1004 lines
30 KiB
HTML
1004 lines
30 KiB
HTML
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<!doctype html>
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<html lang="en" class="no-js">
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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">
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<link rel="shortcut icon" href="../assets/images/favicon.png">
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<meta name="generator" content="mkdocs-1.1.2, mkdocs-material-6.1.4+insiders-1.9.0">
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<title>File Structure - RAPIDS</title>
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<link rel="stylesheet" href="../assets/stylesheets/main.a2a6bca7.min.css">
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<link rel="stylesheet" href="../assets/stylesheets/palette.c308bc62.min.css">
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<link href="https://fonts.gstatic.com" rel="preconnect" crossorigin>
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<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,400,400i,700%7CRoboto+Mono&display=fallback">
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<style>body,input{font-family:"Roboto",-apple-system,BlinkMacSystemFont,Helvetica,Arial,sans-serif}code,kbd,pre{font-family:"Roboto Mono",SFMono-Regular,Consolas,Menlo,monospace}</style>
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<link rel="stylesheet" href="../stylesheets/extra.css">
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</head>
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<body dir="ltr" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="blue">
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<script>var palette=JSON.parse(localStorage.getItem("__palette")||"{}");if(void 0!==palette.color)for(var key in palette.color)document.body.setAttribute("data-md-color-"+key,palette.color[key])</script>
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<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
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<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
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<label class="md-overlay" for="__drawer"></label>
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<div data-md-component="skip">
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<a href="#file-structure" class="md-skip">
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Skip to content
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</a>
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</div>
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<div data-md-component="announce">
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</div>
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<header class="md-header" data-md-component="header">
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<nav class="md-header-nav md-grid" aria-label="Header">
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<a href=".." title="RAPIDS" class="md-header-nav__button md-logo" aria-label="RAPIDS">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 01-2 2H7a2 2 0 01-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V4a2 2 0 012-2h10a2 2 0 012 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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<label class="md-header-nav__button md-icon" for="__drawer">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3V6m0 5h18v2H3v-2m0 5h18v2H3v-2z"/></svg>
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</label>
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<div class="md-header-nav__title" data-md-component="header-title">
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<div class="md-header-nav__ellipsis">
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<div class="md-header-nav__topic">
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<span class="md-ellipsis">
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RAPIDS
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</span>
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</div>
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<div class="md-header-nav__topic" data-md-component="header-topic">
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<span class="md-ellipsis">
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File Structure
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</span>
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</div>
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</div>
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</div>
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<div class="md-header-nav__options">
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<button class="md-header-nav__button md-icon" title="Switch to light mode" aria-label="Switch to light mode" data-md-option="palette" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="blue" data-md-state="hidden">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M17 7H7a5 5 0 00-5 5 5 5 0 005 5h10a5 5 0 005-5 5 5 0 00-5-5m0 8a3 3 0 01-3-3 3 3 0 013-3 3 3 0 013 3 3 3 0 01-3 3z"/></svg>
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</button>
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<button class="md-header-nav__button md-icon" title="Switch to dark mode" aria-label="Switch to dark mode" data-md-option="palette" data-md-color-scheme="slate" data-md-color-primary="blue" data-md-color-accent="blue" data-md-state="hidden">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M7 10a2 2 0 012 2 2 2 0 01-2 2 2 2 0 01-2-2 2 2 0 012-2m10-3a5 5 0 015 5 5 5 0 01-5 5H7a5 5 0 01-5-5 5 5 0 015-5h10M7 9a3 3 0 00-3 3 3 3 0 003 3h10a3 3 0 003-3 3 3 0 00-3-3H7z"/></svg>
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</button>
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</div>
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<label class="md-header-nav__button md-icon" for="__search">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0116 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 019.5 16 6.5 6.5 0 013 9.5 6.5 6.5 0 019.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5z"/></svg>
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</label>
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<div class="md-search" data-md-component="search" role="dialog">
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<label class="md-search__overlay" for="__search"></label>
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<div class="md-search__inner" role="search">
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<form class="md-search__form" name="search">
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<input type="text" class="md-search__input" name="query" aria-label="Search" placeholder="Search" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false" data-md-component="search-query" data-md-state="active">
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<label class="md-search__icon md-icon" for="__search">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0116 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 019.5 16 6.5 6.5 0 013 9.5 6.5 6.5 0 019.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5z"/></svg>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11h12z"/></svg>
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</label>
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<button type="reset" class="md-search__icon md-icon" aria-label="Clear" data-md-component="search-reset" tabindex="-1">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 6.41L17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12 19 6.41z"/></svg>
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</button>
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<div class="md-search__suggest" data-md-component="search-suggest"></div>
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</form>
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<div class="md-search__output">
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<div class="md-search__scrollwrap" data-md-scrollfix>
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<div class="md-search-result" data-md-component="search-result">
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<div class="md-search-result__meta">
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Initializing search
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</div>
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<ol class="md-search-result__list"></ol>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div class="md-header-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05L244 40.45a28.87 28.87 0 00-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 01-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 000 40.81l195.61 195.6a28.86 28.86 0 0040.8 0l194.69-194.69a28.86 28.86 0 000-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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</div>
