higlass 1.11.9 → 1.11.10

package/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Release notes
 
+## v1.11.9
+
+- Remove dependency on `cwise`
+- Fix color issue in GeneAnnotation SVG export
+
 ## v1.11.8
 
 - Remove react-bootstrap from the GenomePositionSearchBox

package/app/scripts/HorizontalGeneAnnotationsTrack.js

@@ -141,6 +141,8 @@ function externalInitTile(track, tile, options) {
     const geneId = track.geneId(geneInfo, td.type);
     const strand = td.strand || geneInfo[5];
 
+    td.strand = td.strand || strand;
+
     let fill = plusStrandColor || DEFAULT_PLUS_STRAND_COLOR;
 
     if (strand === '-') {

package/app/scripts/TrackRenderer.js

@@ -604,7 +604,8 @@ class TrackRenderer extends React.Component {
       ])
       .range([initialXDomain[0], initialXDomain[1]]);
 
-    let startY; let endY;
+    let startY;
+    let endY;
     if (this.currentProps.centerWidth === 0) {
       // If the width of the center track is zero, we do not want to make startY and endY equal.
       startY = this.currentProps.paddingTop + this.currentProps.topHeight;

package/app/scripts/utils/ndarray-assign.js

@@ -1,14 +1,19 @@
-import cwise from 'cwise';
-
 const ndarrayAssign = (target, source) => {
   const numSource = +source;
   const isScalar = !Number.isNaN(numSource);
 
   if (isScalar) {
-    cwise({
-      args: ['array', 'scalar'],
-      body: 'function assigns(a, s) { a = s; }',
-    })(target, numSource);
+    if (target.dimension === 1) {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        target.set(i, numSource);
+      }
+    } else {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        for (let j = 0; j < target.shape[1]; ++j) {
+          target.set(i, j, numSource);
+        }
+      }
+    }
   } else {
     const ty = target.shape[0];
     const tx = target.shape[1];
@@ -26,10 +31,17 @@ const ndarrayAssign = (target, source) => {
       return;
     }
 
-    cwise({
-      args: ['array', 'array'],
-      body: 'function assign(a, b) { a = b; }',
-    })(target, source);
+    if (target.dimension === 1) {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        target.set(i, source.get(i));
+      }
+    } else {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        for (let j = 0; j < target.shape[1]; ++j) {
+          target.set(i, j, source.get(i, j));
+        }
+      }
+    }
   }
 };
 

package/app/scripts/utils/ndarray-to-list.js

@@ -1,16 +1,22 @@
-import cwise from 'cwise';
-
 const ndarrayToList = (arr) => {
   const size = arr.shape.reduce((s, x) => s * x, 1);
   const list = new Array(size);
 
-  cwise({
-    args: ['array', 'scalar', 'scalar'],
-    body: (a, l, i) => {
-      l[i] = a; // eslint-disable-line
-      i++; // eslint-disable-line
-    },
-  })(arr, list, 0);
+  if (arr.dimension === 1) {
+    let l = 0;
+    for (let i = 0; i < arr.shape[0]; ++i) {
+      list[l] = arr.get(i);
+      l++;
+    }
+  } else {
+    let l = 0;
+    for (let i = 0; i < arr.shape[0]; ++i) {
+      for (let j = 0; j < arr.shape[1]; ++j) {
+        list[l] = arr.get(i, j);
+        l++;
+      }
+    }
+  }
 
   return list;
 };

package/app/styles/ViewHeader.module.scss

@@ -19,8 +19,7 @@ $unit: 24px;
   border: 0;
   border-radius: $unit / 8;
   background: $gray-lighter;
-  transition: height $fast $ease,
-              margin $fast $ease;
+  transition: height $fast $ease, margin $fast $ease;
 }
 
 .multitrack-header-dark {
@@ -123,8 +122,7 @@ $unit: 24px;
   width: $unit;
   height: 100%;
   padding: $unit / 4;
-  transition: background $fast $ease,
-              color $fast $ease;
+  transition: background $fast $ease, color $fast $ease;
 
   g {
     stroke: $gray;
@@ -152,7 +150,7 @@ $unit: 24px;
 }
 
 .multitrack-header-icon-squeazed {
-  width: $unit / 1.2  5;
+  width: $unit / 1.2 5;
   padding-left: $unit / 8;
   padding-right: $unit / 8;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "higlass",
-  "version": "1.11.9",
+  "version": "1.11.10",
   "description": "HiGlass Hi-C / genomic / large data viewer",
   "author": "Peter Kerpedjiev <pkerpedjiev@gmail.com>",
   "main": "dist/hglib.js",
@@ -47,7 +47,6 @@
     "ajv": "^6.10.0",
     "box-intersect": "^1.0.1",
     "css-element-queries": "github:marcj/css-element-queries",
-    "cwise": "^1.0.10",
     "d3-array": "^1.2.1",
     "d3-axis": "^1.0.4",
     "d3-brush": "github:flekschas/d3-brush",
@@ -71,7 +70,7 @@
     "path": "^0.12.7",
     "prismjs": "^1.16.0",
     "prop-types": "^15.6.0",
-    "pub-sub-es": "^1.2.1",
+    "pub-sub-es": "^2.0.1",
     "react": "^16.6.3",
     "react-autocomplete": "github:tiemevanveen/react-autocomplete#fix-176",
     "react-bootstrap": "0.32.1",

package/dist/hglib.css

@@ -1 +0,0 @@
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