From c2f3bdd0d6c3b946a566c138e0a84fe00a3bbb00 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Mon, 10 Jul 2017 21:01:15 +0000
Subject: [PATCH 1/8] upgrade plugin

---
 build.sbt           | 8 ++++----
 project/plugins.sbt | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/build.sbt b/build.sbt
index 95da9be..d0e7ea6 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,9 +1,9 @@
 name := "spark-commands"
-version := "1.0.4"
+version := "1.0.5-SNAPSHOT"
 
-providedDeps += spark.value
+providedDeps += spark
 
 deps ++= Seq(
-  libs.value('bdg_utils_cli),
-  libs.value('slf4j)
+  bdg_utils_cli % "0.2.15",
+  slf4j
 )
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 1dd7897..ba64db2 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "2.0.1")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.0.0-SNAPSHOT")

From cd79d03101a605f52fd945f14cb04e1cc02ead89 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Mon, 17 Jul 2017 15:39:00 +0000
Subject: [PATCH 2/8] use SparkConf helper

---
 build.sbt                                                | 3 ++-
 src/main/scala/org/hammerlab/commands/SparkCommand.scala | 5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/build.sbt b/build.sbt
index d0e7ea6..5f55826 100644
--- a/build.sbt
+++ b/build.sbt
@@ -5,5 +5,6 @@ providedDeps += spark
 
 deps ++= Seq(
   bdg_utils_cli % "0.2.15",
-  slf4j
+  slf4j,
+  spark_util % "1.2.0-SNAPSHOT"
 )
diff --git a/src/main/scala/org/hammerlab/commands/SparkCommand.scala b/src/main/scala/org/hammerlab/commands/SparkCommand.scala
index 78e184f..118820f 100644
--- a/src/main/scala/org/hammerlab/commands/SparkCommand.scala
+++ b/src/main/scala/org/hammerlab/commands/SparkCommand.scala
@@ -1,6 +1,7 @@
 package org.hammerlab.commands
 
-import org.apache.spark.{SparkConf, SparkContext}
+import org.apache.spark.{ SparkConf, SparkContext }
+import org.hammerlab.spark.Conf
 
 import scala.collection.mutable
 
@@ -33,7 +34,7 @@ abstract class SparkCommand[T <: Args: Manifest]
    * @return
    */
   private def createSparkContext(): SparkContext = {
-    val config: SparkConf = new SparkConf()
+    val config: SparkConf = Conf()
 
     config.getOption("spark.app.name") match {
       case Some(cmdLineName) => config.setAppName(s"$cmdLineName: $name")

From d378bc849050f07ac82525ae4912eddd466886f2 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Tue, 8 Aug 2017 15:07:28 +0000
Subject: [PATCH 3/8] upgrade plugin, deps

---
 build.sbt                                        | 4 ++--
 project/plugins.sbt                              | 2 +-
 src/main/scala/org/hammerlab/commands/Args.scala | 3 ++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/build.sbt b/build.sbt
index 5f55826..725d91e 100644
--- a/build.sbt
+++ b/build.sbt
@@ -4,7 +4,7 @@ version := "1.0.5-SNAPSHOT"
 providedDeps += spark
 
 deps ++= Seq(
-  bdg_utils_cli % "0.2.15",
+  bdg_utils_cli % "0.2.16",
   slf4j,
-  spark_util % "1.2.0-SNAPSHOT"
+  spark_util % "1.2.1"
 )
diff --git a/project/plugins.sbt b/project/plugins.sbt
index ba64db2..c022d7b 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.0.0-SNAPSHOT")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.1.0")
diff --git a/src/main/scala/org/hammerlab/commands/Args.scala b/src/main/scala/org/hammerlab/commands/Args.scala
index 3ed8ec8..73acc1c 100644
--- a/src/main/scala/org/hammerlab/commands/Args.scala
+++ b/src/main/scala/org/hammerlab/commands/Args.scala
@@ -3,6 +3,7 @@ package org.hammerlab.commands
 import org.apache.spark.SparkContext
 import org.bdgenomics.utils.cli.Args4jBase
 
-trait Args extends Args4jBase {
+trait Args
+  extends Args4jBase {
   def validate(sc: SparkContext): Unit = {}
 }

From 735290d40e75dbc5b0634bf8c9390383a234c994 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Tue, 8 Aug 2017 19:06:47 +0000
Subject: [PATCH 4/8] use spark-util add tests

---
 README.md                                     |  2 +
 build.sbt                                     |  4 +-
 .../org/hammerlab/commands/Command.scala      |  7 +-
 .../org/hammerlab/commands/SparkCommand.scala | 65 +++++++------------
 .../hammerlab/commands/SparkCommandTest.scala | 56 ++++++++++++++++
 5 files changed, 91 insertions(+), 43 deletions(-)
 create mode 100644 src/test/scala/org/hammerlab/commands/SparkCommandTest.scala

diff --git a/README.md b/README.md
index 25997f4..72bd0cc 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,7 @@
 # spark-commands
 
