blacktie/scripts/cummerbund.py:
- removed unused imports
- PEP8 fixes
- added stuff to catch the failure of run due to a new cummerbund behavior that chokes when getting sig genes sometimes
- added PCA and MDS code
tests/test_blacktie_cummerbund.py:
- define nosetests
tests/test_whole_run.py:
- define nosetests
tests/test_whole_run.py:
- define nosetests
- fixed working dir definitions
tests/test_whole_run.py:
- PEP8
/home/gus/Dropbox/repos/git/blacktie/src/blacktie/utils/calls.py:
- PEP8
- altered some imports
- now uses outside `bunch` library
-
blacktie/scripts/blacktie_pipeline.py:
- changed --no-email to --email (now it is default NOT to send emails)
- made --prog option allow giving multiple valid programs (still leaves it up to user to make sure the needed files exist and are pointed to correctly)
- PEP8
- cleaned up imports
- now uses outside `bunch` lib
tests/__init__.py:
- added file
blacktie/utils/misc.py:
- cleaned up imports
- PEP8
- def bunchify(dict_tree):
    - converted type comparison to isinstance()
setup.py:
- cleaned up imports
- PEP8
 Changes to be committed:
	modified:   docs/_build/html/_modules/blacktie/utils/calls.html
	modified:   docs/_build/html/code.html
	modified:   docs/_build/html/genindex.html
	deleted:    requirements.txt
	modified:   test_data

 Changes not staged for commit:
	modified:   test_data (modified content)