Moving sopt to its own project

Previously it was hosted here:
https://github.com/fulcrumgenomics/dagr

.gitignore

@@ -0,0 +1,2 @@
+.idea
+target

.travis.yml

@@ -0,0 +1,23 @@
+sudo: false
+language: scala
+scala:
+- 2.11.7
+jdk:
+- oraclejdk8
+script:
+- sbt +clean coverage +test && sbt coverageReport coverageAggregate
+- find $HOME/.sbt -name "*.lock" | xargs rm
+- find $HOME/.ivy2 -name "ivydata-*.properties" | xargs rm
+cache:
+  directories:
+  - $HOME/.ivy2/cache
+  - $HOME/.sbt/boot/
+before_install:
+- pip install --user codecov
+after_success:
+- codecov
+- test "$TRAVIS_REPO_SLUG" == 'fulcrumgenomics/sopt' && test "$TRAVIS_PULL_REQUEST" == 'false' && test "$TRAVIS_BRANCH" == 'master' && sbt publish
+env:
+  global:
+  - secure: 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
+  - secure: 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

LICENSE

@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) 2015-2016 Fulcrum Genomics LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

@@ -0,0 +1,12 @@
+[![Build Status](https://travis-ci.org/fulcrumgenomics/sopt.svg?branch=master)](https://travis-ci.org/fulcrumgenomics/sopt)
+[![Coverage Status](https://codecov.io/github/fulcrumgenomics/sopt/coverage.svg?branch=master)](https://codecov.io/github/fulcrumgenomics/sopt?branch=master)
+[![Code Review](https://api.codacy.com/project/badge/grade/52e1d786d9784c7192fae2f8e853fa34)](https://www.codacy.com/app/contact_32/sopt)
+[![Maven Central](https://maven-badges.herokuapp.com/maven-central/com.fulcrumgenomics/sopt_2.11/badge.svg)](https://maven-badges.herokuapp.com/maven-central/com.fulcrumgenomics/sopt_2.11)
+[![Dependency Status](https://www.versioneye.com/user/projects/56b2d2d593b95a003c714340/badge.svg)](https://www.versioneye.com/user/projects/56b2d2d593b95a003c714340#dialog_dependency_badge)
+[![License](http://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/fulcrumgenomics/sopt/blob/master/LICENSE)
+[![Language](http://img.shields.io/badge/language-scala-brightgreen.svg)](http://www.scala-lang.org/)
+
+Scala Option Parsing
+====
+
+Coming soon, documentation!

