Fix zoom freezing tips whose radius changed mid-transition

.eslintrc.yaml

@@ -29,10 +29,10 @@ rules:
   # Not possible while strictNullChecks is disabled in tsconfig.
   "@typescript-eslint/no-non-null-assertion": "error"
   no-unused-vars: off
-  "@typescript-eslint/no-unused-vars": ["error", { "argsIgnorePattern": "^_", "destructuredArrayIgnorePattern": "^_" }]
+  "@typescript-eslint/no-unused-vars": ["error", { "argsIgnorePattern": "^_", "destructuredArrayIgnorePattern": "^_", "caughtErrorsIgnorePattern": "^_"}]
   no-use-before-define: off
   "@typescript-eslint/no-use-before-define": ["error", { "functions": false }]
-  "@typescript-eslint/no-var-requires": off # Remove this override once all files use ES6 style imports.
+  "@typescript-eslint/no-require-imports": off # Remove this override once all files use ES6 style imports.
   prefer-const: ["error", {"destructuring": "all"}]
   react/no-array-index-key: error
   react/prop-types: off # Remove this override once all props have been typed using PropTypes or TypeScript.

.github/workflows/ci.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: [20, 22, 24]
+        node: [24, 26]
     steps:
       - uses: actions/checkout@v7
       - uses: actions/setup-node@v6
@@ -30,15 +30,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: [20, 22, 24]
+        node: [24, 26]
     steps:
       - uses: actions/checkout@v7
       - uses: actions/setup-node@v6
         with:
           node-version: ${{ matrix.node }}
       # Build is implicit with the "prepare" life cycle script
       - run: npm ci --loglevel verbose
-      - run: npm run get-data
+      - run: npm run fetch-test-data
       - run: npx playwright install chromium
       - run: npm run smoke-test
 

DEV_DOCS.md

@@ -93,7 +93,7 @@ General advice for writing tests:
 
 > Smoke tests are currently very limited but we may expand these in the future
 
-1. Fetch datasets with `npm run get-data`.
+1. Fetch testing datasets with `npm run fetch-test-data`.
 2. Install the testing browser with `npx playwright install chromium`.
 3. Run `npm run smoke-test`.
 
@@ -110,15 +110,9 @@ If embarking on this journey, consider using Playwright since it is already used
 Linting via eslint: `npm run lint`, typechecking via `npm type-check`
 
 
-## Heroku review apps
-
-
-A Heroku pipeline for this repository is connected to GitHub under the nextstrain-bot user account. The Review Apps feature facilitates manual review of changes by automatically creating a test instance from the PR source branch and adding a link to it on the GitHub PR page. These apps are based on configuration in [app.json](./app.json).
-
-
 #### Test on downstream repositories
 
-Additionally, a GitHub Actions workflow has been set up to generate PRs in downstream repositories that reflect the new changes in Auspice. To use it, add the label [preview on auspice.us](https://github.com/nextstrain/auspice/labels/preview%20on%20auspice.us) and/or [preview on nextstrain.org](https://github.com/nextstrain/auspice/labels/preview%20on%20nextstrain.org).
+A GitHub Actions workflow has been set up to generate PRs in downstream repositories that reflect the new changes in Auspice. To use it, add the label [preview on auspice.us](https://github.com/nextstrain/auspice/labels/preview%20on%20auspice.us) and/or [preview on nextstrain.org](https://github.com/nextstrain/auspice/labels/preview%20on%20nextstrain.org).
 
 ## git-lfs
 

README.md

@@ -39,20 +39,11 @@ See [the relevant page on Auspice docs](https://docs.nextstrain.org/projects/aus
 To get up & running, you'll need datasets to visualise.
 (Please see the [nextstrain docs](https://nextstrain.org/docs/) for tutorials on how to run your own analyses.)
 
