This has been discussed numerous times, but I didn't see an issue devoted to it.

The unit tests currently depend heavily on external resources, e.g. for downloading structures or genbank files. This means that tests cannot be run offline, and that temporary outages cause the build to fail. I suggest

1. Wherever possible, include test resources directly in the repository rather than downloading. Large files (e.g. SCOP files) should be truncated into manageable subsets where possible.
2. Unit tests that legitimately test connections to external resources should be moved to biojava-integrationtest. They should also test connections using junit assume statements (although travis also fails for failed assumptions).
3. All modules except integrationtest should pass when offline