+[![Build Status](https://travis-ci.org/hammerlab/spark-commands.svg?branch=master)](https://travis-ci.org/hammerlab/spark-commands)
+[![Coverage Status](https://coveralls.io/repos/github/hammerlab/spark-commands/badge.svg)](https://coveralls.io/github/hammerlab/spark-commands)
 [![Maven Central](https://img.shields.io/maven-central/v/org.hammerlab/spark-commands_2.11.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Cspark-commands)
 
 Interfaces for creating CLI-runnable and testable Spark commands/apps.
diff --git a/build.sbt b/build.sbt
index 725d91e..633f30a 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,10 +1,10 @@
 name := "spark-commands"
-version := "1.0.5-SNAPSHOT"
+version := "1.1.0-SNAPSHOT"
 
 providedDeps += spark
 
 deps ++= Seq(
-  bdg_utils_cli % "0.2.16",
+  bdg_utils_cli % "0.3.0",
   slf4j,
   spark_util % "1.2.1"
 )
diff --git a/src/main/scala/org/hammerlab/commands/Command.scala b/src/main/scala/org/hammerlab/commands/Command.scala
index c588b41..ec92358 100644
--- a/src/main/scala/org/hammerlab/commands/Command.scala
+++ b/src/main/scala/org/hammerlab/commands/Command.scala
@@ -21,7 +21,12 @@ abstract class Command[T <: Args: Manifest]
    *
    * @param args the command line arguments.
    */
-  def run(args: Array[String]): Unit = run(Args4j[T](args))
+  def run(args: Array[String]): Unit =
+    Args4j[T](args) match {
+      case Left(args) ⇒ run(args)
+      case _ ⇒
+    }
+
   def run(args: String*): Unit = run(args.toArray)
 
   def run(args: T): Unit
diff --git a/src/main/scala/org/hammerlab/commands/SparkCommand.scala b/src/main/scala/org/hammerlab/commands/SparkCommand.scala
index 118820f..6de3cee 100644
--- a/src/main/scala/org/hammerlab/commands/SparkCommand.scala
+++ b/src/main/scala/org/hammerlab/commands/SparkCommand.scala
@@ -1,12 +1,14 @@
 package org.hammerlab.commands
 
+import org.apache.spark.serializer.KryoRegistrator
 import org.apache.spark.{ SparkConf, SparkContext }
-import org.hammerlab.spark.Conf
+import org.hammerlab.spark.{ Conf, SparkConfBase }
 
 import scala.collection.mutable
 
 abstract class SparkCommand[T <: Args: Manifest]
-  extends Command[T] {
+  extends Command[T]
+    with SparkConfBase {
 
   override def run(args: T): Unit = {
     val sc = createSparkContext()
@@ -25,7 +27,22 @@ abstract class SparkCommand[T <: Args: Manifest]
     defaultConfs.update(key, value)
   }
 
-  def defaultRegistrar: String = ""
+  def registrar: Class[_ <: KryoRegistrator] = null
+
+  sparkConf(
+    "spark.master" → "local[*]",
+    "spark.serializer" → "org.apache.spark.serializer.KryoSerializer",
+    "spark.kryoserializer.buffer" → "4mb",
+    "spark.kryo.referenceTracking" → "true",
+    "spark.kryo.registrationRequired" → "true"
+  )
+
+  Option(registrar).foreach(
+    clz ⇒
+      sparkConf(
+        "spark.kryo.registrator" → clz.getCanonicalName
+      )
+  )
 
   /**
    * Return a spark context.
@@ -34,45 +51,13 @@ abstract class SparkCommand[T <: Args: Manifest]
    * @return
    */
   private def createSparkContext(): SparkContext = {
-    val config: SparkConf = Conf()
-
-    config.getOption("spark.app.name") match {
-      case Some(cmdLineName) => config.setAppName(s"$cmdLineName: $name")
-      case _ => config.setAppName(name)
-    }
-
-    if (config.getOption("spark.master").isEmpty) {
-      val numProcessors = Runtime.getRuntime.availableProcessors()
-      config.setMaster(s"local[$numProcessors]")
-      info(s"Running in local mode with $numProcessors 'executors'")
-    }
-
-    if (config.getOption("spark.serializer").isEmpty) {
-      config.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
-    }
-
-    if (config.getOption("spark.kryo.registrator").isEmpty && defaultRegistrar.nonEmpty) {
-      config.set("spark.kryo.registrator", defaultRegistrar)
-    }
-
-    if (config.getOption("spark.kryoserializer.buffer").isEmpty) {
-      config.set("spark.kryoserializer.buffer", "4mb")
-    }
-
-    if (config.getOption("spark.kryo.referenceTracking").isEmpty) {
-      config.set("spark.kryo.referenceTracking", "true")
-    }
-
-    if (config.getOption("spark.kryo.registrationRequired").isEmpty) {
-      config.set("spark.kryo.registrationRequired", "true")
-    }
+    val conf = makeSparkConf
 
-    for {
-      (k, v) <- defaultConfs
-    } {
-      config.set(k, v)
+    conf.getOption("spark.app.name") match {
+      case Some(cmdLineName) => conf.setAppName(s"$cmdLineName: $name")
+      case _ => conf.setAppName(name)
     }
 
