This line fixes an error I was getting compiling with Java 1.8:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project biojava-structure: Compilation failure
[ERROR] /Users/bliven_s/git/biojava_ws/biojava/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:[296,52] reference to newFileSystem is ambiguous
[ERROR]   both method newFileSystem(java.nio.file.Path,java.lang.ClassLoader) in java.nio.file.FileSystems and method newFileSystem(java.nio.file.Path,java.util.Map<java.lang.String,?>) in java.nio.file.FileSystems match

The second form isn't documented, so it could be that this change will cause a warning with different JDKs.

@sbliven
I did initially try to fix this error with the same change. However the TreeMap here, is not fixing this flaky error. The tool still marks it as flaky with error of the sort -

[ERROR] Failures: 
[ERROR]   AlignmentToolsTest.testToConciseAlignmentString:342 1. Cycles. expected:<[1>2>3>1] 7>7> but was:<[2>3>1>2] 7>7>
[INFO] 
[ERROR] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0

@sbliven @josemduarte

Would like to link the Nondex tool here : https://github.com/TestingResearchIllinois/NonDex

The tool requires :

• Adding the plugin as specified in the documentation which applies if you want to run NonDex mutliple times.

• Run for the test -
  mvn -pl biojava-integrationtest nondex:nondex -Dtest=AlignmentToolsTest#testToConciseAlignmentString

• Run for the whole module -
  mvn -pl biojava-integrationtest nondex:nondex.

• Otherwise, one need not add the plugin to pom.xml file(s) and can run just run mvn edu.illinois:nondex-maven-plugin:1.1.2:nondex instead of mvn test. Please check that the command does work for you.

This could be added into travis.yml, so it can be run on new tests too.

It also has the debug feature that can be used to point to the file(s) that could require changes. The link to the tool has all the documentation.