[CANNOLI-215] Add support for Scala 2.12 in build and release scripts

cli/src/main/scala/org/bdgenomics/cannoli/cli/SampleReads.scala

@@ -20,9 +20,11 @@ package org.bdgenomics.cannoli.cli
 import grizzled.slf4j.Logging
 import htsjdk.samtools.ValidationStringency
 import org.apache.spark.SparkContext
+import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.fragment.FragmentDataset
+import org.bdgenomics.formats.avro.Fragment
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
@@ -70,7 +72,7 @@ class SampleReads(protected val args: SampleReadsArgs) extends BDGSparkCommand[S
 
     info("Sampling fraction %f with seed %d".format(args.fraction, args.seed))
     fragments
-      .transform(_.sample(withReplacement = false, args.fraction, args.seed))
+      .transform((rdd: RDD[Fragment]) => rdd.sample(withReplacement = false, args.fraction, args.seed))
       .save(args.outputPath)
   }
 }

scripts/move_to_scala_2.11.sh

@@ -11,11 +11,7 @@ then
     exit 1
 fi
 
-find . -name "pom.xml" -exec sed -e "s/2.10.6/2.11.8/g" \
-    -e "s/2.10/2.11/g" \
+find . -name "pom.xml" -exec sed -e "s/2.12.8/2.11.12/g" \
+    -e "s/2.12/2.11/g" \
     -i.2.11.bak '{}' \;
-# keep parquet-scala at parquet-scala_2.10
-find . -name "pom.xml" -exec sed -e "s/parquet-scala_2.11/parquet-scala_2.10/g" -i.2.11.2.bak '{}' \;
-# keep maven-javadoc-plugin at version 2.10.4
-find . -name "pom.xml" -exec sed -e "s/2.11.4/2.10.4/g" -i.2.11.3.bak '{}' \;
 find . -name "*.2.11.*bak" -exec rm -f {} \;

scripts/move_to_scala_2.12.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+set +x
+
+grep "<scala\.version>" pom.xml | grep -q 2.12
+if [[ $? == 0 ]];
+then
+    echo "Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name)."
+    echo "Cowardly refusing to move to Scala 2.12 a second time..."
+
+    exit 1
+fi
+
+find . -name "pom.xml" -exec sed -e "s/2.11.12/2.12.8/g" \
+    -e "s/2.11/2.12/g" \
+    -i.2.12.bak '{}' \;
+find . -name "*.2.12.*bak" -exec rm -f {} \;

scripts/release/release.sh

@@ -44,6 +44,30 @@ if [ $? != 0 ]; then
   exit 1
 fi
 
+git checkout master
+
+# do spark 2, scala 2.12 release
+git checkout -b maint_spark2_2.12-${release} ${branch}
+
+./scripts/move_to_scala_2.12.sh
+git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.12 release."
+
+mvn --batch-mode \
+  -P distribution \
+  -Dresume=false \
+  -Dtag=cannoli-parent-spark2_2.12-${release} \
+  -DreleaseVersion=${release} \
+  -DdevelopmentVersion=${devel} \
+  -DbranchName=cannoli-spark2_2.12-${release} \
+  release:clean \
+  release:prepare \
+  release:perform
+
+if [ $? != 0 ]; then
+  echo "Releasing Spark 2, Scala 2.12 version failed."
+  exit 1
+fi
+
 if [ $branch = "master" ]; then
   # if original branch was master, update versions on original branch
   git checkout ${branch}