Speck system fix

CHANGELOG.md

@@ -6,64 +6,77 @@
 * Fixed issue with Clustergram rows and columns reordering incorrectly
   on the heatmap when precomputed traces are used to generate the
   figure.
+* Fixed issue with Speck not rendering unless it is attached to a callback.
+* Prevent Speck from trying to calculate a system with no atom.
 
 ### Changed
 * Changed Clustergram to only return a figure by default, so that
   values no longer need to be unpacked.
 
 ### Added
-* Added to Clustergram the ability to generate a "curve dictionary"
-to translate curve number (available in hoverData/clickData) to the
-row or column cluster it represents on the graph.
+* Added to Clustergram the ability to generate a "curve dictionary" to
+  translate curve number (available in hoverData/clickData) to the row
+  or column cluster it represents on the graph.
 
 ## [0.0.8] - 2019-01-04
 
 ### Fixed
-* Fixed issue with Clustergram not reordering rows and columns after clustering.
+* Fixed issue with Clustergram not reordering rows and columns after
+  clustering.
 
 ### Removed
 * Removed mentions of Dash events in OncoPrint component.
 * Removed properties which weren't used in Ideogram component.
 
 ### Changed
-* Changed property `fullChromosomeLabels` so that it can be updated using dash callbacks
-* Changed Imputer (deprecated) to SimpleImputer in Clustergram component.
-* Changed property name `impute_function` to `imputer_parameters` in Clustergram component.
+* Changed property `fullChromosomeLabels` so that it can be updated
+  using dash callbacks.
+* Changed Imputer (deprecated) to SimpleImputer in Clustergram
+  component.
+* Changed property name `impute_function` to `imputer_parameters` in
+  Clustergram component.
 * Changed install requirement to Dash version 0.40.0 or greater.
 
 ### Added
-* Added ability to define custom colours in styles parser for Molecule3D.
+* Added ability to define custom colors in style parser for
+  Molecule3D.
 
 ## [0.0.7] - 2019-26-02
 
 ### Changed
-* Changed unicode right arrow to greater-than sign in Circos for compatibility with Python 2.7.
+* Changed unicode right arrow to greater-than sign in Circos for
+  compatibility with Python 2.7.
 
 ## [0.0.6] - 2019-22-02
 
 ### Added
-* Added requirements from files in `utils`, as well as from pure-Python components, to setup install requirements.
+* Added requirements from files in `utils`, as well as from
+  pure-Python components, to setup install requirements.
 * Added more descriptive prop descriptions for Dash Ideogram.
 
 ## [0.0.5] - 2019-15-02
 
 ### Changed
-* Changed filenames in `dash_bio/utils/` folder to be snake case instead of camel case.
+* Changed filenames in `dash_bio/utils/` folder to be snake case
+  instead of camel case.
 
 ## [0.0.4] - 2019-11-02
 
 ### Added
-* Added recent update to Speck library to fix jumpy behavior on click-and-drag.
+* Added recent update to Speck library to fix jumpy behavior on
+  click-and-drag.
 
 ## [0.0.3] - 2019-06-02
 
 ### Added
-* Added variables to define strings used in `_volcano.py` graph labels.
+* Added variables to define strings used in `_volcano.py` graph
+  labels.
 
 ## [0.0.2] - 2019-05-02
 
 ### Fixed
 * Fixed incompatibility issues with Dash `0.36.0`.
 
 ### Removed
-* Removed all mentions of `fireEvent` and anything else that used Dash events (which have been removed).
+* Removed all mentions of `fireEvent` and anything else that used Dash
+  events (which have been removed).

dash_bio/package.json

@@ -1,6 +1,6 @@
 {
   "name": "dash-bio",
-  "version": "0.0.9-rc4",
+  "version": "0.0.9-rc5",
   "description": "Dash components for bioinformatics",
   "main": "build/index.js",
   "scripts": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "dash-bio",
-  "version": "0.0.9-rc4",
+  "version": "0.0.9-rc5",
   "description": "Dash components for bioinformatics",
   "main": "build/index.js",
   "scripts": {

requirements.txt

@@ -5,8 +5,8 @@
 biopython
 colour==0.1.5
 cython>=0.19
-dash>=0.40.0
-dash-bio==0.0.9-rc4
+dash==0.40.0
+dash-bio==0.0.9-rc5
 dash-daq==0.1.4
 gunicorn
 jsonschema

src/lib/components/Speck.react.js

@@ -10,6 +10,11 @@ import {
 
 export default class Speck extends Component {
     loadStructure(data) {
+        // avoid trying to load an empty system
+        if (data.length === 0) {
+            return;
+        }
+
         const system = speckSystem.new();
 
         for (let i = 0; i < data.length; i++) {
@@ -18,6 +23,7 @@ export default class Speck extends Component {
             // add to the system
             speckSystem.addAtom(system, a.symbol, a.x, a.y, a.z);
         }
+
         speckSystem.center(system);
         speckSystem.calculateBonds(system);