\chapter{The Biopython testing framework}
\label{sec:regr_test}

Biopython has a regression testing framework (the file
\verb|run_tests.py|) based on
\href{https://docs.python.org/3/library/unittest.html}{unittest},
the standard unit testing framework for Python.  Providing comprehensive
tests for modules is one of the most important aspects of making sure that
the Biopython code is as bug-free as possible before going out.
It also tends to be one of the most undervalued aspects of contributing.
This chapter is designed to make running the Biopython tests and
writing good test code as easy as possible.
Ideally, every module that goes into Biopython
should have a test (and should also have documentation!).
All our developers, and anyone installing Biopython from source,
are strongly encouraged to run the unit tests.

\section{Running the tests}

When you download the Biopython source code, or check it out from
our source code repository, you should find a subdirectory call
\verb|Tests|.  This contains the key script \verb|run_tests.py|,
lots of individual scripts named \verb|test_XXX.py|, a subdirectory
called \verb|output| and lots of other subdirectories which
contain input files for the test suite.

As part of building and installing Biopython you will typically
run the full test suite at the command line from the Biopython
source top level directory using the following:
\begin{verbatim}
python setup.py test
\end{verbatim}
This is actually equivalent to going to the \verb|Tests|
subdirectory and running:
\begin{verbatim}
python run_tests.py
\end{verbatim}

You'll often want to run just some of the tests, and this is done
like this:
\begin{verbatim}
python run_tests.py test_SeqIO.py test_AlignIO.py
\end{verbatim}
When giving the list of tests, the \verb|.py| extension is optional,
so you can also just type:
\begin{verbatim}
python run_tests.py test_SeqIO test_AlignIO
\end{verbatim}
To run the docstring tests (see section \ref{section:doctest}), you can use
\begin{verbatim}
python run_tests.py doctest
\end{verbatim}
You can also skip any tests which have been setup with an explicit
online component by adding \verb|--offline|, e.g.
\begin{verbatim}
python run_tests.py --offline
\end{verbatim}
By default, \verb|run_tests.py| runs all tests, including the docstring tests.

If an individual test is failing, you can also try running it
directly, which may give you more information.

Importantly, note that the individual unit test files come in two types:
\begin{itemize}
\item Older simple print-and-compare scripts.  These unit tests are
      essentially short example Python programs, which print out
      various output text.  For a test file named \verb|test_XXX.py|
      there will be a matching text file called \verb|test_XXX| under
      the \verb|output| subdirectory which contains the expected
      output.  All that the test framework does to is run the script,
      and check the output agrees.
\item Standard \verb|unittest|- based tests.  These will \verb|import unittest|
      and then define \verb|unittest.TestCase| classes, each with one
      or more sub-tests as methods starting with \verb|test_| which
      check some specific aspect of the code.
      These tests should not print any output directly.
\end{itemize}
Currently, about half of the Biopython tests are \verb|unittest|-style tests, and half are print-and-compare tests.

Running a simple print-and-compare test directly will usually give lots
of output on screen, but does not check the output matches the expected
output.  If the test is failing with an exception error, it should be
very easy to locate where exactly the script is failing.
For an example of a print-and-compare test, try:
\begin{verbatim}
python test_SeqIO.py
\end{verbatim}

The \verb|unittest|-based tests instead show you exactly which sub-section(s) of
the test are failing. For example,
\begin{verbatim}
python test_Cluster.py
\end{verbatim}

\subsection{Running the tests using Tox}

Like most Python projects, you can also use
\href{https://tox.readthedocs.org/en/latest/}{Tox} to run the tests on multiple
Python versions, provided they are already installed in your system.

We do not provide the configuration \texttt{tox.ini} file in our code base because
of difficulties pinning down user-specific settings (e.g. executable names of the
Python versions). You may also only be interested in testing Biopython only against
a subset of the Python versions that we support.

If you are interested in using Tox, you may start with the example \texttt{tox.ini}
shown below:

\begin{verbatim}
[tox]
envlist = py26, py27, pypy, py33, py34, jython

[testenv]
changedir = Tests
commands = {envpython} run_tests.py --offline
deps =
    numpy
\end{verbatim}

Using the template above, executing \texttt{tox} will test your Biopython code against
Python2.6, Python2.7, PyPy, Python3.3, Python3.4, and Jython. It assumes that those
Pythons' executables are named accordingly: python2.6 for Python2.6, and so on.


\section{Writing tests}

Let's say you want to write some tests for a module called \verb|Biospam|.
This can be a module you wrote, or an existing module that doesn't have
any tests yet.  In the examples below, we assume that
\verb|Biospam| is a module that does simple math.