build.sbt

@@ -1 +1,160 @@
-assemblyJarName in assembly := "dagr-sopt-" + version.value + ".jar"
+import com.typesafe.sbt.SbtGit.GitCommand
+import sbt.Keys._
+import sbt._
+import sbtassembly.AssemblyKeys.assembly
+import sbtassembly.MergeStrategy
+import sbtrelease.ReleasePlugin.autoImport.ReleaseTransformations._
+import scoverage.ScoverageKeys._
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// We have the following "settings" in this build.sbt:
+// - versioning with sbt-release
+// - custom JAR name for the root project
+// - settings to publish to Sonatype
+// - exclude the root, tasks, and pipelines project from code coverage
+// - scaladoc settings
+// - custom merge strategy for assembly
+////////////////////////////////////////////////////////////////////////////////////////////////
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// Use sbt-release to bump the version numbers.
+//
+// see: http://blog.byjean.eu/2015/07/10/painless-release-with-sbt.html
+////////////////////////////////////////////////////////////////////////////////////////////////
+
+// Release settings
+releaseVersionBump := sbtrelease.Version.Bump.Next
+releasePublishArtifactsAction := PgpKeys.publishSigned.value
+releaseProcess := Seq[ReleaseStep](
+  checkSnapshotDependencies,
+  inquireVersions,
+  runClean,
+  runTest,
+  setReleaseVersion,
+  commitReleaseVersion,
+  tagRelease,
+  ReleaseStep(action = Command.process("publishSigned", _)),
+  setNextVersion,
+  commitNextVersion,
+  ReleaseStep(action = Command.process("sonatypeReleaseAll", _)),
+  pushChanges
+)
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// For the aggregate (root) jar, override the name.  For the sub-projects,
+// see the build.sbt in each project folder.
+////////////////////////////////////////////////////////////////////////////////////////////////
+assemblyJarName in assembly := "sopt-" + version.value + ".jar"
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// Sonatype settings
+////////////////////////////////////////////////////////////////////////////////////////////////
+publishMavenStyle := true
+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")
+}
+publishArtifact in Test := false
+pomIncludeRepository := { _ => false }
+// For Travis CI - see http://www.cakesolutions.net/teamblogs/publishing-artefacts-to-oss-sonatype-nexus-using-sbt-and-travis-ci
+credentials ++= (for {
+  username <- Option(System.getenv().get("SONATYPE_USER"))
+  password <- Option(System.getenv().get("SONATYPE_PASS"))
+} yield Credentials("Sonatype Nexus Repository Manager", "oss.sonatype.org", username, password)).toSeq
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// Coverage settings: include all sources
+////////////////////////////////////////////////////////////////////////////////////////////////
+val htmlReportsDirectory: String = "target/test-reports"
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// scaladoc options
+////////////////////////////////////////////////////////////////////////////////////////////////
+val docScalacOptions = Seq("-groups", "-implicits")
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// Common settings for all projects
+////////////////////////////////////////////////////////////////////////////////////////////////
+
+lazy val commonSettings = Seq(
+  organization         := "com.fulcrumgenomics",
+  organizationName     := "Fulcrum Genomics LLC",
+  organizationHomepage := Some(url("http://www.fulcrumgenomics.com")),
+  homepage             := Some(url("http://github.com/fulcrumgenomics/sopt")),
+  startYear            := Some(2015),
+  scalaVersion         := "2.11.8",
+  crossScalaVersions   := Seq("2.11.8", "2.12.1"),
+  scalacOptions        += "-target:jvm-1.8",
+  scalacOptions in (Compile, doc) ++= docScalacOptions,
+  scalacOptions in (Test, doc) ++= docScalacOptions,
+  autoAPIMappings := true,
+  testOptions in Test  += Tests.Argument(TestFrameworks.ScalaTest, "-h", Option(System.getenv("TEST_HTML_REPORTS")).getOrElse(htmlReportsDirectory)),
+  testOptions in Test  += Tests.Argument("-l", "LongRunningTest"), // ignores long running tests
+  // uncomment for full stack traces
+  //testOptions in Test  += Tests.Argument("-oD"),
+  fork in Test         := true,
+  resolvers            += Resolver.jcenterRepo,
+  shellPrompt          := { state => "%s| %s> ".format(GitCommand.prompt.apply(state), version.value) },
+  updateOptions        := updateOptions.value.withCachedResolution(true)
+) ++ Defaults.coreDefaultSettings
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// sopt project
+////////////////////////////////////////////////////////////////////////////////////////////////
+lazy val assemblySettings = Seq(
+  test in assembly     := {},
+  logLevel in assembly := Level.Info
+)
+lazy val root = Project(id="sopt", base=file("."))
+  .settings(commonSettings: _*)
+  .settings(unidocSettings: _*)
+  .settings(assemblySettings: _*)
+  .settings(description := "Scala sopt for Fulcrum Genomics.")
+  .settings(
+    libraryDependencies ++= Seq(
+      "org.scala-lang"            %  "scala-reflect" %  scalaVersion.value,
+      "com.fulcrumgenomics"       %% "commons"       % "0.2.0-SNAPSHOT",
+
+      //---------- Test libraries -------------------//
+      "org.scalatest"             %% "scalatest"     % "3.0.1"  % "test->*" excludeAll ExclusionRule(organization="org.junit", name="junit")
+    )
+  )
+
+////////////////////////////////////////////////////////////////////////////////////////////////
+// Merge strategy for assembly
+////////////////////////////////////////////////////////////////////////////////////////////////
+val customMergeStrategy: String => MergeStrategy = {
+  case x if Assembly.isConfigFile(x) =>
+    MergeStrategy.concat
+  case PathList(ps@_*) if Assembly.isReadme(ps.last) || Assembly.isLicenseFile(ps.last) =>
+    MergeStrategy.rename
+  case PathList("META-INF", xs@_*) =>
+    xs map {
+      _.toLowerCase
+    } match {
+      case ("manifest.mf" :: Nil) | ("index.list" :: Nil) | ("dependencies" :: Nil) =>
+        MergeStrategy.discard
+      case ps@(x :: xt) if ps.last.endsWith(".sf") || ps.last.endsWith(".dsa") =>
+        MergeStrategy.discard
+      case "plexus" :: xt =>
+        MergeStrategy.discard
+      case "spring.tooling" :: xt =>
+        MergeStrategy.discard
+      case "com.google.guava" :: xt =>
+        MergeStrategy.discard
+      case "services" :: xt =>
+        MergeStrategy.filterDistinctLines
+      case ("spring.schemas" :: Nil) | ("spring.handlers" :: Nil) =>
+        MergeStrategy.filterDistinctLines
+      case _ => MergeStrategy.deduplicate
+    }
+  case "asm-license.txt" | "overview.html" =>
+    MergeStrategy.discard
+  case "logback.xml" =>
+    MergeStrategy.first
+  case _ => MergeStrategy.deduplicate
+}
+assemblyMergeStrategy in assembly := customMergeStrategy

