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Move the example XML files to beast-base/examples and beast-fx/examples - #243
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The examples were in beast-base/src/test/resources/beast.base/examples and beast-fx/src/test/resources/beast.fx/examples, which is hard to find. Each folder moves to the top of its module as a whole, including the legacy/ and beast2vs1/ subfolders used by the tests. Each pom maps its examples folder to the resource path the tests already use (beast.base/examples, beast.fx/examples), and the package assemblies read from the new folders, so the test class path and the package zips are unchanged. The migration report and the to-do list of #204 move from the examples folder to scripts/.
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Fixes #241.
What changes
The example XML files move to the top of their modules, as the BEAUti templates did in #238:
beast-base/src/test/resources/beast.base/examples/beast-base/examples/beast-fx/src/test/resources/beast.fx/examples/beast-fx/examples/Each folder moves as a whole, including the
legacy/andbeast2vs1/subfolders used by the tests. This is the layout of theexamples/folder in BEAST 2.Two notes that were in the beast-base examples folder (the migration report and the to-do list of #204) move to
scripts/, so that the folder holds only examples and test XML.How
beast-base/pom.xmlandbeast-fx/pom.xmldeclareexamples/as a test resource with the target path the tests already use (beast.base/examples,beast.fx/examples). No test changes.beast-fx/pom.xmlthat copies the beast-base examples into its test classes reads frombeast-base/examples.package.xmlassemblies read from the new folders. They select the same files as before (top-level XML and JSON,nexus/,fasta/), solegacy/andbeast2vs1/are still not released.README.md, the READMEs in the examples folders,release/Mac/README.md,release/Linux/README.md, a table inscripts/spec-namespace-test-resources.mdand one path in thePackageManagerjavadoc.Checks
Compared with a clean build of master:
BEAST.base.package.*.zipandBEAST.app.package.*.zipare identical.target/test-classesof both modules is identical except for the two notes, which are no longer copied in.mvn teston all modules: beast-pkgmgmt 47, beast-base 605, beast-fx 76 tests, no failures.Not checked: the release scripts for the three platforms run end to end (they take the examples from the package zips, which are unchanged), and importing the project in Eclipse.