Each Biopython test can have three important files and directories involved with it:

\begin{enumerate}
  \item \verb|test_Biospam.py| -- The actual test code for your module.
  \item \verb|Biospam| [optional]-- A directory where any necessary input files
    will be located. If you have any output files that should be manually
    reviewed, output them here (but this is discouraged) to prevent clogging
    up the main Tests directory. In general use a temporary file/folder.
  \item \verb|output/Biospam| -- [for print-and-compare tests only] This
    file contains the expected output from running \verb|test_Biospam.py|.
    This file is not needed for \verb|unittest|-style tests, since there
    the validation is done in the test script \verb|test_Biospam.py| itself.
\end{enumerate}

It's up to you to decide whether you want to write a print-and-compare test script or a \verb|unittest|-style test script. The important thing is that you cannot mix these two styles in a single test script. Particularly, don't use \verb|unittest| features in a print-and-compare test.

Any script with a \verb|test_| prefix in the \verb|Tests| directory will be found and run by \verb|run_tests.py|. Below, we show an example test script \verb|test_Biospam.py| both for a print-and-compare test and for a \verb|unittest|-based test. If you put this script in the Biopython \verb|Tests| directory, then \verb|run_tests.py| will find it and execute the tests contained in it:
\begin{verbatim}
$ python run_tests.py
test_Ace ... ok
test_AlignIO ... ok
test_BioSQL ... ok
test_BioSQL_SeqIO ... ok
test_Biospam ... ok
test_CAPS ... ok
test_Clustalw ... ok
\end{verbatim}
\ldots
\begin{verbatim}
----------------------------------------------------------------------
Ran 107 tests in 86.127 seconds
\end{verbatim}

\subsection{Writing a print-and-compare test}

A print-and-compare style test should be much simpler for beginners
or novices to write - essentially it is just an example script using
your new module.

Here is what you should do to make a print-and-compare test for the
\verb|Biospam| module.

\begin{enumerate}
  \item Write a script called \verb|test_Biospam.py|

  \begin{itemize}

    \item This script should live in the Tests directory

     \item The script should test all of the important functionality
     of the module (the more you test the better your test is, of course!).

     \item Try to avoid anything which might be platform specific,
     such as printing floating point numbers without using an explicit
     formatting string to avoid having too many decimal places
     (different platforms can give very slightly different values).

  \end{itemize}

  \item If the script requires files to do the testing, these should go in
       the directory Tests/Biospam (if you just need something generic, like
       a FASTA sequence file, or a GenBank record, try and use an existing
       sample input file instead).

  \item Write out the test output and verify the output to be correct.

       There are two ways to do this:

  \begin{enumerate}
    \item The long way:

    \begin{itemize}

     \item Run the script and write its output to a file. On UNIX (including
       Linux and Mac OS X) machines, you would do something like:
       \verb|python test_Biospam.py > test_Biospam| which would write the
       output to the file \verb|test_Biospam|.

     \item Manually look at the file \verb|test_Biospam| to make sure the output is correct. When you are sure it is all right and there are no bugs, you need to quickly edit the \verb|test_Biospam| file so that the first line is: `\verb|test_Biospam|' (no quotes).

     \item copy the \verb|test_Biospam| file to the directory Tests/output

   \end{itemize}

   \item The quick way:

   \begin{itemize}
      \item Run \verb|python run_tests.py -g test_Biospam.py|. The
            regression testing framework is nifty enough that it'll put
            the output in the right place in just the way it likes it.

       \item Go to the output (which should be in \verb|Tests/output/test_Biospam|) and double check the output to make sure it is all correct.

   \end{itemize}

 \end{enumerate}

 \item Now change to the Tests directory and run the regression tests
       with \verb|python run_tests.py|. This will run all of the tests, and
       you should see your test run (and pass!).

  \item That's it! Now you've got a nice test for your module ready to check in,
  or submit to Biopython.  Congratulations!
\end{enumerate}

As an example, the \verb|test_Biospam.py| test script to test the
\verb|addition| and \verb|multiplication| functions in the \verb|Biospam|
module  could look as follows:

\begin{verbatim}
from __future__ import print_function
from Bio import Biospam

print("2 + 3 =", Biospam.addition(2, 3))
print("9 - 1 =", Biospam.addition(9, -1))
print("2 * 3 =", Biospam.multiplication(2, 3))
print("9 * (- 1) =", Biospam.multiplication(9, -1))
\end{verbatim}

We generate the corresponding output with \verb|python run_tests.py -g test_Biospam.py|, and check the output file \verb|output/test_Biospam|:

\begin{verbatim}
test_Biospam
2 + 3 = 5
9 - 1 = 8
2 * 3 = 6
9 * (- 1) = -9
\end{verbatim}

Often, the difficulty with larger print-and-compare tests is to keep track which line in the output corresponds to which command in the test script. For this purpose, it is important to print out some markers to help you match lines in the input script with the generated output.

