{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2009/07/15/bioclipse-moving-to-github-cia-hooks.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/6c3ha-gmy93",
      "url": "https://chem-bla-ics.linkedchemistry.info/2009/07/15/bioclipse-moving-to-github-cia-hooks.html",
      "title": "Bioclipse moving to GitHub: CIA hooks enabled",
      "content_html": "<p>Following the CDK and <a href=\"https://chem-bla-ics.linkedchemistry.info/2009/07/08/jchempaint-primary-moving-to-git.html\">JChemPaint Primary <i class=\"fa-solid fa-recycle fa-xs\"></i></a>,\n<a href=\"http://www.bioclipse.net/\">Bioclipe</a> moved to Git just after the <a href=\"http://bioclipse.blogspot.com/2009/07/biocipse-20-released.html\">2.0.0 release</a>.</p>\n\n<p>We decided to split up the repositories, and have one <a href=\"http://mndoci.com/blog/2009/05/07/benevolent-dicators-and-scientific-collaboration/\">benevolent dictator</a>,\nor <a href=\"https://chem-bla-ics.linkedchemistry.info/2009/06/21/dr-whos-of-life-sciences.html\">dr. Who <i class=\"fa-solid fa-recycle fa-xs\"></i></a>, for each repository who will maintain\nthe plugins defined in the repository and coordinate development:</p>\n\n<ul>\n  <li><a href=\"http://github.com/olas/bioclipse.core/tree/master\">bioclipse.core</a></li>\n  <li><a href=\"http://github.com/olas/bioclipse.statistics/tree/master\">bioclipse.statistics</a></li>\n  <li><a href=\"http://github.com/olas/bioclipse.ds/tree/master\">bioclipse.ds</a></li>\n  <li><a href=\"http://github.com/olas/bioclipse.qsar/tree/master\">bioclipse.qsar</a></li>\n  <li><a href=\"http://github.com/egonw/bioclipse.cheminformatics/tree/master\">bioclipse.cheminformatics</a></li>\n  <li><a href=\"http://github.com/egonw/bioclipse.rdf/tree/master\">bioclipse.rdf</a></li>\n  <li><a href=\"http://github.com/masak/bioclipse.bioinformatics/tree/master\">bioclipse.bioinformatics</a></li>\n</ul>\n\n<p>Several plugins are still in the SVN world, but a good deal is now Git-ready. BTW, this move also adds several new accounts\nto watch on GitHub (see Rich’ <a href=\"https://doi.org/10.59350/ps1ms-z0e55\">17 GitHub accounts to watch on Cheminformatics <i class=\"fa-solid fa-recycle fa-xs\"></i></a>).</p>\n\n<p><a href=\"http://www.github.com/\">GitHub</a> turns out to be our big friend here, not <a href=\"http://www.sf.net/\">SourceForge</a>, which only supports one\nGit repository. GitHub recently must have added hooks recently, but I am really happy to see those. The above Bioclipse repositories\nhave hooks turned on for <a href=\"http://cia.vc/stats/project/bioclipse.core\">CIA</a> (so that commit messages end up on our #bioclipse IRC\nchannel) and email (as indicated by the green color):</p>\n\n<p><img src=\"/assets/images/githubHooks.png\" alt=\"\" /></p>\n\n<p>The splitting up, was rather interesting indeed. We wanted to keep the complete commit history, but still reduce the git repositories\nconsiderably. This means removing history of the plugins which should not end up in the repository. Git allows this! Git rules! This\ntime, <a href=\"http://www.kernel.org/pub/software/scm/git/docs/git-filter-branch.html\">git filter-branch</a> is our friend and there are\nbasically two options: constructive and destructive. The first copied bit by bit plugins from the old to the new repository.\nThe second one does the opposite, and removed bit by bit stuff you do not want. Depending on the ratio of plugins you want to\nkeep and those you want to remove, either solution is more appropriate. I have summarized the git commands I used in detail on\n<a href=\"http://wiki.bioclipse.net/index.php?title=Git_Development#Making_your_own_feature_Git_repository\">this Bioclipse wiki page</a>.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Apodaca, R. (2009). Seventeen GitHub Accounts to Watch in Cheminformatics. In <i>Front Matter</i>. Front Matter. https://doi.org/10.59350/ps1ms-z0e55 <a href=\"https://doi.org/10.59350/ps1ms-z0e55\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.59350/ps1ms-z0e55\">Scholia</a></div>\n  </div>",
      "summary": "Following the CDK and JChemPaint Primary , Bioclipe moved to Git just after the 2.0.0 release.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/githubHooks.png",
      "date_published": "2009-07-15T00:00:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["git","bioclipse","github","sourceforge"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.59350/ps1ms-z0e55", "doi": "10.59350/ps1ms-z0e55"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}