-    new SparkContext(config)
+    new SparkContext(conf)
   }
 }
diff --git a/src/test/scala/org/hammerlab/commands/SparkCommandTest.scala b/src/test/scala/org/hammerlab/commands/SparkCommandTest.scala
new file mode 100644
index 0000000..ecf9f18
--- /dev/null
+++ b/src/test/scala/org/hammerlab/commands/SparkCommandTest.scala
@@ -0,0 +1,56 @@
+package org.hammerlab.commands
+
+import com.esotericsoftware.kryo.Kryo
+import org.apache.spark.SparkContext
+import org.apache.spark.serializer.KryoRegistrator
+import org.hammerlab.paths.Path
+import org.hammerlab.test.Suite
+import org.kohsuke.args4j.Argument
+
+class SparkCommandTest
+  extends Suite {
+  test("command") {
+    val outFile = tmpPath()
+    TestCommand.main(Array(outFile.toString()))
+    outFile.lines.toList should be(
+      List(
+        "8mb",
+        "org.hammerlab.commands.TestRegistrar"
+      )
+    )
+  }
+}
+
+class TestArgs
+  extends Args {
+  @Argument(required = true)
+  var outFile: String = _
+}
+
+class TestRegistrar
+  extends KryoRegistrator {
+  override def registerClasses(kryo: Kryo): Unit = {}
+}
+
+object TestCommand
+  extends SparkCommand[TestArgs] {
+  override def name: String = "test"
+  override def description: String = "test command"
+
+  sparkConf(
+    "spark.kryoserializer.buffer" → "8mb"
+  )
+
+
+  override def registrar = classOf[TestRegistrar]
+
+  override def run(args: TestArgs, sc: SparkContext): Unit = {
+    val conf = sc.getConf
+    Path(args.outFile).writeLines(
+      List(
+        conf.get("spark.kryoserializer.buffer"),
+        conf.get("spark.kryo.registrator")
+      )
+    )
+  }
+}

From 1a0c7b77fd1589cd832310736b8d19a129d0bb1c Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Thu, 14 Sep 2017 18:13:28 +0000
Subject: [PATCH 5/8] re-pkg as o.h.cli, add case_app module

---
 .../org/hammerlab/cli/args4j}/Args.scala      |  2 +-
 .../org/hammerlab/cli/args4j}/Command.scala   |  2 +-
 .../hammerlab/cli/args4j/SparkCommand.scala   | 39 ++++++++++
 .../cli/args4j}/SparkCommandTest.scala        | 23 ++++--
 build.sbt                                     | 36 ++++++++--
 .../scala/org/hammerlab/cli/app/App.scala     | 34 +++++++++
 .../org/hammerlab/cli/app/IndexingApp.scala   | 36 ++++++++++
 .../scala/org/hammerlab/cli/app/PathApp.scala | 33 +++++++++
 .../org/hammerlab/cli/app/SparkPathApp.scala  | 72 +++++++++++++++++++
 .../org/hammerlab/cli/args/OutputArgs.scala   | 21 ++++++
 .../hammerlab/cli/app/IndexingAppTest.scala   | 41 +++++++++++
 project/plugins.sbt                           |  2 +-
 .../org/hammerlab/commands/SparkCommand.scala | 63 ----------------
 13 files changed, 325 insertions(+), 79 deletions(-)
 rename {src/main/scala/org/hammerlab/commands => args4j/src/main/scala/org/hammerlab/cli/args4j}/Args.scala (83%)
 rename {src/main/scala/org/hammerlab/commands => args4j/src/main/scala/org/hammerlab/cli/args4j}/Command.scala (96%)
 create mode 100644 args4j/src/main/scala/org/hammerlab/cli/args4j/SparkCommand.scala
 rename {src/test/scala/org/hammerlab/commands => args4j/src/test/scala/org/hammerlab/cli/args4j}/SparkCommandTest.scala (76%)
 create mode 100644 case_app/src/main/scala/org/hammerlab/cli/app/App.scala
 create mode 100644 case_app/src/main/scala/org/hammerlab/cli/app/IndexingApp.scala
 create mode 100644 case_app/src/main/scala/org/hammerlab/cli/app/PathApp.scala
 create mode 100644 case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
 create mode 100644 case_app/src/main/scala/org/hammerlab/cli/args/OutputArgs.scala
 create mode 100644 case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala
 delete mode 100644 src/main/scala/org/hammerlab/commands/SparkCommand.scala

diff --git a/src/main/scala/org/hammerlab/commands/Args.scala b/args4j/src/main/scala/org/hammerlab/cli/args4j/Args.scala
similarity index 83%
rename from src/main/scala/org/hammerlab/commands/Args.scala
rename to args4j/src/main/scala/org/hammerlab/cli/args4j/Args.scala
index 73acc1c..722e5ea 100644
--- a/src/main/scala/org/hammerlab/commands/Args.scala
+++ b/args4j/src/main/scala/org/hammerlab/cli/args4j/Args.scala
@@ -1,4 +1,4 @@
-package org.hammerlab.commands
+package org.hammerlab.cli.args4j
 
