obsolete (#303) 2018-10-09 11:19:19 -07:00
Charlotte Weaver 11ef5ae51b REST Error handling (#299) 
* Use HTTPStatus for all responses

More informative than just the code as an int

* Fill out REST error handling

* Test error routes

* Use HTTP Status for tests too

* factor mime type request into function

* Better mimetype errors

* 404 -> 400 error for bad key
 2018-10-08 14:17:56 -07:00
Charlotte Weaver 8be0833d23 /layout put-> post (#301) 2018-10-08 13:38:13 -07:00
Charlotte Weaver 187bbfdcf7 /data/var (#295) 
* Upgrade version of scanpy

* /data/var

This works for everything except the case where there is only one gene. Anndata flattens X when there is only one var thus causing the transpose to fail.

* Fix edge case when an axis (obs/var) only contains 1 element
 2018-10-03 15:09:46 -07:00
Charlotte Weaver d09c820c1b Commit package-lock.json (#289) 2018-10-02 13:12:57 -07:00
Charlotte Weaver 023fd01957 Added "filter" level for var filter to match other filters (#267) 2018-09-24 15:09:34 -07:00
Charlotte Weaver 1712114c9d Merge pull request #190 from chanzuckerberg/revert-179-csweaver/api-v2-init 
Revert "Format loaded dataset"
 2018-08-14 10:43:15 -07:00
Charlotte Weaver 39414503bd Revert "Format loaded dataset" 2018-08-14 10:40:21 -07:00
Charlotte Weaver 451c930cb5 Merge pull request #186 from chanzuckerberg/csweaver/gitignore 
Cleanup .gitignore
 2018-08-14 09:52:43 -07:00
Charlotte Weaver 9d680cf8d8 Merge pull request #179 from chanzuckerberg/csweaver/api-v2-init 
Format loaded dataset
 2018-08-13 16:02:07 -07:00
Charlotte Weaver b884487789 Merge branch 'master' into csweaver/api-v2-init 2018-08-13 15:48:06 -07:00
Charlotte Weaver ddaa7016a5 Quote formatting 
' => "
 2018-08-13 15:00:23 -07:00
Charlotte Weaver a29ba8da4e Limit pytest ignore warning to only one specific warning 2018-08-13 15:00:06 -07:00
Charlotte Weaver 463cdef08b Cleanup .gitignore 
remove lines related to old separate repo version
add ignore for virtual environments and jupyter notebooks (I use them to test)
 2018-08-13 14:35:41 -07:00
Charlotte Weaver c8c098282d Merge pull request #185 from chanzuckerberg/csweaver/favicon 
Csweaver/favicon
 2018-08-13 10:56:39 -07:00
Charlotte Weaver 8c88f752ea Merge pull request #182 from chanzuckerberg/csweaver/static 
Set static folder to correct location
 2018-08-13 10:48:09 -07:00
Charlotte Weaver a4464d107f Add test to make sure static files are served 
this required that I break up the base url from the api route.
 2018-08-13 10:33:59 -07:00
Charlotte Weaver d44d267bda Initial tests for the rest v2 refactor 
testing the annotations and the data format validation
 2018-08-10 16:57:41 -07:00
Charlotte Weaver 55fa9b892a Splitting the format validation and mandatory annotations 2018-08-10 16:38:07 -07:00
Charlotte Weaver 21a1f00a64 Set static folder to correct location 2018-08-09 14:25:11 -07:00
Charlotte Weaver e96653b826 Serving favicon correctly 2018-08-09 14:14:45 -07:00
Charlotte Weaver 58000c1815 Format loaded dataset 
- create cell and gene ids
- recast numbers to float32/int32
 2018-08-09 11:23:43 -07:00
Charlotte Weaver 3961bdc46d Merge pull request #166 from chanzuckerberg/csweaver/clean 
Added clean script for cellxgene
 2018-08-09 10:22:13 -07:00
Charlotte Weaver 004303300b -f flag for file removal too 2018-08-09 10:09:19 -07:00
Charlotte Weaver ba1e26138f Merge pull request #167 from chanzuckerberg/csweaver/build-anywhere 
Allow build-client to run anywhere
 2018-08-09 09:45:47 -07:00
Charlotte Weaver d093dc2e3b Allow build-client to run anywhere 2018-08-08 15:17:23 -07:00
Charlotte Weaver 3f0bb2ce1d Added clean script for cellxgene 2018-08-08 15:10:33 -07:00
Charlotte Weaver 246f4e41f0 Merge pull request #156 from chanzuckerberg/csweaver/infer-metadata 
Infer schema if none exists
 2018-08-08 11:56:13 -07:00
Charlotte Weaver 67504dcaff Merge pull request #142 from chanzuckerberg/csweaver/cli-subparsers 
Csweaver/cli subparsers
 2018-08-08 11:52:38 -07:00
Charlotte Weaver af85792cce Don't forget unsigned ints! 2018-08-08 11:20:01 -07:00
Charlotte Weaver f4780a9806 Moved add to parser out of try block. 2018-08-08 11:18:06 -07:00
Charlotte Weaver 2a11af2550 Formatting 2018-08-07 17:01:19 -07:00
Charlotte Weaver 2b698cc7d0 Merge remote-tracking branch 'origin/csweaver/cli-subparsers' into csweaver/cli-subparsers 2018-08-07 16:57:13 -07:00
Charlotte Weaver e5c7c0c44a Warn instead if print when scanpy isn't available 2018-08-07 16:57:07 -07:00
