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daniel-jidaniel-ji
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initial work on hivtrace pipeline
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‎.github/workflows/website.yml‎

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name: deploy website
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on:
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# Runs on pushes targeting the default branch
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push:
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branches: ['main']
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# Sets the GITHUB_TOKEN permissions to allow deployment to GitHub Pages
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permissions:
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contents: write
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pages: write
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id-token: write
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# Allow one concurrent deployment
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concurrency:
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group: 'pages'
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cancel-in-progress: true
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jobs:
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deploy:
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timeout-minutes: 60
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-node@v3
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with:
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node-version: 22
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- name: Install dependencies
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run: npm ci
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- name: Build for github pages
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run: npm run build
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- name: Setup Pages
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uses: actions/configure-pages@v5
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.gitignore‎

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# Logs
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logs
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*.log
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npm-debug.log*
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yarn-debug.log*
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yarn-error.log*
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pnpm-debug.log*
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lerna-debug.log*
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node_modules
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dist
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dist-ssr
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*.local
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# Editor directories and files
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.vscode/*
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!.vscode/extensions.json
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.idea
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.DS_Store
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*.suo
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*.ntvs*
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*.njsproj
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*.sln
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*.sw?

‎.nvmrc‎

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v22

‎README.md‎

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# hivtrace-wasm
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a WebAssembly implementation of the HIV-TRACE pipeline.
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# HIV-TRACE WASM
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A WebAssembly implementation of the HIV-TRACE pipeline.
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Uses [cawlign](https://github.com/veg/cawlign/), [tn93](https://github.com/veg/tn93), and [hivnetworkcsv](https://github.com/veg/hivclustering). Implemented using [Biowasm](https://biowasm.com/), [Pyodide](https://pyodide.org/), and [Emscripten](https://emscripten.org/).

‎eslint.config.js‎

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import js from '@eslint/js'
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import globals from 'globals'
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import reactHooks from 'eslint-plugin-react-hooks'
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import reactRefresh from 'eslint-plugin-react-refresh'
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export default [
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{ ignores: ['dist'] },
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{
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files: ['**/*.{js,jsx}'],
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languageOptions: {
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ecmaVersion: 2020,
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globals: globals.browser,
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parserOptions: {
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ecmaVersion: 'latest',
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ecmaFeatures: { jsx: true },
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sourceType: 'module',
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},
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},
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plugins: {
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'react-hooks': reactHooks,
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'react-refresh': reactRefresh,
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},
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rules: {
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...js.configs.recommended.rules,
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...reactHooks.configs.recommended.rules,
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'no-unused-vars': ['error', { varsIgnorePattern: '^[A-Z_]' }],
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'react-refresh/only-export-components': [
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'warn',
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{ allowConstantExport: true },
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],
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},
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},
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]

‎index.html‎

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<link rel="icon" href="/favicon.ico" />
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<title>HIV-TRACE WASM</title>
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</head>
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<body>
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<script type="module" src="/src/main.jsx"></script>
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<script src="/tools/pyodide/pyodide.js"></script>
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<script src="/tools/aioli.js"></script>
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</body>
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</html>

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