Merge pull request #95 from RosettaCommons/kylebarlow/general_dev
Change JD2 to throw exception if a job fails
The prior behavior was for JD2 to exit cleanly and return a zero exit code, even if the only job it tried to run failed. This means that integration tests can sometimes fail silently when they completely fail to run.
JD2 will now count failed jobs (from bad inputs of FAIL_DO_NOT_RETRY), and if this count is above 0, throw a specialized exception at the end of go_main(), which would typically then be caught by the application and result in a non-zero exit code.
I have modified the JD2 integration test to fail against the old case, but it now should still pass.
Integration tests that appear to be broken, and which will now fail continuously after this commit:
coupled_moves
loop_creation
filter_termini_near_interface
antibody_graft
splice_out_shorter_tail
No failed unit tests expected.