--outside_grammar

new features

• --outside_grammar: automatically generate an outside grammar counterpart for user provided grammars to compute e.g. posteriors
• --checkpoint: Thanks to Fynn Muermanns, gapc code generation can now add generic code to periodically (e.g. every hour) dump contents of the partially computed DP matrices to files. Should an execution of a long running job abort prematurely, the binary can be restarted and pick up computation from the last dumped checkpoint.
• --plot-grammar: new levels of detail available for plotting the used grammar. 4: adding yield size information for parsers, 5: optimized table dimensions for non-terminals.
• automatically generated enum algebras will now also report non-terminal parameters for better manual inspection
• --printCall can now be invoked with the generated binaries. Thus, the binary will tell you which gapc command led to its generation. Thanks to Fynn Muermanns.

maintenance:

• CYK code generation is now nicely abstracted into the source file src/cyk.{cc,hh} instead of being intermingled in src/cpp.cc
• plot_grammar code is moved into a dedicated src/plot_grammar.cc file
• librna
  • is exposing additional functions to support Guanine-Quadruplex energy contribution calculation for RNA problems
  • updated the ViennaRNA code base from 2.4.17 to 2.5.1, thanks to Fynn Muermanns
  • significant speed-ups due to clever hashing / pre-computation of energy contributions, thanks to Fynn Muermanns.

fixes:

• --plot-grammar:
  • properly escape & chars
  • unfortunately, graphviz -> dot does not necessarily preserve child node ordering. Using "clusters" mitigates (but does not solve in 100%) this issue significantly
• fixed yield size computation of constant terminal parsers
• guards operate on unsigned int borders, which sometimes led to underflows.
• warn users about negative candidate values when using expsum