Moved org.broadinstitute.hail to is.hail. (hail-is#1265)

bcajes · Jan 17, 2017 · 967e053 · 967e053
1 parent ff7ba73
commit 967e053
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Showing 313 changed files with 1,148 additions and 1,145 deletions.
diff --git a/build.gradle b/build.gradle
@@ -36,7 +36,7 @@ buildScan {
     licenseAgree = 'yes'
 }
 
-mainClassName = "org.broadinstitute.hail.driver.Main"
+mainClassName = "is.hail.driver.Main"
 
 String sparkVersion = System.getProperty("spark.version","2.0.2")
 
@@ -231,15 +231,15 @@ tasks.withType(ShadowJar) {
     manifest {
         attributes 'Implementation-Title': 'Hail',
                 'Implementation-Version': '0.0.1-SNAPSHOT',
-                'Main-Class': 'org.broadinstitute.hail.driver.Main'
+                'Main-Class': 'is.hail.driver.Main'
     }
     baseName = project.name + '-all'
     mergeServiceFiles()
     zip64 true
     // conflict with version in default Hadoop/Spark install
-    relocate 'org.apache.http', 'org.broadinstitute.hail.relocated.org.apache.http'
-    relocate 'com.google.common', 'org.broadinstitute.hail.relocated.com.google.common'
-    relocate 'org.objectweb', 'org.broadinstitute.hail.relocated.org.objectweb'
+    relocate 'org.apache.http', 'is.hail.relocated.org.apache.http'
+    relocate 'com.google.common', 'is.hail.relocated.com.google.common'
+    relocate 'org.objectweb', 'is.hail.relocated.org.objectweb'
 }
 
 shadowJar {
@@ -413,7 +413,7 @@ task makeTutorial(type: Exec, dependsOn: setupDocsDirs) {
 }
 
 task runCommandsJson(type: JavaExec, dependsOn: ['setupDocsDirs', 'classes']) {
-    main 'org.broadinstitute.hail.driver.Main'
+    main 'is.hail.driver.Main'
     args ('commandmeta', '-o', 'build/tmp/docs/commandOptions.json')
     classpath sourceSets.main.runtimeClasspath
 }

diff --git a/python/hail/context.py b/python/hail/context.py
@@ -49,7 +49,10 @@ def __init__(self, sc=None, appName="Hail", master=None, local='local[*]',
         self.gateway = SparkContext._gateway
         self.jvm = SparkContext._jvm
 
-        driver = scala_package_object(self.jvm.org.broadinstitute.hail.driver)
+        # hail package
+        self.hail = getattr(self.jvm, 'is').hail
+
+        driver = scala_package_object(self.hail.driver)
 
         if not sc:
             self.jsc = driver.configureAndCreateSparkContext(
@@ -67,16 +70,16 @@ def __init__(self, sc=None, appName="Hail", master=None, local='local[*]',
         self.sql_context = SQLContext(self.sc, self.jsql_context)
 
     def _jstate(self, jvds):
-        return self.jvm.org.broadinstitute.hail.driver.State(
+        return self.hail.driver.State(
             self.jsc, self.jsql_context, jvds, scala_object(self.jvm.scala.collection.immutable, 'Map').empty())
 
     def _raise_py4j_exception(self, e):
-        msg = scala_package_object(self.jvm.org.broadinstitute.hail.utils).getMinimalMessage(e.java_exception)
+        msg = scala_package_object(self.hail.utils).getMinimalMessage(e.java_exception)
         raise FatalError(msg, e.java_exception)
 
     def run_command(self, vds, pargs):
         jargs = jarray(self.gateway, self.jvm.java.lang.String, pargs)
-        t = self.jvm.org.broadinstitute.hail.driver.ToplevelCommands.lookup(jargs)
+        t = self.hail.driver.ToplevelCommands.lookup(jargs)
         cmd = t._1()
         cmd_args = t._2()
         jstate = self._jstate(vds.jvds if vds != None else None)
@@ -337,7 +340,7 @@ def import_keytable(self, path, key_names, npartitions=None, config=None):
         if not config:
             config = TextTableConfig()
 
