Update README, changelog, build and version numbers

Author: pditommaso

README.md

@@ -208,8 +208,8 @@ The self-contained runnable Nextflow package can be created by using the followi
 Known compilation problems 
 ---------------------------
 
-Nextflow can be compiled both the JDK 7 or JDK 8. However when compiling with the later you **won't** be able
-to run it on a Java 7. The specify the compiler to be used by Gradle build set the 
+Nextflow can be compiled with both JDK 7 or JDK 8. However when compiling with the later you **won't** be able
+to run it on a Java 7. The Java compiler used by the build process can be choose by setting the
 `JAVA_HOME` environment variable accordingly. 
 
 
@@ -219,6 +219,7 @@ this is due to a bug affecting the following Java JDK:
 - 1.7.0 update 55
 - 1.7.0 update 65
 - 1.7.0 update 67
+- 1.7.0 update 71
 - 1.8.0 update 11
 - 1.8.0 update 20
 

build.gradle

@@ -18,7 +18,7 @@
  *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-version = '0.12.0'
+version = '0.12.1'
 apply plugin: 'groovy'
 apply plugin: 'idea'
 

changelog.txt

@@ -1,7 +1,16 @@
 NEXTFLOW CHANGE-LOG
 ===================
 
-0.12.0 - 5 Gen 2014
+0.12.1 - 8 Feb 2014
+- Fixed NoSuchMethodException issue on Java 1.7.0_01 due to missing private constructor
+- Fixed logging issue on Nextflow console
+- Fixed issue `view` operator which hung when used on a dataflow variable
+- Upgrade SLF4J to version 1.7.10
+- Upgrade Capsule to version 0.10.0
+- Removed dependency on jsr166y module
+- Removed `synchronized` declaration on Session cleanUp method
+
+0.12.0 - 5 Jan 2014
 - Added afterScript/beforeScript directives
 - Added tag directive to label task executions with a custom identifier
 - Added dynamic directives evaluation 

docs/conf.py

@@ -50,7 +50,7 @@
 # The short X.Y version.
 version = '0.12'
 # The full version, including alpha/beta/rc tags.
-release = '0.12.0'
+release = '0.12.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/sync-doc.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 TARGET=../../nextflow-website/assets
 LATEST=$TARGET/docs/latest/
-VERSION=$TARGET/docs/v0.12.0/
+VERSION=$TARGET/docs/v0.12.1/
 
 mkdir -p $TARGET/docs/latest/
-mkdir -p $TARGET/docs/v0.12.0/
+mkdir -p $TARGET/docs/v0.12.1/
 
 rsync -r _build/html/* $LATEST
 rsync -r _build/html/* $VERSION

launch.sh

@@ -47,6 +47,8 @@ DEBUG=''
 COLUMNS=${COLUMNS:-`tput cols 2> /dev/tty`}
 MAIN_CLASS='nextflow.cli.Launcher'
 JVM_ARGS+=" -Djava.awt.headless=true -noverify -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
+## flight recorded -- http://docs.oracle.com/javacomponents/jmc-5-4/jfr-runtime-guide/run.htm
+##JVM_ARGS+=" -XX:+UnlockCommercialFeatures -XX:+FlightRecorder -XX:StartFlightRecording=duration=60s,filename=myrecording.jfr"
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 EXTRAE_CONFIG_FILE=${EXTRAE_CONFIG_FILE:-$NXF_HOME/extrae/config}
 NXF_CLI="$0 $@"

nextflow

@@ -102,7 +102,7 @@ if [ "$0" = "bash" ] || [ "$0" = "/bin/bash" ]; then
 fi  
 
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
-NXF_VER=${NXF_VER:-'0.12.0'}
+NXF_VER=${NXF_VER:-'0.12.1'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_ASSETS=${NXF_ASSETS:-$NXF_HOME/assets}
 NXF_CLI="$0 $@"

src/main/groovy/nextflow/Const.groovy

@@ -48,17 +48,17 @@ class Const {
     /**
      * The application version
      */
-    static final String APP_VER = "0.12.0"
+    static final String APP_VER = "0.12.1"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static final long APP_TIMESTAMP = 1420470437645
+    static final long APP_TIMESTAMP = 1423420466067
 
     /**
      * The app build number
      */
-    static final int APP_BUILDNUM = 2580
+    static final int APP_BUILDNUM = 2670
 
     /**
      * The date time formatter string