 import org.apache.spark.SparkContext
 import org.bdgenomics.utils.cli.Args4jBase
diff --git a/src/main/scala/org/hammerlab/commands/Command.scala b/args4j/src/main/scala/org/hammerlab/cli/args4j/Command.scala
similarity index 96%
rename from src/main/scala/org/hammerlab/commands/Command.scala
rename to args4j/src/main/scala/org/hammerlab/cli/args4j/Command.scala
index ec92358..0e8fddf 100644
--- a/src/main/scala/org/hammerlab/commands/Command.scala
+++ b/args4j/src/main/scala/org/hammerlab/cli/args4j/Command.scala
@@ -1,4 +1,4 @@
-package org.hammerlab.commands
+package org.hammerlab.cli.args4j
 
 import grizzled.slf4j.Logging
 import org.bdgenomics.utils.cli.Args4j
diff --git a/args4j/src/main/scala/org/hammerlab/cli/args4j/SparkCommand.scala b/args4j/src/main/scala/org/hammerlab/cli/args4j/SparkCommand.scala
new file mode 100644
index 0000000..e2684ca
--- /dev/null
+++ b/args4j/src/main/scala/org/hammerlab/cli/args4j/SparkCommand.scala
@@ -0,0 +1,39 @@
+package org.hammerlab.cli.args4j
+
+import org.apache.spark.SparkContext
+import org.hammerlab.spark.{ SparkConfBase, confs }
+
+abstract class SparkCommand[T <: Args: Manifest]
+  extends Command[T]
+    with SparkConfBase
+    with confs.Kryo {
+
+  override def run(args: T): Unit = {
+    val sc = createSparkContext()
+    try {
+      args.validate(sc)
+      run(args, sc)
+    } finally {
+      sc.stop()
+    }
+  }
+
+  def run(args: T, sc: SparkContext): Unit
+
+  /**
+   * Return a spark context.
+   *
+   * Typically, most properties are set through config file / cmd-line.
+   * @return
+   */
+  private def createSparkContext(): SparkContext = {
+    val conf = makeSparkConf
+
+    conf.getOption("spark.app.name") match {
+      case Some(cmdLineName) => conf.setAppName(s"$cmdLineName: $name")
+      case _ => conf.setAppName(name)
+    }
+
+    new SparkContext(conf)
+  }
+}
diff --git a/src/test/scala/org/hammerlab/commands/SparkCommandTest.scala b/args4j/src/test/scala/org/hammerlab/cli/args4j/SparkCommandTest.scala
similarity index 76%
rename from src/test/scala/org/hammerlab/commands/SparkCommandTest.scala
rename to args4j/src/test/scala/org/hammerlab/cli/args4j/SparkCommandTest.scala
index ecf9f18..943e40e 100644
--- a/src/test/scala/org/hammerlab/commands/SparkCommandTest.scala
+++ b/args4j/src/test/scala/org/hammerlab/cli/args4j/SparkCommandTest.scala
@@ -1,4 +1,4 @@
-package org.hammerlab.commands
+package org.hammerlab.cli.args4j
 
 import com.esotericsoftware.kryo.Kryo
 import org.apache.spark.SparkContext
@@ -11,11 +11,19 @@ class SparkCommandTest
   extends Suite {
   test("command") {
     val outFile = tmpPath()
-    TestCommand.main(Array(outFile.toString()))
-    outFile.lines.toList should be(
+
+    TestCommand.main(
+      Array(
+        outFile.toString
+      )
+    )
+
+    outFile
+      .lines
+      .toList should be(
       List(
         "8mb",
-        "org.hammerlab.commands.TestRegistrar"
+        "org.hammerlab.cli.args4j.TestRegistrar"
       )
     )
   }
@@ -32,8 +40,12 @@ class TestRegistrar
   override def registerClasses(kryo: Kryo): Unit = {}
 }
 
+import org.hammerlab.spark.test.suite.TestConfs
+
 object TestCommand
-  extends SparkCommand[TestArgs] {
+  extends SparkCommand[TestArgs]
+    with TestConfs {
+
   override def name: String = "test"
   override def description: String = "test command"
 
@@ -41,7 +53,6 @@ object TestCommand
     "spark.kryoserializer.buffer" → "8mb"
   )
 
-
   override def registrar = classOf[TestRegistrar]
 
   override def run(args: TestArgs, sc: SparkContext): Unit = {
diff --git a/build.sbt b/build.sbt
index 633f30a..03a4989 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,10 +1,32 @@
-name := "spark-commands"
-version := "1.1.0-SNAPSHOT"
 
-providedDeps += spark
+lazy val cli =
+  rootProject(
+    args4j,
+    case_app
+  )
 
