fix: minor spelling errors

auspice.js

@@ -15,7 +15,7 @@ const parser = new argparse.ArgumentParser({
   Auspice is an interactive visualisation tool for phylogenomic data.
   It can be used to display local datasets (see "auspice view -h" for details),
   or to build a customised version of the software (see "auspice build -h" for details).
-  This is the software which powers the visualisations on nextstrain.org and auspice.us, amoung others.
+  This is the software which powers the visualisations on nextstrain.org and auspice.us, among others.
   `
 });
 

src/actions/filesDropped/parseCsv.js

@@ -3,7 +3,7 @@ let Papa; /* lazyily imported once a file is dropped on */
 /**
  * A promise-ified version of Papa.parse()
  * A note on encoding here: It will be common that people drop CSVs from microsoft excel
- * in here annd, you guessed it, this causes all sorts of problems.
+ * in here and, you guessed it, this causes all sorts of problems.
  * https://github.com/mholt/PapaParse/issues/169 suggests adding encoding: "ISO-8859-1"
  * to the config, which may work
  * @param {string} csvString a string of delimited text

src/actions/recomputeReduxState.js

@@ -253,7 +253,7 @@ const modifyStateViaMetadata = (state, metadata) => {
               console.error("Skipping 'display_default' for sidebar as it's not 'open' or 'closed'");
             }
           } else {
-            /* most of the time if key=geoResoltion, set both state.geoResolution and state.defaults.geoResolution */
+            /* most of the time if key=geoResolution, set both state.geoResolution and state.defaults.geoResolution */
             state[keysToCheckFor[i]] = metadata.displayDefaults[keysToCheckFor[i]];
             state.defaults[keysToCheckFor[i]] = metadata.displayDefaults[keysToCheckFor[i]];
           }
@@ -491,7 +491,7 @@ const checkAndCorrectErrorsInState = (state, metadata, query, tree, viewingNarra
   if (metadata.geoResolutions) {
     const availableGeoResultions = metadata.geoResolutions.map((i) => i.key);
     if (availableGeoResultions.indexOf(state["geoResolution"]) === -1) {
-      /* fallbacks: JSON defined default, then hardocded default, then any available */
+      /* fallbacks: JSON defined default, then hardcoded default, then any available */
       if (metadata.displayDefaults && metadata.displayDefaults.geoResolution && availableGeoResultions.indexOf(metadata.displayDefaults.geoResolution) !== -1) {
         state.geoResolution = metadata.displayDefaults.geoResolution;
       } else if (availableGeoResultions.indexOf(defaultGeoResolution) !== -1) {
@@ -616,7 +616,7 @@ const modifyTreeStateVisAndBranchThickness = (oldState, zoomSelected, controlsSt
     newIdxRoot = applyInViewNodesToTree(0, oldState);
   }
 
-  /* calculate new branch thickesses & visibility, as this depends on the root note */
+  /* calculate new branch thicknesses & visibility, as this depends on the root note */
   const visAndThicknessData = calculateVisiblityAndBranchThickness(
     oldState,
     controlsState,
@@ -922,7 +922,7 @@ export const createTreeTooState = ({
   secondTreeUrl, /* treeToo URL */
   dispatch
 }) => {
-  /* TODO: reconsile choices (filters, colorBys etc) with this new tree */
+  /* TODO: reconcile choices (filters, colorBys etc) with this new tree */
   /* TODO: reconcile query with visibility etc */
   let controls = oldState.controls;
   const tree = Object.assign({}, oldState.tree);

src/actions/tree.js

@@ -142,7 +142,7 @@ export const updateVisibleTipsAndBranchThicknesses = (
 /**
  * date changes need to update tip visibility & branch thicknesses
  * this can be done in a single action
- * NB calling this without specifing newMin OR newMax is a no-op
+ * NB calling this without specifying newMin OR newMax is a no-op
  * @param  {string|false} newMin optional
  * @param  {string|false} newMax optional
  * @return {null} side-effects: a single action
@@ -333,7 +333,7 @@ const _traverseAndCreateSubtrees = (root, node, attr) => {
   // store original children so we traverse the entire tree
   const originalChildren = node.hasChildren ? [...node.children] : [];
 
