Incompatibility between BEAST 2.7 and babette

[richelbilderbeek]

An email from @mmatschiner:

[...]

I wanted to make you aware that the latest update of BEAST 2.7 is apparently incompatible with Babette, because of changes to the
namespace. I noticed the same for my script snapp_prep.rb that produces XML input files for SNAPP, but I managed to update the
script so that it works with BEAST 2.7.

You'll probably just need to change a number of "spec" attributes, and perhaps @rbouckaert's advice would be helpful for @richelbilderbeek in doing so.

Thanks Micha!

Then an email followed from @rbouckaert:

[...]

Richel, to clarify: most class names have not changed, just the java package they can be found in.
This means that v2.6 XML does not run out of the box with v2.7 (though it might when running the migration script
https://raw.githubusercontent.com/CompEvol/beast2/master/scripts/migrate.pl there are no guarantees).

What will probably help is to use the default namespace below. Since v2.7 requires BEAST packages to use their own java
packages, some classes have moved as well. For example, classes from BEASTLabs that used to be in the beast java package
are now in the beast labs java package. Hope this does not cause too much inconvenience.
Let me know if you run into any trouble.

Thanks @rbouckaert!

[richelbilderbeek]

How nice of them to contact me!

When a user asks to support BEAST2 v2.7 and volunteers to check, I'll look for the time (and/or a BSc or MSc student!) to do so.

[mmatschiner]

I just found out that it's possible to convert files produced by babette for BEAST 2.7 with this script: https://raw.githubusercontent.com/CompEvol/beast2/master/scripts/migrate.pl

[rbouckaert]

Note that the script is not fool-proof. It probably is good enough for many vanilla BEAST analyses, but does not cover all packages. It should be easy enough to extend the script though, since it mostly just does search/replace of spec attributes and contains a mapping in the script.