[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.all-contributorsrc

@@ -1,7 +1,5 @@
 {
-  "files": [
-    "README.md"
-  ],
+  "files": ["README.md"],
   "imageSize": 100,
   "commit": false,
   "contributors": [
@@ -10,67 +8,49 @@
       "name": "Alex Kramer",
       "avatar_url": "https://avatars.githubusercontent.com/u/6502785?v=4",
       "profile": "https://github.com/amkram",
-      "contributions": [
-        "code",
-        "design",
-        "ideas"
-      ]
+      "contributions": ["code", "design", "ideas"]
     },
     {
       "login": "AngieHinrichs",
       "name": "Angie Hinrichs",
       "avatar_url": "https://avatars.githubusercontent.com/u/186983?v=4",
       "profile": "http://genome.ucsc.edu/",
-      "contributions": [
-        "ideas",
-        "data"
-      ]
+      "contributions": ["ideas", "data"]
     },
     {
       "login": "richardgoater",
       "name": "Richard Goater",
       "avatar_url": "https://avatars.githubusercontent.com/u/1429721?v=4",
       "profile": "https://github.com/richardgoater",
-      "contributions": [
-        "design",
-        "code"
-      ]
+      "contributions": ["design", "code"]
     },
     {
       "login": "chaoran-chen",
       "name": "Chaoran Chen",
       "avatar_url": "https://avatars.githubusercontent.com/u/18666552?v=4",
       "profile": "https://github.com/chaoran-chen",
-      "contributions": [
-        "ideas"
-      ]
+      "contributions": ["ideas"]
     },
     {
       "login": "corneliusroemer",
       "name": "Cornelius Roemer",
       "avatar_url": "https://avatars.githubusercontent.com/u/25161793?v=4",
       "profile": "https://github.com/corneliusroemer",
-      "contributions": [
-        "ideas"
-      ]
+      "contributions": ["ideas"]
     },
     {
       "login": "sungyeonkwon",
       "name": "Sung Kwon",
       "avatar_url": "https://avatars.githubusercontent.com/u/25865179?v=4",
       "profile": "https://github.com/sungyeonkwon",
-      "contributions": [
-        "infra"
-      ]
+      "contributions": ["infra"]
     },
     {
       "login": "kvargha",
       "name": "Koorous Vargha",
       "avatar_url": "https://avatars.githubusercontent.com/u/35252220?v=4",
       "profile": "https://kvargha.com/",
-      "contributions": [
-        "code"
-      ]
+      "contributions": ["code"]
     }
   ],
   "contributorsPerLine": 7,

docs/component.md

@@ -49,7 +49,7 @@ D,John,Fish`;
   <script>
     ReactDOM.render(
       React.createElement(Taxonium, { sourceData: sourceData }),
-      document.getElementById("root")
+      document.getElementById("root"),
     );
   </script>
 </body>

taxonium_backend/server.js

@@ -26,7 +26,7 @@ program
   .option("--data_url <data url>", "data url")
   .option(
     "--data_file <data file>",
-    "local data file, as alternative to data url"
+    "local data file, as alternative to data url",
   );
 
 program.parse();
@@ -154,7 +154,7 @@ app.get("/search", function (req, res) {
       result.data.length +
       " results in " +
       (Date.now() - start_time) +
-      "ms"
+      "ms",
   );
   console.log("Result type was " + result.type);
 });
@@ -256,7 +256,7 @@ app.get("/nodes/", function (req, res) {
       max_y,
       min_x,
       max_x,
-      req.query.xType
+      req.query.xType,
     );
   }
   console.log("Ready to send after " + (Date.now() - start_time) + "ms.");
@@ -268,19 +268,19 @@ app.get("/nodes/", function (req, res) {
       (Date.now() - start_time) +
       "ms, and output " +
       result.length +
-      " nodes."
+      " nodes.",
   );
 });
 
 function startListening() {
   if (command_options.ssl) {
     options = {
       key: fs.readFileSync(
-        "/etc/letsencrypt/live/api.taxonium.org/privkey.pem"
+        "/etc/letsencrypt/live/api.taxonium.org/privkey.pem",
       ),
       ca: fs.readFileSync("/etc/letsencrypt/live/api.taxonium.org/chain.pem"),
       cert: fs.readFileSync(
-        "/etc/letsencrypt/live/api.taxonium.org/fullchain.pem"
+        "/etc/letsencrypt/live/api.taxonium.org/fullchain.pem",
       ),
     };
     https.createServer(options, app).listen(command_options.port, "0.0.0.0");
@@ -452,7 +452,7 @@ app.get("/node_details/", async (req, res) => {
   }
   validateSIDandSend(detailed_node, req.query.sid, res);
   console.log(
-    "Request took " + (Date.now() - start_time) + "ms, and output " + node
+    "Request took " + (Date.now() - start_time) + "ms, and output " + node,
   );
 });
 