-  if (node.arrayIdx === 0) { // __ROOT will hold all (expoded) subtrees
+  if (node.arrayIdx === 0) { // __ROOT will hold all (exploded) subtrees
     node.unexplodedChildren = originalChildren;
   } else if (node.hasChildren) {
     const parentTrait = getTraitFromNode(node, attr);

src/components/datasetLoader/index.js

@@ -3,7 +3,7 @@ import { connect } from "react-redux";
 import { loadJSONs } from "../../actions/loadData";
 import { PAGE_CHANGE } from "../../actions/types";
 
-/* The DatsetLoader component simply triggers the (async) loadJSONs action
+/* The DatasetLoader component simply triggers the (async) loadJSONs action
  * and then redirects to the "main" page (via a PAGE_CHANGE action).
  * Note that if the loadJSONs action "fails" it will subsequently redirect to a 404 page
  */

src/components/download/helperFunctions.js

@@ -131,7 +131,7 @@ export const areAuthorsPresent = (tree) => {
 
 /**
  * Create & write a TSV file where each row is an author,
- * with the relevent information (num isolates, journal etcetera)
+ * with the relevant information (num isolates, journal etcetera)
  */
 export const authorTSV = (dispatch, filePrefix, tree) => {
   const lineArray = [];
@@ -170,7 +170,7 @@ export const authorTSV = (dispatch, filePrefix, tree) => {
 
 /**
  * Create & write a TSV file where each row is a strain in the tree,
- * with the relevent information (accession, traits, etcetera).
+ * with the relevant information (accession, traits, etcetera).
  * Only visible nodes (tips) will be included in the file.
  */
 export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibilities) => {
@@ -205,7 +205,7 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibiliti
     }
 
     /* collect values (as writable strings) of the same "traits" as can be viewed by the modal displayed
-    when clicking on tips. Note that "num_date", "author" and "vaccine" are considered seperately below */
+    when clicking on tips. Note that "num_date", "author" and "vaccine" are considered separately below */
     const nodeAttrsToIgnore = ["author", "div", "num_date", "vaccine", "accession"];
     const traits = Object.keys(node.node_attrs).filter((k) => !nodeAttrsToIgnore.includes(k));
     for (const trait of traits) {
@@ -455,7 +455,7 @@ const injectAsSVGStrings = (output, key, data) => {
   output.push("</svg>");
 };
 
-/* define actual writer as a closure, because it may need to be triggered asyncronously */
+/* define actual writer as a closure, because it may need to be triggered asynchronously */
 const writeSVGPossiblyIncludingMap = (dispatch, filePrefix, panelsInDOM, panelLayout, textStrings, map) => {
   const errors = [];
   /* for each panel present in the DOM, create a data structure with the dimensions & the paths/shapes etc */

src/components/entropy/entropyD3.js

@@ -38,7 +38,7 @@ EntropyChart.prototype.render = function render(props) {
   this._drawMainNavElements();
   this._addZoomLayers();
   this._setScales(this.maxNt + 1, props.maxYVal);
-  /* If only a gene/nuc, zoom to that. If zoom min/max as well, that takes precidence */
+  /* If only a gene/nuc, zoom to that. If zoom min/max as well, that takes precedence */
   this.zoomCoordinates = isColorByGenotype(props.colorBy) ?
     this._getZoomCoordinates(decodeColorByGenotype(props.colorBy, props.geneLength), props.geneMap) :
     this.scales.xNav.domain(); // []; /* set zoom to specified gene or to whole genome */
@@ -466,7 +466,7 @@ EntropyChart.prototype._addBrush = function _addBrush() {
     return d3Event && d3Event.sourceEvent && d3Event.sourceEvent.type === 'zoom';
   }
 