\subsection{Writing a unittest-based test}

We want all the modules in Biopython to have unit tests, and a simple
print-and-compare test is better than no test at all.  However, although
there is a steeper learning curve, using the \verb|unittest| framework
gives a more structured result, and if there is a test failure this can
clearly pinpoint which part of the test is going wrong.  The sub-tests can
also be run individually which is helpful for testing or debugging.

The \verb|unittest|-framework has been included with Python since version
2.1, and is documented in the Python Library Reference (which I know you
are keeping under your pillow, as recommended).  There is also
\href{https://docs.python.org/3/library/unittest.html}{online documentaion
for unittest}.
If you are familiar with the \verb|unittest| system (or something similar
like the nose test framework), you shouldn't have any trouble.  You may
find looking at the existing example within Biopython helpful too.

Here's a minimal \verb|unittest|-style test script for \verb|Biospam|,
which you can copy and paste to get started:

\begin{verbatim}
import unittest
from Bio import Biospam

class BiospamTestAddition(unittest.TestCase):

    def test_addition1(self):
        result = Biospam.addition(2, 3)
        self.assertEqual(result, 5)

    def test_addition2(self):
        result = Biospam.addition(9, -1)
        self.assertEqual(result, 8)

class BiospamTestDivision(unittest.TestCase):

    def test_division1(self):
        result = Biospam.division(3.0, 2.0)
        self.assertAlmostEqual(result, 1.5)

    def test_division2(self):
        result = Biospam.division(10.0, -2.0)
        self.assertAlmostEqual(result, -5.0)


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)
\end{verbatim}

In the division tests, we use \verb|assertAlmostEqual| instead of \verb|assertEqual| to avoid tests failing due to roundoff errors; see the \verb|unittest| chapter in the Python documentation for details and for other functionality available in \verb|unittest| (\href{https://docs.python.org/3/library/unittest.html}{online reference}).

These are the key points of \verb|unittest|-based tests:

\begin{itemize}
  \item Test cases are stored in classes that derive from
    \verb|unittest.TestCase| and cover one basic aspect of your code

  \item You can use methods \verb|setUp| and \verb|tearDown| for any repeated
    code which should be run before and after each test method.  For example,
    the \verb|setUp| method might be used to create an instance of the object
    you are testing, or open a file handle.  The \verb|tearDown| should do any
    ``tidying up'', for example closing the file handle.

  \item The tests are prefixed with \verb|test_| and each test should cover
    one specific part of what you are trying to test. You can have as
    many tests as you want in a class.

  \item At the end of the test script, you can use
\begin{verbatim}
if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)
\end{verbatim}
        to execute the tests when the script is run by itself (rather than
        imported from \verb|run_tests.py|).
        If you run this script, then you'll see something like the following:

\begin{verbatim}
$ python test_BiospamMyModule.py
test_addition1 (__main__.TestAddition) ... ok
test_addition2 (__main__.TestAddition) ... ok
test_division1 (__main__.TestDivision) ... ok
test_division2 (__main__.TestDivision) ... ok

----------------------------------------------------------------------
Ran 4 tests in 0.059s

OK
\end{verbatim}

  \item To indicate more clearly what each test is doing, you can add
        docstrings to each test.  These are shown when running the tests,
        which can be useful information if a test is failing.

\begin{verbatim}
import unittest
from Bio import Biospam

class BiospamTestAddition(unittest.TestCase):

    def test_addition1(self):
        """An addition test"""
        result = Biospam.addition(2, 3)
        self.assertEqual(result, 5)

    def test_addition2(self):
        """A second addition test"""
        result = Biospam.addition(9, -1)
        self.assertEqual(result, 8)

class BiospamTestDivision(unittest.TestCase):

    def test_division1(self):
        """Now let's check division"""
        result = Biospam.division(3.0, 2.0)
        self.assertAlmostEqual(result, 1.5)

    def test_division2(self):
        """A second division test"""
        result = Biospam.division(10.0, -2.0)
        self.assertAlmostEqual(result, -5.0)


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)
\end{verbatim}

        Running the script will now show you:

\begin{verbatim}
$ python test_BiospamMyModule.py
An addition test ... ok
A second addition test ... ok
Now let's check division ... ok
A second division test ... ok

