Testing in an IPython Notebook

testing_in_ipynb.ipynb

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      "Testing inside an IPython Notebook\n",
      "===================================\n",
      "\n",
      "In my courses and as part of [Software Carpentry](http://software-carpentry.org)\n",
      "I'm teaching more and more in IPython notebooks. One of the things I/we teach\n",
      "is testing, so I wondered if I could teach it in a notebook as well. With quite\n",
      "a lot of help from [Matthias Bussonnier](https://twitter.com/Mbussonn) I got it\n",
      "working so I thought I'd share."
     ]
    },
    {
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     "metadata": {},
     "source": [
      "An example\n",
      "----------------\n",
      "\n",
      "We will test a function that caluculates the GC-content of a DNA sequence.\n",
      "The GC-content is simply the percentage of bases in the DNA sequence that\n",
      "are either G's or C's. So, for example, the GC-content of 'ATTGC' is 40%.\n",
      "\n",
      "The function we are testing is ``get_gc_content()`` and it takes a single\n",
      "argument, which is a string represting a sequence. This function is in\n",
      "a custom module called ``dna_analysis.py``.\n",
      "\n",
      "### Create the module to test\n",
      "We can use the ``%%file`` magic to save a block of code to a file, so we\n",
      "can use that to create the module that we're going to test."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%file dna_analysis.py\n",
      "\n",
      "\"\"\"Code for analyzing DNA sequences\"\"\"\n",
      "\n",
      "from __future__ import division\n",
      "\n",
      "def get_gc_content(seq):\n",
      "    \"\"\"Determine the GC content of a sequence\"\"\"\n",
      "    seq = seq.upper()\n",
      "    gc_content = 100 * (seq.count('G') + seq.count('C')) / len(seq)\n",
      "    return gc_content"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Writing dna_analysis.py\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### Create the test module\n",
      "1. To use nosetests we need to save the test code to a Python file starting with the word *test*\n",
      "2. We then need to import the function(s) we are going to test\n",
      "3. Then we right a simple function (whose name starts with *test*) that calls the function and\n",
      "checks to see if it returns the right value"
     ]
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     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%file test_dna.py\n",
      "\n",
      "from dna_analysis import get_gc_content\n",
      "\n",
      "def test_get_gc_content_zero():\n",
      "    assert get_gc_content('ATTATTAAA') == 0\n",
      "    \n",
      "def test_get_gc_content_lowercase():\n",
      "    assert get_gc_content('atgcatgc') == 50\n",
      "    \n",
      "def test_get_gc_content_multiline():\n",
      "    sequence = \"\"\"atta\n",
      "gccg\n",
      "attt\n",
      "cccg\"\"\"\n",
      "    assert get_gc_content(sequence) == 50"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Writing test_dna.py\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### Run nosetests\n",
      "We would normally run nosetests from the command line, so in IPython we can just call ``!nosetests``."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!nosetests"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "..F\r\n",
        "======================================================================\r\n",
        "FAIL: test_dna.test_get_gc_content_multiline\r\n",
        "----------------------------------------------------------------------\r\n",
        "Traceback (most recent call last):\r\n",
        "  File \"/usr/lib/python2.7/dist-packages/nose/case.py\", line 197, in runTest\r\n",
        "    self.test(*self.arg)\r\n",
        "  File \"/home/ethan/Dropbox/Teaching/ProgBiol/repo/ipynbs/test_dna.py\", line 15, in test_get_gc_content_multiline\r\n",
        "    assert get_gc_content(sequence) == 50\r\n",
        "AssertionError\r\n",
        "\r\n",
        "----------------------------------------------------------------------\r\n",
        "Ran 3 tests in 0.018s\r\n",
        "\r\n",
        "FAILED (failures=1)\r\n"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "This is exactly we output we want since the original function handles most basic cases,\n",
      "but not multiline strings."
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Value?\n",
      "------\n",
      "I wonder a bit about how valuable this is in the sense that we probably wouldn't\n",
      "normally run tests this way (at least I don't at the moment). But, I think at\n",
      "least for a short workshop where we're teaching all of the Python in a notebook\n",
      "that the value of reducing the cognitive load relative to switching environments\n",
      "for the testing portion might outweigh doing something in a way that might not be exactly\n",
      "how we would do it in day to day work."
     ]
    }
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