Fix issue s1319 Declarations should use Java collection interfaces on biojava-core #1095
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There sometimes seem to be problems with the BerkeleyScopInstallationTest. |
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LGTM thank you!
I've triggered the tests task that failed. But 3 of them have succeeded so I guess the TestCrystallographicMetadata.test1zna is working fine.
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Does this mean that you are going to merge this PR? If so, I'll try to continue resolving this issue. |
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Yes I'd be happy to merge this. Will you do one PR per module then? |
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I don't know yet... Above all, I'm going to try to have a stable situation with each PR. It's likely that this will lead me to do one RP per module. |
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I suggest you do one PR per module. What do you think? |
… biojava-core and dependencies
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This last PR solves other issues of the same type in the core module and dependencies. |
This PR is an experiment to fix the rule Sonar s1319 "Declarations should use Java collection interfaces such as 'List' rather than specific implementation classes such as 'LinkedList'". Note that the scope of this PR is intentionally limited to the biojava-core module and some of its dependencies.
It's a bit complicated on the Biojava project because the Sonar rule raises a few false positives and the project makes extensive use of interface implementations and sometimes methods that are implementation-specific. But after a few manual adjustments to standardise the modifications in the dependent modules, the tests pass with the exception of the TestCrystallographicMetadata.test1zna:92 test in the biojava-integrationtest module. I'm not convinced that the error stems from these modifications, but I'll let you be the judge.
Below is a link to the sonar page describing the problem https://rules.sonarsource.com/java/tag/bad-practice/RSPEC-1319/.
Indepth has fixed 102 issues that would have taken about 2 days to correct manually.