Dummy transition support, rapidprom, many fixes

[javispedro]

New modules

• pn.bound: bounding PetriNets
• pn.replay: new functions for replaying traces in PetriNets
• rapidprom: running RapidProM scripts from python

  Fixes to pmlab modules

• AlphaReencoder with > 27 events: now generates a, b, c, d, ..., aa, ab, ...., ba, ..., aaa
• TransitionSystem: search log2ts, draw_astg in $PATH instead of hardcoding /usr/local/bin/...
• ts_from_sis, pn_from_sis: allow dots ('.') in identifiers; petrify allows this
• TransitionSystem.get_edge() fixed
• TransitionSystem.map_log_frequencies(): raise "UnfitTsError" if the TS does not model the log
• pn_from_sis: support sis files with implicit places
• pn_from_sis: raise exceptions for broken nets (e.g. with place->place arcs).
• pn_from_sis: allow loading PetriNets without initial marking
• pn_from_pnml: "be more liberal in what we accept" (to load nets from ProM)
• PetriNet.save_as_sis: clean up identifiers with invalid characters
• PetriNet.save_as_sis: export place capacities using ".capacity"

  Minor fixes (code style/documentation only)

• ts_from_sis: (use 'newlines' instead of 'Suppress(OneOrMore(LineEnd()))'
• TransitionSystem.set/get_initial_state: document the parameter/return value is the NAME of the state
• TransitionSystem.self_loop_labels: use "generator comprehensions" instead of lists
• TransitionSystem.follow_label: use the new method "find_output_edges"
• TransitionSystem.map_log_frequencies: use the new method "find_output_edges" instead of "follow_label"
• PetriNet.enabled_transitions: use the new method "is_transition_enabled"

  New features with no/minor API changes to existing modules

• log_from_xes: if filename.endswith('.gz') use gzip to automatically uncompress file
• TransitionSystem.save ('sis' format): like Petrify, print the number of states on the header as a comment
• TransitionSystem: add "remove_state" method (slow implementation!)
• TransitionSystem: add "remove_edge" method
• TransitionSystem: add "find_input/output_edges" methods
• TransitionSystem.follow_label: return a Python iterable instead of a list
• ts_from_sis: allow loading from file objects too (to be consistent with other APIs)
• ts_from_pn: add a function to retrieve the TS from a PetriNet object Requires Petrify!
• PetriNet.is_transition_enabled: computes whether transition [t] is enabled in the current marking
• PetriNet.save_as_sis: same as PetriNet.save(file, format='sis')
• PetriNet.save_as_pnml: save as a ProM-compatible PNML file
• PetriNet.save: add new format parameter (to choose between 'sis' and 'pnml' and be consistent with other APIs)
• dummy transition support in PetriNet and TransitionSystem, including loading/saving

  BIG API changes

• log_ts.cases_included_in_ts: change signature of function
• pn_from_pnml: remove "+complete" suffix from transition names if loading from a PNML file