-If you've installed auspice from `npm` you may get datasets to display via:
+If you've installed auspice from `npm` you may get an example dataset to display via:
 
 ```bash
 mkdir data
 curl http://data.nextstrain.org/zika.json --compressed -o data/zika.json
-curl http://data.nextstrain.org/ncov.json --compressed -o data/ncov.json
-...
-```
-
-If you've installed auspice from source, we have a helper script to download a number of datasets for testing:
-
-```bash
-# from the auspice src directory
-npm run get-data
 ```
 
 ### Obtain narratives to view locally

auspice.js

@@ -1,11 +1,11 @@
 #!/usr/bin/env node
 
-const argparse = require('argparse');
-const version = require('./src/version').version;
-const view = require("./cli/view");
-const build = require("./cli/build");
-const develop = require("./cli/develop");
-const convert = require("./cli/convert");
+import argparse from 'argparse';
+import { version } from './src/version.js';
+import * as view from "./cli/view.ts";
+import * as build from "./cli/build.ts";
+import * as develop from "./cli/develop.ts";
+import * as convert from "./cli/convert.js";
 
 const parser = new argparse.ArgumentParser({
   version: version,
@@ -38,5 +38,3 @@ if (args.subcommand === "build") {
 } else if (args.subcommand === "convert") {
   convert.run(args);
 }
-
-// console.dir(args);

babel.config.js → babel.config.cjs

@@ -1,4 +1,4 @@
-const utils = require('./cli/utils');
+const utils = require('./cli/utils.ts');
 
 /* What variables does this config depend on?
  * process.env.BABEL_EXTENSION_PATH -- a resolved path
@@ -31,6 +31,9 @@ module.exports = function babelConfig(api) {
   if (api.env("development")) {
     plugins.push(["react-hot-loader/babel", { safetyNet: false }]);
   }
+  if (api.env('test')) {
+    plugins.push("babel-plugin-transform-import-meta");
+  }
   if (process.env.BABEL_INCLUDE_TIMING_FUNCTIONS === "false") {
     plugins.push(["strip-function-call", {strip: ["timerStart", "timerEnd"]}]);
   }

cli/build.js → cli/build.ts

@@ -1,14 +1,20 @@
-const webpack = require("webpack");
-const path = require("path");
-const generateWebpackConfig = require("../webpack.config.js").default;
-const utils = require("./utils");
+import webpack from "webpack";
+import path from "path";
+import { fileURLToPath } from 'url';
+import { createRequire } from 'module';
+import * as utils from "./utils.ts";
+
+const require = createRequire(import.meta.url);
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+
+const generateWebpackConfig = require("../webpack.config.cjs").default;
 const SUPPRESS = require('argparse').Const.SUPPRESS;
 
-const addParser = (parser) => {
+const addParser = (parser): void => {
   const description = `Build the client source code bundle.
   For development, you may want to use "auspice develop" which recompiles code on the fly as changes are made.
   You may provide customisations (e.g. code, options) to this step to modify the functionality and appearance of auspice.
-  To serve the bundle you will need a server such as "auspice view". 
+  To serve the bundle you will need a server such as "auspice view".
   `;
 
   const subparser = parser.addParser('build', {addHelp: true, description});
@@ -24,7 +30,7 @@ const addParser = (parser) => {
   subparser.addArgument('--serverless', {action: "storeTrue", help: SUPPRESS});
 };
 
-const run = (args) => {
+const run = (args): void => {
 
   /* webpack set up */
   const extensionPath = args.extend ? path.resolve(args.extend) : undefined;
@@ -64,14 +70,14 @@ const run = (args) => {
 /* Where should the built files be saved? (or sourced??)
  * This may grow more complex over time
  */
-function getCustomOutputPath(extensions) {
+function getCustomOutputPath(extensions): string | false {
   if (extensions && path.resolve(__dirname, "..") !== process.cwd()) {
     return process.cwd();
   }
   return false;
 }
 
-module.exports = {
+export {
   addParser,
   run
 };

cli/convert.js

@@ -1,7 +1,7 @@
 /* eslint no-console: off */
-const fs = require("fs");
-const convertFromV1 = require("./server/convertJsonSchemas").convertFromV1;
-const utils = require("./utils");
+import fs from "fs";
+import { convertFromV1 } from "./server/convertJsonSchemas.js";
+import * as utils from "./utils.ts";
 
 
 const addParser = (parser) => {
@@ -35,7 +35,7 @@ const run = (args) => {
   fs.writeFileSync(args.output, JSON.stringify(v2, null, args.minify_json ? 0 : 2));
 };
 