-  /* zooms in by modifing the domain of xMain scale */
+  /* zooms in by modifying the domain of xMain scale */
   this._zoom = function _zoom(start, end) {
     const s = [start, end];
     this.scales.xMain.domain(s);

src/components/entropy/index.js

@@ -111,7 +111,7 @@ class Entropy extends React.Component {
     if (newMutType !== this.props.mutType) {
       /* 1. switch the redux colorBy back to the default */
       this.props.dispatch(changeColorBy(this.props.defaultColorBy));
-      /* 2. update the mut type in redux & re-calulate entropy */
+      /* 2. update the mut type in redux & re-calculate entropy */
       this.props.dispatch(changeMutType(newMutType));
     }
   }

src/components/framework/footer.js

@@ -156,8 +156,8 @@ const FooterStyles = styled.div`
 
 export const getAcknowledgments = (metadata, dispatch) => {
   /**
-   * If the metadata contains a description key, then it will take precendence the hard-coded
-   * acknowledgements. Expects the text in the description to be in Mardown format.
+   * If the metadata contains a description key, then it will take precedence the hard-coded
+   * acknowledgements. Expects the text in the description to be in Markdown format.
    * Jover. December 2019.
   */
   if (metadata.description) {

src/components/main/index.js

@@ -48,7 +48,7 @@ const Measurements = lazy(() => import("../measurements"));
 class Main extends React.Component {
   constructor(props) {
     super(props);
-    /* window listner employed to toggle switch to mobile display.
+    /* window listener employed to toggle switch to mobile display.
     NOTE: this used to toggle sidebar open boolean when that was stored
     as state here, but his has since ben moved to redux state. The mobile
     display should likewise be lifted to redux state */

src/components/main/utils.js

@@ -3,7 +3,7 @@ import { controlsWidth, controlsPadding } from "../../util/globals";
 
 
 export const calcPanelDims = (panels, narrativeIsDisplayed, availableWidth, availableHeight) => {
-  /* Calculate reponsive geometries. chart: entropy, frequencies. full/grid: map, tree, measurements */
+  /* Calculate responsive geometries. chart: entropy, frequencies. full/grid: map, tree, measurements */
   const chartWidthFraction = 1;
   const fullWidthFraction = 1;
   const gridWidthFraction = 0.5;

src/components/map/map.js

@@ -244,7 +244,7 @@ class Map extends React.Component {
         this.props.showTransmissionLines,
       );
 
-      // don't redraw on every rerender - need to seperately handle virus change redraw
+      // don't redraw on every rerender - need to separately handle virus change redraw
       this.setState({
         boundsSet: true,
         d3elems,
@@ -296,7 +296,7 @@ class Map extends React.Component {
 
       if (!this.state.demeData || !this.state.transmissionData) {
         /* this seems to happen when the data takes a particularly long time to create.
-        and the map is ready before the data (??). It's imperitive that this method runs
+        and the map is ready before the data (??). It's imperative that this method runs
         so if the data's not ready yet we try to rerun it after a short time.
         This could be improved */
         window.setTimeout(() => this.respondToLeafletEvent(leafletEvent), 50);
@@ -358,7 +358,7 @@ class Map extends React.Component {
   /**
    * updates demes & transmissions when redux (tree) visibility or colorScale (i.e. colorBy) has changed
    * returns early if the map or tree isn't ready
-   * uses deme & transmission indicies for smart (quick) updating
+   * uses deme & transmission indices for smart (quick) updating
    */
   maybeUpdateDemesAndTransmissions(nextProps) {
     if (!this.state.map || !this.props.treeLoaded || !this.state.d3elems) { return; }

src/components/map/mapHelpersLatLong.js

@@ -146,7 +146,7 @@ const setupDemeData = (nodes, visibility, geoResolution, nodeColors, triplicate,
       const coords = leafletLatLongToLayerPoint(lat, long, map);
 
       /* add entries to
-       * (1) `demeIndicies` -- a dict of "deme value" to the indicies of `demeData` & `arcData` where they appear
+       * (1) `demeIndices` -- a dict of "deme value" to the indices of `demeData` & `arcData` where they appear
        * (2) `demeData` -- an array of objects, each with {name, count etc.}
        *      if pie charts, then `demeData.arcs` exists, if colour-blended circles, `demeData.color` exists
        */

src/components/measurements/index.js

@@ -48,7 +48,7 @@ const isVisible = (visibility) => visibility === NODE_VISIBLE;
  * are relevant for the Measurement's panel. Uses the colorScale redux state to
  * find the current color attribute per strain.
  *
- * tree.visiblity and tree.nodeColors need to be an arrays that have the same
+ * tree.visibility and tree.nodeColors need to be arrays that have the same
  * order as tree.nodes
  * @param {Object} state
  * @returns {Object<string,Object>}

