Failing integration tests DocumentationTest

[kche309]

Building package fails beast integration test with the error below

junit_phylonco:
    [mkdir] Created dir: /home/kylie/Repos-new/beast-phylonco/build/junitreport
    [junit] Running test.beast.integration.DocumentationTest
    [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.763 sec
    [junit] Test test.beast.integration.DocumentationTest FAILED

@kche309 to fix DocumentationTest

[J-Moravec]

Seems like what is being tested is BEAST2 code, not phylonco code. Integration tests might not be properly set up?

[kche309]

I agree, it looks like the failing classes are from BEAST2 and other packages rather than the phylonco package. It is strange it is not picked up in the beast2 github continuous integration workflow (e.g. https://github.com/CompEvol/beast2/runs/4925469365?check_suite_focus=true).

On further inspection, it seems only beast-core tests are run for BEAST2 CI

[walterxie]

If you did not change any Java classes, I used the Gradle to run all tests just now and they were passed:

[J-Moravec]

@walterxie This is about integration tests, not unit tests.

[kche309]

Ant builds are no longer used, this is being replaced with Gradle.
Integration tests will be setup on Docker similar to https://github.com/tgvaughan/bacter

TODO: @kche309 to set up Docker file for integration tests

[kche309]

I've had a quick look into Gradle documentation, setting up integration tests looks a bit tricky https://docs.gradle.org/current/userguide/java_testing.html#sec:configuring_java_integration_tests
Beast2 does not package tests in the jar, so we can't load integration tests directly from the jar.
Probably it is easier to have a Docker + ant setup that can run and test in a clean environment.