-module.exports = {
+export {
   addParser,
   run
 };

cli/dev/reverse-proxy.js

@@ -1,7 +1,6 @@
-
-const utils = require("../utils");
-const { URL } = require("url");
-const fetch = require("node-fetch");
+import * as utils from "../utils.ts";
+import { URL } from "url";
+import fetch from "node-fetch";
 
 const PROXY = process.env.PROXY || `http://localhost:5000`
 
@@ -59,8 +58,6 @@ async function proxy(req, res) {
   }
 }
 
-module.exports = {
-  getAvailable: proxy,
-  getDataset: proxy,
-  getNarrative: proxy,
-};
+export const getAvailable = proxy;
+export const getDataset = proxy;
+export const getNarrative = proxy;

cli/develop.js → cli/develop.ts

@@ -1,17 +1,26 @@
 /* eslint no-console: off */
-const path = require("path");
-const express = require("express");
-const webpack = require("webpack");
-const webpackDevMiddleware = require("webpack-dev-middleware");
-const webpackHotMiddleware = require("webpack-hot-middleware");
-const utils = require("./utils");
-const { loadAndAddHandlers, serveRelativeFilepaths } = require("./view");
-const version = require('../src/version').version;
-const chalk = require('chalk');
-const generateWebpackConfig = require("../webpack.config.js").default;
+import path from "path";
+import { fileURLToPath } from 'url';
+import { createRequire } from 'module';
+import express from "express";
+import webpack from "webpack";
+import webpackDevMiddleware from "webpack-dev-middleware";
+import webpackHotMiddleware from "webpack-hot-middleware";
+import * as utils from "./utils.ts";
+import * as view from "./view.ts";
+import { version } from '../src/version.js';
+import _chalk from 'chalk';
+/* eslint-disable-next-line @typescript-eslint/consistent-type-assertions */
+const chalk = _chalk as any as import('chalk').Chalk;
+import { processPathArguments } from "./server/processPaths.ts";
+
+const require = createRequire(import.meta.url);
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+
+const generateWebpackConfig = require("../webpack.config.cjs").default;
 const SUPPRESS = require('argparse').Const.SUPPRESS;
 
-const addParser = (parser) => {
+const addParser = (parser): void => {
   const description = `Launch auspice in development mode.
     This runs a local server and uses hot-reloading to allow automatic updating as you edit the code.
     NOTE: there is a speed penalty for this ability and this should never be used for production.
@@ -21,24 +30,25 @@ const addParser = (parser) => {
   subparser.addArgument('--verbose', {action: "storeTrue", help: "Print more verbose progress messages in the terminal."});
   subparser.addArgument('--extend', {action: "store", metavar: "JSON", help: "Client customisations to be applied. See documentation for more details. Note that hot reloading does not currently work for these customisations."});
   subparser.addArgument('--handlers', {action: "store", metavar: "JS", help: "Overwrite the provided server handlers for client requests. See documentation for more details."});
-  subparser.addArgument('--datasetDir', {metavar: "PATH", help: "Directory where datasets (JSONs) are sourced. This is ignored if you define custom handlers."});
-  subparser.addArgument('--narrativeDir', {metavar: "PATH", help: "Directory where narratives (Markdown files) are sourced. This is ignored if you define custom handlers."});
+  view.addDatasetNarrativePathArgs(subparser)
   subparser.addArgument('--includeTiming', {action: "storeTrue", help: "Do not strip timing functions. With these included the browser console will print timing measurements for a number of functions."});
 
   /* there are some options which we deliberately do not document via `--help`. See build.js for explanations. */
   subparser.addArgument('--gh-pages', {action: "store", help: SUPPRESS});
 };
 