src/components/measurements/measurementsD3.js

@@ -187,7 +187,7 @@ export const drawMeasurementsSVG = (ref, svgData) => {
   // Create a subplot for each grouping
   let prevSubplotBottom = layout.topPadding;
   groupedMeasurements.forEach(([groupingValue, measurements], index) => {
-    // Make each subplot it's own SVG to re-use the same subplot yScale
+    // Make each subplot its own SVG to re-use the same subplot yScale
     const subplot = svg.append("svg")
       .attr("class", classes.subplot)
       .attr("id", getSubplotDOMId(groupingOrderedValues.indexOf(groupingValue)))
@@ -222,7 +222,7 @@ export const drawMeasurementsSVG = (ref, svgData) => {
         // If necessary, scale down the text to fit in the available space for the y-Axis labels
         // This does mean that if the text is extremely long, it can be unreadable.
         // We can improve on this by manually splitting the text into parts that can fit on multiple lines,
-        // but there's always limits of the available space so punting that for now.
+        // but there're always limits of the available space so punting that for now.
         //    -Jover, 20 September 2022
         g.selectAll('text')
           .attr("transform", (_, i, element) => {
@@ -283,7 +283,7 @@ export const colorMeasurementsSVG = (ref, treeStrainColors) => {
 export const drawMeansForColorBy = (ref, svgData, treeStrainColors, legendValues) => {
   const { xScale, groupingOrderedValues, groupedMeasurements } = svgData;
   const svg = select(ref);
-  // Re move all current color by means
+  // Remove all current color by means
   svg.selectAll(`.${classes.colorMean}`).remove();
   // Calc and draw color by means for each group
   groupedMeasurements.forEach(([groupingValue, measurements]) => {

src/components/narrative/MainDisplayMarkdown.js

@@ -8,8 +8,8 @@ const MarkdownDisplay = lazy(() => import("../markdownDisplay"));
 /**
  * The following code borrows heavily from the Footer
  * but is here in order to allow modifications with no side
- * effects to the Footer. This work was done in an expidited fashion
- * for nCoV but this should be revisted and improved when we have
+ * effects to the Footer. This work was done in an expedited fashion
+ * for nCoV but this should be revisited and improved when we have
  * time.                                          james. Jan 24 2020
  */
 

src/components/narrative/MobileNarrativeDisplay.js

@@ -28,7 +28,7 @@ const scrollToTop = () => {
 
 const explanationParagraph=`
   <p class="explanation">
-  Narratives are interleaved sections of text and associated nextstrain visualisations of the genomic data.
+  Narratives are interleaved sections of text and associated Nextstrain visualisations of the genomic data.
   Click the coloured arrows at the top & bottom of each page to move through this narrative.
   Within each page, you can scroll through the text to see visualisations of the genomic data.
   </p>
@@ -79,7 +79,7 @@ class MobileNarrativeDisplay extends React.Component {
       ));
       scrollToTop();
     };
-    // TODO: bind down & up arrows (is this ok since we also have scollable content?)
+    // TODO: bind down & up arrows (is this ok since we also have scrollable content?)
   }
 
   pageNarrativeContent() {

src/components/narrative/index.js

@@ -63,7 +63,7 @@ class Narrative extends React.Component {
       this.reactPageScroller.goToPage(this.props.currentInFocusBlockIdx);
     }
     /* bind arrow keys to move around in narrative */
-    /* Note that "normal" page scrolling is not avaialble in narrative mode
+    /* Note that "normal" page scrolling is not available in narrative mode
     and that scrolling the sidebar is associated with changing the narrative slide */
     Mousetrap.bind(['left', 'up'], this.goToPreviousSlide);
     Mousetrap.bind(['right', 'down'], this.goToNextSlide);

src/components/narrativeEditor/markdownInput.js

@@ -96,7 +96,7 @@ export const MarkdownInput = ({fileName, setNarrative, setError}) => {
 
