{
  "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/2007/12/19/test-results-for-cdk-10x-branch.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/ry980-qya21",
      "url": "https://chem-bla-ics.linkedchemistry.info/2007/12/19/test-results-for-cdk-10x-branch.html",
      "title": "Test results for the CDK 1.0.x branch",
      "content_html": "<p>The <a href=\"http://cdk.sf.net/\">Chemistry Development Kit</a> has never really been without any bugs, which is reflected in the number\nof failing JUnit tests. For <a href=\"http://cdk.svn.sourceforge.net/viewvc/cdk/trunk/cdk/\">trunk/</a> this is today 106 failing tests\n(<a href=\"http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/junitsummary.html\">live stats</a>). The stable\n<a href=\"http://cdk.svn.sourceforge.net/viewvc/cdk/branches/cdk-1.0.x/\">cdk-1.0.x/</a> branch, however, the number of failing tests\nis not much lower: 64 failing tests today (<a href=\"http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly-1.0.x/junitsummary.html\">live stats</a>).</p>\n\n<p>Overall, only a low percentage of the tests fails (&lt;2% for cdk-1.0.x/ and &lt;3% for trunk/), and, more importantly, it is\nparticular algorithms that are typically broken. For example, in the structgen module 8 tests fail, for both CDK versions.\nIn the <code class=\"language-plaintext highlighter-rouge\">cdk-1.0.x/</code> branch it is the valency checker code that causes quite a few fails, which I discussed in\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2007/07/01/atom-typing-in-cdk.html\">Atom typing in the CDK <i class=\"fa-solid fa-recycle fa-xs\"></i></a> and which is the reason for\nthe atom type perception refactoring in progress in trunk/ (see <a href=\"https://chem-bla-ics.linkedchemistry.info/2007/11/06/evidence-of-aromaticity.html\">Evidence of Aromaticity <i class=\"fa-solid fa-recycle fa-xs\"></i></a>).\nNot all code in trunk/ has yet been updated yet, and this causes quite a few failing tests for <code class=\"language-plaintext highlighter-rouge\">trunk/</code> in the <code class=\"language-plaintext highlighter-rouge\">reaction</code>,\n<code class=\"language-plaintext highlighter-rouge\">qsarAtomic</code> and <code class=\"language-plaintext highlighter-rouge\">qsarBond</code> modules.</p>\n\n<p>Back to the <code class=\"language-plaintext highlighter-rouge\">cdk-1.0.x/</code> branch. Previous CDK releases tended to have around 40 failing tests, so I was worried about\nthe number of tests failing now. Maybe backported patches causes additional fails? To study that I had my machine run\nthe JUnit tests for all revisions of the <code class=\"language-plaintext highlighter-rouge\">cdk-1.0.x/</code> branch since the branch was made in commit\n<a href=\"http://cdk.svn.sourceforge.net/viewvc/cdk?view=rev&amp;revision=8343\">8343</a>. The result looks like:</p>\n\n<p><img src=\"/assets/images/results.png\" alt=\"\" /></p>\n\n<p>Indeed, it is a number of backports that cause the clear increase in bugs between commit 9044 and 9058. Nothing particular I can see, and worse, the intermediate revisions do not compile and do not have test restults:</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>104 9044 3731  84  73  979.709  0\n105 9045    0   0   0    0.000  0\n106 9046    0   0   0    0.000  0\n107 9047    0   0   0    0.000  0\n108 9048    0   0   0    0.000  0\n109 9049    0   0   0    0.000  0\n110 9050    0   0   0    0.000  0\n111 9051    0   0   0    0.000  0\n112 9052    0   0   0    0.000  0\n113 9053    0   0   0    0.000  0\n114 9054    0   0   0    0.000  0\n115 9055    0   0   0    0.000  0\n116 9056    0   0   0    0.000  0\n117 9057    0   0   0    0.000  0\n118 9058 3740 104 146  989.566  0\n</code></pre></div></div>\n\n<p>I should have taken more care when merging in these patches, even though they are supposed to fix issues:</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>Merged r8697: Add a method to the query atom container creator which creates an\n  queryatomcontainer. This replaces each pseudoatom to an anyatom.\nMerged r8699 and r8700: Added test file by Volker (see cdk-user) for the shortest path problem;\n  JUnit test provided by Volker Haehnke (haehnke - bioinformatik uni-frankfurt de), somewhat\n  rewritten.\nMerged r8701: Renamed a variable to comply with http://en.wikipedia.org/wiki/Dijkstra's_algorithm\nMerged r8751: Bug fixes for bugs #1783367 'SmilesParser incorrectly assigns double bonds' and \n  #1783381 'SmilesParser uses Molecule instead of IMolecule'. Test case for bug #1783367.\nMerged r8754 and r8773: Fix and test case for bug #1783547 and #1783546 'Lost aromaticity in \n  SmilesParser with Biphenyl and Benzene'\nMerged r8774: Add a MDL RXN reader which uses the MDLV2000Reader instead of the MDLReader\nMerged r8775, r8776, r8777: bug fixes for #150354 #1783774 #1778479 in the SmilesParser, \n  SmilesGenerator and MDLWriter/PseudoAtom.\nMerged r8791: Code for v,mass atom two digits mass atom and exception handeling\nMerged r8800: Fixed reading of MDL molfiles with exactly 12 columns (==valid) in the bond block\nMerged r8802: Made a little more memory efficient by removing unnesscary cloning operations\nMerged r8803: Fixed it so that we make a deep copy of the input molecule\nMerged r8809: Added code to work on a local copy of theinput molecule\nMerged r8811: Updated Javadocs\nMerged 8824 8821 8820 8819 8817 8816: Added code to properly work on a local copy\n</code></pre></div></div>\n\n<p>I’m quite sure it must be the deep-cloning fix ported from the commits 8800-8824. I already fixed a number of bugs in the IP calculation\ncode which is still a good deal of the failing tests in the cdk-1.0.x/ branch (and affects trunk/ too), as can be seen by the drop in\nbugs just after the big increase:</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>r9079 | egonw | 2007-10-15 13:24:10 +0200 (Mon, 15 Oct 2007) | 1 line\n\nRenamed container to localClone to clear up code. Fixed a bug where the uncloned atoms was\nsearched in the cloned atomcontainer. More bugs like this are in the code. Miguel is contacted\nabout this problem.\n------------------------------------------------------------------------\nr9082 | egonw | 2007-10-15 13:48:15 +0200 (Mon, 15 Oct 2007) | 1 line\n\nRenamed container to localClone to clear up code. Fixed a bug where the uncloned atoms was\nsearched in the cloned atomcontainer.\n</code></pre></div></div>\n\n<p>The big drop in number of fails is caused by the removal of the SMARTS code from the branch, which has been present since\nthe start of the branch (see <a href=\"http://cdk.svn.sourceforge.net/viewvc/cdk/branches/cdk-1.0.x/src/org/openscience/cdk/smiles/?pathrev=8343\">this page</a>).</p>\n\n<p>From this analysis I conclude that CDK 1.0.2 can soon be released. With the note that the ionization potential calculation\nis not safe to use.</p>",
      "summary": "The Chemistry Development Kit has never really been without any bugs, which is reflected in the number of failing JUnit tests. For trunk/ this is today 106 failing tests (live stats). The stable cdk-1.0.x/ branch, however, the number of failing tests is not much lower: 64 failing tests today (live stats).",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/results.png",
      "date_published": "2007-12-19T00:00:00+00:00",
      "date_modified": "2025-04-20T00:00:00+00:00",
      "tags": ["cdk"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}