-        return KeyTable(self, self.jvm.org.broadinstitute.hail.keytable.KeyTable.importTextTable(
+        return KeyTable(self, self.hail.keytable.KeyTable.importTextTable(
             self.jsc, jarray(self.gateway, self.jvm.java.lang.String, path_args), key_names, npartitions, config.to_java(self)))
 
     def import_plink(self, bed, bim, fam, npartitions=None, delimiter='\\\\s+', missing='NA', quantpheno=False):

diff --git a/python/hail/dataset.py b/python/hail/dataset.py
@@ -650,7 +650,7 @@ def annotate_samples_vds(self, right, root=None, code=None):
 
         return VariantDataset(
             self.hc,
-            self.hc.jvm.org.broadinstitute.hail.driver.AnnotateSamplesVDS.annotate(
+            self.hc.hail.driver.AnnotateSamplesVDS.annotate(
                 self.jvds, right.jvds, code, root))
 
     def annotate_variants_bed(self, input, root, all=False):
@@ -968,7 +968,7 @@ def annotate_variants_vds(self, other, code=None, root=None):
 
         return VariantDataset(
             self.hc,
-            self.hc.jvm.org.broadinstitute.hail.driver.AnnotateVariantsVDS.annotate(
+            self.hc.hail.driver.AnnotateVariantsVDS.annotate(
                 self.jvds, other.jvds, code, root))
 
     def cache(self):
@@ -994,7 +994,7 @@ def concordance(self, right):
 
         """
 
-        result = self.hc.jvm.org.broadinstitute.hail.driver.Concordance.calculate(
+        result = self.hc.hail.driver.Concordance.calculate(
             self.jvds, right.jvds)
         return (VariantDataset(self.hc, result._1()),
                 VariantDataset(self.hc, result._2()))
@@ -1008,7 +1008,7 @@ def count(self, genotypes=False):
         """
 
         try:
-            return (scala_package_object(self.hc.jvm.org.broadinstitute.hail.driver)
+            return (scala_package_object(self.hc.hail.driver)
                     .count(self.jvds, genotypes)
                     .toJavaMap())
         except Py4JJavaError as e:
@@ -1956,7 +1956,7 @@ def join(self, right):
 
         """
         try:
-            return VariantDataset(self.hc, self.hc.jvm.org.broadinstitute.hail.driver.Join.join(self.jvds, right.jvds))
+            return VariantDataset(self.hc, self.hc.hail.driver.Join.join(self.jvds, right.jvds))
         except Py4JJavaError as e:
             self._raise_py4j_exception(e)
 
@@ -3176,7 +3176,7 @@ def make_keytable(self, variant_condition, genotype_condition, key_names):
         if isinstance(genotype_condition, list):
             genotype_condition = ','.join(genotype_condition)
 
-        jkt = (scala_package_object(self.hc.jvm.org.broadinstitute.hail.driver)
+        jkt = (scala_package_object(self.hc.hail.driver)
                .makeKT(self.jvds, variant_condition, genotype_condition,
                        jarray(self.hc.gateway, self.hc.jvm.java.lang.String, key_names)))
         return KeyTable(self.hc, jkt)
diff --git a/python/hail/keytable.py b/python/hail/keytable.py
@@ -535,7 +535,7 @@ def to_dataframe(self, expand=True, flatten=True):
             self._raise_py4j_exception(e)
 
     def export_mongodb(self, mode='append'):
-        (scala_package_object(self.hc.jvm.org.broadinstitute.hail.driver)
+        (scala_package_object(self.hc.hail.driver)
          .exportMongoDB(self.hc.jsql_context, self.jkt, mode))
 
     def explode(self, column_names):

