Prep for v2.7.0 release

[rbouckaert]

Though the public release is still a bit off since we need to decide what will be included, this is a catch all issue for dealing with anything to do with assisting this release.

Currently, it contains two packages: beast.pkgmgmt and beast.base.

The beast.app package is move to BEAST.app, which is Swing based and BeastFX, which is JavaFX based. The former does not allow GUI unit testing with java version over 8, while the latter does, and has a number of new features built int like help me choose buttons, theme chooser and method section generation.

scripts/migrate.md contains some information on how to migrate v2.6 packages to v2.7. Most notably, classes moved to get a more logical structure so imports need to be adjusted (a script is available to assist), and all BEAST objects need to be declared in the version.xml file.

There is a v2.6 branch containing the v2.6.7 code + recent updates.

[tgvaughan]

Wow, these are huge changes. Very brave! Roughly what is the timeline here?

[rbouckaert]

Currently working on the release script, trying to get a pre-release out asap, but then depending on how much work is involved in migrating packages and whatever issues pop up along the way, we have to see how things develop. I think this is a big step forward in modernising BEAST, so worth the big change. But given there are a growing number of packages, I would not want to go through this exercise any time soon, so want to be sure that everyone is happy with the proposed changes.

This is also a good time to get things in, like deprecating log(int) :-).

Let me know if you have other things that make life easier, or raise an issue.

[rbouckaert]

The release script works for Java 8 and Linux with JRE now (which I prefer to be the default to make the installation process as smooth as possible). Have a try and see whether you like the new look of BEAUti. BEAST and TreeAnnotator had a facelift as well -- BEAST is still rather experimental, and needs a bit of work. There are no packages available yet, other than BEAST.base and BEAST.app. The release includes the JavaFX version of BEAST.app.

[tgvaughan]

Exciting! I haven't had a chance to look at this yet (busy few weeks) and am on holidays next week, but hopefully I'll get a chance to poke around the week after.

[rbouckaert]

Managed to get an OS X with Azul zulu Java 17 to work with JavaFX. JavaFX is not distributed by most JREs, and Adoptium (which we used for v2.6.x releases) has no plans to do so.

The easiest way to distribute BEAST with JRE is to include a distribution that already has JavaFX included, such as Azul zulu. There does not seem to be a license issue distributing it with BEAST, but I may have overlooked something.

Anyone noticing issues with Azul? Is there a better distribution?