IO optimization #164
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IO optimization #164
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implented some small speedups
still inexplicably have an order-of-magnitude speed difference between calling `parse_newick` on a newick string and doing the _exact same thing_ within the io code...
e-koch
requested changes
Dec 7, 2021
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I added a few minor comments. Some of the test failures are legitimate and at least one seems to be related to this PR (https://travis-ci.org/github/dendrograms/astrodendro/jobs/523668907#L1286).
| self._smallest_index = min(self._indices) | ||
| try: | ||
| self._smallest_index = min(self._indices) | ||
| except ValueError: |
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What causes the ValueError in min? Is there a check somewhere if _indices is empty?
parse_newick right now)
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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.