1.10.0 (March 19, 2025)
=======================

New feature release in the 1.10.x series.

This release adds GPUs to multiprocess resource management.
In general, no changes to existing code should be required if the GPU-enabled
interface has a ``use_gpu`` input.
The ``n_gpu_procs`` can be used to set the number of GPU processes that may
be run in parallel, which will override the default of GPUs identified by
``nvidia-smi``, or 1 if no GPUs are detected.

  * FIX: Reimplement ``gpu_count()`` (https://github.com/nipy/nipype/pull/3718)
  * FIX: Avoid 0D array in ``algorithms.misc.merge_rois`` (https://github.com/nipy/nipype/pull/3713)
  * FIX: Allow nipype.sphinx.ext.apidoc Config to work with Sphinx 8.2.1+ (https://github.com/nipy/nipype/pull/3716)
  * FIX: Resolve crashes when running workflows with updatehash=True (https://github.com/nipy/nipype/pull/3709)
  * ENH: Support for gpu queue (https://github.com/nipy/nipype/pull/3642)
  * ENH: Update to .wci.yml (https://github.com/nipy/nipype/pull/3708)
  * ENH: Add Workflow Community Initiative (WCI) descriptor (https://github.com/nipy/nipype/pull/3608)


1.9.2 (December 17, 2024)
=========================

Bug fix release in the 1.9.x series.

  * FIX: Missed np.savetxt bstring (https://github.com/nipy/nipype/pull/3704)
  * MAINT: Bump astral-sh/setup-uv from 3 to 4 (https://github.com/nipy/nipype/pull/3702)
  * MAINT: Bump codecov/codecov-action from 4 to 5 (https://github.com/nipy/nipype/pull/3703)


1.9.1 (November 19, 2024)
=========================

Bug fix release in the 1.9.x series.

This release adds support for Numpy 2 and Python 3.13.

  * FIX: Restore generate_gantt_chart functionality (https://github.com/nipy/nipype/pull/3290)
  * FIX: Address numpy and traits deprecations (https://github.com/nipy/nipype/pull/3699)
  * FIX: `ts_Z_corr` → `ts_wb_Z` (https://github.com/nipy/nipype/pull/3697)
  * ENH: Remove unused and recently unsupported antsRegistration flag (https://github.com/nipy/nipype/pull/3695)
  * MAINT: Bump codecov/codecov-action from 4 to 5 (https://github.com/nipy/nipype/pull/3698)


1.9.0 (October 31, 2024)
========================

New feature release in the 1.9.x series.

