[HLS-351] Release prep

.gitignore

@@ -1,12 +1,30 @@
+# Java targets
 target
 core/target
 project/target
-.idea
-*.swp
-*.swo
-adam.log
+
+# Distribution / packaging
+build/
+dist/
+maven-repo/
+*.egg-info/
+
+# Mac
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
 **/__pycache__
 *.pyc
-.DS_Store
+
+# Sphinx documentation
 docs/build
+
+# Editor files
+*.swp
+*.swo
+*.iml
+.idea
+
+# Logs
+adam.log
 unit-tests.log

build.sbt

@@ -6,9 +6,9 @@ val sparkVersion = "2.4.3"
 val scalaMajorMinor = "2.11"
 
 ThisBuild / scalaVersion := s"$scalaMajorMinor.12"
-ThisBuild / version := "0.1.0-SNAPSHOT"
 ThisBuild / organization := "io.projectglow"
 ThisBuild / scalastyleConfig := baseDirectory.value / "scalastyle-config.xml"
+ThisBuild / publish / skip := true
 
 ThisBuild / organizationName := "The Glow Authors"
 ThisBuild / startYear := Some(2019)
@@ -61,48 +61,78 @@ lazy val commonSettings = Seq(
       MergeStrategy.first
   },
   scalacOptions += "-target:jvm-1.8"
-  )
+)
+
+lazy val dependencies = Seq(
+  "org.apache.spark" %% "spark-catalyst" % sparkVersion % "provided",
+  "org.apache.spark" %% "spark-core" % sparkVersion % "provided",
+  "org.apache.spark" %% "spark-mllib" % sparkVersion % "provided",
+  "org.apache.spark" %% "spark-sql" % sparkVersion % "provided",
+  "org.seqdoop" % "hadoop-bam" % "7.9.1",
+  "log4j" % "log4j" % "1.2.17",
+  "org.slf4j" % "slf4j-api" % "1.7.16",
+  "org.slf4j" % "slf4j-log4j12" % "1.7.16",
+  "org.jdbi" % "jdbi" % "2.63.1",
+  "com.typesafe.scala-logging" %% "scala-logging-slf4j" % "2.1.2",
+  // Exclude extraneous GATK dependencies
+  ("org.broadinstitute" % "gatk" % "4.0.11.0")
+    .exclude("biz.k11i", "xgboost-predictor")
+    .exclude("com.esotericsoftware", "kryo")
+    .exclude("com.esotericsoftware", "reflectasm")
+    .exclude("com.github.jsr203hadoop", "jsr203hadoop")
+    .exclude("com.google.cloud", "google-cloud-nio")
+    .exclude("com.google.cloud.bigdataoss", "gcs-connector")
+    .exclude("com.intel", "genomicsdb")
+    .exclude("com.intel.gkl", "gkl")
+    .exclude("com.opencsv", "opencsv")
+    .exclude("commons-io", "commons-io")
+    .exclude("gov.nist.math.jama", "gov.nist.math.jama")
+    .exclude("it.unimi.dsi", "fastutil")
+    .exclude("org.aeonbits.owner", "owner")
+    .exclude("org.apache.commons", "commons-lang3")
+    .exclude("org.apache.commons", "commons-math3")
+    .exclude("org.apache.commons", "commons-collections4")
+    .exclude("org.apache.commons", "commons-vfs2")
+    .exclude("org.apache.hadoop", "hadoop-client")
+    .exclude("org.apache.spark", s"spark-mllib_$scalaMajorMinor")
+    .exclude("org.bdgenomics.adam", s"adam-core-spark2_$scalaMajorMinor")
+    .exclude("org.broadinstitute", "barclay")
+    .exclude("org.broadinstitute", "hdf5-java-bindings")
+    .exclude("org.broadinstitute", "gatk-native-bindings")
+    .exclude("org.broadinstitute", "gatk-bwamem-jni")
+    .exclude("org.broadinstitute", "gatk-fermilite-jni")
+    .exclude("org.jgrapht", "jgrapht-core")
+    .exclude("org.objenesis", "objenesis")
+    .exclude("org.ojalgo", "ojalgo")
+    .exclude("org.ojalgo", "ojalgo-commons-math3")
+    .exclude("org.reflections", "reflections")
+    .exclude("org.seqdoop", "hadoop-bam")
+    .exclude("org.xerial", "sqlite-jdbc"),
+  // Test dependencies
+  "org.scalatest" %% "scalatest" % "3.0.3" % "test",
+  "org.scalacheck" %% "scalacheck" % "1.12.5" % "test",
+  "org.mockito" % "mockito-all" % "1.9.5" % "test",
+  "org.apache.spark" %% "spark-core" % sparkVersion % "test" classifier "tests",
+  "org.apache.spark" %% "spark-catalyst" % sparkVersion % "test" classifier "tests",
+  "org.apache.spark" %% "spark-sql" % sparkVersion % "test" classifier "tests",
+  "org.bdgenomics.adam" %% "adam-apis-spark2" % "0.28.0" % "test",
+  "org.bdgenomics.bdg-formats" % "bdg-formats" % "0.11.3" % "test",
+  "org.xerial" % "sqlite-jdbc" % "3.20.1" % "test"
+).map(_.exclude("com.google.code.findbugs", "jsr305"))
 
