forked from fulcrumgenomics/dagr
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbuild.sbt
221 lines (205 loc) · 10 KB
/
build.sbt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
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,
releaseStepCommand("publishSigned"),
setNextVersion,
commitNextVersion,
releaseStepCommand("sonatypeReleaseAll"),
pushChanges
)
////////////////////////////////////////////////////////////////////////////////////////////////
// For the aggregate (root) jar, override the name. For the sub-projects,
// see the build.sbt in each project folder.
////////////////////////////////////////////////////////////////////////////////////////////////
assembly / assemblyJarName := "dagr-" + version.value + ".jar"
////////////////////////////////////////////////////////////////////////////////////////////////
// Sonatype settings
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val sonatypeSettings = Seq(
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")
},
Test / publishArtifact := 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: only count coverage of dagr.core
////////////////////////////////////////////////////////////////////////////////////////////////
coverageExcludedPackages := "<empty>;dagr\\.tasks.*;dagr\\.pipelines.*;dagr\\.cmdline.*"
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/dagr")),
startYear := Some(2015),
scalaVersion := "2.13.8",
crossScalaVersions := Seq("2.13.8"),
scalacOptions ++= Seq("-target:jvm-1.8", "-deprecation"),
Compile / doc / scalacOptions ++= docScalacOptions,
Test / doc/ scalacOptions ++= docScalacOptions,
useCoursier := false,
autoAPIMappings := true,
Test / testOptions += Tests.Argument(TestFrameworks.ScalaTest, "-h", Option(System.getenv("TEST_HTML_REPORTS")).getOrElse(htmlReportsDirectory)),
Test / testOptions += Tests.Argument("-l", "LongRunningTest"), // ignores long running tests
// uncomment for full stack traces
//testOptions in Test += Tests.Argument("-oD"),
Test / fork := true,
resolvers += Resolver.jcenterRepo,
resolvers += Resolver.sonatypeRepo("public"),
resolvers += Resolver.mavenLocal,
shellPrompt := { state => "%s| %s> ".format(GitCommand.prompt.apply(state), version.value) },
coverageExcludedPackages := "<empty>;dagr\\.tasks.*;dagr\\.pipelines.*",
updateOptions := updateOptions.value.withCachedResolution(true),
Test / javaOptions += "-Ddagr.color-status=false",
// Needed to avoid "sbt.ForkMain failed with exit code 137"
//in Travis with `sudo: false`.
// See https://github.com/sbt/sbt/issues/653
// and https://github.com/travis-ci/travis-ci/issues/3775
Test / javaOptions += "-Xmx1G",
libraryDependencies += "org.scalatest" %% "scalatest" % "3.0.8" % "test->*" excludeAll ExclusionRule(organization="org.junit", name="junit"),
assembly / assemblyJarName := s"${name.value}-${version.value}.jar"
) ++ Defaults.coreDefaultSettings ++ sonatypeSettings
////////////////////////////////////////////////////////////////////////////////////////////////
// core project
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val core = Project(id="dagr-core", base=file("core"))
.settings(commonSettings: _*)
.settings(description := "Core methods and classes to execute tasks in dagr.")
.settings(
libraryDependencies ++= Seq(
"com.fulcrumgenomics" %% "commons" % "1.4.0",
"com.fulcrumgenomics" %% "sopt" % "1.1.0",
"com.github.oshi" % "oshi-core" % "6.1.4",
"org.scala-lang" % "scala-reflect" % scalaVersion.value,
"org.scala-lang" % "scala-compiler" % scalaVersion.value,
"org.reflections" % "reflections" % "0.9.10",
"com.typesafe" % "config" % "1.4.2",
"javax.servlet" % "javax.servlet-api" % "3.1.0",
"jline" % "jline" % "2.14.6"
)
)
.disablePlugins(sbtassembly.AssemblyPlugin)
////////////////////////////////////////////////////////////////////////////////////////////////
// tasks project
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val htsjdkAndPicardExcludes = Seq(
ExclusionRule(organization="org.apache.ant"),
ExclusionRule(organization="gov.nih.nlm.ncbi"),
ExclusionRule(organization="org.testng"),
ExclusionRule(organization="com.google.cloud.genomics")
)
lazy val tasks = Project(id="dagr-tasks", base=file("tasks"))
.settings(description := "A set of example dagr tasks.")
.settings(commonSettings: _*)
.settings(
libraryDependencies ++= Seq(
"com.github.samtools" % "htsjdk" % "2.24.1" excludeAll(htsjdkAndPicardExcludes: _*),
"com.github.broadinstitute" % "picard" % "2.26.11" excludeAll(htsjdkAndPicardExcludes: _*)
)
)
.disablePlugins(sbtassembly.AssemblyPlugin)
.dependsOn(core)
////////////////////////////////////////////////////////////////////////////////////////////////
// pipelines project
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val pipelines = Project(id="dagr-pipelines", base=file("pipelines"))
.settings(description := "A set of example dagr pipelines.")
.settings(commonSettings: _*)
.disablePlugins(sbtassembly.AssemblyPlugin)
.dependsOn(tasks, core)
////////////////////////////////////////////////////////////////////////////////////////////////
// root (dagr) project
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val assemblySettings = Seq(
assembly / test := {},
assembly / logLevel := Level.Info
)
lazy val root = Project(id="dagr", base=file("."))
.settings(commonSettings: _*)
.settings(assemblySettings: _*)
.settings(description := "A tool to execute tasks in directed acyclic graphs.")
.settings(publishArtifact := false)
.aggregate(core, tasks, pipelines)
.dependsOn(core, tasks, pipelines)
////////////////////////////////////////////////////////////////////////////////////////////////
// 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
}
assembly / assemblyMergeStrategy := customMergeStrategy