Change gatkDoc and gatkTabComplete build tasks to include Picard. #3683
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Fixes #3627. |
Codecov Report
@@ Coverage Diff @@
## master #3683 +/- ##
===============================================
+ Coverage 79.402% 79.408% +0.007%
- Complexity 17369 17370 +1
===============================================
Files 1139 1139
Lines 62690 62681 -9
Branches 9527 9526 -1
===============================================
- Hits 49777 49774 -3
+ Misses 9112 9109 -3
+ Partials 3801 3798 -3
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magicDGS
reviewed
Oct 11, 2017
build.gradle
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| @@ -112,7 +113,8 @@ dependencies { | |||
| testCompile(javadocJDKFiles) | |||
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| compile 'org.broadinstitute:barclay:1.2.1' | |||
| compile 'com.github.broadinstitute:picard:2.12.2' | |||
| compile 'com.github.broadinstitute:picard:' + picardVersion | |||
| compileOnly 'com.github.broadinstitute:picard:' + picardVersion + ':sources' | |||
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I'd add a new configuration for this, to being able to include more in the future:
configurations {
## requires the ":sources" marker
docgen {
transitive false
}
}
..
dependencies {
..
docgen 'com.github.broadinstitute:picard:' + picardVersion + ':sources'
..
}
build.gradle
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| @@ -481,7 +496,7 @@ task gatkDoc(type: Javadoc, dependsOn: classes) { | |||
| into gatkDocDir | |||
| } | |||
| } | |||
| source = sourceSets.main.allJava | |||
| source = sourceSets.main.allJava + getPicardJavaSourceFiles(picardVersion) | |||
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I guess that getPicardJavaSourceFiles can be removed and being simplify the gatkDoc/gatkTabComplete by using:
final docSources = configurations.docgen.collect { zipTree(it) }
source = files(docSources) + sourceSets.main.allJava
include '**/*.java'This will also help to include new dependencies in the code and not only Picard....
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@magicDGS - thanks - I'll try that. Although I don't imagine we'll add any more source sets like this, your suggestion seems cleaner all around.
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@lbergelson You want to have a look at this one before merge? |
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@droazen Do we want merged javadoc as well (I included that here) ? |
lbergelson
reviewed
Oct 13, 2017
build.gradle
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| compile.exclude group: 'com.esotericsoftware.kryo' | ||
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| externalSourceConfiguration { | ||
| // External sources we need for doc and tab completion generation tasks )i.e., Picard sources) |
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typo ) is facing the wrong way
lbergelson
approved these changes
Oct 13, 2017
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@magicDGS Thanks for that suggestion. |
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