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Major optimizations for database population and global stemma generation

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@jjmccollum jjmccollum released this 03 Feb 15:47

With this major release (thanks to the invaluable contributions of @dopeyduck), the open-cbgm library and the open-cbgm-standalone utility now make use of multithreading to parallelize the creation of the genealogical cache database and the generation of global stemmata, resulting in significant speedups for each. The core library also features a new optimization to speed up the set cover solver when only one minimum-cost solution is desired, which further accelerates the generation of global stemmata. In addition, several modules in the standalone utility (compare_witnesses, find_relatives, optimize_substemmata, print_textual_flow, print_global_stemma) now support an -e option for excluding specific witnesses from calculations and a -p option for excluding witnesses extant at fewer than a given proportion of variation units (to facilitate the exclusion of fragmentary witnesses).