16 Commits

Author SHA1 Message Date
Bruce Martin
32f60a1547 clean up type inferencing (#2332)
* unit tests for 64 bit conversion

* clean up type handling

* type inference tests

* more type inference fixes

* use schema to determine user intent for data typing

* stop using deprecated API

* fbs type encoding test

* add missing test

* add more tests

* correctly infer X type for CXG adaptor

* lint

* fix typo

* ts migration

* cleanup from PR review

* lint

* PR review changes
2021-07-28 15:10:12 -07:00
Bruce Martin
0b1ab02a60 rename X_approx_distribution to X_approximate_distribution (#2337) 2021-07-27 13:43:04 -07:00
Bruce Martin
1ea2b7fe80 fix for incorrect stats computation in diff exp t-test (#2318)
* 2211 fixes

* lint

* lint

* add missing test and bug found by test

* change terminology for count distribution

* update scanpy requirement

* update scanpy requirement
2021-07-23 11:36:26 -07:00
Bruce Martin
0667ad0274 remove experimental reembedding support (#2301)
* remove experimental reembedding support

* lint

* lint

* add prepare requirements to requirements-dev

* oops, revert accidental deletion of import

* more test modifications

* remove obsolete unit tests
2021-07-15 13:55:26 -07:00
Bruce Martin
e334fbe96e remove experimental ontology support (#2300)
* remove experimental ontology support

* lint

* remove ontologies from unit tests

* additional test changes
2021-07-14 07:23:38 -07:00
Severiano Badajoz
07816c2f93 docs: release 0.17.0 (#2278)
* Bump version: 0.16.7 → 0.17.0-rc.0

* Bump version: 0.17.0-rc.0 → 0.17.0
2021-07-07 15:07:37 -07:00
Severiano Badajoz
90da04b6c7 fix: update server version to 0.16.7 (#2276) 2021-07-06 23:25:34 +00:00
Severiano Badajoz
5f976cc4fc fix: convert sparse numpy matrix to ndarray (#2271) 2021-07-06 21:04:50 +00:00
Severiano Badajoz
28b526b3fc feat: diffexp returns two genesets (#2230)
* feat: return two lists for diffexp (#2221)

* sp

* split out derive sort order, tests passing

* sp

* return diff exp results in two lists

* update

* copy implementation over to desktop

* add tests for two lists

* small fixes to complete backend implementation

* accept new diffexp response

* map diff exp response to genesets

* delete )

* name diffexp genesets with population names

* take constants out of state and allow width prop to override

* shorten mini-histo properly truncate and resize depending on expansion

* prepend new genesets

* rename data within diffexp action

* backend

* move diffexp ttest to common code module, update tests

* update for unit tests

* reference actual var

Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
Co-authored-by: Madison Dunitz <dunitzm@gmail.com>
2021-06-08 21:02:19 +00:00
maniarathi
59ec3afbb9 Pin versions of flatbuffer and Flask to be less than 2.0 (#2199) 2021-05-12 15:13:10 -07:00
Colin Megill
d04dba225f Filename dialogue includes gene sets (#2185)
* change filenames

* gene-sets to anno dialogue

* logging, lambda

* celllabels

* cell dash labels

* space

* fix 2182 - annotation file name change on the backend

Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
2021-05-07 17:32:11 -04:00
Bruce Martin
f2e9aecebe hosted gene sets routes, plus a few bug fixes (#2155)
* first cut at hosted gs routes

* lint

* update tests to match csv parser changes

* update tests to new API

* update gene set name validation rules to match requirements

* add path mapping from dataset to geneset

* add test cases for geneset GET route

* fix test assertion

* remove debugging code

* update gene set uri mapping function

* fix error message

* allow extra user-specified headers in gene set csv file

* clarify comment
2021-04-27 13:58:58 -07:00
Bruce Martin
860547ced1 update requirements for server (#2172) 2021-04-21 17:12:16 -07:00
Bruce Martin
ae30b66123 gene set summary progress (#2127)
* revert removal of cache control headers

* checkpoint work on revising summary route

* add summary query support to annoMatrix

* summarize route cleanup

* add mising file

* clean up summarize route

* add summary histogram

* update deps

* lint

* more lint

* lint

* manage crossfiler during gene set state changes

* remove obsolete debugging code

* correctly perform async watch in histogram

* better error handling
2021-03-30 14:43:53 -07:00
Bruce Martin
b494dd31f4 revert removal of cache control headers (#2118)
* revert removal of cache control headers

* always generate cache header for health route
2021-03-26 08:49:44 -07:00
Madison Dunitz
78c9d24ed4 Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
2021-03-26 00:27:07 -05:00