Fix 3dmol zoom and expose zoom props

.circleci/config.yml

@@ -44,8 +44,7 @@ jobs:
                     python -m venv venv
                     . venv/bin/activate
                     git clone --depth 1 https://github.com/plotly/dash.git dash-main
-                    cd dash-main && pip install -e .[dev,testing]
-                    cd dash-renderer && npm ci && npm run build && pip install -e . && cd ../..
+                    cd dash-main && pip install -e .[dev,testing] --progress-bar off && renderer build && cd ../
                     npm run build
 
             - run:

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## UNRELEASED
+
+### Fixed
+* [#561](https://github.com/plotly/dash-bio/pull/561) Repeated re-rendering of the Molecule3dViewer component caused the viewer zoom to decrease multiplicatively.
+This fix also exposes the `zoom` and `zoomTo` props for this component.
+
+
 ## [0.7.0] - 2021-04-19
 
 ### Fixed
@@ -12,7 +19,7 @@
 * [#554](https://github.com/plotly/dash-bio/pull/554) Added additional props and arbitrary layout arguments to VolcanoPlot.
 
 ### Changed
-- [#550](https://github.com/plotly/dash-bio/pull/548) Updated CONTRIBUTING.md andbasic demo app structure. In addition, removed residual code and pre-deploy scripts associated with now-discontinued Dash Bio gallery. 
+- [#550](https://github.com/plotly/dash-bio/pull/548) Updated CONTRIBUTING.md andbasic demo app structure. In addition, removed residual code and pre-deploy scripts associated with now-discontinued Dash Bio gallery.
 
 ## [0.6.1] - 2021-02-15
 ### Fixed

R/dashbioAlignmentChart.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioAlignmentChart <- function(id=NULL, eventDatum=NULL, data=NULL, extension=NULL, colorscale=NULL, opacity=NULL, textcolor=NULL, textsize=NULL, showlabel=NULL, showid=NULL, showconservation=NULL, conservationcolor=NULL, conservationcolorscale=NULL, conservationopacity=NULL, conservationmethod=NULL, correctgap=NULL, showgap=NULL, gapcolor=NULL, gapcolorscale=NULL, gapopacity=NULL, groupbars=NULL, showconsensus=NULL, tilewidth=NULL, tileheight=NULL, overview=NULL, numtiles=NULL, scrollskip=NULL, tickstart=NULL, ticksteps=NULL, width=NULL, height=NULL) {
+dashbioAlignmentChart <- function(id=NULL, colorscale=NULL, conservationcolor=NULL, conservationcolorscale=NULL, conservationmethod=NULL, conservationopacity=NULL, correctgap=NULL, data=NULL, eventDatum=NULL, extension=NULL, gapcolor=NULL, gapcolorscale=NULL, gapopacity=NULL, groupbars=NULL, height=NULL, numtiles=NULL, opacity=NULL, overview=NULL, scrollskip=NULL, showconsensus=NULL, showconservation=NULL, showgap=NULL, showid=NULL, showlabel=NULL, textcolor=NULL, textsize=NULL, tickstart=NULL, ticksteps=NULL, tileheight=NULL, tilewidth=NULL, width=NULL) {
 
