diff --git a/assembly/.gitignore b/assembly/.gitignore
deleted file mode 100644
index faac96765..000000000
--- a/assembly/.gitignore
+++ /dev/null
@@ -1,21 +0,0 @@
-.DS_Store
-*.class
-*.log
-.idea
-.idea/*
-*.iml
-core/*.iml
-.#*
-
-# sbt specific
-dist/*
-target/
-lib_managed/
-src_managed/
-project/boot/
-project/plugins/project/
-
-# Scala-IDE specific
-.scala_dependencies
-
-out/
diff --git a/assembly/.sbtopts b/assembly/.sbtopts
deleted file mode 100644
index e4b7e3ada..000000000
--- a/assembly/.sbtopts
+++ /dev/null
@@ -1 +0,0 @@
--J-Xmx5G
diff --git a/assembly/.travis.yml b/assembly/.travis.yml
deleted file mode 100644
index a668ea2d9..000000000
--- a/assembly/.travis.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-sudo: required
-dist: trusty
-language: scala
-scala:
- - 2.11.6
-branches:
- only:
- - master
- - dev
diff --git a/assembly/LICENSE b/assembly/LICENSE
deleted file mode 100644
index 8dada3eda..000000000
--- a/assembly/LICENSE
+++ /dev/null
@@ -1,201 +0,0 @@
- Apache License
- Version 2.0, January 2004
- http://www.apache.org/licenses/
-
- TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
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- appropriateness of using or redistributing the Work and assume any
- risks associated with Your exercise of permissions under this License.
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- 8. Limitation of Liability. In no event and under no legal theory,
- whether in tort (including negligence), contract, or otherwise,
- unless required by applicable law (such as deliberate and grossly
- negligent acts) or agreed to in writing, shall any Contributor be
- liable to You for damages, including any direct, indirect, special,
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- has been advised of the possibility of such damages.
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- of any other Contributor, and only if You agree to indemnify,
- defend, and hold each Contributor harmless for any liability
- incurred by, or claims asserted against, such Contributor by reason
- of your accepting any such warranty or additional liability.
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-
- APPENDIX: How to apply the Apache License to your work.
-
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- boilerplate notice, with the fields enclosed by brackets "{}"
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-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
diff --git a/assembly/README.md b/assembly/README.md
index fbe4213c9..c58fcac8b 100644
--- a/assembly/README.md
+++ b/assembly/README.md
@@ -1,6 +1,3 @@
-[![Build Status](https://travis-ci.org/clulab/reach-assembly.svg?branch=master)](https://travis-ci.org/clulab/reach-assembly)
-[![Maven Central](https://maven-badges.herokuapp.com/maven-central/org.clulab/reach-assembly_2.11/badge.svg)](https://maven-badges.herokuapp.com/maven-central/org.clulab/reach-assembly_2.11)
-
`reach-assembly`
=====
@@ -21,9 +18,6 @@ For more details on the sieve-based assembly system, please refer to the followi
}
```
-# Licensing
-All our own code is licensed under Apache License Version 2.0. **However, some of the libraries used here, most notably CoreNLP, are GPL v2.** If `BioNLPProcessor` is not removed from this package, technically our whole code becomes GPL v2 since `BioNLPProcessor` builds on Stanford's `CoreNLP` functionality. Soon, we will split the code into multiple components, so licensing becomes less ambiguous.
-
# Changes
+ **0.0.1** - Assembly system from `reach` v1.3.2
+ [more...](CHANGES.md)
@@ -58,11 +52,11 @@ More publications from the Reach project are available [here](https://github.com
This software requires Java 1.8.
