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Author SHA1 Message Date
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
Charlotte Weaver 8b0d7d5cf6 Clarify install docs for python3 and venvs 2018-07-17 16:03:33 -07:00
Charlotte Weaver 28d341cf1c Fix default path for dataset 2018-07-17 16:03:06 -07:00
Charlotte Weaver 59022d7a9c Merge pull request #117 from chanzuckerberg/csweaver/tests 
Csweaver/tests
 2018-07-17 13:29:48 -07:00
Charlotte Weaver fdaaaf69a2 use unittest assert methods instead of assert 2018-07-17 11:01:38 -07:00
Charlotte Weaver 6961b64d87 Updated readme for python packaged version 2018-07-16 14:20:50 -07:00
Charlotte Weaver a5423a6911 Adding minor tests to scanpy calculation code 2018-07-16 11:48:53 -07:00
Charlotte Weaver 05b9a6833d Add tests for scanpy engine 2018-07-16 11:48:53 -07:00
Charlotte Weaver b8f501a46c Move to running tests after installing 
to avoid the sys.path.insert
 2018-07-16 11:48:53 -07:00
Charlotte Weaver b6f253e843 Initial packaging working 
pip install works if client files are built and moved manually
 2018-07-16 11:48:53 -07:00
Charlotte Weaver 851ddde130 Merge pull request #116 from chanzuckerberg/csweaver/packaging 
Csweaver/packaging
 2018-07-16 11:44:56 -07:00
Charlotte Weaver 2e1da27a31 Merge branch 'webgl-pause' 2018-07-16 11:11:23 -07:00
Charlotte Weaver d375c48b6a Merge branch 'master' into webgl-pause 2018-07-16 11:10:51 -07:00
Charlotte Weaver 82c4d2948c Merge branch 'csweaver/addbackend' 2018-07-16 10:58:46 -07:00
Charlotte Weaver 5a15f5a915 mergining addbackend 2018-07-16 10:58:33 -07:00
Charlotte Weaver 8aafd7d271 fix eslint-scope vulnerability 2018-07-12 13:05:27 -07:00
Charlotte Weaver 02799cea8e No relative imports "up" 2018-07-12 12:59:34 -07:00
Charlotte Weaver ba9e5f1e41 flake8/lint cleanup 2018-07-12 11:52:24 -07:00
Charlotte Weaver f466ef6553 Added entry point to run cellxgene from console 2018-07-10 12:56:42 -07:00
Charlotte Weaver a3bf802aec Add example dataset 2018-07-06 16:03:24 -07:00
Charlotte Weaver 071c24d0f4 Add client build script 2018-07-06 15:59:20 -07:00
Charlotte Weaver d937485034 Merge branch 'csweaver/packaging' of github.com:chanzuckerberg/cellxgene into csweaver/packaging 2018-07-06 15:51:08 -07:00
Charlotte Weaver 0639759a90 Initial packaging working 
pip install works if client files are built and moved manually
 2018-07-06 15:44:22 -07:00
Charlotte Weaver 558950852e Merge remote-tracking branch 'origin/csweaver/addbackend' into csweaver/addbackend 2018-07-06 15:43:37 -07:00
Charlotte Weaver cd1b67fd09 Rename diffexpression 2018-07-06 15:41:08 -07:00
Charlotte Weaver 5b9ddfa1a6 Added documentation to filter 2018-07-06 15:40:21 -07:00
Charlotte Weaver 354eacc3c8 Remove cell ids from engine 
Previously I just removed them from the driver
 2018-07-06 15:38:42 -07:00
Charlotte Weaver cf12acd47c Added documentation to filter 2018-07-06 10:26:46 -07:00
Charlotte Weaver 6652c07495 Remove cell ids from engine 
Previously I just removed them from the driver
 2018-07-06 10:26:33 -07:00
Charlotte Weaver e3bf06ca61 Config file no longer necessary 
Config is solely from environment variables instead.
 2018-07-06 10:13:24 -07:00
Charlotte Weaver 01de23c533 Fixed some faulty requirements 
Not tested on latest flask version yet
The latest anndata is causing problems with sorting  numeric indexes. I made a separate issue to actually fix that at a later point.
 2018-07-06 10:12:32 -07:00
Charlotte Weaver 451f95b0a4 Initial packaging working 
pip install works if client files are built and moved manually
 2018-07-05 17:06:51 -07:00
Charlotte Weaver 85506db971 Updating to latest cellxgene client code 
Fixes the build error in the old version. 

Reverted the API version since we changed directions from updating the API to refactoring the server structure instead.
 2018-07-05 13:37:26 -07:00