Merge branch 'V2' into production

.github/workflows/github-pages.yml_

@@ -0,0 +1,18 @@
+name: Build and deploy Jekyll site to GitHub Pages
+
+on:
+    push:
+        branches:
+            - master
+
+jobs:
+    github-pages:
+        runs-on: ubuntu-16.04
+        steps:
+            - uses: actions/checkout@v2
+            - uses: helaili/[email protected]
+              env:
+                  JEKYLL_PAT: ${{ secrets.JEKYLL_PAT }}
+              with:
+                  jekyll_src: "docs"
+                  target_branch: "gh-pages"

.gitignore

@@ -30,14 +30,17 @@ build
 *.properties
 
 # needed for gradle-plugin
-!app/carnival-gradle/src/main/resources/META-INF/gradle-plugins/edu.upenn.pmbb.carnival.properties
+!app/carnival-gradle/src/main/resources/META-INF/gradle-plugins/*
 
 # do not ignore the docker-compose file
 !docker-compose.yml
 
 #do not ignore travis file
 !.travis.yml
 
+# add github workflows
+!.github/workflows/github-pages.yml
+
 # Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
 !gradle-wrapper.jar
 

README.md

@@ -10,8 +10,7 @@
 
 ## Quick Links
 
--   [Documentation](docs/index.markdown)
--   [Documentation Website](https://pmbb-ibi.github.io/carnival/)
+-   [Documentation Website Hosted by Github](https://pmbb-ibi.github.io/carnival/)
 
 ## Contents
 
@@ -46,7 +45,7 @@ Carnival’s property graph database:
 
 ## <a name="github-pages-site"></a> Github Pages
 
-The Github pages site is stored in the `docs` directory and makes use of [jekyll](https://jekyllrb.com). See the [jekyll docs](https://jekyllrb.com/docs/) for jekyll installation and usage instructions.
+The Github pages site is stored in the `/docs` directory and makes use of [jekyll](https://jekyllrb.com). See the [jekyll docs](https://jekyllrb.com/docs/) for jekyll installation and usage instructions.
 
 ### Prerequisites
 - Install [Ruby](https://www.ruby-lang.org/en/)

app/build.gradle

@@ -11,7 +11,7 @@
 buildscript {
     repositories {
         mavenCentral()
-        jcenter()
+        mavenLocal()
     }
     dependencies {
         classpath group: 'org.yaml', name: 'snakeyaml', version: '1.27'
@@ -37,10 +37,6 @@ plugins {
 ///////////////////////////////////////////////////////////////////////////////
 // Java
 ///////////////////////////////////////////////////////////////////////////////
-java {
-    sourceCompatibility = JavaVersion.toVersion('11')
-    targetCompatibility = JavaVersion.toVersion('11')
-}
 task printJavaVersion {
     println "[Carnival] Java version: ${JavaVersion.current()}"
 }
@@ -54,13 +50,13 @@ compileGroovy.dependsOn('printJavaVersion')
 // common plugins
 ///////////////////////////////////////////////////////////////////////////////
 allprojects {
-    group = 'edu.upenn.pmbb'
-    sourceCompatibility = JavaVersion.toVersion('11')
-    version = '2.0.0'   // see https://semver.org/
+    group = carnivalGroup
+    version = carnivalVersion   // see https://semver.org/
+    sourceCompatibility = JavaVersion.toVersion("${javaVersion}")
+    targetCompatibility = JavaVersion.toVersion("${javaVersion}")
 
     repositories {
         mavenCentral()
-        jcenter()
         mavenLocal()
         flatDir(dir: 'libs', name: 'Local libs')  
     }
@@ -228,73 +224,6 @@ def browse(path) {
 }
 
 
-///////////////////////////////////////////////////////////////////////////////
-// convenience local publishing tasks
-///////////////////////////////////////////////////////////////////////////////
-task refreshUtil {
-    dependsOn 'carnival-util:publishToMavenLocal'
-}
-
-task publishGraph {
-    dependsOn refreshUtil
-    dependsOn 'carnival-graph:publishToMavenLocal'
-}
-
-task publishCore {
-    dependsOn publishGraph
-    dependsOn 'carnival-core:publishToMavenLocal'
-}
-
-task publishAll {
-    dependsOn publishCore
-    dependsOn 'carnival-gradle:publishToMavenLocal'
-}
-
-task deleteLocalRepos {
-    doLast {
-        [
-            "${System.getProperty('user.home')}/.m2/repository/edu/upenn/pmbb/", 
-            "${System.getProperty('user.home')}/.groovy/grapes/edu.upenn.pmbb/"
-        ].each { bd ->
-            ant.echo(bd)
-
-            def file = new File(bd)
-            if (!file.exists()) return
-
-            def path = ant.path {
-                dirset(dir:bd, includes:'carnival-*')
-            }
-            path.list().each {
-                println it
-                ant.delete(includeEmptyDirs:true, verbose:true, dir:it)
-            }        
-            //ant.delete(includeEmptyDirs:true, verbose:true) {
-            //    dirset(dir:bd, includes:'carnival-*')
-            //}
-        }
-    }
-}
-
-task cleanBuild {
-    subprojects.each { dependsOn("${it.name}:clean") } 
-    subprojects.each { finalizedBy("${it.name}:compileGroovy") } 
-    doLast {println 'cleanBuild'} 
-}
-
-task localRebuildAndPublish { 
-    dependsOn cleanBuild
-    dependsOn deleteLocalRepos
-    finalizedBy publishAll
-    doLast {println 'localRebuildAndPublish'} 
-}
-
-task localBuildAndPublish { 
-    subprojects.each { dependsOn("${it.name}:compileGroovy") } 
-    dependsOn deleteLocalRepos
-    finalizedBy publishAll
-    doLast {println 'localBuildAndPublish'} 
-}
-
 
 ///////////////////////////////////////////////////////////////////////////////
 // JaCoCo code coverage

app/carnival-core/build.gradle

@@ -118,8 +118,6 @@ dependencies {
 
     // http libraries
     // http-builder was deprecated by http-builder-ng
-    // - carnival-core/vine/http.groovy uses the updated http-builder-ng library
-    // - carnival-pmbb/vine/redcapVine.groovy uses the old http-builder library; should be updated to use http.groovy
     implementation 'org.codehaus.groovy.modules.http-builder:http-builder:0.7.1'
     implementation 'io.github.http-builder-ng:http-builder-ng-core:1.0.4'