-deps ++= Seq(
-  bdg_utils_cli % "0.3.0",
-  slf4j,
-  spark_util % "1.2.1"
+val defaults = Seq(
+  organization := "org.hammerlab.cli",
+  deps ++= Seq(
+    slf4j,
+    spark_util % "1.3.0"
+  )
+) ++ addSparkDeps
+
+lazy val args4j = project.settings(
+  defaults,
+  version := "1.1.0-SNAPSHOT",
+  deps += bdg_utils_cli % "0.3.0",
+  testDeps += Parent.autoImport.args4j
+)
+
+lazy val case_app = project.settings(
+  defaults,
+  name := "case-app",
+  version := "1.0.0-SNAPSHOT",
+  deps ++= Seq(
+    Parent.autoImport.case_app,
+    io % "1.2.0",
+    paths % "1.2.0"
+  )
 )
diff --git a/case_app/src/main/scala/org/hammerlab/cli/app/App.scala b/case_app/src/main/scala/org/hammerlab/cli/app/App.scala
new file mode 100644
index 0000000..d723355
--- /dev/null
+++ b/case_app/src/main/scala/org/hammerlab/cli/app/App.scala
@@ -0,0 +1,34 @@
+package org.hammerlab.cli.app
+
+import caseapp.core.Messages
+import caseapp.{ CaseApp, Parser, RemainingArgs }
+import grizzled.slf4j.Logging
+
+abstract class App[Args : Parser : Messages]
+  extends CaseApp[Args]
+    with Logging {
+
+  final override def run(options: Args, remainingArgs: RemainingArgs): Unit =
+    remainingArgs match {
+      case RemainingArgs(args, Nil) ⇒
+        run(
+          options,
+          args
+        )
+      case RemainingArgs(args, unparsed) ⇒
+        throw new IllegalArgumentException(
+          s"Unparsed arguments: ${unparsed.mkString(" ")}"
+        )
+    }
+
+  def done(): Unit = {}
+
+  final def run(options: Args, remainingArgs: Seq[String]): Unit =
+    try {
+      _run(options, remainingArgs)
+    } finally {
+      done()
+    }
+
+  protected def _run(options: Args, remainingArgs: Seq[String]): Unit
+}
diff --git a/case_app/src/main/scala/org/hammerlab/cli/app/IndexingApp.scala b/case_app/src/main/scala/org/hammerlab/cli/app/IndexingApp.scala
new file mode 100644
index 0000000..e6256cf
--- /dev/null
+++ b/case_app/src/main/scala/org/hammerlab/cli/app/IndexingApp.scala
@@ -0,0 +1,36 @@
+package org.hammerlab.cli.app
+
+import caseapp.Parser
+import caseapp.core.Messages
+import org.hammerlab.io.Printer
+import org.hammerlab.paths.Path
+
+trait OutPathArgs {
+  def out: Option[Path]
+}
+
+/**
+ * Interface for apps that take a [[Path]] and "index" it in some way, generating an output file that is by default
+ * named by appending an extension to the input path.
+ *
+ * @param defaultSuffix if [[OutPathArgs.out]] is empty, construct an output path by appending this string to the argument
+ *                      value [[PathApp.path]].
+ */
+abstract class IndexingApp[Args <: OutPathArgs : Parser : Messages](defaultSuffix: String)
+  extends PathApp[Args] {
+  implicit var printer: Printer = _
+
+  override def init(options: Args): Unit = {
+    printer =
+      Printer(
+        options
+          .out
+          .getOrElse(
+            path + defaultSuffix
+          )
+      )
+  }
+
+  override def close(): Unit =
+    printer.close()
+}
diff --git a/case_app/src/main/scala/org/hammerlab/cli/app/PathApp.scala b/case_app/src/main/scala/org/hammerlab/cli/app/PathApp.scala
new file mode 100644
index 0000000..ac5816d
--- /dev/null
+++ b/case_app/src/main/scala/org/hammerlab/cli/app/PathApp.scala
@@ -0,0 +1,33 @@
+package org.hammerlab.cli.app
+
+import java.io.Closeable
+
+import caseapp.Parser
+import caseapp.core.Messages
+import org.hammerlab.paths.Path
+
+abstract class PathApp[Args : Parser : Messages]
+  extends App[Args]
+    with Closeable {
+
+  @transient implicit var path: Path = _
+
+  def init(options: Args): Unit = {}
+  def close(): Unit = {}
+
+  final protected override def _run(options: Args, args: Seq[String]): Unit = {
+    if (args.size != 1) {
+      throw new IllegalArgumentException(
+        s"Exactly one argument (a BAM file path) is required"
+      )
+    }
+
+    path = Path(args.head)
+
+    init(options)
+    run(options)
+    close()
+  }
+
+  protected def run(options: Args): Unit
+}
diff --git a/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala b/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
new file mode 100644
index 0000000..f8a4d3d
--- /dev/null
+++ b/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
@@ -0,0 +1,72 @@
+package org.hammerlab.cli.app
+
+import caseapp.Parser
+import caseapp.core.Messages
+import grizzled.slf4j.Logging
+import org.apache.spark.SparkContext
+import org.apache.spark.serializer.KryoRegistrator
+import org.hammerlab.cli.args.OutputArgs
+import org.hammerlab.hadoop.Configuration
+import org.hammerlab.io.{ Printer, SampleSize }
+import org.hammerlab.spark.{ SparkConfBase, confs }
+
+trait SparkPathAppArgs {
+  def output: OutputArgs
+}
+
+trait HasSparkConf
+  extends SparkConfBase
+    with confs.Kryo
+    with confs.DynamicAllocation
+    with confs.EventLog
+    with confs.Speculation
+
+trait SparkApp[Args]
+  extends HasSparkConf {
+
+  self: App[Args] with Logging ⇒
+
+  @transient private var _sc: SparkContext = _
+
+  implicit def sc: SparkContext = {
+    if (_sc == null) {
+      info("Creating SparkContext")
+      _sc = new SparkContext(makeSparkConf)
+    }
+    _sc
+  }
+
