Cythonized files now deleted after setup. (closes #667)

Default behavior now depends on release or dev status. When in dev mode
default is to use Cython and delete cythonized files. When in release
mode default is to skip Cython but keep existing cythonized files.

setup.py now reads the version string directly from version.py.

Environment variable handling in setup.py enhanced to recognize strings
with boolean meaning (fixes #629).

Travis' minimal build now also rebuilds cythonized files.

.travis.yml

@@ -16,14 +16,14 @@ env:
 matrix:
   allow_failures:
      - python: "3.3"
-       env: SETUP=full CYTHONIZE=true
+       env: SETUP=full 
   include:
      - python: "2.7"
-       env: SETUP=minimal CYTHONIZE=false
+       env: SETUP=minimal
      - python: "2.7"
-       env: SETUP=full CYTHONIZE=true
+       env: SETUP=full
      - python: "3.3"
-       env: SETUP=full CYTHONIZE=true
+       env: SETUP=full
 # command to install dependencies
 addons:
   apt:
@@ -45,8 +45,9 @@ install:
   - if [[ $SETUP == 'minimal' ]]; then conda create --yes -q -n pyenv python=2.7 numpy=1.9.2 nose=1.3.7 sphinx=1.3; fi
   - source activate pyenv
   - if [[ $SETUP == 'full' ]]; then conda install --yes python=$TRAVIS_PYTHON_VERSION cython biopython matplotlib networkx netcdf4; fi
-  - if [[ $SETUP == 'minimal' ]]; then conda install --yes python=$TRAVIS_PYTHON_VERSION biopython networkx; fi
-  - if [[ $CYTHONIZE == 'true' ]]; then find . -name '*.pyx' -exec touch '{}' \; ;fi
+  - if [[ $SETUP == 'minimal' ]]; then conda install --yes python=$TRAVIS_PYTHON_VERSION cython biopython networkx; fi
+# ensure that cython files are rebuilt
+  - find . -name '*.pyx' -exec touch '{}' \;
   - pip install -v package/
   - pip install testsuite/
   - pip install coveralls tempdir