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‎_sources/index.rst.txt

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.. card::
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Latest release (2024-07-07):
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Latest release (2025-01-13):
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.. button-link:: https://github.com/scikit-bio/scikit-bio/releases/tag/0.6.2
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.. button-link:: https://github.com/scikit-bio/scikit-bio/releases/tag/0.6.3
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:color: success
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:shadow:
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scikit-bio 0.6.2
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scikit-bio 0.6.3
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.. card::
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‎_sources/install.rst.txt

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Python
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------
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scikit-bio requires `Python <https://www.python.org/>`_ 3.8 or later installed in your system.
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scikit-bio requires `Python <https://www.python.org/>`_ 3.9 or later installed in your system.
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‎_static/basic.css

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‎about.html

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© Copyright 2014-2024, scikit-bio development team.
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‎contribute.html

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<p>You will want to test your code like a <em>user</em> would do: import the function, execute it on some input data, and examine whether the results are correct. You may install additional software such as <a class="reference external" href="https://jupyter.org/">Jupyter</a> in the same conda environment to make the testing process convenient and pleasant. There is no need to reinstall the modified scikit-bio package in a separate environment in order to test. As soon as you edit the code, the changes will immediately reflect when you use the code.</p>
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<p>For example, you wrote a function <code class="docutils literal notranslate"><span class="pre">gc_content</span></code>, which calculates the fraction of <code class="docutils literal notranslate"><span class="pre">G</span></code> and <code class="docutils literal notranslate"><span class="pre">C</span></code> in a nucleotide sequence:</p>
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<span class="k">return</span> <span class="nb">sum</span><span class="p">(</span><span class="mi">1</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">seq</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="s2">&quot;GC&quot;</span><span class="p">)</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">seq</span><span class="p">)</span>
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<p>Now test the function on some data. For example, you would expect that <code class="docutils literal notranslate"><span class="pre">gc_content(&quot;ACGT&quot;)</span></code> and <code class="docutils literal notranslate"><span class="pre">gc_content(&quot;GGATCCGC&quot;)</span></code> return 0.5 and 0.75, respectively. Is that the case?</p>
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<p><a class="reference external" href="https://en.wikipedia.org/wiki/Unit_testing">Unit testing</a> involves testing the smallest units of your code, such as classes, functions, and methods, to ensure they function correctly in isolation. It is a fundamental best practice in software engineering, but is often overlooked by beginners. Unit testing is made easier by writing test code alongside the algorithm code. Both types of code are integrated into the scikit-bio codebase. This test code is then regularly executed whenever changes are made to ensure that the intended behavior remains consistent over time.</p>
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<p>Below is a very simple example for the <code class="docutils literal notranslate"><span class="pre">gc_content</span></code>. The lines between the triple double quotes (<code class="docutils literal notranslate"><span class="pre">&quot;&quot;&quot;</span></code>) are the docstring:</p>
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