upgrade sbt, plugin

hammerlab · Jan 13, 2018 · e52e0a8 · e52e0a8
1 parent 4fc7711
commit e52e0a8
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Showing 26 changed files with 24 additions and 26 deletions.
diff --git a/Hadoop-BAM b/Hadoop-BAM
diff --git a/adam-core b/adam-core
diff --git a/args4s b/args4s
diff --git a/cli b/cli
diff --git a/coverage-depth b/coverage-depth
diff --git a/guacamole b/guacamole
diff --git a/io b/io
diff --git a/iterator b/iterator
diff --git a/loci b/loci
diff --git a/magic-rdds b/magic-rdds
diff --git a/math b/math
diff --git a/path-utils b/path-utils
diff --git a/project/build.properties b/project/build.properties
diff --git a/project/plugins.sbt b/project/plugins.sbt
diff --git a/reads b/reads
diff --git a/readsets b/readsets
diff --git a/reference b/reference
diff --git a/sbt-parent b/sbt-parent
diff --git a/shapeless b/shapeless
diff --git a/spark-bam b/spark-bam
diff --git a/spark-tests b/spark-tests
diff --git a/spark-util b/spark-util
diff --git a/string-utils b/string-utils
diff --git a/test-utils b/test-utils
diff --git a/utils b/utils
diff --git a/utils-cli b/utils-cli
+8 −13		build.sbt
+1 −1		project/build.properties
+1 −1		project/plugins.sbt
+2 −2		build.sbt
+1 −1		project/build.properties
+1 −1		project/plugins.sbt
+25 −40		build.sbt
+1 −1		project/build.properties
+1 −2		project/plugins.sbt
+1 −1		src/main/scala/org/hammerlab/guacamole/Main.scala
+5 −3		src/main/scala/org/hammerlab/guacamole/commands/GuacCommand.scala
+1 −1		src/main/scala/org/hammerlab/guacamole/commands/PartitionLoci.scala
+1 −1		src/main/scala/org/hammerlab/guacamole/commands/PartitionReads.scala
+1 −1		src/main/scala/org/hammerlab/guacamole/commands/SomaticJointCaller.scala
+1 −1		src/main/scala/org/hammerlab/guacamole/commands/SomaticStandardCaller.scala
+2 −2		src/main/scala/org/hammerlab/guacamole/commands/VAFHistogram.scala
+1 −1		src/main/scala/org/hammerlab/guacamole/commands/VariantSupport.scala
+1 −1		src/main/scala/org/hammerlab/guacamole/readsets/args/GermlineCallerArgs.scala
+1 −1		src/main/scala/org/hammerlab/guacamole/variants/GenotypeOutputArgs.scala
+2 −2		src/main/scala/org/hammerlab/guacamole/variants/GenotypeOutputCaller.scala
+1 −1		src/test/scala/org/hammerlab/guacamole/main/GeneratePartialFasta.scala
+2 −0		src/test/scala/org/hammerlab/guacamole/windowing/SlidingWindowSuite.scala
+5 −4		build.sbt
+1 −1		project/build.properties
+1 −1		project/plugins.sbt
+3 −1		src/test/scala/org/hammerlab/genomics/reference/PositionSerializationTest.scala
+16 −0		.travis.yml
+28 −135		README.md
+34 −0		assembly/README.md
+3 −3		assembly/src/main/scala/org/hammerlab/sbt/plugin/Assembly.scala
+15 −0		base/README.md
+16 −29		base/src/main/scala/org/hammerlab/sbt/plugin/HammerLab.scala
+31 −0		base/src/sbt-test/base/test-deps/build.sbt
+5 −0		base/src/sbt-test/base/test-deps/project/plugins.sbt
+1 −0		base/src/sbt-test/base/test-deps/test
+91 −58		build.sbt
+54 −0		deps/README.md
+13 −9		deps/src/main/scala/org/hammerlab/sbt/plugin/Deps.scala
+15 −0		deps/src/sbt-test/deps/dsl/build.sbt
+5 −0		deps/src/sbt-test/deps/dsl/project/plugins.sbt
+1 −0		deps/src/sbt-test/deps/dsl/test
+31 −0		github/README.md
+73 −0		github/src/main/scala/org/hammerlab/sbt/plugin/GitHub.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/Util.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/Artifact.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/Classifier.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/Configuration.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/Configurations.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/CrossVersion.scala
+5 −11		lib/src/main/scala/org/hammerlab/sbt/deps/Dep.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/Group.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/GroupArtifact.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/Scope.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/Version.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/deps/VersionsMap.scala
+0 −0		lib/src/main/scala/org/hammerlab/sbt/plugin/Plugin.scala
+16 −0		maven/README.md
+47 −0		maven/src/main/scala/org/hammerlab/sbt/plugin/Maven.scala
+9 −0		parent/README.md
+29 −29		parent/src/main/scala/org/hammerlab/sbt/plugin/Parent.scala
+34 −0		parent/src/sbt-test/parent/settings/build.sbt
+32 −0		parent/src/sbt-test/parent/settings/pom.xml
+5 −0		parent/src/sbt-test/parent/settings/project/plugins.sbt
+1 −0		parent/src/sbt-test/parent/settings/test
+16 −0		project/Scripted.scala
+3 −1		project/plugins.sbt
+1 −0		project/scripted.sbt
+29 −0		root/README.md
+31 −10		root/src/main/scala/org/hammerlab/sbt/plugin/Root.scala
+28 −0		root/src/sbt-test/root/repo/build.sbt
+5 −0		root/src/sbt-test/root/repo/project/plugins.sbt
+1 −0		root/src/sbt-test/root/repo/test
+16 −0		scala/README.md
+10 −25		scala/src/main/scala/org/hammerlab/sbt/plugin/Scala.scala
+1 −1		scripts/create-scala-project
+23 −0		spark/README.md
+7 −9		spark/src/main/scala/org/hammerlab/sbt/plugin/Spark.scala
+0 −47		src/main/scala/org/hammerlab/sbt/plugin/Maven.scala
+0 −30		src/main/scala/org/hammerlab/sbt/plugin/Scalariform.scala
+18 −0		test/README.md
+6 −7		test/src/main/scala/org/hammerlab/sbt/plugin/Test.scala
+17 −0		travis/README.md
+0 −0		travis/src/main/scala/org/hammerlab/sbt/plugin/Travis.scala
+53 −0		versions/README.md
+20 −23		versions/src/main/scala/org/hammerlab/sbt/plugin/Versions.scala
+3 −2		build.sbt
+1 −1		project/build.properties
+1 −1		project/plugins.sbt
+3 −1		src/test/scala/org/hammerlab/genomics/bases/BasesSerializerTest.scala