16. For developers

16.1. The GDSCTools test suite

The GDSCTools package has a large set of tests in the ./test/gdsctools directory. In version 0.10, about 80% of the functionalities are covered. If you add a new module or function, please add a corresponding test file in ./test/gdsctools directory.

The test suite uses the nosetests utility and is integrated within the Travis continuous integration (see below).

To run the tests locally, you will need nose and coverage packages:

pip install nose coverage

Then, in the directory where is the setup.py file, type

python setup.py nosetests

You may also go directly in the ./test/gdsctools directory but some tests may required extra files or permission.

16.2. Documentation

The documentation is based on Sphinx. This means that all code is documented using the REST syntax. Docstring are added in classes and functions as much as possible with code examples.

See for example the file in gdsctools/anova.py and in particular the class ANOVA.

In addition, in the ./doc directory there are a set of files encoded using the REST syntax. If you go to that directory and type:

make html

then the entire documentation included Tutorial and Developer guide will be parsed and interpreted. The resulting html documentation can then be found in doc/build/html. For the Sphinx documentation to be generated, the GDSCTools package must be installed.

Note

the command above will work only if GDSCTools source code is available and installed in the shell where the command is executed.

The documentation can then be uploaded on pypi. Go to the directory were is the file setup.py and type:

python setup.py upload_docs

16.3. Continuous Integration

This is based on Travis. The reports should be available here: https://travis-ci.org/CancerRxGene/gdsctools and the status is also reported in the main github page (https://github.com/CancerRxGene/gdsctools) as an icon (build) that will be green or red depending on the status of the build within Travis.

The required files is in the main directory and called .travis.yml

16.4. ReadTheDocs

The doc is built on read the docs. The required files are readthedocs.yml and requirements.txt.