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0.13.1

0.13.1 (May 20, 2017)

=====================

* FIX: Make release compatible with conda-forge build process (nipy#2017)
* ENH: Update some minimum versions in compliance with Debian Jessie (nipy#2017)
* ENH: Circle builds use cached docker layers (nipy#2017)
* ENH: Base docker to use FS6 and ANTS 2.2.0 (nipy#2024)
* FIX: Mailmap and contributor acknowledgment (nipy#2017)
* FIX: Preserve node properties in sub nodes of MapNode (nipy#2019)
* FIX: Fix interfaces 3DUnifize, ICA_AROMA, BinaryMaths, RegAverage, BBRegister,
  AffineInitializer (nipy#2025, nipy#2027,
  nipy#2036, nipy#2037,
  nipy#2031, nipy#2010)
* ENH: Add Anisotropic Power interface (nipy#2039)
* FIX: Bayesian estimation in SPM (nipy#2030)

0.13.0 (May 11, 2017)
=====================

* ENH: Multi-stage recon-all directives (nipy#1991)
* FIX: FEAT "folder does not exist" error (nipy#2000)
* ENH: Niftyfit interfaces (nipy#1910)
* FIX: Define ANTSPATH for BrainExtraction automatically (nipy#1986)
* ENH: New trait for imaging files (nipy#1949)
* ENH: Niftyseg interfaces (nipy#1911)
* ENH: Niftyreg interfaces (nipy#1913)
* MRG: Allow more support for CLI (nipy#1908)
* ENH: 3dQwarpPlusMinus interface (nipy#1974)
* FIX: PY3.6 support (nipy#1977)
* FIX: PY3 and stream fixes for MRTrix2TrackVis (nipy#1804)
* ENH: More mask options for CompCor interfaces (nipy#1968 + nipy#1992)
* ENH: Additional TOPUP outputs (nipy#1976)
* ENH: Additional Eddy flags (nipy#1967)
* ENH: ReconAll handlers for less common cases (nipy#1966)
* ENH: FreeSurferSource now finds graymid/midthickness surfs (nipy#1972)
* ENH: Additional fslmaths dimensional reduction operations (nipy#1956)
* ENH: More options for RobustFOV interface (nipy#1923)
* ENH: Add MRIsCombine to FreeSurfer utils (nipy#1948)
* FIX: Level1Design EV parameter substitution (nipy#1953)
* FIX: Dcm2niix outputs can be uncompressed (nipy#1951)
* FIX: Ensure build fails in Circle when tests fail (nipy#1981)
* ENH: Add interface to antsAffineInitializer (nipy#1980)
* ENH: AFNI motion parameter support for FrameWiseDisplacement (nipy#1840)
* ENH: Add ANTs KellyKapowski interface (nipy#1845)
* FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (nipy#1728)
* FIX: Select Eddy run command at runtime (nipy#1871)
* FIX: Increase FLIRT's flexibility with apply_xfm (nipy#1875)
* DOC: Update FSL preprocess docstrings (nipy#1881)
* ENH: Support GIFTI outputs in SampleToSurface (nipy#1886)
* FIX: Configparser differences between PY2 and PY3 (nipy#1890)
* ENH: Add mris_expand interface (nipy#1893)
* FIX: Split over-eager globs in FreeSurferSource (nipy#1894)
* FIX: Store undefined by default so that xor checks don't trip (nipy#1903)
* FIX: Gantt chart generator PY3 compatibility (nipy#1907)
* FIX: Add DOF and --fsl-dof options to BBRegister (nipy#1917)
* ENH: Auto-derive input_names in Function (nipy#1918)
* FIX: Minor fixes for NonSteadyStateDetector (nipy#1926)
* DOC: Add duecredit references for AFNI and FSL (nipy#1930)
* ENH: Added zenodo (https://zenodo.org/) file (nipy#1924)
* ENH: Disable symlinks on CIFS filesystems (nipy#1941)
* ENH: Sphinx extension to plot workflows (nipy#1896)
* ENH: Added non-steady state detector for EPI data (nipy#1839)
* ENH: Enable new BBRegister init options for FSv6+ (nipy#1811)
* REF: Splits nipype.interfaces.utility into base, csv, and wrappers (nipy#1828)
* FIX: Makespec now runs with nipype in current directory (nipy#1813)
* FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (nipy#1796 + nipy#1831)
* ENH: DVARS includes intensity normalization feature - turned on by default (nipy#1827)
* FIX: DVARS is correctly using sum of squares instead of standard deviation (nipy#1827)
* ENH: Refactoring of nipype.interfaces.utility (nipy#1828)
* FIX: CircleCI were failing silently. Some fixes to tests (nipy#1833)
* FIX: Issues in Docker image permissions, and docker documentation (nipy#1825)
* ENH: Revised all Dockerfiles and automated deployment to Docker Hub
       from CircleCI (nipy#1815)
* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (nipy#1790)
* FIX: Cast DVARS float outputs to avoid memmap error (nipy#1777)
* FIX: FSL FNIRT intensity mapping files (nipy#1799)
* ENH: Additional outputs generated by FSL EDDY (nipy#1793)
* TST: Parallelize CircleCI build across 4 containers (nipy#1769)