+  implicit def conf: Configuration = sc.hadoopConfiguration
+
+  override def done(): Unit = {
+    if (_sc != null && !_sc.isStopped) {
+      info("Stopping SparkContext")
+      _sc.stop()
+    }
+    _sc = null
+  }
+}
+
+/**
+ * [[SparkApp]] that takes an input path and prints some information to stdout or a path, with optional truncation of
+ * such output.
+ */
+abstract class SparkPathApp[Args <: SparkPathAppArgs : Parser : Messages](override val registrar: Class[_ <: KryoRegistrator])
+  extends PathApp[Args]
+    with SparkApp[Args] {
+
+  @transient implicit var printer: Printer = _
+  @transient implicit var printLimit: SampleSize = _
+
+  override def init(options: Args): Unit = {
+    val OutputArgs(printLim, path, overwrite) = options.output
+
+    if (path.exists(_.exists) && !overwrite)
+      throw new IllegalArgumentException(
+        s"Output path $path exists and overwrite (-f) not set"
+      )
+
+    printer = Printer(path)
+    printLimit = printLim
+  }
+}
diff --git a/case_app/src/main/scala/org/hammerlab/cli/args/OutputArgs.scala b/case_app/src/main/scala/org/hammerlab/cli/args/OutputArgs.scala
new file mode 100644
index 0000000..0034d0d
--- /dev/null
+++ b/case_app/src/main/scala/org/hammerlab/cli/args/OutputArgs.scala
@@ -0,0 +1,21 @@
+package org.hammerlab.cli.args
+
+import caseapp.{ ValueDescription, ExtraName ⇒ O, HelpMessage ⇒ M }
+import org.hammerlab.io.SampleSize
+import org.hammerlab.paths.Path
+
+case class OutputArgs(
+  @O("l")
+  @ValueDescription("num=1000000")
+  @M("When collecting samples of records/results for displaying to the user, limit to this many to avoid overloading the driver")
+  printLimit: SampleSize = SampleSize(1000000),
+
+  @O("o")
+  @ValueDescription("path")
+  @M("Print output to this file, otherwise to stdout")
+  outputPath: Option[Path] = None,
+
+  @O("f")
+  @M("Whether to overwrite the output file, if it already exists")
+  overwrite: Boolean = false
+)
diff --git a/case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala b/case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala
new file mode 100644
index 0000000..e4db763
--- /dev/null
+++ b/case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala
@@ -0,0 +1,41 @@
+package org.hammerlab.cli.app
+
+import caseapp.{ AppName, ExtraName ⇒ O }
+import org.hammerlab.paths.Path
+import org.hammerlab.test.Suite
+
+class IndexingAppTest
+  extends Suite {
+
+  test("sample app") {
+    val in = tmpPath()
+    in.writeLines(1 to 10 map(_.toString))
+    SumNumbers.main(
+      Array(
+        in.toString()
+      )
+    )
+    (in + ".sum").read should be("55\n")
+  }
+
+}
+
+@AppName("Add up numbers from an input file, write result to a sibling file with extension '.sum'")
+case class Args(@O("o") out: Option[Path] = None)
+  extends OutPathArgs
+
+object SumNumbers
+  extends IndexingApp[Args](".sum") {
+  override protected def run(options: Args): Unit = {
+
+    import org.hammerlab.io.Printer._
+    import cats.implicits.catsStdShowForInt
+
+    echo(
+      path
+        .lines
+        .map(_.toInt)
+        .sum
+    )
+  }
+}
diff --git a/project/plugins.sbt b/project/plugins.sbt
index c022d7b..33635f8 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.1.0")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.1.3-SNAPSHOT")
diff --git a/src/main/scala/org/hammerlab/commands/SparkCommand.scala b/src/main/scala/org/hammerlab/commands/SparkCommand.scala
deleted file mode 100644
index 6de3cee..0000000
--- a/src/main/scala/org/hammerlab/commands/SparkCommand.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package org.hammerlab.commands
-
-import org.apache.spark.serializer.KryoRegistrator
-import org.apache.spark.{ SparkConf, SparkContext }
-import org.hammerlab.spark.{ Conf, SparkConfBase }
-
-import scala.collection.mutable
-
-abstract class SparkCommand[T <: Args: Manifest]
-  extends Command[T]
-    with SparkConfBase {
-
-  override def run(args: T): Unit = {
-    val sc = createSparkContext()
-    try {
-      args.validate(sc)
-      run(args, sc)
-    } finally {
-      sc.stop()
-    }
-  }
-
-  def run(args: T, sc: SparkContext): Unit
-
-  private val defaultConfs = mutable.HashMap[String, String]()
-  def setDefaultConf(key: String, value: String): Unit = {
-    defaultConfs.update(key, value)
-  }
-
-  def registrar: Class[_ <: KryoRegistrator] = null
-
-  sparkConf(
-    "spark.master" → "local[*]",
-    "spark.serializer" → "org.apache.spark.serializer.KryoSerializer",
-    "spark.kryoserializer.buffer" → "4mb",
-    "spark.kryo.referenceTracking" → "true",
-    "spark.kryo.registrationRequired" → "true"
-  )
-
-  Option(registrar).foreach(
-    clz ⇒
-      sparkConf(
-        "spark.kryo.registrator" → clz.getCanonicalName
-      )
-  )
-
-  /**
-   * Return a spark context.
-   *
-   * Typically, most properties are set through config file / cmd-line.
-   * @return
-   */
-  private def createSparkContext(): SparkContext = {
-    val conf = makeSparkConf
-
-    conf.getOption("spark.app.name") match {
-      case Some(cmdLineName) => conf.setAppName(s"$cmdLineName: $name")
-      case _ => conf.setAppName(name)
-    }
-
-    new SparkContext(conf)
-  }
-}