 lazy val core = (project in file("core"))
   .settings(
     commonSettings,
     name := "glow",
-    libraryDependencies ++= Seq(
-      "org.apache.spark" %% "spark-catalyst" % sparkVersion % "provided",
-      "org.apache.spark" %% "spark-core" % sparkVersion % "provided",
-      "org.apache.spark" %% "spark-mllib" % sparkVersion % "provided",
-      "org.apache.spark" %% "spark-sql" % sparkVersion % "provided",
-      "com.github.samtools" % "htsjdk" % "2.20.0",
-      "com.fasterxml.jackson.module" %% "jackson-module-scala" % "2.9.9",
-      "org.seqdoop" % "hadoop-bam" % "7.9.1",
-      "log4j" % "log4j" % "1.2.17",
-      "org.slf4j" % "slf4j-api" % "1.7.16",
-      "org.slf4j" % "slf4j-log4j12" % "1.7.16",
-      "org.jdbi" % "jdbi" % "2.63.1",
-      "com.typesafe.scala-logging" %% "scala-logging-slf4j" % "2.1.2",
-      // Exclude extraneous GATK dependencies
-      ("org.broadinstitute" % "gatk" % "4.0.11.0")
-        .exclude("biz.k11i", "xgboost-predictor")
-        .exclude("com.google.cloud.bigdataoss", "gcs-connector")
-        .exclude("com.intel", "genomicsdb")
-        .exclude("org.apache.spark", s"spark-mllib_$scalaMajorMinor")
-        .exclude("org.bdgenomics.adam", s"adam-core-spark2_$scalaMajorMinor")
-        .exclude("com.google.cloud", "google-cloud-nio"),
-      // Test dependencies
-      "org.scalatest" %% "scalatest" % "3.0.3" % "test",
-      "org.scalacheck" %% "scalacheck" % "1.12.5" % "test",
-      "org.mockito" % "mockito-all" % "1.9.5" % "test",
-      "org.apache.spark" %% "spark-core" % sparkVersion % "test" classifier "tests",
-      "org.apache.spark" %% "spark-catalyst" % sparkVersion % "test" classifier "tests",
-      "org.apache.spark" %% "spark-sql" % sparkVersion % "test" classifier "tests",
-      "org.bdgenomics.adam" %% "adam-apis-spark2" % "0.28.0" % "test",
-      "org.bdgenomics.bdg-formats" % "bdg-formats" % "0.11.3" % "test"
-    ),
+    publish / skip := false,
+    bintrayRepository := "glow",
+    libraryDependencies ++= dependencies,
     // Fix versions of libraries that are depended on multiple times
     dependencyOverrides ++= Seq(
       "org.apache.hadoop" % "hadoop-client" % "2.7.3",
       "io.netty" % "netty" % "3.9.9.Final",
-      "io.netty" % "netty-all" % "4.1.17.Final"
+      "io.netty" % "netty-all" % "4.1.17.Final",
+      "com.github.samtools" % "htsjdk" % "2.20.1"
     )
   )
 
