Bye submodules.
No more submodule
Makefile fun.
Please compile on Clavius now.
It compiles.
Makefile install
A little cleaner.
Patching.
Fixing RNAspectral
The amount of time that took to find was annoying.
Way too much debug in -v flag
Finer grained runs
Multi-param support and a new flag for MFPT (print all MFPT), and better Spectral verbosity.
Erro on radial_probability for MFPT, spectral_usage and remove the energy_grid_file option, since that's made redundant by the RNApopulation code.
FFTbor2D prints a CSV file compatible with RNAmfpt using the -c flag, and updated the README.md files to contain example calls.
A ton of new changes surrounding the RNAspectral code to permit the serialization and deserialization of the eigensystem. This will be useful for doing population proportion experiments on systems where you want to look at the rates multiple times, without having to regenerate the system.
Changing the way the parse_*_args functions work to take parameters struct as input. Better for multi_param
Better commandline for MFPT
Better commandline for FFTbor2D
Fixing 3 bugs. (1) argv[0] in each subparam is the subparam name. This fakes out getopt (otherwise it doesn't parse right.) (2,3) subparam argv flags are prefixed with a '-' and terminated with '\0'