From f84e7301498bc57b4e89e8623330664897c1bfd1 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Tue, 19 Sep 2017 18:40:24 +0000
Subject: [PATCH 6/8] add spark default eventLog guard

---
 build.sbt                                           | 13 +++++++------
 .../scala/org/hammerlab/cli/app/SparkPathApp.scala  | 11 ++++++++++-
 project/plugins.sbt                                 |  2 +-
 3 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/build.sbt b/build.sbt
index 03a4989..aad3982 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,10 +1,4 @@
 
-lazy val cli =
-  rootProject(
-    args4j,
-    case_app
-  )
-
 val defaults = Seq(
   organization := "org.hammerlab.cli",
   deps ++= Seq(
@@ -30,3 +24,10 @@ lazy val case_app = project.settings(
     paths % "1.2.0"
   )
 )
+
+lazy val cli_root =
+  rootProject(
+    "cli-root",
+    args4j,
+    case_app
+  )
diff --git a/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala b/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
index f8a4d3d..68a873e 100644
--- a/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
+++ b/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
@@ -8,6 +8,7 @@ import org.apache.spark.serializer.KryoRegistrator
 import org.hammerlab.cli.args.OutputArgs
 import org.hammerlab.hadoop.Configuration
 import org.hammerlab.io.{ Printer, SampleSize }
+import org.hammerlab.paths.Path
 import org.hammerlab.spark.{ SparkConfBase, confs }
 
 trait SparkPathAppArgs {
@@ -31,7 +32,15 @@ trait SparkApp[Args]
   implicit def sc: SparkContext = {
     if (_sc == null) {
       info("Creating SparkContext")
-      _sc = new SparkContext(makeSparkConf)
+      val conf = makeSparkConf
+      if (
+        conf.get("spark.eventLog.enabled", "true") == "true" &&
+          conf.get("spark.eventLog.dir", "") == "" &&
+          !Path("/tmp/spark-events").exists) {
+        conf.set("spark.eventLog.enabled", "false")
+        warn("Disabling event-logging because default destination /tmp/spark-events doesn't exist")
+      }
+      _sc = new SparkContext(conf)
     }
     _sc
   }
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 33635f8..c67154a 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.1.3-SNAPSHOT")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "3.2.0")

From 901927a84490900d44e1e6704c37d26d1200971d Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Tue, 19 Sep 2017 18:41:17 +0000
Subject: [PATCH 7/8] travis config

---
 .travis.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index f330307..28ad4ae 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ jdk:
 scala:
   - 2.11.8
 
-script: sbt ++$TRAVIS_SCALA_VERSION clean compile
+script: sbt ++$TRAVIS_SCALA_VERSION clean coverageTest
 
 cache:
   directories:
@@ -14,6 +14,8 @@ cache:
   - $HOME/.sbt/boot/
   - $HOME/.zinc
 
+after_success: sbt ++$TRAVIS_SCALA_VERSION travis-report
+
 before_cache:
   # Tricks to avoid unnecessary cache updates
   - find $HOME/.ivy2 -name "ivydata-*.properties" -delete

From 050835e0dbd9eb21f248202f0889896932cad130 Mon Sep 17 00:00:00 2001
From: Ryan Williams <ryan.blake.williams@gmail.com>
Date: Tue, 19 Sep 2017 18:58:15 +0000
Subject: [PATCH 8/8] add SparkPathApp test

---
 README.md                                     | 14 ++++++-
 .../org/hammerlab/cli/app/SparkPathApp.scala  |  2 +-
 case_app/src/test/resources/numbers           | 10 +++++
 .../hammerlab/cli/app/IndexingAppTest.scala   |  9 +----
 .../hammerlab/cli/app/SparkPathAppTest.scala  | 37 +++++++++++++++++++
 5 files changed, 62 insertions(+), 10 deletions(-)
 create mode 100644 case_app/src/test/resources/numbers
 create mode 100644 case_app/src/test/scala/org/hammerlab/cli/app/SparkPathAppTest.scala

diff --git a/README.md b/README.md
index 72bd0cc..6cf5789 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,16 @@
 