-    props <- list(id=id, eventDatum=eventDatum, data=data, extension=extension, colorscale=colorscale, opacity=opacity, textcolor=textcolor, textsize=textsize, showlabel=showlabel, showid=showid, showconservation=showconservation, conservationcolor=conservationcolor, conservationcolorscale=conservationcolorscale, conservationopacity=conservationopacity, conservationmethod=conservationmethod, correctgap=correctgap, showgap=showgap, gapcolor=gapcolor, gapcolorscale=gapcolorscale, gapopacity=gapopacity, groupbars=groupbars, showconsensus=showconsensus, tilewidth=tilewidth, tileheight=tileheight, overview=overview, numtiles=numtiles, scrollskip=scrollskip, tickstart=tickstart, ticksteps=ticksteps, width=width, height=height)
+    props <- list(id=id, colorscale=colorscale, conservationcolor=conservationcolor, conservationcolorscale=conservationcolorscale, conservationmethod=conservationmethod, conservationopacity=conservationopacity, correctgap=correctgap, data=data, eventDatum=eventDatum, extension=extension, gapcolor=gapcolor, gapcolorscale=gapcolorscale, gapopacity=gapopacity, groupbars=groupbars, height=height, numtiles=numtiles, opacity=opacity, overview=overview, scrollskip=scrollskip, showconsensus=showconsensus, showconservation=showconservation, showgap=showgap, showid=showid, showlabel=showlabel, textcolor=textcolor, textsize=textsize, tickstart=tickstart, ticksteps=ticksteps, tileheight=tileheight, tilewidth=tilewidth, width=width)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'AlignmentChart',
         namespace = 'dash_bio',
-        propNames = c('id', 'eventDatum', 'data', 'extension', 'colorscale', 'opacity', 'textcolor', 'textsize', 'showlabel', 'showid', 'showconservation', 'conservationcolor', 'conservationcolorscale', 'conservationopacity', 'conservationmethod', 'correctgap', 'showgap', 'gapcolor', 'gapcolorscale', 'gapopacity', 'groupbars', 'showconsensus', 'tilewidth', 'tileheight', 'overview', 'numtiles', 'scrollskip', 'tickstart', 'ticksteps', 'width', 'height'),
+        propNames = c('id', 'colorscale', 'conservationcolor', 'conservationcolorscale', 'conservationmethod', 'conservationopacity', 'correctgap', 'data', 'eventDatum', 'extension', 'gapcolor', 'gapcolorscale', 'gapopacity', 'groupbars', 'height', 'numtiles', 'opacity', 'overview', 'scrollskip', 'showconsensus', 'showconservation', 'showgap', 'showid', 'showlabel', 'textcolor', 'textsize', 'tickstart', 'ticksteps', 'tileheight', 'tilewidth', 'width'),
         package = 'dashBio'
         )
 

R/dashbioCircos.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioCircos <- function(enableDownloadSVG=NULL, enableZoomPan=NULL, id=NULL, style=NULL, eventDatum=NULL, selectEvent=NULL, layout=NULL, config=NULL, size=NULL, tracks=NULL) {
+dashbioCircos <- function(id=NULL, config=NULL, enableDownloadSVG=NULL, enableZoomPan=NULL, eventDatum=NULL, layout=NULL, selectEvent=NULL, size=NULL, style=NULL, tracks=NULL) {
 
-    props <- list(enableDownloadSVG=enableDownloadSVG, enableZoomPan=enableZoomPan, id=id, style=style, eventDatum=eventDatum, selectEvent=selectEvent, layout=layout, config=config, size=size, tracks=tracks)
+    props <- list(id=id, config=config, enableDownloadSVG=enableDownloadSVG, enableZoomPan=enableZoomPan, eventDatum=eventDatum, layout=layout, selectEvent=selectEvent, size=size, style=style, tracks=tracks)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'Circos',
         namespace = 'dash_bio',
-        propNames = c('enableDownloadSVG', 'enableZoomPan', 'id', 'style', 'eventDatum', 'selectEvent', 'layout', 'config', 'size', 'tracks'),
+        propNames = c('id', 'config', 'enableDownloadSVG', 'enableZoomPan', 'eventDatum', 'layout', 'selectEvent', 'size', 'style', 'tracks'),
         package = 'dashBio'
         )
 

R/dashbioFornaContainer.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioFornaContainer <- function(id=NULL, height=NULL, width=NULL, sequences=NULL, nodeFillColor=NULL, colorScheme=NULL, customColors=NULL, allowPanningAndZooming=NULL) {
+dashbioFornaContainer <- function(id=NULL, allowPanningAndZooming=NULL, colorScheme=NULL, customColors=NULL, height=NULL, nodeFillColor=NULL, sequences=NULL, width=NULL) {
 
-    props <- list(id=id, height=height, width=width, sequences=sequences, nodeFillColor=nodeFillColor, colorScheme=colorScheme, customColors=customColors, allowPanningAndZooming=allowPanningAndZooming)
+    props <- list(id=id, allowPanningAndZooming=allowPanningAndZooming, colorScheme=colorScheme, customColors=customColors, height=height, nodeFillColor=nodeFillColor, sequences=sequences, width=width)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'FornaContainer',
         namespace = 'dash_bio',
-        propNames = c('id', 'height', 'width', 'sequences', 'nodeFillColor', 'colorScheme', 'customColors', 'allowPanningAndZooming'),
+        propNames = c('id', 'allowPanningAndZooming', 'colorScheme', 'customColors', 'height', 'nodeFillColor', 'sequences', 'width'),
         package = 'dashBio'
         )
 