@@ -463,7 +463,7 @@ app.get("/tip_atts", async (req, res) => {
   const atts = filtering.getTipAtts(processedData.nodes, node_id, att);
   validateSIDandSend(atts, req.query.sid, res);
   console.log(
-    "Request took " + (Date.now() - start_time) + "ms, and output " + atts
+    "Request took " + (Date.now() - start_time) + "ms, and output " + atts,
   );
 });
 
@@ -474,11 +474,11 @@ app.get("/nextstrain_json/:root_id", async (req, res) => {
     root_id,
     processedData.nodes,
     config,
-    processedData.mutations
+    processedData.mutations,
   );
   res.setHeader(
     "Content-Disposition",
-    "attachment; " + "filename=" + root_id + ".nextstrain.json"
+    "attachment; " + "filename=" + root_id + ".nextstrain.json",
   );
   res.send(json);
 });
@@ -505,7 +505,7 @@ const loadData = async () => {
   processedData = await importing.processJsonl(
     supplied_object,
     logStatusMessage,
-    ReadableWebToNodeStream.ReadableWebToNodeStream
+    ReadableWebToNodeStream.ReadableWebToNodeStream,
   );
 
   logStatusMessage({
@@ -517,7 +517,7 @@ const loadData = async () => {
   }
 
   processedData.genes = new Set(
-    processedData.mutations.map((mutation) => mutation.gene)
+    processedData.mutations.map((mutation) => mutation.gene),
   );
   // as array
   processedData.genes = Array.from(processedData.genes);
@@ -530,7 +530,7 @@ const loadData = async () => {
     processedData.overallMaxY,
     processedData.overallMinX,
     processedData.overallMaxX,
-    "x_dist"
+    "x_dist",
   );
 
   cached_starting_values = result;

taxonium_component/README.md

@@ -73,7 +73,7 @@ If you're working with basic HTML, you can include the Taxonium component using
   <script>
     ReactDOM.render(
       React.createElement(Taxonium, { sourceData: sourceData }),
-      document.getElementById("root")
+      document.getElementById("root"),
     );
   </script>
 </body>

taxonium_component/src/Deck.jsx

@@ -66,7 +66,7 @@ function Deck({
   // Treenome state
   const setMouseXY = useCallback(
     (info) => view.setMouseXY([info.x, info.y]),
-    [view]
+    [view],
   );
   const [treenomeReferenceInfo, setTreenomeReferenceInfo] = useState(null);
 
@@ -91,7 +91,7 @@ function Deck({
         mouseDownPos.current &&
         Math.sqrt(
           Math.pow(mouseDownPos.current[0] - event.clientX, 2) +
-            Math.pow(mouseDownPos.current[1] - event.clientY, 2)
+            Math.pow(mouseDownPos.current[1] - event.clientY, 2),
         ) > pan_threshold
       ) {
         return false;
@@ -148,7 +148,7 @@ function Deck({
       onViewStateChange,
       xzoom,
       deckRef,
-    ]
+    ],
   );
 
   const [hoverInfo, setHoverInfoRaw] = useState(null);
@@ -166,7 +166,7 @@ function Deck({
         hoverDetails.clearNodeDetails();
       }
     },
-    [hoverDetails]
+    [hoverDetails],
   );
 
   const { layers, layerFilter, keyStuff } = useLayers({

taxonium_component/src/Taxonium.jsx

@@ -77,7 +77,7 @@ function Taxonium({
     backendUrl ? backendUrl : query.backend,
     query.sid,
     url_on_fail,
-    sourceData
+    sourceData,
   );
   let hoverDetails = useHoverDetails();
   const gisaidHoverDetails = useNodeDetails("gisaid-hovered", backend);
@@ -93,7 +93,7 @@ function Taxonium({
     setTitle,
     query,
     configDict,
-    configUrl
+    configUrl,
   );
   const colorBy = useColorBy(config, query, updateQuery);
   const colorMapping = useMemo(() => {
@@ -110,7 +110,7 @@ function Taxonium({
     (xType) => {
       updateQuery({ xType });
     },
-    [updateQuery]
+    [updateQuery],
   );
 