 
-const run = (args) => {
+const run = async (args): Promise<void> => {
+  const dataPaths = processPathArguments(args)
+
   /* Basic server set up */
   const app = express();
   app.set('port', process.env.PORT || 4000);
   app.set('host', process.env.HOST || "localhost");
 
   const baseDir = path.resolve(__dirname, "..");
   utils.verbose(`Serving index / favicon etc from  "${baseDir}"`);
-  app.get("/favicon.png", (req, res) => {res.sendFile(path.join(baseDir, "favicon.png"));});
+  app.get("/favicon.png", (_req, res) => {res.sendFile(path.join(baseDir, "favicon.png"));});
 
   /* webpack set up */
   const extensionPath = args.extend ? path.resolve(args.extend) : undefined;
@@ -51,7 +61,7 @@ const run = (args) => {
   process.env.BABEL_EXTENSION_PATH = extensionPath;
 
   /* Redirects / to webpack-generated index */
-  app.use((req, res, next) => {
+  app.use((req, _res, next) => {
     if (!/^\/__webpack_hmr|^\/charon|\.[A-Za-z0-9]{1,5}$/.test(req.path)) {
       req.url = webpackConfig.output.publicPath;
     }
@@ -69,12 +79,20 @@ const run = (args) => {
 
   let handlerMsg = "";
   if (args.gh_pages) {
-    handlerMsg = serveRelativeFilepaths({app, dir: path.resolve(args.gh_pages)});
+    handlerMsg = view.serveRelativeFilepaths({app, dir: path.resolve(args.gh_pages)});
+  } else if (args.handlers) {
+    handlerMsg = await view.customRouteHandlers(app, path.resolve(args.handlers));
   } else {
-    handlerMsg = loadAndAddHandlers({app, handlersArg: args.handlers, datasetDir: args.datasetDir, narrativeDir: args.narrativeDir});
+    handlerMsg = view.defaultRouteHandlers({app, dataPaths});
   }
+  /* Handle unhandled API (charon) routes */
+  app.get("/charon*", (req, res) => {
+    const errorMessage = "Query unhandled -- " + req.originalUrl;
+    utils.warn(errorMessage);
+    return res.status(500).type("text/plain").send(errorMessage);
+  });
 
-  app.get("*", (req, res) => res.redirect("/"));
+  app.get("*", (_req, res) => res.redirect("/"));
 
   const server = app.listen(app.get('port'), app.get('host'), () => {
     utils.log("\n\n---------------------------------------------------");
@@ -95,8 +113,8 @@ const run = (args) => {
       utils.error(`Host ${app.get('host')} is not a valid address. The server could not be started. If you did not provide a HOST environment variable when starting the app you may have HOST already set in your system. You can either change that variable, or override HOST when starting the app.
 
       Example commands to fix:
-        ${chalk.yellow('HOST="localhost" auspice develop')}
-        ${chalk.yellow('HOST="localhost" npm run develop')}`);
+        ${chalk.yellow('HOST="localhost" auspice develop <PATH>')}
+        ${chalk.yellow('HOST="localhost" npm run develop -- <PATH>')}`);
     }
 
     utils.error(`Uncaught error in app.listen(). Code: ${error.code}`);
@@ -105,7 +123,7 @@ const run = (args) => {
 
 };
 
-module.exports = {
+export {
   addParser,
   run
 };

cli/server/convertJsonSchemas.js

@@ -1,4 +1,4 @@
-const utils = require("../utils");
+import * as utils from "../utils.ts";
 
 /** In auspice v1, the `prettyString` function was used extensively to transform values
  * for "nicer" display. v2 JSONs intentially avoid this -- the strings are intended to
@@ -397,7 +397,7 @@ const setNodeBranchAttrs = (v2) => {
 };
 
 
-const convertFromV1 = ({tree, meta}) => {
+export const convertFromV1 = ({tree, meta}) => {
   const v2 = {version: "v2", meta: { extensions: { original_version: "v1" }}};
   // set metadata
   setColorings(v2["meta"], meta);
@@ -411,8 +411,3 @@ const convertFromV1 = ({tree, meta}) => {
   removeNonV2TreeProps(v2);
   return v2;
 };
-
-
-module.exports = {
-  convertFromV1
-};