{
  "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/2010/05/10/how-to-use-github-for-cdkbioclipse-code.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/nfcyx-jxj82",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/05/10/how-to-use-github-for-cdkbioclipse-code.html",
      "title": "How to use GitHub for [CDK|Bioclipse] code review",
      "content_html": "<p>Triggered by posts in the past <a href=\"https://chem-bla-ics.linkedchemistry.info/2010/05/08/web-20-technologies-in-student.html\">three <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2010/05/10/github-simplifies-code-review-and.html\">days <i class=\"fa-solid fa-recycle fa-xs\"></i></a>, I though about writing up a short\ntutorial on how to perform code review for existing code on <a href=\"http://www.github.com/\">GitHub</a>. Therefore, this applied to\n<a href=\"http://cdk.sf.net/\">CDK</a> and <a href=\"http://www.bioclipse.net/\">Bioclipse</a> source code, many but will work for any project hosted\nin GitHub. Even if it is not, you could consider putting up a copy there yourself. This example will demonstrate the\nprocedure on CDK functionality in Bioclipse in the <a href=\"http://github.com/egonw/bioclipse.cheminformatics/\">bioclipse.cheminformatics</a>\nrepository.</p>\n\n<p><em>Click on the images to get a higher resolution version.</em></p>\n\n<h2 id=\"step-1-find-the-class-you-want-to-review\">Step 1: find the class you want to review</h2>\n\n<p>Use the GitHub web interface to browse your way towards the source code of the class you want to review. For example,\nthe <a href=\"http://github.com/egonw/bioclipse.cheminformatics/blob/master/plugins/net.bioclipse.cdk.smartsmatching/src/net/bioclipse/cdk/smartsmatching/SmartsMatchingHelper.java\">SmartsMatchingHelper.java</a>:</p>\n\n<p><img src=\"/assets/images/codeReview1.png\" alt=\"\" /></p>\n\n<h2 id=\"step-2-identify-something-you-like-to-comment-on\">Step 2: identify something you like to comment on</h2>\n\n<p>Next step is to perform some code reviewing. For example, we might want to ask something about how parseProperty() works:</p>\n\n<p><img src=\"/assets/images/codeReview2.png\" alt=\"\" /></p>\n\n<p>Now, this page on GitHub does not provide the means to leave comments; instead, you comment on commits.</p>\n\n<h2 id=\"step-3-find-the-last-commit-that-touched-the-line-you-like-to-comment-on\">Step 3: find the last commit that touched the line you like to comment on</h2>\n\n<p>Git has a <a href=\"http://ftp.sunet.se/pub//Linux/kernel.org/software/scm/git/docs/git-blame.html\">blame option</a> (also called annotate)\nwhich will show you for each line who last changed that line. The GitHub web page makes this functionality available with the\n‘blame’ link just above the first line of the source code:</p>\n\n<p><img src=\"/assets/images/codeReview3.png\" alt=\"\" /></p>\n\n<p>This link will lead us to a page with a new column on the left side showing commit hashes, name of the commit author,\nand the first few characters of the commit message. For example, the\n<a href=\"http://github.com/egonw/bioclipse.cheminformatics/blame/master/plugins/net.bioclipse.cdk.smartsmatching/src/net/bioclipse/cdk/smartsmatching/SmartsMatchingHelper.java\">web page</a>\nbits relevant to code we want to comment on, looks like:</p>\n\n<p><img src=\"/assets/images/codeReview4.png\" alt=\"\" /></p>\n\n<p>This shows us that commit <a href=\"http://github.com/egonw/bioclipse.cheminformatics/commit/3ce78ba572e0fbb32536cfb24ae9848297057575\">3ce78ba5</a>\nis the one we are interested in:</p>\n\n<p><img src=\"/assets/images/codeReview5.png\" alt=\"\" /></p>\n\n<h2 id=\"step-4-look-up-the-line-again-and-add-a-comment\">Step 4: Look up the line again and add a comment</h2>\n\n<p>In the web page with the appropriate commit looked in the previous step, you scroll down to the line you want to comment on.\nIf you hover over that line, a blue comment bubble will show up on the left side:</p>\n\n<p><img src=\"/assets/images/codeReview6.png\" alt=\"\" /></p>\n\n<p>Clicking that blue comment icon, you get a dialog where you can enter your comment:</p>\n\n<p><img src=\"/assets/images/codeReview7.png\" alt=\"\" /></p>\n\n<p>The ‘Add Line Note’ button confirms and saves your comment:</p>\n\n<p><img src=\"/assets/images/codeReview8.png\" alt=\"\" /></p>\n\n<h2 id=\"step-5-inform-the-commiter-about-your-review\">Step 5: inform the commiter about your review</h2>\n\n<p>The next step would be to inform the commit author. GitHub actually helps here, and should send a message,\nlike this one:</p>\n\n<p><img src=\"/assets/images/codeReview9.png\" alt=\"\" /></p>\n\n<p>But it would certainly not hurt of you filed a bug report or sent an email.</p>\n\n<p><em>Now, I should only convert this into a screencast…</em></p>",
      "summary": "Triggered by posts in the past three days , I though about writing up a short tutorial on how to perform code review for existing code on GitHub. Therefore, this applied to CDK and Bioclipse source code, many but will work for any project hosted in GitHub. Even if it is not, you could consider putting up a copy there yourself. This example will demonstrate the procedure on CDK functionality in Bioclipse in the bioclipse.cheminformatics repository.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview6.png",
      "date_published": "2010-05-10T00:10:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["cdk","bioclipse","github"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}