diff --git a/python/hail/utils.py b/python/hail/utils.py
@@ -58,8 +58,8 @@ def to_java(self, hc):
         :param :class:`.HailContext` The Hail context.
         """
         try:
-            return hc.jvm.org.broadinstitute.hail.utils.TextTableConfiguration.apply(self.types, self.comment,
-                                                             self.delimiter, self.missing,
-                                                             self.noheader, self.impute)
+            return hc.hail.utils.TextTableConfiguration.apply(self.types, self.comment,
+                                                              self.delimiter, self.missing,
+                                                              self.noheader, self.impute)
         except Py4JJavaError as e:
             self._raise_py4j_exception(e)
diff --git a/...nstitute/hail/io/compress/BGzipCodec.java → .../java/is/hail/io/compress/BGzipCodec.java b/...nstitute/hail/io/compress/BGzipCodec.java → .../java/is/hail/io/compress/BGzipCodec.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.io.compress;
+package is.hail.io.compress;
 
 import org.apache.hadoop.io.compress.*;
 

diff --git a/...titute/hail/io/compress/BGzipCodecGZ.java → ...ava/is/hail/io/compress/BGzipCodecGZ.java b/...titute/hail/io/compress/BGzipCodecGZ.java → ...ava/is/hail/io/compress/BGzipCodecGZ.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.io.compress;
+package is.hail.io.compress;
 
 public class BGzipCodecGZ extends BGzipCodec {
 

diff --git a/...te/hail/io/compress/BGzipInputStream.java → ...is/hail/io/compress/BGzipInputStream.java b/...te/hail/io/compress/BGzipInputStream.java → ...is/hail/io/compress/BGzipInputStream.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.io.compress;
+package is.hail.io.compress;
 
 import org.apache.hadoop.fs.Seekable;
 import org.apache.hadoop.io.compress.SplitCompressionInputStream;

diff --git a/...stitute/hail/annotations/Annotation.scala → ...cala/is/hail/annotations/Annotation.scala b/...stitute/hail/annotations/Annotation.scala → ...cala/is/hail/annotations/Annotation.scala
@@ -1,9 +1,9 @@
-package org.broadinstitute.hail.annotations
+package is.hail.annotations
 
 import org.apache.spark.sql.Row
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.utils.Interval
-import org.broadinstitute.hail.variant._
+import is.hail.expr._
+import is.hail.utils.Interval
+import is.hail.variant._
 
 object Annotation {
 

diff --git a/...dinstitute/hail/annotations/package.scala → ...n/scala/is/hail/annotations/package.scala b/...dinstitute/hail/annotations/package.scala → ...n/scala/is/hail/annotations/package.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail
+package is.hail
 
 package object annotations {
 

diff --git a/.../org/broadinstitute/hail/asm4s/Code.scala → src/main/scala/is/hail/asm4s/Code.scala b/.../org/broadinstitute/hail/asm4s/Code.scala → src/main/scala/is/hail/asm4s/Code.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.asm4s
+package is.hail.asm4s
 
 import java.lang.reflect.{Constructor, Field, Method, Modifier}
 

diff --git a/...nstitute/hail/asm4s/FunctionBuilder.scala → ...scala/is/hail/asm4s/FunctionBuilder.scala b/...nstitute/hail/asm4s/FunctionBuilder.scala → ...scala/is/hail/asm4s/FunctionBuilder.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.asm4s
+package is.hail.asm4s
 
 import java.io.PrintWriter
 

diff --git a/...g/broadinstitute/hail/asm4s/package.scala → src/main/scala/is/hail/asm4s/package.scala b/...g/broadinstitute/hail/asm4s/package.scala → src/main/scala/is/hail/asm4s/package.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail
+package is.hail
 
 import java.lang.reflect.Method
 

diff --git a/...broadinstitute/hail/check/Arbitrary.scala → src/main/scala/is/hail/check/Arbitrary.scala b/...broadinstitute/hail/check/Arbitrary.scala → src/main/scala/is/hail/check/Arbitrary.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.check
+package is.hail.check
 
 import scala.collection.generic.CanBuildFrom
 import scala.math.Numeric.Implicits._

diff --git a/...a/org/broadinstitute/hail/check/Gen.scala → src/main/scala/is/hail/check/Gen.scala b/...a/org/broadinstitute/hail/check/Gen.scala → src/main/scala/is/hail/check/Gen.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.check
+package is.hail.check
 
 import breeze.linalg.DenseMatrix
 import breeze.storage.Zero

diff --git a/.../org/broadinstitute/hail/check/Prop.scala → src/main/scala/is/hail/check/Prop.scala b/.../org/broadinstitute/hail/check/Prop.scala → src/main/scala/is/hail/check/Prop.scala
@@ -1,6 +1,6 @@
-package org.broadinstitute.hail.check
+package is.hail.check
 