R/dashbioIdeogram.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioIdeogram <- function(id=NULL, style=NULL, className=NULL, annotationsLayout=NULL, annotations=NULL, annotationsPath=NULL, annotationsData=NULL, annotationTracks=NULL, annotationHeight=NULL, annotationsColor=NULL, histogramScaling=NULL, barWidth=NULL, showAnnotTooltip=NULL, assembly=NULL, brush=NULL, brushData=NULL, container=NULL, chrHeight=NULL, chrMargin=NULL, chrWidth=NULL, chromosomes=NULL, dataDir=NULL, organism=NULL, localOrganism=NULL, homology=NULL, perspective=NULL, fullChromosomeLabels=NULL, resolution=NULL, filterable=NULL, orientation=NULL, ploidy=NULL, ploidyDesc=NULL, ancestors=NULL, rangeSet=NULL, rotatable=NULL, rotated=NULL, sex=NULL, showChromosomeLabels=NULL, showBandLabels=NULL, showFullyBanded=NULL, showNonNuclearChromosomes=NULL) {
+dashbioIdeogram <- function(id=NULL, ancestors=NULL, annotationHeight=NULL, annotationTracks=NULL, annotations=NULL, annotationsColor=NULL, annotationsData=NULL, annotationsLayout=NULL, annotationsPath=NULL, assembly=NULL, barWidth=NULL, brush=NULL, brushData=NULL, chrHeight=NULL, chrMargin=NULL, chrWidth=NULL, chromosomes=NULL, className=NULL, container=NULL, dataDir=NULL, filterable=NULL, fullChromosomeLabels=NULL, histogramScaling=NULL, homology=NULL, localOrganism=NULL, organism=NULL, orientation=NULL, perspective=NULL, ploidy=NULL, ploidyDesc=NULL, rangeSet=NULL, resolution=NULL, rotatable=NULL, rotated=NULL, sex=NULL, showAnnotTooltip=NULL, showBandLabels=NULL, showChromosomeLabels=NULL, showFullyBanded=NULL, showNonNuclearChromosomes=NULL, style=NULL) {
 
-    props <- list(id=id, style=style, className=className, annotationsLayout=annotationsLayout, annotations=annotations, annotationsPath=annotationsPath, annotationsData=annotationsData, annotationTracks=annotationTracks, annotationHeight=annotationHeight, annotationsColor=annotationsColor, histogramScaling=histogramScaling, barWidth=barWidth, showAnnotTooltip=showAnnotTooltip, assembly=assembly, brush=brush, brushData=brushData, container=container, chrHeight=chrHeight, chrMargin=chrMargin, chrWidth=chrWidth, chromosomes=chromosomes, dataDir=dataDir, organism=organism, localOrganism=localOrganism, homology=homology, perspective=perspective, fullChromosomeLabels=fullChromosomeLabels, resolution=resolution, filterable=filterable, orientation=orientation, ploidy=ploidy, ploidyDesc=ploidyDesc, ancestors=ancestors, rangeSet=rangeSet, rotatable=rotatable, rotated=rotated, sex=sex, showChromosomeLabels=showChromosomeLabels, showBandLabels=showBandLabels, showFullyBanded=showFullyBanded, showNonNuclearChromosomes=showNonNuclearChromosomes)
+    props <- list(id=id, ancestors=ancestors, annotationHeight=annotationHeight, annotationTracks=annotationTracks, annotations=annotations, annotationsColor=annotationsColor, annotationsData=annotationsData, annotationsLayout=annotationsLayout, annotationsPath=annotationsPath, assembly=assembly, barWidth=barWidth, brush=brush, brushData=brushData, chrHeight=chrHeight, chrMargin=chrMargin, chrWidth=chrWidth, chromosomes=chromosomes, className=className, container=container, dataDir=dataDir, filterable=filterable, fullChromosomeLabels=fullChromosomeLabels, histogramScaling=histogramScaling, homology=homology, localOrganism=localOrganism, organism=organism, orientation=orientation, perspective=perspective, ploidy=ploidy, ploidyDesc=ploidyDesc, rangeSet=rangeSet, resolution=resolution, rotatable=rotatable, rotated=rotated, sex=sex, showAnnotTooltip=showAnnotTooltip, showBandLabels=showBandLabels, showChromosomeLabels=showChromosomeLabels, showFullyBanded=showFullyBanded, showNonNuclearChromosomes=showNonNuclearChromosomes, style=style)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'Ideogram',
         namespace = 'dash_bio',
-        propNames = c('id', 'style', 'className', 'annotationsLayout', 'annotations', 'annotationsPath', 'annotationsData', 'annotationTracks', 'annotationHeight', 'annotationsColor', 'histogramScaling', 'barWidth', 'showAnnotTooltip', 'assembly', 'brush', 'brushData', 'container', 'chrHeight', 'chrMargin', 'chrWidth', 'chromosomes', 'dataDir', 'organism', 'localOrganism', 'homology', 'perspective', 'fullChromosomeLabels', 'resolution', 'filterable', 'orientation', 'ploidy', 'ploidyDesc', 'ancestors', 'rangeSet', 'rotatable', 'rotated', 'sex', 'showChromosomeLabels', 'showBandLabels', 'showFullyBanded', 'showNonNuclearChromosomes'),
+        propNames = c('id', 'ancestors', 'annotationHeight', 'annotationTracks', 'annotations', 'annotationsColor', 'annotationsData', 'annotationsLayout', 'annotationsPath', 'assembly', 'barWidth', 'brush', 'brushData', 'chrHeight', 'chrMargin', 'chrWidth', 'chromosomes', 'className', 'container', 'dataDir', 'filterable', 'fullChromosomeLabels', 'histogramScaling', 'homology', 'localOrganism', 'organism', 'orientation', 'perspective', 'ploidy', 'ploidyDesc', 'rangeSet', 'resolution', 'rotatable', 'rotated', 'sex', 'showAnnotTooltip', 'showBandLabels', 'showChromosomeLabels', 'showFullyBanded', 'showNonNuclearChromosomes', 'style'),
         package = 'dashBio'
         )
 