 [![Build Status](https://travis-ci.org/hammerlab/spark-commands.svg?branch=master)](https://travis-ci.org/hammerlab/spark-commands)
 [![Coverage Status](https://coveralls.io/repos/github/hammerlab/spark-commands/badge.svg)](https://coveralls.io/github/hammerlab/spark-commands)
-[![Maven Central](https://img.shields.io/maven-central/v/org.hammerlab/spark-commands_2.11.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Cspark-commands)
 
-Interfaces for creating CLI-runnable and testable Spark commands/apps.
+Interfaces for creating CLI-runnable and testable commands/apps, with [Spark](http://spark.apache.org/)-based and non-Spark flavors.
+
+## args4j
+[![Maven Central](https://img.shields.io/maven-central/v/org.hammerlab.cli/args4j_2.11.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Chammerlab%20args4j)
+
+
+## case-app
+[![Maven Central](https://img.shields.io/maven-central/v/org.hammerlab.cli/case-app_2.11.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Chammerlab%20case-app)
+
+
+
+
diff --git a/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala b/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
index 68a873e..e20cbe0 100644
--- a/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
+++ b/case_app/src/main/scala/org/hammerlab/cli/app/SparkPathApp.scala
@@ -60,7 +60,7 @@ trait SparkApp[Args]
  * [[SparkApp]] that takes an input path and prints some information to stdout or a path, with optional truncation of
  * such output.
  */
-abstract class SparkPathApp[Args <: SparkPathAppArgs : Parser : Messages](override val registrar: Class[_ <: KryoRegistrator])
+abstract class SparkPathApp[Args <: SparkPathAppArgs : Parser : Messages](override val registrar: Class[_ <: KryoRegistrator] = null)
   extends PathApp[Args]
     with SparkApp[Args] {
 
diff --git a/case_app/src/test/resources/numbers b/case_app/src/test/resources/numbers
new file mode 100644
index 0000000..f00c965
--- /dev/null
+++ b/case_app/src/test/resources/numbers
@@ -0,0 +1,10 @@
+1
+2
+3
+4
+5
+6
+7
+8
+9
+10
diff --git a/case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala b/case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala
index e4db763..a4e9a61 100644
--- a/case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala
+++ b/case_app/src/test/scala/org/hammerlab/cli/app/IndexingAppTest.scala
@@ -6,10 +6,8 @@ import org.hammerlab.test.Suite
 
 class IndexingAppTest
   extends Suite {
-
-  test("sample app") {
-    val in = tmpPath()
-    in.writeLines(1 to 10 map(_.toString))
+  test("SumNumbers") {
+    val in = fileCopy(path("numbers"), tmpPath())
     SumNumbers.main(
       Array(
         in.toString()
@@ -17,7 +15,6 @@ class IndexingAppTest
     )
     (in + ".sum").read should be("55\n")
   }
-
 }
 
 @AppName("Add up numbers from an input file, write result to a sibling file with extension '.sum'")
@@ -27,10 +24,8 @@ case class Args(@O("o") out: Option[Path] = None)
 object SumNumbers
   extends IndexingApp[Args](".sum") {
   override protected def run(options: Args): Unit = {
-
     import org.hammerlab.io.Printer._
     import cats.implicits.catsStdShowForInt
-
     echo(
       path
         .lines
diff --git a/case_app/src/test/scala/org/hammerlab/cli/app/SparkPathAppTest.scala b/case_app/src/test/scala/org/hammerlab/cli/app/SparkPathAppTest.scala
new file mode 100644
index 0000000..d7f76c1
--- /dev/null
+++ b/case_app/src/test/scala/org/hammerlab/cli/app/SparkPathAppTest.scala
@@ -0,0 +1,37 @@
+package org.hammerlab.cli.app
+
+import caseapp.Recurse
+import org.hammerlab.cli.args.OutputArgs
+import org.hammerlab.spark.test.suite.MainSuite
+import org.hammerlab.test.Suite
+
+class SparkPathAppTest
+  extends MainSuite {
+  test("SumNumbersSpark") {
+    val out = tmpPath()
+    SumNumbersSpark.main(
+      Array(
+        path("numbers").toString,
+        "-o", out.toString
+      )
+    )
+    out.read should be("55\n")
+  }
+}
+
+case class SparkArgs(@Recurse output: OutputArgs)
+  extends SparkPathAppArgs
+
+object SumNumbersSpark
+  extends SparkPathApp[SparkArgs] {
+  override protected def run(options: SparkArgs): Unit = {
+    import org.hammerlab.io.Printer._
+    import cats.implicits.catsStdShowForInt
+    echo(
+      sc
+        .textFile(path.toString)
+        .map(_.toInt)
+        .reduce(_ + _)
+    )
+  }
+}