A PHP 5.3+ Mutation Testing framework
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A PHP 5.3+ Mutation Testing framework.

Mutagenesis is released under a New BSD License.

Mutation Testing

According to Wikipedia:

Mutation testing (or Mutation analysis or Program mutation) is a method of software testing, which involves modifying programs' source code or byte code in small ways. In short, any tests which pass after code has been mutated are considered defective. These so-called mutations are based on well-defined mutation operators that either mimic typical programming errors (such as using the wrong operator or variable name) or force the creation of valuable tests (such as driving each expression to zero). The purpose is to help the tester develop effective tests or locate weaknesses in the test data used for the program or in sections of the code that are seldom or never accessed during execution.


Mutagenesis requires PHP 5.3 with PHP Tokenizer support enabled.

In addition, Mutagenesis relies on the PECL runkit extension in order to mutate source code already in memory. Unfortunately, the current version of runkit in PHP's official subversion repository is in turns incomplete or bugged. However an updated runkit is maintained on Github at http://github.com/zenovich/runkit. Mutagenesis requires that this specific version of runkit is used with PHP 5.3.

To install the runkit extension, the following commands should be sufficient:

git clone http://github.com/zenovich/runkit.git runkit
cd runkit
sudo make install

Once the runkit extension has been installed, you should edit your relevant php.ini file to add the extension for loading, e.g.


Huge thanks to http://github.com/zenovich (zenovich on Github) for maintaining this runkit copy!


The preferred installation method is via PEAR. At present no PEAR channel has been provided but this does not prevent a simple install! The simplest method of installation is:

git clone git://github.com/padraic/mutagenesis.git mutagenesis
cd mutagenesis
sudo pear install pear.xml

The above process will install Mutagenesis as a PEAR library.

Note: If installing from a git clone, you may need to delete any previous Mutagenesis install via PEAR using:

sudo pear uninstall Mutagenesis

While the git repository tracks code in development, I will add an official PEAR channel in the near future once a stable release is made.

Note: Mutagenesis supports PHPUnit 3.5 by default, the current stable version. Earlier versions of PHPUnit may or not work and it is suggested to ensure PHPUnit is updated prior to using Mutagenesis.


Mutagenesis is used from the command line using the installed 'mutagenesis' script or 'mutagenesis.bat' from Windows. It hooks into the underlying test suite for a library or application by using an adapter. Currently, a PHPUnit adapter is bundled and used by default.

After an initial test run to ensure all unit tests are passing, Mutagenesis examines the source code of what is being tested. Based on this examination, it generates a set of "mutations" (i.e. deliberate errors). For example, it may locate the boolean value TRUE and generate a mutation to change it to FALSE. For each generated mutation, the test suite is rerun (via the adapter) with the mutation applied to the relevant class method using the runkit extension. Each such test run is performed in a new PHP process.

If the test suite passes, this is interpreted as meaning that the test suite did not detect the deliberately introduced error. This is referred to as an "escaped mutant". It demonstrates that your test suite was insufficient to detect that particular mutation (a possible sign you need more unit tests!).

If the test suite reports a failure, error or exception, this is interpreted as a successful mutant capture. Your test suite was sufficient to detect the deliberate error.

After all mutations have been tested, a final report is provided with a small diff description of each escaped mutant to assist in composing any new unit tests required.

On a final note, Mutation Testing is a semi-blind process. Not all mutations introduce true errors. Changing a TRUE to a FALSE where a variable is being initialised (and is definitely changed later) would not cause a test failure. Such a reported mutant is a false positive (or ghost). These are unavoidable but should be examined in context to ensure they are indeed harmless. Updating source code to remove such false positives will still assist in getting more relevant Mutation Testing reports in the future.

Command Line Options

A typical mutagenesis command is issued with:

mutagenesis --src="/path/project/library" --tests="/path/project/tests"

The basic parameters let you control the directory depth, i.e. which subset of the source code and/or tests will be utilised. Additional options may be passed to direct the unit test framework adapter:

  • --adapter: The name of the unit test adapter to use; defaults to "phpunit"
  • --options: String containing command line switches to pass to the unit test framework
  • --timeout: Sets the number of seconds after which a test run is considered timout
  • --bootstrap: Sets a bootstrap file to include prior to running tests
  • --constraint: PHPUnit class and/or file path for test execution
  • --detail-captures: Shows mutation diffs and testing reports for captured mutants

Note: The default timeout is 120 seconds. Any test suite exceeding this should have a relevant timeout set using --timeout or else all test runs would timeout. A reported timeout is not a bad thing, it simply means a mutation may have created a noticeable infinite loop in the source code.

Important: The bootstrap option is essential where your source code relies on autoloading. Mutagenesis needs to include class files prior to the test adapter running, so setting a relevant bootstrap prevents include errors. For example, PHPUnit test suites often use a TestHelper.php or Bootstrap.php file.

For example, imagine we usually employ the following to run some PHPUnit tests:

phpunit AllTests.php --exclude-group disabled

In addition, we use the file TestHelper.php to setup autloading for the tests (this would normally be included from within AllTests.php manually but Mutagenesis needs to load it as early as possible).

We can pass this to mutagenesis as:

mutagenesis --src="/path/project/library" --tests="/path/project/tests" \
    --options="--exclude-group disabled" --constraint="AllTests.php" \

Note: "\" merely marks a line break for this README. The command should be on a single line with the \ removed.

This affords a very flexible means of allowing users to use Mutagenesis on narrower subsets of their test suites.

Understand Mutagenesis Output

Mutagenesis outputs an initial and final report. The initial report is the result of a pretest, a test run to ensure the test suite is in a passing state before attempting any mutations. Tests must be in a non-fail state or else mutation testing cannot be performed (i.e. all mutants would escape!).

The final report renders all escaped mutants with a description of the class, method and file mutated, along with a diff of the method code that was changed. Here's a quick exerpt of a mutation test run with escaped mutants (containing the first escaped example - the remainder are omitted for brevity).

Mutagenesis 0.5: Mutation Testing for PHP

All initial checks successful! The mutagenic slime has been activated.

    > PHPUnit 3.4.12 by Sebastian Bergmann.
    > ............................................................ 60 / 62
    > ..
    > Time: 0 seconds, Memory: 16.50Mb
    > OK (62 tests, 156 assertions)

Stand by...Mutation Testing commencing.


40 Mutants born out of the mutagenic slime!

16 Mutants escaped; the integrity of your source code may be compromised by the following Mutants:

Difference on Idun_Validate_And::isValid() in library/Idun/Validate/And.php
@@ @@
                 $this->_errors = $conditional->getErrors();
-                return false;
+                return true;
         return true;

The progress output uses the following markers:

  • .: Current mutation was detected by test suite
  • E: Current mutation was undetected by test suite
  • T: Test suite timed out (see --timeout option)

Supported Mutations

Work on Mutagenesis is ongoing, and more mutations will be added over time. Please refer to the included SupportedMutations file for the current list.


Mutation Testing relies on running a test suite repeatedly for each mutation generated. It is not a fast process, and is better suited to occassional use or in continuous integration. Mutagenesis has implemented a number of heuristics first utilised by the Java Jumbler framework in order to speed things up.

  1. Exit Early

Mutagenesis only requires a single test in a suite to fail to know when a mutation has been detected. Therefore, once any test fails, the test suite run is terminated immediately so we're not pointlessly executed whole test suites unnecessarily.

  1. Execute Fastest First

During the initial test suite check, Mutagenesis compiles execution times for each test case encountered. In subsequent runs, it will execute test cases in order of their execution times starting with the fastest. This leaves very slow test cases to the very end thus relying on the probability that any mutation detections will often be detected earlier by faster tests thus reducing the net time spent in running test suites.

  1. Rinse And Repeat

Mutagenesis mutates file by file, meaning that any test case detecting a mutation has a better change of detecting other mutations on the same file. Therefore, Mutagenesis first executes the last two tests cases to detect a mutation before any other test cases to leverage off their probable success.