diff --git a/README.md b/README.md index 470ccd33f4..fe326bd567 100644 --- a/README.md +++ b/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=` > to the Maven command. diff --git a/adam-assembly/pom.xml b/adam-assembly/pom.xml index 6e3234e9b2..2f0a9c46b3 100644 --- a/adam-assembly/pom.xml +++ b/adam-assembly/pom.xml @@ -74,7 +74,7 @@ workaround - + diff --git a/docs/api/overview.rst b/docs/api/overview.rst index 9106771d9a..aab7f90003 100644 --- a/docs/api/overview.rst +++ b/docs/api/overview.rst @@ -27,6 +27,18 @@ Central `__ under the groupId ${adam.version} + +From ADAM version 0.27.0, Scala 2.12 artifacts are also available: + +:: + + + org.bdgenomics.adam + adam-core-spark2_2.12 + ${adam.version} + + + Scala apps should depend on ``adam-core``, while Java applications should also depend on ``adam-apis``: diff --git a/docs/downstream/cli.rst b/docs/downstream/cli.rst index adee818aed..20392be488 100644 --- a/docs/downstream/cli.rst +++ b/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 `__ Logger via the ``log`` field, -mix in the org.bdgenomics.utils.misc.Logging trait by adding +to `slf4j `__ 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 } } diff --git a/docs/downstream/library.rst b/docs/downstream/library.rst index 0c06f5f307..6a808e1c3d 100644 --- a/docs/downstream/library.rst +++ b/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 `__ or any other argument parsing +library `__ or any other argument parsing library. .. code:: scala diff --git a/docs/installation/source.rst b/docs/installation/source.rst index 47f84002ad..c01863a0ab 100644 --- a/docs/installation/source.rst +++ b/docs/installation/source.rst @@ -4,7 +4,7 @@ Building ADAM from Source You will need to have `Apache Maven `__ 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=`` to the Maven command. diff --git a/pom.xml b/pom.xml index 399b2e8a65..e6ea29315c 100644 --- a/pom.xml +++ b/pom.xml @@ -58,12 +58,9 @@ - massie - Matt Massie - massie@cs.berkeley.edu - http://www.cs.berkeley.edu/~massie - U.C. Berkeley Computer Science - http://www.cs.berkeley.edu/ + heuermh + Michael L Heuer + University of California Berkeley diff --git a/scripts/publish-scaladoc.sh b/scripts/publish-scaladoc.sh deleted file mode 100755 index 01cf4fa382..0000000000 --- a/scripts/publish-scaladoc.sh +++ /dev/null @@ -1,51 +0,0 @@ -#!/bin/bash - -set -x -v -e - -version=${1:-latest} - -# clone repo -git clone -b gh-pages git@github.com:bigdatagenomics/adam.git adam-docs - -# get current sha1 -sha1=$(git log -1 --pretty=format:%H) - -# generate scaladoc -mvn generate-sources scala:doc - -# get current scaladoc dir -scaladoc=${PWD}/adam-core/target/site/scaladocs/ - -# make directory to copy docs to, if it does not already exist -mkdir -p adam-docs/${version} - -# copy docs over -cp -rvf ${scaladoc} adam-docs/${version}/scaladocs - -# step into repo -cd adam-docs - -# mark for add and commit -if [[ ${version} == "latest" ]]; -then - git commit --author "Big Data Genomics " \ - -a -m "Updating docs for ADAM commit ${sha1}." -else - - # insert new version html into index.html - mv index.html index.old - head -n 17 index.old > index.html - echo "
  • ${version}:" >> index.html - echo " Scaladoc" >> index.html - echo "
    • " >> index.html - tail -n +18 index.old >> index.html - rm index.old - - git add index.html ${version} - git commit -m "Adding docs for ADAM ${version} release." -fi -git push origin gh-pages - -# remove adam docs clone -cd .. -rm -rf adam-docs diff --git a/scripts/release/README.md b/scripts/release/README.md index 0e49c74d4a..7d29d8d4d3 100644 --- a/scripts/release/README.md +++ b/scripts/release/README.md @@ -10,26 +10,18 @@ Setup your environment Once your environment is setup, you'll be able to do a release. -First update CHANGES.md with closed issues and closed and merged pull requests and commit to master. -Since version 0.18.2 this is a manual process, see issue #936 and e.g. commit 48e2930a4bb026928b31e5bef03b305f0dbeb41d. +Then from the project root directory, run `./scripts/release/release.sh`. This script requires +parameters for release version, next development version, and release Github Milestone identifier, e.g. -Then from the project root directory, run `./scripts/release/release.sh`. -If you have any problems, run `./scripts/release/rollback.sh`. +```bash +$ ./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. \ No newline at end of file +Finally, be sure to announce the release on the ADAM mailing list, Gitter, Big Data Genomics blog, and Twitter (@bigdatagenomics). diff --git a/scripts/release/release.sh b/scripts/release/release.sh index 72ae1f6336..ce525a68eb 100755 --- a/scripts/release/release.sh +++ b/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 \ diff --git a/scripts/release/rollback.sh b/scripts/release/rollback.sh deleted file mode 100755 index 75a6513283..0000000000 --- a/scripts/release/rollback.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/sh - -mvn -P distribution release:rollback