Setup Development Environment

Virtual Environments

We recommend using virtual environments with virtualenvwrapper. Since MDAnalysis is split into the actual package and a testsuite you need to install both modules in development mode.

cd <to where ever you checked out MDAnalysis>
mkvirtualenv mdanalysis
pip install numpy
pip install cython
pip install -e package/
pip install -e testsuite/

The -e flag will cause pip to call setup with the develop option. This means that any changes on the source code will immediately be reflected in your virtual environment.

Testing

• To run the unit-tests

cd testsuite/MDAnalsysisTests
./mda_nosetests

• Run specific tests

./mda_nosetests test_analysis.py
./mda_nosetests test_analysis.py:TestContactMatrix

• test with coverage

./mda_nosetest --with-coverage --cover-erase --cover-package=MDAnalsysis

If you also want to get a HTML output of the coverage report

./mda_nosetest --with-coverage --cover-erase --cover-package=MDAnalsysis --cover-html --cover-html-dir=coverage