davidbgk
/
larlet-fr-david-cache


			
							123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172
							<!doctype html><!-- This is a valid HTML5 document. -->
<!-- Screen readers, SEO, extensions and so on. -->
<html lang="fr">
<!-- Has to be within the first 1024 bytes, hence before the `title` element
  See: https://www.w3.org/TR/2012/CR-html5-20121217/document-metadata.html#charset -->
<meta charset="utf-8">
<!-- Why no `X-UA-Compatible` meta: https://stackoverflow.com/a/6771584 -->
<!-- The viewport meta is quite crowded and we are responsible for that.
  See: https://codepen.io/tigt/post/meta-viewport-for-2015 -->
<meta name="viewport" content="width=device-width,initial-scale=1">
<!-- Required to make a valid HTML5 document. -->
<title>The Rise of GitHub in Scholarly Publications (archive) — David Larlet</title>
<meta name="description" content="Publication mise en cache pour en conserver une trace.">
<!-- That good ol' feed, subscribe :). -->
<link rel="alternate" type="application/atom+xml" title="Feed" href="/david/log/">
<!-- Generated from https://realfavicongenerator.net/ such a mess. -->
<link rel="apple-touch-icon" sizes="180x180" href="/static/david/icons2/apple-touch-icon.png">
<link rel="icon" type="image/png" sizes="32x32" href="/static/david/icons2/favicon-32x32.png">
<link rel="icon" type="image/png" sizes="16x16" href="/static/david/icons2/favicon-16x16.png">
<link rel="manifest" href="/static/david/icons2/site.webmanifest">
<link rel="mask-icon" href="/static/david/icons2/safari-pinned-tab.svg" color="#07486c">
<link rel="shortcut icon" href="/static/david/icons2/favicon.ico">
<meta name="msapplication-TileColor" content="#f7f7f7">
<meta name="msapplication-config" content="/static/david/icons2/browserconfig.xml">
<meta name="theme-color" content="#f7f7f7" media="(prefers-color-scheme: light)">
<meta name="theme-color" content="#272727" media="(prefers-color-scheme: dark)">
<!-- Documented, feel free to shoot an email. -->
<link rel="stylesheet" href="/static/david/css/style_2021-01-20.css">
<!-- See https://www.zachleat.com/web/comprehensive-webfonts/ for the trade-off. -->
<link rel="preload" href="/static/david/css/fonts/triplicate_t4_poly_regular.woff2" as="font" type="font/woff2" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)" crossorigin>
<link rel="preload" href="/static/david/css/fonts/triplicate_t4_poly_bold.woff2" as="font" type="font/woff2" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)" crossorigin>
<link rel="preload" href="/static/david/css/fonts/triplicate_t4_poly_italic.woff2" as="font" type="font/woff2" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)" crossorigin>
<link rel="preload" href="/static/david/css/fonts/triplicate_t3_regular.woff2" as="font" type="font/woff2" media="(prefers-color-scheme: dark)" crossorigin>
<link rel="preload" href="/static/david/css/fonts/triplicate_t3_bold.woff2" as="font" type="font/woff2" media="(prefers-color-scheme: dark)" crossorigin>
<link rel="preload" href="/static/david/css/fonts/triplicate_t3_italic.woff2" as="font" type="font/woff2" media="(prefers-color-scheme: dark)" crossorigin>
<script>
    function toggleTheme(themeName) {
        document.documentElement.classList.toggle(
            'forced-dark',
            themeName === 'dark'
        )
        document.documentElement.classList.toggle(
            'forced-light',
            themeName === 'light'
        )
    }
    const selectedTheme = localStorage.getItem('theme')
    if (selectedTheme !== 'undefined') {
        toggleTheme(selectedTheme)
    }
</script>

  <meta name="robots" content="noindex, nofollow">
  <meta content="origin-when-cross-origin" name="referrer">
  <!-- Canonical URL for SEO purposes -->
  <link rel="canonical" href="https://arxiv.org/abs/2208.04895">

<body class="remarkdown h1-underline h2-underline h3-underline em-underscore hr-center ul-star pre-tick" data-instant-intensity="viewport-all">


