Closed tomwhite closed 5 years ago
did you only open this to get the tests? is this a serious candidate for merging? in the current state, of course that would not be possible...
Merging #1269 into master will decrease coverage by
1.843%
. The diff coverage isn/a
.
@@ Coverage Diff @@
## master #1269 +/- ##
===============================================
- Coverage 69.358% 67.515% -1.843%
+ Complexity 8302 8151 -151
===============================================
Files 555 558 +3
Lines 33118 33397 +279
Branches 5572 5632 +60
===============================================
- Hits 22970 22548 -422
- Misses 7886 8665 +779
+ Partials 2262 2184 -78
Impacted Files | Coverage Δ | Complexity Δ | |
---|---|---|---|
...ain/java/htsjdk/samtools/util/MergingIterator.java | 85.714% <ø> (ø) |
11 <0> (ø) |
:arrow_down: |
.../main/java/htsjdk/samtools/sra/ReferenceCache.java | 0% <0%> (-81.818%) |
0% <0%> (-4%) |
|
src/main/java/htsjdk/samtools/sra/SRAUtils.java | 0% <0%> (-81.818%) |
0% <0%> (-3%) |
|
src/main/java/htsjdk/samtools/SRAIndex.java | 0% <0%> (-77.273%) |
0% <0%> (-18%) |
|
src/main/java/htsjdk/samtools/SRAIterator.java | 0% <0%> (-72.857%) |
0% <0%> (-18%) |
|
...java/htsjdk/samtools/sra/SRAAlignmentIterator.java | 0% <0%> (-72%) |
0% <0%> (-15%) |
|
...c/main/java/htsjdk/samtools/sra/SRALazyRecord.java | 0% <0%> (-71.591%) |
0% <0%> (-130%) |
|
src/main/java/htsjdk/samtools/BinList.java | 0% <0%> (-70.588%) |
0% <0%> (-2%) |
|
...va/htsjdk/samtools/sra/SRAUnalignmentIterator.java | 0% <0%> (-65.574%) |
0% <0%> (-14%) |
|
...va/htsjdk/samtools/sra/SRAIndexedSequenceFile.java | 0% <0%> (-64.865%) |
0% <0%> (-7%) |
|
... and 54 more |
@yfarjoun the goal here is to check we can build and run htsjdk tests with Java 11. The source and target Java versions are not changed - they are still Java 8 - so this is just to ensure that we can use a Java 11 compiler and runtime with the current htsjdk source. It does not replace the Java 8-based build.
There were a few things I had to change to get this to work:
This is a serious candidate for merging, since none of these changes interfere with the current Java 8 build. I also added a openjdk11
target to Travis so that every change is checked on Java 11. This will mean that htsjdk doesn't regress in its ability to be built with and run on Java 11.
Wow, those two javadoc comments were the issue? I assumed it would be much worse than that. Bizarre. That shouldn't cause a javadoc null point exception...
@tomwhite This still had some issues with it, I pushed lb_java11 which should resolve them. Would you like to incorporate those changes into yours or should I create a new pr?
@lbergelson thanks for looking at this. I had a look at your branch, but it wasn't clear how the changes related to Java 11. That said, please go ahead and merge as you see fit.
@tomwhite They fix problems introduce by moving to gradle 5. It broke the maven
publication so I switched it to the newer maven-publish
which seemed to fix the problem. I bumped a few versions of things and did a little cleanup to remove newly deprecated stuff as well.
closing this since I've taken it over in #1291
Description
Runs htsjdk's unit tests on Java 11.
Checklist