0.13.0-rc1 (January 4, 2017)
============================

* FIX: Compatibility with traits 4.6 (nipy#1770)
* FIX: Multiproc deadlock (nipy#1756)
* TST: Replace nose and unittest with pytest (nipy#1722, nipy#1751)
* FIX: Semaphore capture using MultiProc plugin (nipy#1689)
* REF: Refactor AFNI interfaces (nipy#1678, nipy#1680)
* ENH: Move nipype commands to group command using click (nipy#1608)
* FIX: AFNI Retroicor interface fixes (nipy#1669)
* FIX: Minor errors after migration to setuptools (nipy#1671)
* ENH: Add AFNI 3dNote interface (nipy#1637)
* ENH: Abandon distutils, only use setuptools (nipy#1627)
* FIX: Minor bugfixes related to unicode literals (nipy#1656)
* TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
* ENH: Add signal extraction interface (nipy#1647)
* ENH: Add a DVARS calculation interface (nipy#1606)
* ENH: New interface to b0calc of FSL-POSSUM (nipy#1399)
* ENH: Add CompCor (nipy#1599)
* ENH: Add duecredit entries (nipy#1466)
* FIX: Python 3 compatibility fixes (nipy#1572)
* REF: Improved PEP8 compliance for fsl interfaces (nipy#1597)
* REF: Improved PEP8 compliance for spm interfaces (nipy#1593)
* TST: Replaced coveralls with codecov (nipy#1609)
* ENH: More BrainSuite interfaces (nipy#1554)
* ENH: Convenient load/save of interface inputs (nipy#1591)
* ENH: Add a Framewise Displacement calculation interface (nipy#1604)
* FIX: Use builtins open and unicode literals for py3 compatibility (nipy#1572)
* TST: reduce the size of docker images & use tags for images (nipy#1564)
* ENH: Implement missing inputs/outputs in FSL AvScale (nipy#1563)
* FIX: Fix symlink test in copyfile (nipy#1570, nipy#1586)
* ENH: Added support for custom job submission check in SLURM (nipy#1582)
* ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
       (nipy#1654)

0.13.0

Release 0.13.0 (May 11, 2017)