<article>
  <header>
    <h1>The Rise of GitHub in Scholarly Publications</h1>
  </header>
  <nav>
    <p class="center">
      <a href="/david/" title="Aller à l’accueil"><svg class="icon icon-home">
        <use xlink:href="/static/david/icons2/symbol-defs-2021-12.svg#icon-home"></use>
      </svg> Accueil</a> •
      <a href="https://arxiv.org/abs/2208.04895" title="Lien vers le contenu original">Source originale</a>
    </p>
  </nav>
  <hr>
  <p>The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters. To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora. We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub. The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera. </p>
</article>


<hr>

<footer>
  <p>
    <a href="/david/" title="Aller à l’accueil"><svg class="icon icon-home">
        <use xlink:href="/static/david/icons2/symbol-defs-2021-12.svg#icon-home"></use>
      </svg> Accueil</a> •
    <a href="/david/log/" title="Accès au flux RSS"><svg class="icon icon-rss2">
        <use xlink:href="/static/david/icons2/symbol-defs-2021-12.svg#icon-rss2"></use>
      </svg> Suivre</a> •
    <a href="http://larlet.com" title="Go to my English profile" data-instant><svg class="icon icon-user-tie">
        <use xlink:href="/static/david/icons2/symbol-defs-2021-12.svg#icon-user-tie"></use>
      </svg> Pro</a> •
    <a href="mailto:david%40larlet.fr" title="Envoyer un courriel"><svg class="icon icon-mail">
        <use xlink:href="/static/david/icons2/symbol-defs-2021-12.svg#icon-mail"></use>
      </svg> Email</a> •
    <abbr class="nowrap" title="Hébergeur : Alwaysdata, 62 rue Tiquetonne 75002 Paris, +33184162340"><svg class="icon icon-hammer2">
        <use xlink:href="/static/david/icons2/symbol-defs-2021-12.svg#icon-hammer2"></use>
      </svg> Légal</abbr>
  </p>
  <template id="theme-selector">
      <form>
          <fieldset>
              <legend><svg class="icon icon-brightness-contrast">
                <use xlink:href="/static/david/icons2/symbol-defs-2021-12.svg#icon-brightness-contrast"></use>
              </svg> Thème</legend>
              <label>
                  <input type="radio" value="auto" name="chosen-color-scheme" checked> Auto
              </label>
              <label>
                  <input type="radio" value="dark" name="chosen-color-scheme"> Foncé
              </label>
              <label>
                  <input type="radio" value="light" name="chosen-color-scheme"> Clair
              </label>
          </fieldset>
      </form>
  </template>
</footer>
<script src="/static/david/js/instantpage-5.1.0.min.js" type="module"></script>
<script>
    function loadThemeForm(templateName) {
        const themeSelectorTemplate = document.querySelector(templateName)
        const form = themeSelectorTemplate.content.firstElementChild
        themeSelectorTemplate.replaceWith(form)

        form.addEventListener('change', (e) => {
            const chosenColorScheme = e.target.value
            localStorage.setItem('theme', chosenColorScheme)
            toggleTheme(chosenColorScheme)
        })

        const selectedTheme = localStorage.getItem('theme')
        if (selectedTheme && selectedTheme !== 'undefined') {
            form.querySelector(`[value="${selectedTheme}"]`).checked = true
        }
    }

    const prefersColorSchemeDark = '(prefers-color-scheme: dark)'
    window.addEventListener('load', () => {
        let hasDarkRules = false
        for (const styleSheet of Array.from(document.styleSheets)) {
            let mediaRules = []
            for (const cssRule of styleSheet.cssRules) {
                if (cssRule.type !== CSSRule.MEDIA_RULE) {
                    continue
                }
                // WARNING: Safari does not have/supports `conditionText`.
                if (cssRule.conditionText) {
                    if (cssRule.conditionText !== prefersColorSchemeDark) {
                        continue
                    }
                } else {
                    if (cssRule.cssText.startsWith(prefersColorSchemeDark)) {
                        continue
                    }
                }
                mediaRules = mediaRules.concat(Array.from(cssRule.cssRules))
            }

            // WARNING: do not try to insert a Rule to a styleSheet you are
            // currently iterating on, otherwise the browser will be stuck
            // in a infinite loop…
            for (const mediaRule of mediaRules) {
                styleSheet.insertRule(mediaRule.cssText)
                hasDarkRules = true
            }
        }
        if (hasDarkRules) {
            loadThemeForm('#theme-selector')
        }
    })
</script>
</body>
</html>