visualization parameter updates/fixes

• changed --t-lin, --t-log defaults and fixed --t-lin=1, --t-log=1
• fixed potential issues with --t-end = --t-ext
• adapted README example to publication

using lonley base-pairs

• removed the --noLP default (added parameter setting)
• added profiling option for runtime optimization
• using --cg-auto default parameter
• using k0=1e5, t-ext=0.04 default parameter
• added new visulization types and fixed motif file input
• added epsilon to t-fast sanity check

DrTransformer and DrPlotter

The first release of DrTransformer as standalone package (no more ribolands). Incorporates many changes to prior versions, many of which were never officially released:

• all essential functions with major updates (expansion, coarse graining, simulation and pruning).
• interface changes and partial rewrites
• new parameters and parameter defaults
• no more plotting for DrTransformer, this is the job for DrPlotter
• new plotting layout with transcript length ticks, repaired code to enable plotting including pause sites
• using scipy and numpy for matrix exponentials (instead of treekin)
• and probably more ...