Break the graphviz layout engine up a bit so we can call sfdp with 3D switched on
Global constants should be capitalized
Merge remote-tracking branch 'gh/dev' into dev
Update tests to current structure
Update reference particles
Ignore input files that find their way here
Merge branch 'fix_tests' into dev
Cleaned up files with most errors
Clean a few more files
Remove old git script
Remove bash scripts
Improve hepmc event iteration
Massive pep8 pass

Striped whitespace, renamed variables, broke import cycles...
Further pep8 improvements
Add some doc strings
PEP8-ify options parsing
Add an abstract method to the Tool class
Scrub warnings in __init__ files