@@ -127,33 +157,37 @@ lazy val python =
           "SPARK_HOME" -> (ThisBuild / baseDirectory).value.absolutePath
         ).!
         require(ret == 0, "Python tests failed")
-      }
+      },
+      publish / skip := true
     )
 
-// Uncomment the following for publishing to Sonatype.
-// See https://www.scala-sbt.org/1.x/docs/Using-Sonatype.html for more detail.
+// Publish to Bintray
+ThisBuild / description := "An open-source toolkit for large-scale genomic analysis"
+ThisBuild / homepage := Some(url("https://projectglow.io"))
+ThisBuild / scmInfo := Some(
+  ScmInfo(
+    url("https://github.com/projectglow/glow"),
+    "scm:[email protected]:projectglow/glow.git"
+  )
+)
+ThisBuild / pomIncludeRepository := { _ =>
+  false
+}
+ThisBuild / publishMavenStyle := true
+
+ThisBuild / bintrayOrganization := Some("projectglow")
+ThisBuild / bintrayRepository := "glow"
 
-// ThisBuild / description := "Some descripiton about your project."
-// ThisBuild / licenses    := List("Apache 2" -> new URL("http://www.apache.org/licenses/LICENSE-2.0.txt"))
-// ThisBuild / homepage    := Some(url("https://github.com/example/project"))
-// ThisBuild / scmInfo := Some(
-//   ScmInfo(
-//     url("https://github.com/your-account/your-project"),
-//     "scm:[email protected]:your-account/your-project.git"
-//   )
-// )
-// ThisBuild / developers := List(
-//   Developer(
-//     id    = "Your identifier",
-//     name  = "Your Name",
-//     email = "your@email",
-//     url   = url("http://your.url")
-//   )
-// )
-// ThisBuild / pomIncludeRepository := { _ => false }
-// ThisBuild / publishTo := {
-//   val nexus = "https://oss.sonatype.org/"
-//   if (isSnapshot.value) Some("snapshots" at nexus + "content/repositories/snapshots")
-//   else Some("releases" at nexus + "service/local/staging/deploy/maven2")
-// }
-// ThisBuild / publishMavenStyle := true
+import ReleaseTransformations._
+
+releaseProcess := Seq[ReleaseStep](
+  checkSnapshotDependencies,
+  inquireVersions,
+  runTest,
+  setReleaseVersion,
+  commitReleaseVersion,
+  tagRelease,
+  publishArtifacts,
+  setNextVersion,
+  commitNextVersion
+)

core/src/main/scala/io/projectglow/bgen/BgenSchemaInferrer.scala

@@ -17,7 +17,7 @@
 package io.projectglow.bgen
 
 import com.google.common.io.LittleEndianDataInputStream
-import org.apache.hadoop.fs.FileStatus
+import org.apache.hadoop.fs.{FileStatus, Path}
 import org.apache.spark.sql.SparkSession
 import org.apache.spark.sql.types.StructType
 
@@ -45,19 +45,20 @@ object BgenSchemaInferrer {
 
     val serializableConf = new SerializableConfiguration(spark.sparkContext.hadoopConfiguration)
     val ignoreExtension = options.get(BgenFileFormat.IGNORE_EXTENSION_KEY).exists(_.toBoolean)
-    val bgenFiles =
+    val bgenPaths =
       files.filter { fs =>
         fs.getLen > 0 && (fs
           .getPath
           .toString
           .endsWith(BgenFileFormat.BGEN_SUFFIX) || ignoreExtension)
-      }
+      }.map(_.getPath.toString)
     val hasSampleIds = spark
       .sparkContext
-      .parallelize(bgenFiles)
-      .map { fs =>
-        val hadoopFs = fs.getPath.getFileSystem(serializableConf.value)
-        WithUtils.withCloseable(hadoopFs.open(fs.getPath)) { stream =>
+      .parallelize(bgenPaths)
+      .map { path =>
+        val hPath = new Path(path)
+        val hadoopFs = hPath.getFileSystem(serializableConf.value)
+        WithUtils.withCloseable(hadoopFs.open(hPath)) { stream =>
           val littleEndianDataInputStream = new LittleEndianDataInputStream(stream)
           new BgenHeaderReader(littleEndianDataInputStream)
             .readHeader(None)

core/src/main/scala/io/projectglow/vcf/VCFFileFormat.scala

@@ -457,13 +457,15 @@ private[vcf] object SchemaDelegate {
       files: Seq[FileStatus]): (Seq[VCFInfoHeaderLine], Seq[VCFFormatHeaderLine]) = {
     val serializableConf = new SerializableConfiguration(spark.sessionState.newHadoopConf())
 
