Wire up BEAST X dependency and add JC69 tile#38
Open
alexeid wants to merge 1 commit into
Open
Conversation
Adds an install-beast-mcmc.sh helper that downloads the official BEAST X v10.5.0 release tgz and registers the bundled fat beast.jar as dr:beast-mcmc:10.5.0 in the local Maven repository, plus a README documenting the one-time setup. The integrations/beastx/java pom now declares this dependency. Adds a first concrete tile, JC69Tile, mirroring the BEAST 2 pattern. BEAST X has no dedicated JukesCantor class, so the tile builds an HKY with kappa=1.0 and equal nucleotide frequencies, which is equivalent. Registers the tile in BeastXCoreTileLibrary and adds a unit test exercising the BEAST X classpath at runtime.
Collaborator
|
Looks good to me, thank you! |
Collaborator
|
The failed tests are due to the fact that the Rev parser is not yet fully updated to 03-2026, so indeed unrelated to this. |
tochsner
approved these changes
May 6, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
install-beast-mcmc.sh+ README that download the BEAST X v10.5.0 release tgz and register the bundled fatbeast.jarasdr:beast-mcmc:10.5.0in the local Maven repo.integrations/beastx/java/pom.xmlnow depends on that artifact.JC69Tilefrom the BEAST 2 integration. BEAST X has no dedicatedJukesCantorclass, so the tile buildsHKYwith kappa=1.0 and equal nucleotide frequencies. Registered inBeastXCoreTileLibrary.JC69Tile.applyTile(...)and asserts on the resultingHKY— exercises the BEAST X classpath at runtime.Test plan
./integrations/beastx/install-beast-mcmc.shon a fresh clonemvn -pl integrations/beastx/java -am compilesucceedsmvn -pl integrations/beastx/java test -Dtest=JC69TileTestpasses (2/2)Notes
beastx-parser, notmain.phylospec-coreRevConverterTest(The function nexus does not exist) on thebeastx-parserbranch block a top-levelmvn test. Unrelated to this change but worth flagging.