=============================

* ENH: Multi-stage recon-all directives (nipy#1991)
* FIX: FEAT "folder does not exist" error (nipy#2000)
* ENH: Niftyfit interfaces (nipy#1910)
* FIX: Define ANTSPATH for BrainExtraction automatically (nipy#1986)
* ENH: New trait for imaging files (nipy#1949)
* ENH: Niftyseg interfaces (nipy#1911)
* ENH: Niftyreg interfaces (nipy#1913)
* MRG: Allow more support for CLI (nipy#1908)
* ENH: 3dQwarpPlusMinus interface (nipy#1974)
* FIX: PY3.6 support (nipy#1977)
* FIX: PY3 and stream fixes for MRTrix2TrackVis (nipy#1804)
* ENH: More mask options for CompCor interfaces (nipy#1968 + nipy#1992)
* ENH: Additional TOPUP outputs (nipy#1976)
* ENH: Additional Eddy flags (nipy#1967)
* ENH: ReconAll handlers for less common cases (nipy#1966)
* ENH: FreeSurferSource now finds graymid/midthickness surfs (nipy#1972)
* ENH: Additional fslmaths dimensional reduction operations (nipy#1956)
* ENH: More options for RobustFOV interface (nipy#1923)
* ENH: Add MRIsCombine to FreeSurfer utils (nipy#1948)
* FIX: Level1Design EV parameter substitution (nipy#1953)
* FIX: Dcm2niix outputs can be uncompressed (nipy#1951)
* FIX: Ensure build fails in Circle when tests fail (nipy#1981)
* ENH: Add interface to antsAffineInitializer (nipy#1980)
* ENH: AFNI motion parameter support for FrameWiseDisplacement (nipy#1840)
* ENH: Add ANTs KellyKapowski interface (nipy#1845)
* FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (nipy#1728)
* FIX: Select Eddy run command at runtime (nipy#1871)
* FIX: Increase FLIRT's flexibility with apply_xfm (nipy#1875)
* DOC: Update FSL preprocess docstrings (nipy#1881)
* ENH: Support GIFTI outputs in SampleToSurface (nipy#1886)
* FIX: Configparser differences between PY2 and PY3 (nipy#1890)
* ENH: Add mris_expand interface (nipy#1893)
* FIX: Split over-eager globs in FreeSurferSource (nipy#1894)
* FIX: Store undefined by default so that xor checks don't trip (nipy#1903)
* FIX: Gantt chart generator PY3 compatibility (nipy#1907)
* FIX: Add DOF and --fsl-dof options to BBRegister (nipy#1917)
* ENH: Auto-derive input_names in Function (nipy#1918)
* FIX: Minor fixes for NonSteadyStateDetector (nipy#1926)
* DOC: Add duecredit references for AFNI and FSL (nipy#1930)
* ENH: Added zenodo (https://zenodo.org/) file (nipy#1924)
* ENH: Disable symlinks on CIFS filesystems (nipy#1941)
* ENH: Sphinx extension to plot workflows (nipy#1896)
* ENH: Added non-steady state detector for EPI data (nipy#1839)
* ENH: Enable new BBRegister init options for FSv6+ (nipy#1811)
* REF: Splits nipype.interfaces.utility into base, csv, and wrappers (nipy#1828)
* FIX: Makespec now runs with nipype in current directory (nipy#1813)
* FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (nipy#1796 + nipy#1831)
* ENH: DVARS includes intensity normalization feature - turned on by default (nipy#1827)
* FIX: DVARS is correctly using sum of squares instead of standard deviation (nipy#1827)
* ENH: Refactoring of nipype.interfaces.utility (nipy#1828)
* FIX: CircleCI were failing silently. Some fixes to tests (nipy#1833)
* FIX: Issues in Docker image permissions, and docker documentation (nipy#1825)
* ENH: Revised all Dockerfiles and automated deployment to Docker Hub
       from CircleCI (nipy#1815)
* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (nipy#1790)
* FIX: Cast DVARS float outputs to avoid memmap error (nipy#1777)
* FIX: FSL FNIRT intensity mapping files (nipy#1799)
* ENH: Additional outputs generated by FSL EDDY (nipy#1793)
* TST: Parallelize CircleCI build across 4 containers (nipy#1769)
* FIX: Compatibility with traits 4.6 (nipy#1770)
* FIX: Multiproc deadlock (nipy#1756)
* TST: Replace nose and unittest with pytest (nipy#1722, nipy#1751)
* FIX: Semaphore capture using MultiProc plugin (nipy#1689)
* REF: Refactor AFNI interfaces (nipy#1678, nipy#1680)
* ENH: Move nipype commands to group command using click (nipy#1608)
* FIX: AFNI Retroicor interface fixes (nipy#1669)
* FIX: Minor errors after migration to setuptools (nipy#1671)
* ENH: Add AFNI 3dNote interface (nipy#1637)
* ENH: Abandon distutils, only use setuptools (nipy#1627)
* FIX: Minor bugfixes related to unicode literals (nipy#1656)
* TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
* ENH: Add signal extraction interface (nipy#1647)
* ENH: Add a DVARS calculation interface (nipy#1606)
* ENH: New interface to b0calc of FSL-POSSUM (nipy#1399)
* ENH: Add CompCor (nipy#1599)
* ENH: Add duecredit entries (nipy#1466)
* FIX: Python 3 compatibility fixes (nipy#1572)
* REF: Improved PEP8 compliance for fsl interfaces (nipy#1597)
* REF: Improved PEP8 compliance for spm interfaces (nipy#1593)
* TST: Replaced coveralls with codecov (nipy#1609)
* ENH: More BrainSuite interfaces (nipy#1554)
* ENH: Convenient load/save of interface inputs (nipy#1591)
* ENH: Add a Framewise Displacement calculation interface (nipy#1604)
* FIX: Use builtins open and unicode literals for py3 compatibility (nipy#1572)
* TST: reduce the size of docker images & use tags for images (nipy#1564)
* ENH: Implement missing inputs/outputs in FSL AvScale (nipy#1563)
* FIX: Fix symlink test in copyfile (nipy#1570, nipy#1586)
* ENH: Added support for custom job submission check in SLURM (nipy#1582)
* ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
       (nipy#1654)

0.13.0-rc1

Merge pull request nipy#1772 from satra/rel/0.13.0-rc1

Rel/0.13.0 rc1

0.12.1

Update CHANGES

0.12.0

Update requirements.txt

0.12.0-rc2

Merge pull request nipy#1519 from satra/rel/0.12.0-rc2

updates for 0.12.0-rc2

0.12.0-rc1

Merge pull request nipy#1449 from satra/rel/0.12rc1

final changes before tagging release candidate

0.11.0

fix: version compilation

0.11.0-rc1

Update .travis.yml

0.10.0

release 0.10.0