+    val filePaths = files.map(_.getPath.toString)
     spark
       .sparkContext
-      .parallelize(files.map(_.getPath.toString))
+      .parallelize(filePaths)
       .map { path =>
         val (header, _) = VCFFileFormat.createVCFCodec(path, serializableConf.value)
-
-        (header.getInfoHeaderLines.asScala.toSeq, header.getFormatHeaderLines.asScala.toSeq)
+        val infoHeaderLines = header.getInfoHeaderLines.asScala.toSet
+        val formatHeaderLines = header.getFormatHeaderLines.asScala.toSet
+        (infoHeaderLines, formatHeaderLines)
       }
       .collect()
       .foldLeft((Seq.empty[VCFInfoHeaderLine], Seq.empty[VCFFormatHeaderLine])) {

core/src/test/resources/log4j.properties

@@ -9,3 +9,4 @@ log4j.appender.file.File=unit-tests.log
 log4j.logger.akka=ERROR
 log4j.logger.Remoting=ERROR
 log4j.logger.org.eclipse.jetty=ERROR
+log4j.logger.org.apache.hadoop=WARN

core/src/test/scala/io/projectglow/sql/GlowBaseTest.scala

@@ -37,7 +37,6 @@ abstract class GlowBaseTest
   override protected def sparkConf: SparkConf = {
     super
       .sparkConf
-      .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
       .set("spark.driver.maxResultSize", "0")
       .set("spark.kryo.registrator", "org.broadinstitute.hellbender.engine.spark.GATKRegistrator")
       .set("spark.kryoserializer.buffer.max", "2047m")

project/plugins.sbt

@@ -1,5 +1,7 @@
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.14.10")
+addSbtPlugin("com.github.gseitz" % "sbt-release" % "1.0.11")
 addSbtPlugin("net.virtual-void" % "sbt-dependency-graph" % "0.9.2")
+addSbtPlugin("org.foundweekends" % "sbt-bintray" % "0.5.4")
 addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.0.0")
 addSbtPlugin("org.scalastyle" %% "scalastyle-sbt-plugin" % "1.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.5.1")

python/README.rst

@@ -0,0 +1,16 @@
+=======================================================
+An open-source toolkit for large-scale genomic analysis
+=======================================================
+
+|circle-ci|
+
+.. |circle-ci| image:: https://circleci.com/gh/projectglow/glow.svg?style=svg&circle-token=7511f70b2c810a18e88b5c537b0410e82db8617d
+    :target: https://circleci.com/gh/projectglow/glow
+
+Glow is an open-source toolkit for working with genomic data at biobank-scale and beyond. The toolkit is natively built
+on Apache Spark, the leading unified engine for big data processing and machine learning, enabling the scale of the
+cloud for genomics workflows.
+
+`Read the docs`_ to start using Glow.
+
+.. _Read the docs: https://glow.readthedocs.io

python/environment.yml

@@ -5,4 +5,6 @@ dependencies:
   - pip
   - pip:
     - pyspark==2.4.2
+    - setuptools==41.2.0 # Python packaging
     - typeguard==2.5.0
+    - twine==2.0.0 # Pypi publishing

python/setup.py

@@ -0,0 +1,20 @@
+from setuptools import setup
+
+setup(
+    name='glow.py',
+    version='0.1.0',
+    packages=['glow'],
+    install_requires=[
+        'typeguard==2.5.0',
+    ],
+    author='The Glow Authors',
+    description='An open-source toolkit for large-scale genomic analysis',
+    long_description=open('README.rst').read(),
+    long_description_content_type='text/x-rst',
+    license='Apache License 2.0',
+    classifiers=[
+        'Intended Audience :: Developers',
+        'Programming Language :: Python :: 3.7',
+    ],
+    url='https://projectglow.io'
+)

version.sbt

@@ -0,0 +1 @@
+version in ThisBuild := "0.1.0"