Merge branch 'master' into enh/nstdstate

Author: chrisgorgo

CHANGES

@@ -1,14 +1,31 @@
-Upcoming release 0.13
+Upcoming Release
 =====================
 
 * ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839)
+* ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)
+* REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828)
+* FIX: Makespec now runs with nipype in current directory (https://github.com/nipy/nipype/pull/1813)
+* FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (https://github.com/nipy/nipype/pull/1796 + https://github.com/nipy/nipype/pull/1831)
 * ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827)
 * FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827)
 * ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828)
 * FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833)
 * FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825)
 * ENH: Revised all Dockerfiles and automated deployment to Docker Hub
        from CircleCI (https://github.com/nipy/nipype/pull/1815)
+* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
+* FIX: Cast DVARS float outputs to avoid memmap error (https://github.com/nipy/nipype/pull/1777)
+* FIX: FSL FNIRT intensity mapping files (https://github.com/nipy/nipype/pull/1799)
+* ENH: Additional outputs generated by FSL EDDY (https://github.com/nipy/nipype/pull/1793)
+* TST: Parallelize CircleCI build across 4 containers (https://github.com/nipy/nipype/pull/1769)
+
+
+0.13.0-rc1 (January 4, 2017)
+===============================
+ 
+* FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770)
+* FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756)
+* TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751)
 * FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689)
 * REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680)
 * ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
@@ -37,7 +54,6 @@ Upcoming release 0.13
 * ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
 * ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
        (https://github.com/nipy/nipype/pull/1654)
-* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
 
 Release 0.12.1 (August 3, 2016)
 ===============================

circle.yml

@@ -25,10 +25,11 @@ dependencies:
     - mkdir -p $SCRATCH && sudo setfacl -d -m group:ubuntu:rwx $SCRATCH && sudo setfacl -m group:ubuntu:rwx $SCRATCH
     - mkdir -p $HOME/docker $HOME/examples $SCRATCH/pytest $SCRATCH/logs
   override:
+    - if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; else echo 'No docker image found in cache'; fi :
+        timeout: 6000
     - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
     - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-fsl_course_data.tar.gz "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
     - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
-    - if [[ -e $HOME/docker/image.tar ]]; then docker load --input $HOME/docker/image.tar; else echo 'No docker image found in cache'; fi
     - docker images
     - sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" nipype/info.py
     - e=1 && for i in {1..5}; do docker build -t nipype/nipype:latest --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
@@ -37,8 +38,8 @@ dependencies:
         timeout: 1600
     - e=1 && for i in {1..5}; do docker build -f docker/Dockerfile_py35 -t nipype/nipype_test:py35 . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
         timeout: 1600
-    - docker save -o $HOME/docker/image.tar nipype/nipype:latest nipype/nipype_test:py27 nipype/nipype_test:py35 :
-        timeout: 1600
+    - docker save -o $HOME/docker/cache.tar nipype/nipype:latest nipype/nipype_test:py27 nipype/nipype_test:py35 :
+        timeout: 6000
 
 test:
   override: