This is a WIP to speed up the reading and parsing of dendrograms from disk.
One key change in speeding up the parsing was removing a conversion from an array of coordinates to a list of tuples of coordinates. Creating N tuples was a very expensive step, apparently, and eliminating it cut the time by >50% in the _fast_reader.
The WIP is (1) to make sure that we didn't break anything, really and (2) to try to speed up parse_newick.
This is a WIP to speed up the reading and parsing of dendrograms from disk.
One key change in speeding up the parsing was removing a conversion from an array of coordinates to a list of tuples of coordinates. Creating N tuples was a very expensive step, apparently, and eliminating it cut the time by >50% in the
_fast_reader.The WIP is (1) to make sure that we didn't break anything, really and (2) to try to speed up
parse_newick.