R/dashbioIgv.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioIgv <- function(id=NULL, style=NULL, className=NULL, genome=NULL, reference=NULL, locus=NULL, minimumBases=NULL, tracks=NULL) {
+dashbioIgv <- function(id=NULL, className=NULL, genome=NULL, locus=NULL, minimumBases=NULL, reference=NULL, style=NULL, tracks=NULL) {
 
-    props <- list(id=id, style=style, className=className, genome=genome, reference=reference, locus=locus, minimumBases=minimumBases, tracks=tracks)
+    props <- list(id=id, className=className, genome=genome, locus=locus, minimumBases=minimumBases, reference=reference, style=style, tracks=tracks)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'Igv',
         namespace = 'dash_bio',
-        propNames = c('id', 'style', 'className', 'genome', 'reference', 'locus', 'minimumBases', 'tracks'),
+        propNames = c('id', 'className', 'genome', 'locus', 'minimumBases', 'reference', 'style', 'tracks'),
         package = 'dashBio'
         )
 

R/dashbioMolecule2dViewer.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioMolecule2dViewer <- function(id=NULL, selectedAtomIds=NULL, width=NULL, height=NULL, modelData=NULL) {
+dashbioMolecule2dViewer <- function(id=NULL, height=NULL, modelData=NULL, selectedAtomIds=NULL, width=NULL) {
 
-    props <- list(id=id, selectedAtomIds=selectedAtomIds, width=width, height=height, modelData=modelData)
+    props <- list(id=id, height=height, modelData=modelData, selectedAtomIds=selectedAtomIds, width=width)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'Molecule2dViewer',
         namespace = 'dash_bio',
-        propNames = c('id', 'selectedAtomIds', 'width', 'height', 'modelData'),
+        propNames = c('id', 'height', 'modelData', 'selectedAtomIds', 'width'),
         package = 'dashBio'
         )
 

R/dashbioMolecule3dViewer.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioMolecule3dViewer <- function(id=NULL, selectionType=NULL, backgroundColor=NULL, backgroundOpacity=NULL, styles=NULL, modelData=NULL, atomLabelsShown=NULL, selectedAtomIds=NULL, labels=NULL, orbital=NULL, shapes=NULL, onRenderNewData=NULL, onChangeSelection=NULL) {
+dashbioMolecule3dViewer <- function(id=NULL, atomLabelsShown=NULL, backgroundColor=NULL, backgroundOpacity=NULL, labels=NULL, modelData=NULL, onChangeSelection=NULL, onRenderNewData=NULL, orbital=NULL, selectedAtomIds=NULL, selectionType=NULL, shapes=NULL, styles=NULL, zoom=NULL, zoomTo=NULL) {
 