-import org.broadinstitute.hail.utils._
+import is.hail.utils._
 import org.apache.commons.math3.random.RandomDataGenerator
 
 import scala.collection.mutable.ArrayBuffer

diff --git a/...tute/hail/driver/AggregateIntervals.scala → ...a/is/hail/driver/AggregateIntervals.scala b/...tute/hail/driver/AggregateIntervals.scala → ...a/is/hail/driver/AggregateIntervals.scala
@@ -1,12 +1,12 @@
-package org.broadinstitute.hail.driver
-
-import org.broadinstitute.hail.utils._
-import org.broadinstitute.hail.annotations.Annotation
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.io.annotators.IntervalListAnnotator
-import org.broadinstitute.hail.methods._
-import org.broadinstitute.hail.utils.Interval
-import org.broadinstitute.hail.variant._
+package is.hail.driver
+
+import is.hail.utils._
+import is.hail.annotations.Annotation
+import is.hail.expr._
+import is.hail.io.annotators.IntervalListAnnotator
+import is.hail.methods._
+import is.hail.utils.Interval
+import is.hail.variant._
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 import scala.collection.mutable

diff --git a/...stitute/hail/driver/AnnotateAlleles.scala → ...cala/is/hail/driver/AnnotateAlleles.scala b/...stitute/hail/driver/AnnotateAlleles.scala → ...cala/is/hail/driver/AnnotateAlleles.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
 object AnnotateAlleles extends SuperCommand {
   def name = "annotatealleles"

diff --git a/...ute/hail/driver/AnnotateAllelesExpr.scala → .../is/hail/driver/AnnotateAllelesExpr.scala b/...ute/hail/driver/AnnotateAllelesExpr.scala → .../is/hail/driver/AnnotateAllelesExpr.scala
@@ -1,9 +1,9 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
-import org.broadinstitute.hail.utils._
-import org.broadinstitute.hail.annotations._
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.methods.Aggregators
+import is.hail.utils._
+import is.hail.annotations._
+import is.hail.expr._
+import is.hail.methods.Aggregators
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 import scala.collection.mutable

diff --git a/...nstitute/hail/driver/AnnotateGlobal.scala → ...scala/is/hail/driver/AnnotateGlobal.scala b/...nstitute/hail/driver/AnnotateGlobal.scala → ...scala/is/hail/driver/AnnotateGlobal.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
 object AnnotateGlobal extends SuperCommand {
   def name = "annotateglobal"

diff --git a/...tute/hail/driver/AnnotateGlobalExpr.scala → ...a/is/hail/driver/AnnotateGlobalExpr.scala b/...tute/hail/driver/AnnotateGlobalExpr.scala → ...a/is/hail/driver/AnnotateGlobalExpr.scala
@@ -1,9 +1,9 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
-import org.broadinstitute.hail.annotations._
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.methods.Aggregators
-import org.broadinstitute.hail.variant.Variant
+import is.hail.annotations._
+import is.hail.expr._
+import is.hail.methods.Aggregators
+import is.hail.variant.Variant
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 import scala.collection.mutable

diff --git a/...tute/hail/driver/AnnotateGlobalList.scala → ...a/is/hail/driver/AnnotateGlobalList.scala b/...tute/hail/driver/AnnotateGlobalList.scala → ...a/is/hail/driver/AnnotateGlobalList.scala
@@ -1,10 +1,10 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
-import org.broadinstitute.hail.utils._
-import org.broadinstitute.hail.annotations._
-import org.broadinstitute.hail.expr
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.methods.Aggregators
+import is.hail.utils._
+import is.hail.annotations._
+import is.hail.expr
+import is.hail.expr._
+import is.hail.methods.Aggregators
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 import scala.collection.mutable