   const { data, boundsForQueries, isCurrentlyOutsideBounds } =

taxonium_component/src/components/Basic.jsx

@@ -17,7 +17,7 @@ export const Button = ({
         className={classNames(
           "tx-button no-underline",
           "border border-gray-400 shadow-sm rounded py-1 px-2 bg-gray-100 hover:bg-gray-200 text-sm text-gray-700",
-          className
+          className,
         )}
         href={href}
         title={title}
@@ -32,7 +32,7 @@ export const Button = ({
         className={classNames(
           "tx-button",
           "border border-gray-400 shadow-sm rounded py-1 px-2 bg-gray-100 hover:bg-gray-200 text-sm text-gray-700",
-          className
+          className,
         )}
         onClick={onClick}
         title={title}
@@ -49,7 +49,7 @@ export const Select = ({ onChange, className, children, value, title }) => {
       className={classNames(
         "border bg-white text-gray-900 text-sm hover:text-gray-700 py-1 pl-2 pr-6",
         "focus:ring-gray-800 focus:border-gray-800",
-        className
+        className,
       )}
       onChange={onChange}
       value={value}

taxonium_component/src/components/DeckSettingsModal.jsx

@@ -50,7 +50,7 @@ const DeckSettingsModal = ({
               checked={settings.displayTextForInternalNodes}
               onChange={() =>
                 settings.setDisplayTextForInternalNodes(
-                  !settings.displayTextForInternalNodes
+                  !settings.displayTextForInternalNodes,
                 )
               }
             />{" "}
@@ -65,7 +65,7 @@ const DeckSettingsModal = ({
               checked={settings.displayPointsForInternalNodes}
               onChange={() =>
                 settings.setDisplayPointsForInternalNodes(
-                  !settings.displayPointsForInternalNodes
+                  !settings.displayPointsForInternalNodes,
                 )
               }
             />{" "}
@@ -81,7 +81,7 @@ const DeckSettingsModal = ({
               value={settings.thresholdForDisplayingText}
               onChange={(e) =>
                 settings.setThresholdForDisplayingText(
-                  parseFloat(e.target.value)
+                  parseFloat(e.target.value),
                 )
               }
               step="0.1"
@@ -120,7 +120,7 @@ const DeckSettingsModal = ({
                   onChange={() =>
                     settings.setMutationTypeEnabled(
                       key,
-                      !settings.mutationTypesEnabled[key]
+                      !settings.mutationTypesEnabled[key],
                     )
                   }
                 />{" "}

taxonium_component/src/components/JBrowseErrorBoundary.jsx

@@ -23,7 +23,7 @@ export class JBrowseErrorBoundary extends React.Component {
       error.message === "Invalid array length"
     ) {
       toast.error(
-        "Error displaying track. Please make sure your file is well-formatted (e.g., validated with https://github.com/EBIvariation/vcf-validator)."
+        "Error displaying track. Please make sure your file is well-formatted (e.g., validated with https://github.com/EBIvariation/vcf-validator).",
       );
     }
   }

taxonium_component/src/components/JBrowsePanel.jsx

@@ -283,7 +283,7 @@ function JBrowsePanel(props) {
       state.session.view
     ) {
       freezeTracks.forEach((t) =>
-        state.session.view.showTrack(t.configuration.trackId)
+        state.session.view.showTrack(t.configuration.trackId),
       );
     }
   }, [freezeTracks, state]);
@@ -308,7 +308,7 @@ function JBrowsePanel(props) {
       const widget = state.session.addWidget(
         "AddTrackWidget",
         "addTrackWidget",
-        { view: state.session.view.id }
+        { view: state.session.view.id },
       );
       // AddTrackWidget calls session.addTrackConf, which
       // doesn't appear to be defined in the session object
@@ -332,7 +332,7 @@ function JBrowsePanel(props) {
         ":" +
         props.treenomeState.ntBoundsExt[0] +
         ".." +
-        props.treenomeState.ntBoundsExt[1]
+        props.treenomeState.ntBoundsExt[1],
     );
     props.treenomeState.setNtBoundsExt(null);
   }, [props.settings.chromosomeName, props.treenomeState, state.session.view]);

taxonium_component/src/components/Key.jsx

@@ -27,7 +27,7 @@ const Key = ({
     <div
       className={classNames(
         "px-2 border-right border  bg-white opacity-90 absolute bottom-2 left-2 pt-1 pb-2",
-        collapsed ? "w-20" : "w-32"
+        collapsed ? "w-20" : "w-32",
       )}
     >
       <h3

taxonium_component/src/components/NodeHoverTip.jsx

@@ -119,7 +119,7 @@ const NodeHoverTip = ({
                 hoveredNode[key]
               )}
             </div>
-          )
+          ),
       )}
 
       {config.mutations.length > 0 && (
@@ -164,7 +164,7 @@ const NodeHoverTip = ({
             <div className="mt-1 justify">
               <b className="font-semibold">Authors:</b>{" "}
               {fixAuthors(
-                hoverDetails.nodeDetails.acknowledgements.covv_authors
+                hoverDetails.nodeDetails.acknowledgements.covv_authors,
               )}
             </div>
           </div>