biopython/biopython — pull request #78 by brandoninvergo (2012-10-13 22:45:48+00:00)
Title: PAML 4.6 fixes

New PAML version = new parsing breakage ("let's arbitrarily put spaces where they weren't before").

Most of the changes are in the test output files used in the parsing unit tests. You don't have to look at any of them (in Tests/PAML/Results), since I was mainly cleaning up, adding some missing ones, and then adding ones for the new version. I also cleaned up the script that I use to generate these test files, so it'll be a bit more flexible and easier to use in the future.

As for actual code, only one regexp needed to be changed (in Bio/Phylo/PAML/_parse_codeml.py), and one minor change was needed in test_PAML_codeml.py.