Charlotte Weaver 11f88a9eb2 Warn instead if print when scanpy isn't available 2018-08-07 16:49:40 -07:00
Charlotte Weaver bf19bb7dce Formatting 2018-08-07 16:38:25 -07:00
Charlotte Weaver c2b3f331cf Add layout and diffexp calculations to cli options 2018-08-07 16:37:47 -07:00
Charlotte Weaver 499b9551f1 moved scanpy parser to scanpy class 2018-08-07 16:37:02 -07:00
Charlotte Weaver 0969854e9e Merge pull request #162 from chanzuckerberg/csweaver/require 
Trimming out secondary dependencies from requirements
 2018-08-07 16:14:28 -07:00
Charlotte Weaver 247b89ab0c Update README.md 2018-08-07 15:54:25 -07:00
Charlotte Weaver ccee3e0a38 api host 0.0.0.0 -> 127.0.0.1 2018-08-07 15:43:13 -07:00
Charlotte Weaver c11ae77de4 Trimming out secondary dependencies from requirements 2018-08-07 12:53:48 -07:00
Charlotte Weaver 0db24a6c07 Merge pull request #157 from chanzuckerberg/csweaver/readme-data 
Added instructions on how to load your own data in scanpy
 2018-08-07 10:19:31 -07:00
Charlotte Weaver 9236f02637 Merge branch 'master' into csweaver/readme-data 2018-08-07 10:18:57 -07:00
Charlotte Weaver 16d7fac88e Added instructions on how to load your own data in scanpy 2018-08-06 17:15:35 -07:00
Charlotte Weaver a2b699b05d Infer schema if none exists 2018-08-06 16:39:18 -07:00
Charlotte Weaver 12b8232327 Merge pull request #155 from chanzuckerberg/csweaver/pip-install 
Use pip instead of python setup.py
 2018-08-06 16:03:39 -07:00
Charlotte Weaver a22a4e2473 Use pip instead of python setup.py 2018-08-06 14:56:42 -07:00
Charlotte Weaver 8401d1dd3d Merge pull request #154 from chanzuckerberg/build-fix 
Fix build
 2018-08-06 12:23:41 -07:00
Charlotte Weaver 0c8b86d1c4 Merge pull request #141 from chanzuckerberg/csweaver/datatoapp 
Move data to a property of the app object
 2018-08-03 13:03:34 -07:00
Charlotte Weaver e682028b8e Use flask's current_app 2018-08-03 10:54:43 -07:00
Charlotte Weaver 8dbb131afd Move data to a property of the app object 2018-08-02 16:18:17 -07:00
Charlotte Weaver 64bfb7416e Merge pull request #121 from chanzuckerberg/csweaver/cli 
Csweaver/cli
 2018-08-02 15:12:11 -07:00
Charlotte Weaver ee5fe8f37b Merge pull request #138 from chanzuckerberg/csweaver/cache 
Add simple cache to backend
 2018-08-02 11:55:21 -07:00
Charlotte Weaver e11b905836 Cleaning up import statements 2018-08-02 11:34:00 -07:00
Charlotte Weaver 116cef551c Switch to default timeout for cache 2018-08-02 11:28:44 -07:00
Charlotte Weaver 489a2dd5db Add flask-caching to requirements 2018-08-01 16:29:38 -07:00
Charlotte Weaver 0a36fac142 10 day cache (down from 1000) 
I can expect a scientist to leave this running over the weekend on their laptop and still expect fast results. If someone leaves it running for a few years the data can probably be safely recalculated.
 2018-08-01 15:48:56 -07:00
Charlotte Weaver 69fca7ea8b Using flask_caching instead 
More recent module, same API
 2018-08-01 15:46:04 -07:00
Charlotte Weaver 7642251d44 Add simple cache to backend 2018-08-01 13:32:04 -07:00
Charlotte Weaver 516ecc2ad3 Merge pull request #123 from chanzuckerberg/csweaver/rm-duplicate-tests 
Removed duplicate jest tests
 2018-07-20 13:58:00 -07:00
Charlotte Weaver d77accc858 Update travis for CLI 2018-07-20 13:15:17 -07:00
Charlotte Weaver 83e7685f57 Update readme for CLI 2018-07-20 11:47:42 -07:00
Charlotte Weaver de5e0f4ea7 Address PR review issues 2018-07-20 11:43:31 -07:00
Charlotte Weaver 4b2f24cb40 Removed duplicate jest tests 2018-07-20 11:06:59 -07:00
Charlotte Weaver fec055ede3 Merge pull request #122 from chanzuckerberg/csweaver/branding-template 
Updated obvious areas to cellxgene branding
 2018-07-20 09:21:29 -07:00
Charlotte Weaver fdd9b1d0bd Updated obvious areas to cellxgene branding 2018-07-19 17:37:40 -07:00
Charlotte Weaver 9c72f2c2d5 Updating travis file to match new cli 2018-07-19 17:23:30 -07:00
Charlotte Weaver 2c7a11ab80 Added cli command for run 2018-07-19 17:21:28 -07:00
Charlotte Weaver 45f61d87d7 Initial CLI 
added basic cli for running
 2018-07-18 21:45:07 -07:00
Charlotte Weaver 71d1cd250c Merge pull request #119 from chanzuckerberg/csweaver/travis 
Setup travis integration
 2018-07-18 14:14:13 -07:00
Charlotte Weaver 558e8f522a Style for travis build files 2018-07-18 14:07:04 -07:00
Charlotte Weaver 895cfcebe0 Added initial travis config file 2018-07-18 10:21:24 -07:00
Charlotte Weaver cd7c06c822 Merge pull request #120 from chanzuckerberg/csweaver/packaging-improvements 
Csweaver/packaging improvements
 2018-07-17 16:25:31 -07:00