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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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Cleaning up old stuff - including old likelihood native libraries #1189

Open rambaut opened 5 months ago

rambaut commented 5 months ago

This is a large purge of obsolete stuff starting with the oldevomodel/* and oldevomodelxml/ packages that are based around the original TreeLikelihood that uses TreeLikelihoodCore - the original native library. Most uses of this package were simply to get constant strings for parsers that were also available in newer files.

The biggest loss is the whole of the evomodel.arg package which was entirely dependent on oldevolmodel. It was easiest to delete it. Legacy use can be through BEAST v1.10.4 and at some point someone can reimplement using BEAGLE tree likelihoods.

There were a few other things that were easier to delete than to update and have likely been unused for years.

msuchard commented 4 months ago

am seeing this error:

    [junit] Running test.dr.evomodel.substmodel.GeneralSubstitutionModelTest
    [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.101 sec

and many, many other errors. @rambaut -- can this wait until after our ..0 release?

rambaut commented 4 months ago

The tests all used the old TreeLikelihood and likelihood core. Which is not much use. I am not sure our unit tests are really worth it at present.