-The `jar` is available on Maven Central. To use, simply add the following dependency to your `build.sbt`:
+The `jar` is available on Maven Central. To use, simply add the following dependency to your `build.sbt` (NOTE: replace yourVersion with the version you wish to use):
```scala
libraryDependencies ++= Seq(
- "org.clulab" %% "reach" % "1.3.2"
+ "org.clulab" %% "reach-assembly" % "yourVersion"
)
```
@@ -78,7 +72,7 @@ Add the generated jar files under `target/` to your `$CLASSPATH`, along with the
You can run interactively explore assembly output for various snippets of text using the assembly shell:
```scala
-sbt "runMain org.clulab.assembly.AssemblyShell"
+sbt "runMain org.clulab.reach.assembly.AssemblyShell"
```
# Modifying the code
diff --git a/assembly/build.sbt b/assembly/build.sbt
index 9b52f73b7..4f5ad47e0 100644
--- a/assembly/build.sbt
+++ b/assembly/build.sbt
@@ -1,99 +1,16 @@
-import ReleaseTransformations._
-
name := "reach-assembly"
-organization := "org.clulab"
-
-scalaVersion := "2.11.8"
-
-scalacOptions ++= Seq("-feature", "-unchecked", "-deprecation")
-
-testOptions in Test += Tests.Argument("-oD")
-
-parallelExecution in Test := false
-
-// forward sbt's stdin to forked process
-connectInput in run := true
-
-// don't show output prefix
-outputStrategy := Some(StdoutOutput)
-
-//
-// publishing settings
-//
-
-// these are the steps to be performed during release
-releaseProcess := Seq[ReleaseStep](
- checkSnapshotDependencies,
- inquireVersions,
- runClean,
- runTest,
- setReleaseVersion,
- ReleaseStep(action = Command.process("publishSigned", _)),
- ReleaseStep(action = Command.process("sonatypeReleaseAll", _)),
- commitReleaseVersion,
- tagRelease,
- setNextVersion,
- commitNextVersion,
- pushChanges
-)
-
-// publish to a maven repo
-publishMavenStyle := true
-
-// the standard maven repository
-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")
-}
-
-// let’s remove any repositories for optional dependencies in our artifact
-pomIncludeRepository := { _ => false }
-
-// mandatory stuff to add to the pom for publishing
-pomExtra := (
- https://github.com/clulab/reach-assembly
-
-
- Apache License, Version 2.0
- http://www.apache.org/licenses/LICENSE-2.0.html
- repo
-
-
-
- https://github.com/clulab/reach-assembly
- https://github.com/clulab/reach-assembly
-
-
-
- ghp
- Gus Hahn-Powell
- gushahnpowell@gmail.com
-
- )
-
-//
-// end publishing settings
-//
-
//resolvers += "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots"
libraryDependencies ++= {
val akkaV = "2.4.3"
Seq(
"org.scalatest" %% "scalatest" % "2.2.4" % "test",
- "org.clulab" %% "reach" % "1.3.2",
- "org.clulab" %% "processors-main" % "6.0.0",
- "org.clulab" %% "processors-corenlp" % "6.0.0",
- "org.clulab" %% "processors-models" % "6.0.0",
- "com.typesafe" % "config" % "1.2.1",
- "commons-io" % "commons-io" % "2.4",
+ //"com.typesafe" % "config" % "1.2.1",
+ //"commons-io" % "commons-io" % "2.4",
// logging
- "ch.qos.logback" % "logback-classic" % "1.1.7",
- "com.typesafe.scala-logging" %% "scala-logging" % "3.4.0",
+ //"ch.qos.logback" % "logback-classic" % "1.1.7",
+ //"com.typesafe.scala-logging" %% "scala-logging" % "3.4.0",
// graph-based CSP
"org.choco-solver" % "choco-graph" % "3.3.0",
// Twirl
@@ -109,14 +26,4 @@ libraryDependencies ++= {
"com.typesafe.akka" %% "akka-slf4j" % akkaV,
"com.typesafe.akka" %% "akka-http-xml-experimental" % akkaV
)
-}
-
-// settings for building project website
-
-site.settings
-// include documentation
-site.includeScaladoc()
-
-ghpages.settings
-
-git.remoteRepo := "git@github.com:clulab/reach-assembly.git"
+}
\ No newline at end of file
diff --git a/assembly/project/build.properties b/assembly/project/build.properties
deleted file mode 100644
index d638b4f34..000000000
--- a/assembly/project/build.properties
+++ /dev/null
@@ -1 +0,0 @@
-sbt.version = 0.13.8
\ No newline at end of file
diff --git a/assembly/project/plugins.sbt b/assembly/project/plugins.sbt