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</nav>
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</header>
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<div class="md-container" data-md-component="container">
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<main class="md-main" data-md-component="main">
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<div class="md-main__inner md-grid">
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<div class="md-sidebar md-sidebar--primary" data-md-component="navigation" >
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<div class="md-sidebar__scrollwrap">
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<div class="md-sidebar__inner">
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<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
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<label class="md-nav__title" for="__drawer">
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<a href=".." title="RAPIDS" class="md-nav__button md-logo" aria-label="RAPIDS">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 01-2 2H7a2 2 0 01-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V4a2 2 0 012-2h10a2 2 0 012 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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RAPIDS
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</label>
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<div class="md-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05L244 40.45a28.87 28.87 0 00-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 01-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 000 40.81l195.61 195.6a28.86 28.86 0 0040.8 0l194.69-194.69a28.86 28.86 0 000-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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</div>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href=".." class="md-nav__link">
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Home
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</a>
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</li>
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-2" type="checkbox" id="nav-2" checked>
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<label class="md-nav__link" for="nav-2">
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Setup
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Setup" data-md-level="1">
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<label class="md-nav__title" for="nav-2">
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<span class="md-nav__icon md-icon"></span>
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Setup
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item md-nav__item--active">
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<input class="md-nav__toggle md-toggle" data-md-toggle="toc" type="checkbox" id="__toc">
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<a href="./" class="md-nav__link md-nav__link--active">
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File Structure
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../setup/installation/" class="md-nav__link">
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Installation
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../setup/configuration/" class="md-nav__link">
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Initial Configuration
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../setup/execution/" class="md-nav__link">
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Execution
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</a>
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-3" type="checkbox" id="nav-3" >
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<label class="md-nav__link" for="nav-3">
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Example Workflows
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Example Workflows" data-md-level="1">
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<label class="md-nav__title" for="nav-3">
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<span class="md-nav__icon md-icon"></span>
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Example Workflows
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../workflow-examples/minimal/" class="md-nav__link">
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Minimal
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</a>
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-4" type="checkbox" id="nav-4" >
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<label class="md-nav__link" for="nav-4">
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Behavioral Features
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Behavioral Features" data-md-level="1">
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<label class="md-nav__title" for="nav-4">
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<span class="md-nav__icon md-icon"></span>
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Behavioral Features
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../features/feature-introduction/" class="md-nav__link">
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Introduction
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</a>
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</li>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-4-2" type="checkbox" id="nav-4-2" >
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<label class="md-nav__link" for="nav-4-2">
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Phone
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25z"/></svg>
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<h1 id="file-structure">File Structure<a class="headerlink" href="#file-structure" title="Permanent link">¶</a></h1>
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<p>Read this page if you want to learn more about how RAPIDS is structured. If you want to start using it go to <a href="../setup/installation/">Installation</a> and then to <a href="../setup/configuration/">Initial Configuration</a></p>
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<p>All paths mentioned in this page are relative to RAPIDS’ root folder.</p>
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<p>If you want to extract the behavioral features that RAPIDS offers, you will only have to create or modify the <a href="../setup/configuration/#database-credentials"><code>.env</code> file</a>, <a href="../setup/configuration/#participant-files">participants files</a>, <a href="../setup/configuration/#day-segments">day segment files</a>, and the <code>config.yaml</code> file. The <code>config.yaml</code> file is the heart of RAPIDS and includes parameters to manage participants, data sources, sensor data, visualizations and more.</p>
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<p>All data is saved in <code>data/</code>. The <code>data/external/</code> folder stores any data imported or created by the user, <code>data/raw/</code> stores sensor data as imported from your database, <code>data/interim/</code> has intermediate files necessary to compute behavioral features from raw data, and <code>data/processed/</code> has all the final files with the behavioral features in folders per participant and sensor.</p>
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<p>All the source code is saved in <code>src/</code>. The <code>src/data/</code> folder stores scripts to download, clean and pre-process sensor data, <code>src/features</code> has scripts to extract behavioral features organized in their respective subfolders , <code>src/models/</code> can host any script to create models or statistical analyses with the behavioral features you extract, and <code>src/visualization/</code> has scripts to create plots of the raw and processed data.</p>
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<p>There are other important files and folders but only relevant if you are interested in extending RAPIDS (e.g. virtual env files, docs, tests, Dockerfile, the Snakefile, etc.). In the figure below, we represent the interactions between users and files. After a user modifies <code>config.yaml</code> and <code>.env</code> the <code>Snakefile</code> file will decide what Snakemake rules have to be executed to produce the required output files (behavioral features) and what scripts are in charge of producing such files. In addition, users can add or modifiy files in the <code>data</code> folder (for example to configure the <a href="../setup/configuration/#participant-files">participants files</a> or the <a href="../setup/configuration/#day-segments">day segment files</a>).</p>
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})
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