-    props <- list(id=id, selectionType=selectionType, backgroundColor=backgroundColor, backgroundOpacity=backgroundOpacity, styles=styles, modelData=modelData, atomLabelsShown=atomLabelsShown, selectedAtomIds=selectedAtomIds, labels=labels, orbital=orbital, shapes=shapes, onRenderNewData=onRenderNewData, onChangeSelection=onChangeSelection)
+    props <- list(id=id, atomLabelsShown=atomLabelsShown, backgroundColor=backgroundColor, backgroundOpacity=backgroundOpacity, labels=labels, modelData=modelData, onChangeSelection=onChangeSelection, onRenderNewData=onRenderNewData, orbital=orbital, selectedAtomIds=selectedAtomIds, selectionType=selectionType, shapes=shapes, styles=styles, zoom=zoom, zoomTo=zoomTo)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'Molecule3dViewer',
         namespace = 'dash_bio',
-        propNames = c('id', 'selectionType', 'backgroundColor', 'backgroundOpacity', 'styles', 'modelData', 'atomLabelsShown', 'selectedAtomIds', 'labels', 'orbital', 'shapes', 'onRenderNewData', 'onChangeSelection'),
+        propNames = c('id', 'atomLabelsShown', 'backgroundColor', 'backgroundOpacity', 'labels', 'modelData', 'onChangeSelection', 'onRenderNewData', 'orbital', 'selectedAtomIds', 'selectionType', 'shapes', 'styles', 'zoom', 'zoomTo'),
         package = 'dashBio'
         )
 

R/dashbioNeedlePlot.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioNeedlePlot <- function(id=NULL, mutationData=NULL, xlabel=NULL, ylabel=NULL, rangeSlider=NULL, needleStyle=NULL, domainStyle=NULL) {
+dashbioNeedlePlot <- function(id=NULL, domainStyle=NULL, mutationData=NULL, needleStyle=NULL, rangeSlider=NULL, xlabel=NULL, ylabel=NULL) {
 
-    props <- list(id=id, mutationData=mutationData, xlabel=xlabel, ylabel=ylabel, rangeSlider=rangeSlider, needleStyle=needleStyle, domainStyle=domainStyle)
+    props <- list(id=id, domainStyle=domainStyle, mutationData=mutationData, needleStyle=needleStyle, rangeSlider=rangeSlider, xlabel=xlabel, ylabel=ylabel)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'NeedlePlot',
         namespace = 'dash_bio',
-        propNames = c('id', 'mutationData', 'xlabel', 'ylabel', 'rangeSlider', 'needleStyle', 'domainStyle'),
+        propNames = c('id', 'domainStyle', 'mutationData', 'needleStyle', 'rangeSlider', 'xlabel', 'ylabel'),
         package = 'dashBio'
         )
 

R/dashbioNglMoleculeViewer.R

@@ -1,16 +1,16 @@
 # AUTO GENERATED FILE - DO NOT EDIT
 
-dashbioNglMoleculeViewer <- function(id=NULL, width=NULL, height=NULL, stageParameters=NULL, imageParameters=NULL, downloadImage=NULL, pdbString=NULL, data=NULL, molStyles=NULL) {
+dashbioNglMoleculeViewer <- function(id=NULL, data=NULL, downloadImage=NULL, height=NULL, imageParameters=NULL, molStyles=NULL, pdbString=NULL, stageParameters=NULL, width=NULL) {
 
-    props <- list(id=id, width=width, height=height, stageParameters=stageParameters, imageParameters=imageParameters, downloadImage=downloadImage, pdbString=pdbString, data=data, molStyles=molStyles)
+    props <- list(id=id, data=data, downloadImage=downloadImage, height=height, imageParameters=imageParameters, molStyles=molStyles, pdbString=pdbString, stageParameters=stageParameters, width=width)
     if (length(props) > 0) {
         props <- props[!vapply(props, is.null, logical(1))]
     }
     component <- list(
         props = props,
         type = 'NglMoleculeViewer',
         namespace = 'dash_bio',
-        propNames = c('id', 'width', 'height', 'stageParameters', 'imageParameters', 'downloadImage', 'pdbString', 'data', 'molStyles'),
+        propNames = c('id', 'data', 'downloadImage', 'height', 'imageParameters', 'molStyles', 'pdbString', 'stageParameters', 'width'),
         package = 'dashBio'
         )