deleted file mode 100644
index 07c111baa..000000000
--- a/assembly/project/plugins.sbt
+++ /dev/null
@@ -1,7 +0,0 @@
-// used for building project website
-resolvers += "jgit-repo" at "http://download.eclipse.org/jgit/maven"
-addSbtPlugin("com.typesafe.sbt" % "sbt-ghpages" % "0.5.4")
-
-addSbtPlugin("com.jsuereth" % "sbt-pgp" % "1.0.0")
-addSbtPlugin("org.xerial.sbt" % "sbt-sonatype" % "1.1")
-addSbtPlugin("com.github.gseitz" % "sbt-release" % "1.0.3")
diff --git a/assembly/src/main/resources/logback.xml b/assembly/src/main/resources/logback.xml
deleted file mode 100644
index 9127da939..000000000
--- a/assembly/src/main/resources/logback.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-
-
-
-
- logging.loglevel
-
-
-
- logging.logfile
-
-
-
- %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n
-
-
-
-
-
- ${logfile}
-
- %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n
-
-
-
-
-
-
-
-
-
diff --git a/assembly/src/main/resources/application.conf b/assembly/src/main/resources/reference.conf
similarity index 72%
rename from assembly/src/main/resources/application.conf
rename to assembly/src/main/resources/reference.conf
index 4468d2737..8aeeb0551 100644
--- a/assembly/src/main/resources/application.conf
+++ b/assembly/src/main/resources/reference.conf
@@ -2,43 +2,8 @@
# Configuration file for reach-assembly
#
-# the encoding of input and output files
-encoding = "utf-8"
-
-# this is a list of sections that we should ignore
-ignoreSections = ["references", "materials", "materials|methods", "methods", "supplementary-material"]
-
-# context engine config
-contextEngine {
- type = Policy4
- params = {
- bound = 3
- }
-}
-
-logging {
- # defines project-wide logging level
- loglevel = INFO
- # this log file gets overwritten every time ReachCLI is executed
- # so you should copy it if you want to keep it around
- logfile = ${HOME}/reach-assembly.log
-}
-
-# grounding configuration
-grounding: {
- # List of AdHoc grounding files to insert, in order, into the grounding search sequence.
- # Each element of the list is a map of KB filename and optional meta info (not yet used):
- # example: { kb: "adhoc.tsv", source: "NMZ at CMU" }
- adHocFiles: [
- { kb: "NER-Grounding-Override.tsv.gz", source: "MITRE/NMZ/BG feedback overrides" }
- ]
-
- # flag to turn off the influence of species on grounding
- overrideSpecies = true
-}
-
# number of simultaneous threads to use for parallelization
-threadLimit = 2
+#threadLimit = 2
# settings for assembly
assembly {
diff --git a/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala b/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala
index 0937ef848..f766ebfb9 100644
--- a/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala
+++ b/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala
@@ -8,7 +8,7 @@ import jline.console.ConsoleReader
import jline.console.history.FileHistory
import org.clulab.reach.display._
import org.clulab.reach.{context, ReachSystem}
-import org.clulab.assembly.display._
+import org.clulab.reach.assembly.display._
object AssemblyShell extends App {
diff --git a/assembly/version.sbt b/assembly/version.sbt
deleted file mode 100644
index 7131d3537..000000000
--- a/assembly/version.sbt
+++ /dev/null
@@ -1 +0,0 @@
-version in ThisBuild := "0.0.2-SNAPSHOT"
diff --git a/build.sbt b/build.sbt
index c1fbf29ca..1c39f543b 100644
--- a/build.sbt
+++ b/build.sbt
@@ -68,16 +68,20 @@ lazy val root = (project in file("."))
(Keys.`package` in (main, Compile)).value
}
)
- .aggregate(main, export)
- .dependsOn(main, export) // so that we can import from the console
+ .aggregate(main, assembly, export)
+ .dependsOn(main, assembly, export) // so that we can import from the console
lazy val main = project
.settings(commonSettings:_*)
-lazy val export = project
+lazy val assembly = project
.settings(commonSettings:_*)
.dependsOn(main)
+lazy val export = project
+ .settings(commonSettings:_*)
+ .dependsOn(main, assembly)
+
//
// publishing settings
//