diff --git a/...ute/hail/driver/AnnotateGlobalTable.scala → .../is/hail/driver/AnnotateGlobalTable.scala b/...ute/hail/driver/AnnotateGlobalTable.scala → .../is/hail/driver/AnnotateGlobalTable.scala
@@ -1,8 +1,8 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
-import org.broadinstitute.hail.annotations._
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.utils.{TextTableOptions, TextTableReader}
+import is.hail.annotations._
+import is.hail.expr._
+import is.hail.utils.{TextTableOptions, TextTableReader}
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 object AnnotateGlobalTable extends Command with JoinAnnotator {

diff --git a/...stitute/hail/driver/AnnotateSamples.scala → ...cala/is/hail/driver/AnnotateSamples.scala b/...stitute/hail/driver/AnnotateSamples.scala → ...cala/is/hail/driver/AnnotateSamples.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
 object AnnotateSamples extends SuperCommand {
   def name = "annotatesamples"

diff --git a/...ute/hail/driver/AnnotateSamplesExpr.scala → .../is/hail/driver/AnnotateSamplesExpr.scala b/...ute/hail/driver/AnnotateSamplesExpr.scala → .../is/hail/driver/AnnotateSamplesExpr.scala
@@ -1,9 +1,9 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
-import org.broadinstitute.hail.utils._
-import org.broadinstitute.hail.annotations.{Annotation, Inserter}
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.methods.Aggregators
+import is.hail.utils._
+import is.hail.annotations.{Annotation, Inserter}
+import is.hail.expr._
+import is.hail.methods.Aggregators
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 import scala.collection.mutable

diff --git a/...tute/hail/driver/AnnotateSamplesFam.scala → ...a/is/hail/driver/AnnotateSamplesFam.scala b/...tute/hail/driver/AnnotateSamplesFam.scala → ...a/is/hail/driver/AnnotateSamplesFam.scala
@@ -1,9 +1,9 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
-import org.broadinstitute.hail.utils._
-import org.broadinstitute.hail.annotations.Annotation
-import org.broadinstitute.hail.expr.Parser
-import org.broadinstitute.hail.io.plink.{FamFileConfig, PlinkLoader}
+import is.hail.utils._
+import is.hail.annotations.Annotation
+import is.hail.expr.Parser
+import is.hail.io.plink.{FamFileConfig, PlinkLoader}
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 object AnnotateSamplesFam extends Command {

diff --git a/...ute/hail/driver/AnnotateSamplesList.scala → .../is/hail/driver/AnnotateSamplesList.scala b/...ute/hail/driver/AnnotateSamplesList.scala → .../is/hail/driver/AnnotateSamplesList.scala
@@ -1,8 +1,8 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
-import org.broadinstitute.hail.utils._
-import org.broadinstitute.hail.annotations.Annotation
-import org.broadinstitute.hail.expr._
+import is.hail.utils._
+import is.hail.annotations.Annotation
+import is.hail.expr._
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 object AnnotateSamplesList extends Command {

diff --git a/...te/hail/driver/AnnotateSamplesTable.scala → ...is/hail/driver/AnnotateSamplesTable.scala b/...te/hail/driver/AnnotateSamplesTable.scala → ...is/hail/driver/AnnotateSamplesTable.scala
@@ -1,10 +1,10 @@
-package org.broadinstitute.hail.driver
+package is.hail.driver
 
 import org.apache.spark.sql.Row
-import org.broadinstitute.hail.utils._
-import org.broadinstitute.hail.annotations._
-import org.broadinstitute.hail.expr._
-import org.broadinstitute.hail.utils._
+import is.hail.utils._
+import is.hail.annotations._
+import is.hail.expr._
+import is.hail.utils._
 import org.kohsuke.args4j.{Option => Args4jOption}
 
 object AnnotateSamplesTable extends Command with JoinAnnotator {