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Testing Howto

How to test your Biskit installation.
  • Each Biskit module comes with its own test class (derrived from Biskit.test.BiskitTest).
  • All the input data needed to run the tests is checked into the project and can be found in the folder ~biskit/test.
  • The tests are independent of each other and there is no need to execute them in a specific order.
  • Many of the tests write an output to disc. The directory used for the output is the folder given by tempfile.tempdir, normally /tmp.
  • TAGS classify tests into categories that can be included or excluded from a test run, currently these are: LONG, OLD, EXE, PVM

Testing a single module:

To test a single module just execute the module, for example:

cd biskit/Biskit
python -i PDBModel.py

...will run the PDBModel test case and release you into an interactive interpreter to inspect the result.

Testing the full installation:

Testing of the full installation is facilitated by a script ~biskit/Biskit/test.py (in fact, test.py also is the module that defines the whole Biskit testing infrastructure ). This script accepts a few options. The most useful option may be -e to exclude tests by their tags and -p which allows you to narrow down testing to a Biskit sub-package

To get some help from the script, call it without arguments:

python test.py
Example 1,

test everything:

python test.py -v 2

(give any default option to prevent the printing of the help screen). After having typed that, going for lunch or a walk may be a good idea, especially if your docking and homology modeling installation is complete.

Example 2,

only test core Biskit without external programs or pvm-dependent code:

python test.py -p Biskit -e exe pvm
Example 3,

only test docking and homology modeling external programs:

python test.py -p Biskit.Mod Biskit.Dock -i exe

Writing your own test:

Biskit.test automatically collects all BiskitTest-derrived test cases from all Biskit modules. The documentation in Biskit.test contains a ready-made template for your own test case and all the necessary (or maybe unnecessary) instructions.