build.gradle

plugins {
  id 'org.xtext.xtend' version '3.0.2'
  id 'org.xtext.builder' version '3.0.2'
  id 'java'
  id 'eclipse'
  id 'application'
  id 'maven'
}

dependencies {
  xtextLanguages "com.github.UBC-Stat-ML.blangDSL:ca.ubc.stat.blang:4.0.1"
  compile group: 'com.github.UBC-Stat-ML', name: 'conifer', version: '2.0.7'
  compile group: 'com.github.UBC-Stat-ML', name: 'blangSDK', version: '2.18.4'
}

xtext {
  languages {
    blang {
      setup = 'ca.ubc.stat.blang.BlangDslStandaloneSetup'
      fileExtension = 'bl'
      generator.outlet.producesJava = true
      generator.javaSourceLevel = '1.8'
    }
  }
}

repositories {
  mavenCentral()
  jcenter()
  maven { url "file:///${System.properties['user.home']}/artifacts/" }
  maven { url 'https://jitpack.io' }
  maven { url "https://ubc-stat-ml.github.io/artifacts/" }
  maven { url "https://www.stat.ubc.ca/~bouchard/maven/" }
}

xtend {
  generator {
    javaSourceLevel = 1.8
  }
}


def createScript(project, mainClass, name) {
  project.tasks.create(name: name, type: CreateStartScripts) {
    outputDir       = new File(project.buildDir, 'scripts')
    mainClassName   = mainClass
    applicationName = name
    classpath       = project.tasks[JavaPlugin.JAR_TASK_NAME].outputs.files + project.configurations.runtime
  }
  project.tasks[name].dependsOn(project.jar)

  project.applicationDistribution.with {
    into("bin") {
      from(project.tasks[name])
      fileMode = 0755
    }
  }
}

startScripts.enabled = false
run.enabled = false

createScript(project, 'corrupt.FixedMatrixModel',       'corrupt-infer')
createScript(project, 'corrupt.NoisyBinaryModel',       'corrupt-infer-with-noisy-params')
createScript(project, 'corrupt.distances.L1Decoder',    'corrupt-l1-decode')
createScript(project, 'corrupt.GenerateData',           'corrupt-generate')
createScript(project, 'corrupt.post.AverageCLMatrices', 'corrupt-average')
createScript(project, 'corrupt.Greedy',                 'corrupt-greedy')
createScript(project, 'corrupt.Distances',              'corrupt-distance')
createScript(project, 'corrupt.post.ScoreTrees',        'corrupt-batch-distances')
createScript(project, 'corrupt.viz.PerfectPhyloViz',    'corrupt-viz')
createScript(project, 'corrupt.viz.TreeGrowthViz',      'corrupt-viz-growth')
createScript(project, 'corrupt.pre.StraightenJitter',   'corrupt-straighten')
createScript(project, 'corrupt.pre.Tidify',             'corrupt-tidify')
createScript(project, 'corrupt.pre.Filter',             'corrupt-filter')
createScript(project, 'corrupt.pre.Tidy2MutationCell',  'corrupt-tidy2mutcellmtx')
createScript(project, 'corrupt.pre.GraphViz2Newick',    'corrupt-graphviz2newick')
createScript(project, 'corrupt.post.NoiseEstimator',    'corrupt-noise-estimate')
createScript(project, 'corrupt.post.RankLoci',          'corrupt-rank-loci')
createScript(project, 'corrupt.GrowTree',               'corrupt-grow')
createScript(project, 'corrupt.post.TreeEval',          'corrupt-eval')

createScript(project, 'humi.Preprocess',                'humi-preprocess')
createScript(project, 'humi.freq.DeltaMethod',          'humi-delta')
createScript(project, 'humi.posets.Intervals2Poset',    'humi-poset')
createScript(project, 'humi.posets.ComparePosets',      'humi-compare-posets')

createScript(project, 'humi.models.BNB',      'humi-bnb')
createScript(project, 'humi.models.MixBNB',   'humi-mixbnb')
createScript(project, 'humi.models.MixGNB',   'humi-mixgnb')
createScript(project, 'humi.models.MixYS',    'humi-mixys')
createScript(project, 'humi.models.NB',       'humi-nb')
createScript(project, 'humi.models.YS',       'humi-ys')
createScript(project, 'humi.models.MixNB',    'humi-mixnb')
createScript(project, 'humi.models.Poi',      'humi-poi')

uploadArchives {
  repositories {
    mavenDeployer {
      repository(url: "file:///${System.properties['user.home']}/artifacts/")
      snapshotRepository(url: "file:///${System.properties['user.home']}/artifacts/")
      pom.version = "1.0.6"
      pom.artifactId = "nowellpack"
      pom.groupId = "com.github.UBC-Stat-ML"
    }
  }
}