 /** promisify FileReader's readAsText() so we can use it within
  * async functions via `await readJson(file)`.
- * Originally addapted from https://stackoverflow.com/a/51026615
+ * Originally adapted from https://stackoverflow.com/a/51026615
  * Taken from https://github.com/nextstrain/auspice.us/blob/427c138dcfce1f0e6fff8049dacc4e416304ff7a/auspice_client_customisation/handleDroppedFiles.js#L24-L44
  */
 function readFile(file, isJSON=true) {

src/components/tree/legend/legend.js

@@ -213,7 +213,7 @@ class Legend extends React.Component {
   }
 
   render() {
-    // catch the case where we try to render before anythings ready
+    // catch the case where we try to render before anything's ready
     if (!this.props.colorScale) return null;
     return (
       <svg

src/components/tree/phyloTree/grid.js

@@ -141,7 +141,7 @@ const calculateTemporalGridSeperation = (timeRange, pxAvailable) => {
   }
   /* how many of those "units" should ideally fit into each major grid separation? */
   majorStep.n = Math.floor(timeBetweenMajorGrids/levels[majorStep.unit].t) || 1;
-  /* if the numer of units (per major grid) is above the allowed max, use a bigger unit */
+  /* if the number of units (per major grid) is above the allowed max, use a bigger unit */
   if (levels[majorStep.unit].max && majorStep.n > levels[majorStep.unit].max) {
     majorStep.unit = levelsKeys[levelsKeys.indexOf(majorStep.unit)-1];
     majorStep.n = Math.floor(timeBetweenMajorGrids/levels[majorStep.unit].t) || 1;

src/components/tree/phyloTree/helpers.js

@@ -48,7 +48,7 @@ export const setDisplayOrderRecursively = (node, yCounter) => {
     node.displayOrderRange = [yCounter, yCounter];
     return yCounter;
   }
-  /* if here, then all children have displayOrders, but we dont. */
+  /* if here, then all children have displayOrders, but we don't. */
   node.displayOrder = children.reduce((acc, d) => acc + d.shell.displayOrder, 0) / children.length;
   node.displayOrderRange = [children[0].shell.displayOrder, children[children.length - 1].shell.displayOrder];
   return yCounter;

src/components/tree/phyloTree/layouts.js

@@ -50,7 +50,7 @@ export const setLayout = function setLayout(layout, scatterVariables) {
 };
 
 /**
- * assignes x,y coordinates for a rectancular layout
+ * assignes x,y coordinates for a rectangular layout
  * @return {null}
  */
 export const rectangularLayout = function rectangularLayout() {

src/components/tree/reactD3Interface/change.js

@@ -11,7 +11,7 @@ export const changePhyloTreeViaPropsComparison = (mainTree, phylotree, oldProps,
   Note that updating properties itself won't trigger any visual changes */
   phylotree.dateRange = [newProps.dateMinNumeric, newProps.dateMaxNumeric];
 
-  /* catch selectedStrain dissapearence seperately to visibility and remove modal */
+  /* catch selectedStrain disappearance separately to visibility and remove modal */
   if (oldTreeRedux.selectedStrain && !newTreeRedux.selectedStrain) {
     /* TODO change back the tip radius */
     newState.selectedNode = {};

src/components/tree/reactD3Interface/initialRender.js

@@ -39,7 +39,7 @@ export const renderTree = (that, main, phylotree, props) => {
       onTipLeave: callbacks.onTipLeave.bind(that),
       tipLabel: makeTipLabelFunc(props.tipLabelKey)
     },
-    treeState.branchThickness, /* guarenteed to be in redux by now */
+    treeState.branchThickness, /* guaranteed to be in redux by now */
     treeState.visibility,
     props.temporalConfidence.on, /* drawConfidence? */
     treeState.vaccines,

src/components/tree/tangle/unusedUntanglingCode.js

@@ -1,6 +1,6 @@
 
 /** applyToNodesPostOrder
- * recursivly apply the callback to each node postorder (root to tip, go left as far as you can, then backtrack...)
+ * recursively apply the callback to each node postorder (root to tip, go left as far as you can, then backtrack...)
  */
 // const applyToNodesPostOrder = (node, callback) => {
 //   if (node.children) {