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Author SHA1 Message Date
Jeremy Freeman 6ea3b7f3cf use collapsable details to improve FAQ formatting (#503) 2018-12-07 21:07:57 +01:00
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
Bruce Martin 48e0ea542b clarifications to release recipe (#499) 
* clarifications to release recipe

* fix spelling errors
 2018-12-05 16:58:53 -08:00
Bruce Martin 95fd20b405 bump version to 0.3 (#498) 0.3.0 2018-12-05 14:35:17 -08:00
Charlotte Weaver 5c6cc597c8 Default warning in debug mode (#497) 2018-12-05 13:38:34 -08:00
Bruce Martin 3bfeadc2b9 improve handling of non-finite floating point values (#490) 
* improve HTTP error reporting

* generate standards-compatible JSON

* add --nan-to-num work-around for non-finite floating point values

* lint

* update tests

* correctly set Infinities to min/max

* REAMDE update for --nan-to-num

* define constant for repetitive warning message

* clarify where NaN errors will occure
 2018-12-04 14:56:16 -08:00
Bruce Martin 296ed752fa Improved summary counts of annotation values (#478) 
* convert annotation summary to a Map

* add 2d annotation count summary

* add memoization on 2D annotation counting

* add tests for annotation summarization

* fix import/exports

* rename WorldOps to WorldUtil

* rename WorldOps to WorldUtil

* add comment
 2018-12-03 09:15:03 -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
Bruce Martin af0d1f6fb2 issue #480 workaround (#484) 
* only load annotation var names

* remove incorrect usage of var annotation data

* temporary workaround for issue #480

* lint

* issue warnings only once per item
 2018-11-29 16:33:21 -08:00
fionagriffin a83ec60308 add FAQs to readme (#482) 
Added question and answer to FAQ; added link to scanpy documentation on scientific recipes.
 2018-11-29 13:59:10 -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
Colin Megill 00b9a8fa72 Fuzzy search on genes (#473) 
* proof of concept blueprint typeahead

* poc with fuzzysearch lib

* typeahead adds gene on enter

* add gene on menu click

* typeahead clears correctly

* cleanup
 2018-11-28 09:50:02 -08:00
Charlotte Weaver 28f5263c88 bump version (#475) 0.2.3 2018-11-27 15:43:19 -08:00
Bruce Martin 933fac5fff Allow float64 to down-cast to float32 (#472) 
* warn if annotations will down-cast to float32

* correctly handle falsey data values
 2018-11-27 11:17:30 -08:00
Charlotte Weaver 0c26f227fe bump version (#470) 0.2.2 2018-11-26 15:38:47 -08:00
Marcus Kinsella 2b90c747f5 Fix readme images on PyPi (#467) 
But this time actually do that
 2018-11-26 15:27:05 -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) 0.2.1 2018-11-26 11:42:56 -08:00
Bruce Martin 138d30909a improve type handling for non-string annotation data (#465) 
* improve type handling for non-string annotation data

* improve clarity of code
 2018-11-26 10:32:29 -08:00
Charlotte Weaver 2b5094665f version 0.2.0 (#456) 0.2.0 2018-11-16 15:12:54 -08:00
Jeremy Freeman a81258bc0d remove printing (#455) 2018-11-16 14:45:06 -08:00
Bruce Martin 141f802824 differential expression improvements (#452) 
* add cutoff for low expression genes in topN selection

* remove debugging printfs

* change cli param name for diffexp cutoff

* change CLI param name

* second try at diffexp - using lfc sort with pval cutoff

* use lfc cutoff

* update comments to match code; cap p-value adjustment to max of 1

* lint

* explain diffexp in readme

* add link

* add diffexp-lfc-cutoff to test config

* update test to match revised diffexp spec

* fix latent bug in GET arg handling that was breaking tests

* lint

* comment cleanup

* fix variance overestimation so it is symmetric

* lint
 2018-11-16 14:44:56 -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
Jeremy Freeman dff2526077 warm to cool (#454) 2018-11-16 14:33:32 -08:00
Marcus Kinsella 2b4aa92f67 Use externally-reachable image urls (#453) 
This is needed for the images to show up in pypi.
 2018-11-16 13:02:49 -08:00
Jeremy Freeman 3151306d7e readme updates (#436) 
lots of updates to the readme to: improve scientific and technical clarity, reflect all recent changes to the CLI (especially the addition of prepare), reflect all recent changes to our installation, improve explanation of how to handle a few different kinds of data, and expand instructions on contributing and developing
 2018-11-15 18:18:30 -08:00
Colin Megill ef80c8df2a Change color scales to rainbow (#449) 
* rainbow

* eslint

* remove comments
 2018-11-15 18:17:55 -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) 0.0.4 2018-11-15 11:56:22 -08:00
Marcus Kinsella 523048de43 Set long_description_content_type (#439) 
This _should_ make it look more attractive on pypi.
 2018-11-15 11:19:34 -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
Bruce Martin 00a68276a2 diffexp performance & UX improvements (#431) 
* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments
 2018-11-14 12:51:24 -08:00
Charlotte Weaver bc0cecbd1c Release Test (#427) 
* bump-update

* Release Test!
 2018-11-14 11:03:52 -08:00
Colin Megill dbff824854 Viewport fills entire screen (#430) 
* full pane webgl and svg

* fixes for full pane selection and centering

* force graph remount, clear brush state
 2018-11-13 11:45:38 -05:00
Colin Megill 9decf134e0 fixed scatterplot infinite render (#429) 
* add more to state from componentDidMount

* always brush

* destructure

* move render to function

* fixed scatterplot infinite render

* remove logging
 2018-11-09 20:28:22 -05:00
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
Bruce Martin 6916aec6c3 update package dependencies (#417) 2018-11-07 13:58:21 -08:00
Bruce Martin 9f7e1f1cb0 use quicksort instead of default system sort (#413) 2018-11-07 13:35:00 -08:00
Bruce Martin 121360c0a5 remove extraneous package-lock.json file (#412) 2018-11-07 13:34:41 -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
Bruce Martin a9189017c7 first draft of release process (#408) 
* first draft of release process

* additional release process changes

* specify semver
 2018-11-06 07:17:35 -08:00
Bruce Martin 2d5bc9d0c9 Performance work, plus fix #405 (#406) 
* remove memoization

* update to flash 1.0.2; turn on threading

* stand-alone helper routines for array slicing

* fix issue #405

* reset diffexp state when world changes

* performance work in dimension creation; fix world slicing bug

* update tests to match new state mgmt api

* update flask

* do not make dimensions for useless annotations

* update test to match optimizations
 2018-11-05 13:57:58 -08:00