codecov.yml

@@ -0,0 +1,8 @@
+coverage:
+  status:
+    patch:
+      default:
+        target: '80'
+    project:
+      default:
+        target: auto

project/build.properties

@@ -0,0 +1 @@
+sbt.version=0.13.9

project/plugins.sbt

@@ -0,0 +1,9 @@
+resolvers += Resolver.url("fix-sbt-plugin-releases", url("http://dl.bintray.com/sbt/sbt-plugin-releases"))(Resolver.ivyStylePatterns)
+
+addSbtPlugin("com.typesafe.sbt"  % "sbt-git"       % "0.8.5")
+addSbtPlugin("com.github.gseitz" % "sbt-release"   % "1.0.3")
+addSbtPlugin("com.eed3si9n"      % "sbt-assembly"  % "0.14.3")
+addSbtPlugin("org.scoverage"     % "sbt-scoverage" % "1.5.0")
+addSbtPlugin("org.xerial.sbt"    % "sbt-sonatype"  % "1.1")
+addSbtPlugin("com.jsuereth"      % "sbt-pgp"       % "1.0.1")
+addSbtPlugin("com.eed3si9n"      % "sbt-unidoc"    % "0.3.3")

sonatype.sbt

@@ -0,0 +1,26 @@
+sonatypeProfileName := "com.fulcrumgenomics"
+
+pomExtra in Global := {
+    <licenses>
+      <license>
+        <name>MIT License</name>
+        <url>http://www.opensource.org/licenses/mit-license.html</url>
+      </license>
+    </licenses>
+    <scm>
+      <url>git@github.com:fulcrumgenomics/sopt</url>
+      <connection>scm:git:git@github.com:fulcrumgenomics/sopt.git</connection>
+    </scm>
+    <developers>
+      <developer>
+        <id>nh13</id>
+        <name>Nils Homer</name>
+        <url>http://github.com/nh13</url>
+      </developer>
+      <developer>
+        <id>tfenne</id>
+        <name>Tim Fennell</name>
+        <url>http://github.com/tfenne</url>
+      </developer>
+    </developers>
+}

src/main/java/dagr/sopt/cmdline/ArgAnnotation.java → src/main/java/com/fulcrumgenomics/sopt/cmdline/ArgAnnotation.java

@@ -21,7 +21,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package dagr.sopt.cmdline;
+package com.fulcrumgenomics.sopt.cmdline;
 
 import java.lang.annotation.*;
 

src/main/java/dagr/sopt/cmdline/ClpAnnotation.java → src/main/java/com/fulcrumgenomics/sopt/cmdline/ClpAnnotation.java

