Merge d80ceee into f032086

README.md

@@ -68,7 +68,7 @@ R and Python.
 You will need to have [Apache Maven](http://maven.apache.org/) version 3.1.1 or
 later installed in order to build ADAM.
 
-> **Note:** The default configuration is for Hadoop 2.7.3. If building against
+> **Note:** The default configuration is for Hadoop 2.7.5. If building against
 > a different version of Hadoop, please pass `-Dhadoop.version=<HADOOP_VERSION>`
 > to the Maven command.
 

adam-assembly/pom.xml

@@ -74,7 +74,7 @@
             <configuration>
               <shaderHint>workaround</shaderHint>
               <transformers>
-                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
               </transformers>
             </configuration>
           </execution>

docs/api/overview.rst

@@ -27,6 +27,18 @@ Central <http://search.maven.org>`__ under the groupId
       <version>${adam.version}</version>
     </dependency>
 
+
+From ADAM version 0.27.0, Scala 2.12 artifacts are also available:
+
+::
+
+    <dependency>
+      <groupId>org.bdgenomics.adam</groupId>
+      <artifactId>adam-core-spark2_2.12</artifactId>
+      <version>${adam.version}</version>
+    </dependency>
+
+
 Scala apps should depend on ``adam-core``, while Java applications
 should also depend on ``adam-apis``:
 

docs/downstream/cli.rst

@@ -54,8 +54,8 @@ method. The ``MyCommandArgs`` class defined above is provided in the
 constructor and specifies the CLI command for ``BDGSparkCommand``. We
 must define a companion object because the command cannot run without
 being added to the list of accepted commands described below. For access
-to an `slf4j <http://www.slf4j.org/>`__ Logger via the ``log`` field,
-mix in the org.bdgenomics.utils.misc.Logging trait by adding
+to `slf4j <http://www.slf4j.org/>`__ Logger methods, such as ``info``,
+mix in the grizzled.slf4j.Logging trait by adding
 ``with Logging`` to the class definition.
 
 .. code:: scala
@@ -64,7 +64,7 @@ mix in the org.bdgenomics.utils.misc.Logging trait by adding
       val companion = MyCommand
 
       def run(sc: SparkContext) {
-        log.info("Doing something...")
+        info("Doing something...")
         // do something
       }
     }

docs/downstream/library.rst

@@ -5,7 +5,7 @@ To use ADAM as a library in new applications:
 
 Create an object with a ``main(args: Array[String])`` method and handle
 command line arguments. Feel free to use the `args4j
-library <http://www.slf4j.org/>`__ or any other argument parsing
+library <https://args4j.kohsuke.org>`__ or any other argument parsing
 library.
 
 .. code:: scala

docs/installation/source.rst

@@ -4,7 +4,7 @@ Building ADAM from Source
 You will need to have `Apache Maven <http://maven.apache.org/>`__
 version 3.1.1 or later installed in order to build ADAM.
 
-    **Note:** The default configuration is for Hadoop 2.7.3. If building
+    **Note:** The default configuration is for Hadoop 2.7.5. If building
     against a different version of Hadoop, please pass
     ``-Dhadoop.version=<HADOOP_VERSION>`` to the Maven command.
 

pom.xml

@@ -58,12 +58,9 @@
   </scm>
   <developers>
     <developer>
-      <id>massie</id>
-      <name>Matt Massie</name>
-      <email>massie@cs.berkeley.edu</email>
-      <url>http://www.cs.berkeley.edu/~massie</url>
-      <organization>U.C. Berkeley Computer Science</organization>
-      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
+      <id>heuermh</id>
+      <name>Michael L Heuer</name>
+      <organization>University of California Berkeley</organization>
     </developer>
   </developers>
   <issueManagement>

scripts/release/README.md

@@ -10,26 +10,18 @@ Setup your environment
 
 Once your environment is setup, you'll be able to do a release.
 
-First update CHANGES.md with closed issues and closed and merged pull requests and commit to master.
-Since version 0.18.2 this is a manual process, see issue #936 and e.g. commit 48e2930a4bb026928b31e5bef03b305f0dbeb41d.
+Then from the project root directory, run `./scripts/release/release.sh`.  This script requires
+parameters for release version, next development version, and release Github Milestone identifier, e.g.
 
-Then from the project root directory, run `./scripts/release/release.sh`.
-If you have any problems, run `./scripts/release/rollback.sh`.
+```bash
+$ ./scripts/release/release.sh 0.27.0 0.28.0-SNAPSHOT 21
+```
 
 Once you've successfully published the release, you will need to "close" and "release" it following the instructions at
 http://central.sonatype.org/pages/releasing-the-deployment.html#close-and-drop-or-release-your-staging-repository
 
 After the release is rsynced to the Maven Central repository, confirm checksums match and verify signatures.
 
-Create a new pull request against [Homebrew Science](https://github.com/Homebrew/homebrew-science) for the new release version.
-Often this will just require a version bump and checksum update.  See e.g. https://github.com/Homebrew/homebrew-science/pull/3375.
+The ADAM Homebrew formula and Bioconda recipe may need updating, if the auto-update bots are not able to pick up the release.
 
-Also, register the new release at [Spark Packages](https://spark-packages.org/). This will make it easy for people to pull in
-and use ADAM in Spark, or on Databricks. We already have registered [ADAM on Spark
-Packages](https://spark-packages.org/package/bigdatagenomics/adam). You'll just need to update the Maven coordinates/release
-version, give the commit hash of the release commit (from the 2.10 release) and attach a release ZIP. This is generated by
-the release script.
-
-Finally, be sure to announce the release on the ADAM mailing list and Twitter (@bigdatagenomics).
-
-Additionally, once the release is done, you will need to bump the R and Python development versions on trunk.
+Finally, be sure to announce the release on the ADAM mailing list, Gitter, Big Data Genomics blog, and Twitter (@bigdatagenomics).

scripts/release/release.sh

@@ -96,11 +96,14 @@ if [ $? != 0 ]; then
   exit 1
 fi
 
+git checkout master
+
 # do spark 2, scala 2.12 release
 git checkout -b maint_spark2_2.12-${release} ${branch}
 
-git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.12 release."
 ./scripts/move_to_scala_2.12.sh
+git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.12 release."
+
 mvn --batch-mode \
   -P distribution \
   -Dresume=false \