----------------------------------------------------------------------
Ran 4 tests in 0.001s

OK
\end{verbatim}
\end{itemize}

If your module contains docstring tests (see section \ref{section:doctest}),
you \emph{may} want to include those in the tests to be run. You can do so as
follows by modifying the code under \verb|if __name__ == "__main__":|
to look like this:

\begin{verbatim}
if __name__ == "__main__":
    unittest_suite = unittest.TestLoader().loadTestsFromName("test_Biospam")
    doctest_suite = doctest.DocTestSuite(Biospam)
    suite = unittest.TestSuite((unittest_suite, doctest_suite))
    runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
    runner.run(suite)
\end{verbatim}

This is only relevant if you want to run the docstring tests when you
execute \verb|python test_Biospam.py| if it has some complex run-time
dependency checking.

In general instead include the docstring tests by adding them to the
\verb|run_tests.py| as explained below.

\section{Writing doctests}
\label{section:doctest}

Python modules, classes and functions support built in documentation using
docstrings.  The \href{https://docs.python.org/3/library/doctest.html}{doctest
framework} (included with Python) allows the developer to embed working
examples in the docstrings, and have these examples automatically tested.

Currently only a small part of Biopython includes doctests. The
\verb|run_tests.py| script takes care of running the doctests.
For this purpose, at the top of the \verb|run_tests.py| script is a
manually compiled list of modules to test, which
allows us to skip modules with optional external dependencies which may
not be installed (e.g. the Reportlab and NumPy libraries).  So, if you've
added some doctests to the docstrings in a Biopython module, in order to
have them included in the Biopython test suite, you must update
\verb|run_tests.py| to include your module. Currently, the relevant part
of \verb|run_tests.py| looks as follows:

\begin{verbatim}
# This is the list of modules containing docstring tests.
# If you develop docstring tests for other modules, please add
# those modules here.
DOCTEST_MODULES = ["Bio.Seq",
                   "Bio.SeqRecord",
                   "Bio.SeqIO",
                   "...",
                  ]
#Silently ignore any doctests for modules requiring numpy!
try:
    import numpy
    DOCTEST_MODULES.extend(["Bio.Statistics.lowess"])
except ImportError:
    pass
\end{verbatim}

Note that we regard doctests primarily as documentation, so you should
stick to typical usage. Generally complicated examples dealing with error
conditions and the like would be best left to a dedicated unit test.

Note that if you want to write doctests involving file parsing, defining
the file location complicates matters.  Ideally use relative paths assuming
the code will be run from the \verb|Tests| directory, see the
\verb|Bio.SeqIO| doctests for an example of this.

To run the docstring tests only, use
\begin{verbatim}
$ python run_tests.py doctest
\end{verbatim}

Note that the doctest system is fragile and care is needed to ensure
your output will match on all the different versions of Python that
Biopython supports (e.g. differences in floating point numbers).

\section{Writing doctests in the Tutorial}
\label{section:doctest-tutorial}

This Tutorial you are reading has a lot of code snippets, which are
often formatted like a doctest. We have our own system in file
\verb|test_Tutorial.py| to allow tagging code snippets in the
Tutorial source to be run as Python doctests. This works by adding
special \verb|%doctest| comment lines before each verbatim block,
e.g.

\begin{lstlisting}
%doctest
\begin{verbatim}
>>> from Bio.Alphabet import generic_dna
>>> from Bio.Seq import Seq
>>> len("ACGT")
4
\end{verbatim}
\end{lstlisting}

\noindent Often code examples are not self-contained, but
continue from the previous verbatim block. Here we use the
magic comment \verb|%cont-doctest| as shown here:

\begin{lstlisting}
%cont-doctest
\begin{verbatim}
>>> Seq("ACGT") == Seq("ACGT", generic_dna)
True
\end{verbatim}
\end{lstlisting}

The special \verb|%doctest| comment line can take a working directory
(relative to the \verb|Doc/| folder) to use if you have any example
data files, e.g. \verb|%doctest examples| will use the
\verb|Doc/examples| folder, while  \verb|%doctest ../Tests/GenBank|
will use the \verb|Tests/GenBank| folder.

After the directory argument, you can specify any Python dependencies
which must be present in order to run the test by adding \verb|lib:XXX|
to indicate \verb|import XXX| must work, e.g.
\verb|%doctest examples lib:numpy|

You can run the Tutorial doctests via:

\begin{verbatim}
$ python test_Tutorial.py
\end{verbatim}

or:

\begin{verbatim}
$ python run_tests.py test_Tutorial.py
\end{verbatim}