@@ -21,7 +21,10 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-package dagr.sopt.cmdline;
+package com.fulcrumgenomics.sopt.cmdline;
+
+import com.fulcrumgenomics.sopt.cmdline.ClpGroup;
+import com.fulcrumgenomics.sopt.cmdline.Clps;
 
 import java.lang.annotation.*;
 

src/main/scala/dagr/sopt/cmdline/ClpArgumentDefinitionPrinting.scala → src/main/scala/com/fulcrumgenomics/sopt/cmdline/ClpArgumentDefinitionPrinting.scala

@@ -22,13 +22,14 @@
  * THE SOFTWARE.
  */
 
-package dagr.sopt.cmdline
+package com.fulcrumgenomics.sopt.cmdline
 
 import java.util
 
-import dagr.commons.reflect.ReflectionUtil
-import dagr.sopt.util._
-import dagr.commons.util.StringUtil
+import com.fulcrumgenomics.commons.reflect.ReflectionUtil
+import com.fulcrumgenomics.commons.util.StringUtil
+import com.fulcrumgenomics.sopt.util.{KCYN, KGRN}
+import com.fulcrumgenomics.sopt.util._
 
 import scala.util.{Failure, Success}
 

src/main/scala/dagr/sopt/cmdline/ClpGroup.scala → src/main/scala/com/fulcrumgenomics/sopt/cmdline/ClpGroup.scala

@@ -22,7 +22,7 @@
  * THE SOFTWARE.
  */
 
-package dagr.sopt.cmdline
+package com.fulcrumgenomics.sopt.cmdline
 
 /**
   * Trait for groups of CommandLinePrograms.

src/main/scala/dagr/sopt/cmdline/ClpReflectiveBuilder.scala → src/main/scala/com/fulcrumgenomics/sopt/cmdline/ClpReflectiveBuilder.scala

@@ -22,11 +22,11 @@
  * THE SOFTWARE.
  */
 
-package dagr.sopt.cmdline
+package com.fulcrumgenomics.sopt.cmdline
 
-import dagr.commons.reflect.{ReflectionUtil, Argument, ArgumentLookup, ReflectiveBuilder}
-import dagr.commons.util.StringUtil
-import dagr.sopt.{arg, clp}
+import com.fulcrumgenomics.commons.reflect.{Argument, ArgumentLookup, ReflectionUtil, ReflectiveBuilder}
+import com.fulcrumgenomics.commons.util.StringUtil
+import dagr.sopt.arg
 
 import scala.collection.mutable
 import scala.collection.mutable.ListBuffer

src/main/scala/dagr/sopt/cmdline/CommandLineException.scala → src/main/scala/com/fulcrumgenomics/sopt/cmdline/CommandLineException.scala

@@ -22,7 +22,7 @@
  * THE SOFTWARE.
  */
 
-package dagr.sopt.cmdline
+package com.fulcrumgenomics.sopt.cmdline
 
 object CommandLineException {
   /** Prepends the exception name to the message. */

src/main/scala/dagr/sopt/cmdline/CommandLineParser.scala → src/main/scala/com/fulcrumgenomics/sopt/cmdline/CommandLineParser.scala

@@ -22,13 +22,13 @@
  * THE SOFTWARE.
  */
 
-package dagr.sopt.cmdline
+package com.fulcrumgenomics.sopt.cmdline
 
-import dagr.commons.reflect.ReflectionUtil
-import dagr.commons.util.StringUtil
+import com.fulcrumgenomics.commons.reflect.ReflectionUtil
+import com.fulcrumgenomics.sopt.util._
 import dagr.sopt.clp
-import dagr.sopt.util.ParsingUtil._
-import dagr.sopt.util._
+import com.fulcrumgenomics.sopt.util.ParsingUtil._
+import com.fulcrumgenomics.sopt.util._
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable.ListBuffer