binary wire format with flatbuffers (#509)

* first flatbuffer schema

* do not lint auto-generated files

* add flatbuffers package

* add flatbuffer module

* wire up /data/X/T route

* use flatbuffers for matrix data fetc

* clarity and comments

* add flatbuffer layout route

* clean up obsolete code

* fix tests

* move flake8 config to setup.cfg

* add comments

* lint

* rework layout routes for fbs

* add more type support to fbs

* lint

* add flatbuffer support for annotations

* function name improvements

* fix botched merge with master

* remove unused import

* route cleanup for flatbuffers

* rename function for clarity

* add missing globals to Jest tests

* fix client JS tests

* fix routes for Python tests

* comments for clarity

* non-finite floating point hardening

* more non-finite number handling

* lint

* fix tests for summarizeAnnotations

* harden diffexp calculation against FP errors

* cleanup unused code

* lint

* add encoding tests for flatbuffers

* application type specified as strings

* fix spelling error

* improve variable names

* add note about documentation gap

* rename FBS DataFrame to Matrix

client/src/components/brushableHistogram/index.js

@@ -13,6 +13,7 @@ import memoize from "memoize-one";
 import { kvCache } from "../../util/stateManager";
 import * as globals from "../../globals";
 import actions from "../../actions";
+import finiteExtent from "../../util/finiteExtent";
 
 @connect(state => ({
   world: state.controls.world,
@@ -56,7 +57,7 @@ class HistogramBrush extends React.Component {
       histogramCache.x = d3
         .scaleLinear()
         .domain(
-          d3.extent(varValues)
+          finiteExtent(varValues)
         ) /* replace this if we have ranges for genes back from server like we do for annotations on cells */
         .range([0, this.width]);
 

client/src/components/geneExpression/index.js

@@ -3,7 +3,6 @@
 
 import React from "react";
 import _ from "lodash";
-import * as d3 from "d3";
 import fuzzysort from "fuzzysort";
 
 import { connect } from "react-redux";
@@ -14,6 +13,7 @@ import * as globals from "../../globals";
 import actions from "../../actions";
 import { postUserErrorToast } from "../framework/toasters";
 import ExpressionButtons from "./expressionButtons";
+import finiteExtent from "../../util/finiteExtent";
 
 const renderGene = (fuzzySortResult, { handleClick, modifiers, query }) => {
   if (!modifiers.matchesPredicate) {
@@ -155,7 +155,7 @@ class GeneExpression extends React.Component {
                     key={geneName}
                     field={geneName}
                     zebra={index % 2 === 0}
-                    ranges={d3.extent(values)}
+                    ranges={finiteExtent(values)}
                     isUserDefined
                   />
                 );
@@ -185,7 +185,7 @@ class GeneExpression extends React.Component {
                     key={name}
                     field={name}
                     zebra={index % 2 === 0}
-                    ranges={d3.extent(values)}
+                    ranges={finiteExtent(values)}
                     isDiffExp
                     logFoldChange={value[1]}
                     pval={value[2]}

client/src/components/scatterplot/scatterplot.js

@@ -20,6 +20,7 @@ import scaleLinear from "../../util/scaleLinear";
 
 import { margin, width, height } from "./util";
 import { kvCache } from "../../util/stateManager";
+import finiteExtent from "../../util/finiteExtent";
 
 @connect(state => {
   const {
@@ -227,11 +228,11 @@ class Scatterplot extends React.Component {
   static setupScales(expressionX, expressionY) {
     const xScale = d3
       .scaleLinear()
-      .domain(d3.extent(expressionX))
+      .domain(finiteExtent(expressionX))
       .range([0, width]);
     const yScale = d3
       .scaleLinear()
-      .domain(d3.extent(expressionY))
+      .domain(finiteExtent(expressionY))
       .range([height, 0]);
 
     return {