Added --profile option to run Python profiler
Add --profile option
Convert findMeanSD script to a method in calibration.py
Replaced findThresholds script with method in calibration.py
Split findMeanSD into smaller and more manageable methods
Edited comments
Bugfix in arguments to runMultiple
Write profile output to file
Removed obsolete scripts
Write pstats to named temporary file (pasted from cython branch)
Added option to activate profiling by default in config.ini
Removed cython imports, previously added in error
Replace 'for range' with 'while' and list append with assignment, for greater efficiency
Replace 'for range' with 'while', list append with assignment, and file with StringIO, for greater efficiency
Bugfix for output array length in callsToBinary
Fix minor bug in handling --text argument with profiler
Changed copyright notice for multiple authors
Use class in utilities.py for generic argument validation
Merge pull request #5 from iainrb/devel

Merge changes from iainrb/devel for release 3.1
Merge branch 'devel'