diff --git a/build.sbt b/build.sbt index c055593..187dc70 100644 --- a/build.sbt +++ b/build.sbt @@ -1,19 +1,20 @@ group("org.hammerlab.genomics") name := "loci" - -github.repo("genomic-loci") +v"2.0.3" addSparkDeps +import genomics.reference + dep( - args4j, - args4s % "1.3.1", - htsjdk, - iterators % "2.0.0", - paths % "1.4.0", - reference % "1.4.2" + testtest, - scalautils, - spark_util % "2.0.2", + args4j, + args4s % "1.3.1", + htsjdk, + iterators % "2.1.0", + paths % "1.5.0", + reference % "1.4.3" + testtest, + scalautils, + spark_util % "2.0.3", string_utils % "1.2.0" ) @@ -28,3 +29,5 @@ shadeRenames += "com.google.thirdparty.**" → "org.hammerlab.guava.@1" publishThinShadedJar publishTestJar + +github.repo("genomic-loci") diff --git a/project/build.properties b/project/build.properties index 8b697bb..31334bb 100644 --- a/project/build.properties +++ b/project/build.properties @@ -1 +1 @@ -sbt.version=1.1.0 +sbt.version=1.1.1 diff --git a/project/plugins.sbt b/project/plugins.sbt index 0003a9d..93d8288 100644 --- a/project/plugins.sbt +++ b/project/plugins.sbt @@ -1 +1 @@ -addSbtPlugin("org.hammerlab.sbt" % "base" % "4.2.0") +addSbtPlugin("org.hammerlab.sbt" % "base" % "4.4.2") diff --git a/src/test/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIteratorSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIteratorSuite.scala index 3a1c178..50041c2 100644 --- a/src/test/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIteratorSuite.scala +++ b/src/test/scala/org/hammerlab/genomics/loci/iterator/SkippableLociIteratorSuite.scala @@ -1,9 +1,9 @@ package org.hammerlab.genomics.loci.iterator +import hammerlab.test.Suite import org.hammerlab.genomics.reference.test.IntervalsUtil import org.hammerlab.genomics.reference.test.LociConversions._ import org.hammerlab.genomics.reference.{ Interval, Locus } -import org.hammerlab.test.Suite class SkippableLociIteratorSuite extends Suite diff --git a/src/test/scala/org/hammerlab/genomics/loci/map/ContigSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/map/ContigSuite.scala index 11d45f8..4a6fb20 100644 --- a/src/test/scala/org/hammerlab/genomics/loci/map/ContigSuite.scala +++ b/src/test/scala/org/hammerlab/genomics/loci/map/ContigSuite.scala @@ -1,10 +1,10 @@ package org.hammerlab.genomics.loci.map import com.google.common.collect.{ ImmutableRangeMap, Range } +import hammerlab.test.Suite import org.hammerlab.genomics.reference.Locus -import org.hammerlab.genomics.reference.test.{ ClearContigNames, ContigNameConversions } import org.hammerlab.genomics.reference.test.LociConversions._ -import org.hammerlab.test.Suite +import org.hammerlab.genomics.reference.test.{ ClearContigNames, ContigNameConversions } class ContigSuite extends Suite diff --git a/src/test/scala/org/hammerlab/genomics/loci/map/LociMapSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/map/LociMapSuite.scala index 7cb20db..363b257 100644 --- a/src/test/scala/org/hammerlab/genomics/loci/map/LociMapSuite.scala +++ b/src/test/scala/org/hammerlab/genomics/loci/map/LociMapSuite.scala @@ -1,10 +1,10 @@ package org.hammerlab.genomics.loci.map +import hammerlab.test.Suite import org.hammerlab.genomics.loci.set.test.LociSetUtil import org.hammerlab.genomics.reference.Interval import org.hammerlab.genomics.reference.test.LociConversions.intToLocus import org.hammerlab.genomics.reference.test.{ ClearContigNames, ContigNameConversions } -import org.hammerlab.test.Suite class LociMapSuite extends Suite diff --git a/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala index 830fd0b..b1e5eb5 100644 --- a/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala +++ b/src/test/scala/org/hammerlab/genomics/loci/parsing/ParsedLociSuite.scala @@ -1,9 +1,9 @@ package org.hammerlab.genomics.loci.parsing +import hammerlab.test.Suite import org.hammerlab.genomics.loci.set.test.LociSetUtil import org.hammerlab.genomics.reference.test.ClearContigNames import org.hammerlab.genomics.reference.test.LociConversions.intToLocus -import org.hammerlab.test.Suite import org.hammerlab.test.resources.File class ParsedLociSuite diff --git a/src/test/scala/org/hammerlab/genomics/loci/set/LociIteratorSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/set/LociIteratorSuite.scala index 322127a..0459d91 100644 --- a/src/test/scala/org/hammerlab/genomics/loci/set/LociIteratorSuite.scala +++ b/src/test/scala/org/hammerlab/genomics/loci/set/LociIteratorSuite.scala @@ -1,9 +1,9 @@ package org.hammerlab.genomics.loci.set +import hammerlab.test.Suite import org.hammerlab.genomics.loci.iterator.LociIterator import org.hammerlab.genomics.reference.Interval import org.hammerlab.genomics.reference.test.LociConversions._ -import org.hammerlab.test.Suite class LociIteratorSuite extends Suite { diff --git a/src/test/scala/org/hammerlab/genomics/loci/set/SerializerSuite.scala b/src/test/scala/org/hammerlab/genomics/loci/set/SerializerSuite.scala index 0b86377..83b5ba8 100644 --- a/src/test/scala/org/hammerlab/genomics/loci/set/SerializerSuite.scala +++ b/src/test/scala/org/hammerlab/genomics/loci/set/SerializerSuite.scala @@ -109,7 +109,7 @@ object Helpers { /** * Isolate this method in its own object because otherwise ClosureCleaner will attempt to Java-serialize the enclosing - * [[org.hammerlab.test.Suite]], which errors due to a non-serializable [[org.scalatest.Assertions]].AssertionsHelper + * [[hammerlab.test.Suite]], which errors due to a non-serializable [[org.scalatest.Assertions]].AssertionsHelper * member inherited from [[org.scalatest.FunSuite]]. See https://github.com/scalatest/scalatest/issues/1013. */ def mapTask(implicit factory: Factory) =