  * FIX: Remove exists=True from fsl.MotionOutliers output that might not exist (https://github.com/nipy/nipype/pull/1428)
  * FIX: Improve evaluate_connect_function errors across Python versions (https://github.com/nipy/nipype/pull/3655)
  * FIX: Changed inheritance of TensorMetricsInputSpec (https://github.com/nipy/nipype/pull/3663)
  * FIX: Add cropped files to dcm2niix output  (https://github.com/nipy/nipype/pull/3609)
  * FIX: Deduplicate dcm2niix output (https://github.com/nipy/nipype/pull/3610)
  * FIX: Parse commas in CSV fields (https://github.com/nipy/nipype/pull/3637)
  * FIX: MRTrix3 change inputs position for MRTransform (https://github.com/nipy/nipype/pull/3611)
  * FIX: Use out_prefix instead of "w" in spm.Normalize12 (https://github.com/nipy/nipype/pull/3600)
  * FIX: Fix typo in spm.Normalize12 process (https://github.com/nipy/nipype/pull/3599)
  * FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596)
  * FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596)
  * FIX: Fix bugs with ``fsl_out=True`` and ``lta_out=True`` (https://github.com/nipy/nipype/pull/3583)
  * FIX: Test failures (https://github.com/nipy/nipype/pull/3587)
  * FIX: update merge_imgs input type of dcm2niix Node (https://github.com/nipy/nipype/pull/3548)
  * FIX: update sample_random_points and random_seed type of ProbTrackXBaseInputSpec (https://github.com/nipy/nipype/pull/3556)
  * FIX: update self.inputs.optimization in outputs for GTMPVC (https://github.com/nipy/nipype/pull/3571)
  * ENH: Support HDF5 (mat 7.3) SPM.mat files (https://github.com/nipy/nipype/pull/3650)
  * ENH: FILMGLS gifti output support in surface mode (https://github.com/nipy/nipype/pull/3652)
  * ENH: Added available inputs for MRTrix3's 5ttgen (https://github.com/nipy/nipype/pull/3658)
  * ENH: Add functions to mrtrix3 interface (https://github.com/nipy/nipype/pull/3613)
  * ENH: Update PETsurfer interface (https://github.com/nipy/nipype/pull/3602)
  * ENH: Add 'hsvs' option to 5ttgen + mrtransform fix (https://github.com/nipy/nipype/pull/3630)
  * ENH: add STC PVC to PETPVC interface (https://github.com/nipy/nipype/pull/3634)
  * ENH: Add GenericLabel to ANTS ApplyTransforms. (https://github.com/nipy/nipype/pull/3617)
  * ENH: Issue 3553 add mvecs to dcm2niix (https://github.com/nipy/nipype/pull/3554)
  * ENH: add contrast outputs for EstimatedModel  (https://github.com/nipy/nipype/pull/3577)
  * ENH: Issue 3345: Adding FreeSurfer longitudinal interfaces (https://github.com/nipy/nipype/pull/3529)
  * ENH: Enable SPM voxel-based FDR (https://github.com/nipy/nipype/pull/3558)
  * REF: Replace deprecated pkgutil.find_loader with importlib.util.find_spec (https://github.com/nipy/nipype/pull/3692)
  * REF: io.open() → open() (https://github.com/nipy/nipype/pull/3575)
  * REF: Stop using deprecated import internally (https://github.com/nipy/nipype/pull/3561)
  * DOC: Patch doc/conf.py to work with latest ReadTheDocs (https://github.com/nipy/nipype/pull/3691)
  * DOC/FIX: Fix wrong name, should be al_ea (https://github.com/nipy/nipype/pull/3629)
  * DOC: Fix typos newly found by codespell (https://github.com/nipy/nipype/pull/3606)
  * STY: Apply ruff/pycodestyle rules (E) (https://github.com/nipy/nipype/pull/3689)
  * STY: Apply ruff rules (RUF) again (https://github.com/nipy/nipype/pull/3688)
  * STY: Apply ruff/Pyflakes rules (F) (https://github.com/nipy/nipype/pull/3681)
  * STY: Apply ruff/Perflint rules (PERF) again (https://github.com/nipy/nipype/pull/3687)
  * STY: Apply ruff/flake8-comprehensions preview rules (C4) (https://github.com/nipy/nipype/pull/3686)
  * STY: Apply ruff/flake8-simplify rules (SIM) (https://github.com/nipy/nipype/pull/3676)
  * STY: Apply ruff/flake8-bugbear rules (B) (https://github.com/nipy/nipype/pull/3671)
  * STY: Apply ruff/flake8-comprehensions rules (C4)  (https://github.com/nipy/nipype/pull/3680)
  * STY: Apply ruff/Perflint rules (PERF) (https://github.com/nipy/nipype/pull/3674)
  * STY: Apply ruff/flake8-implicit-str-concat rules (ISC) (https://github.com/nipy/nipype/pull/3679)
  * STY: Apply ruff/flake8-pie rules (PIE) (https://github.com/nipy/nipype/pull/3678)
  * STY: Apply ruff/flake8-raise rules (RSE) (https://github.com/nipy/nipype/pull/3677)
  * STY: Apply ruff/flynt rules (FLY) (https://github.com/nipy/nipype/pull/3675)
  * STY: Apply ruff rules (RUF) (https://github.com/nipy/nipype/pull/3673)
  * STY: Codespell (https://github.com/nipy/nipype/pull/3672)
  * STY: Apply ruff/refurb rules (https://github.com/nipy/nipype/pull/3648)
  * STY: Apply ruff/pyupgrade rules (https://github.com/nipy/nipype/pull/3647)
  * STY: Adjusted variable names for clarity and codespell false positives (https://github.com/nipy/nipype/pull/3627)
  * STY: Remove duplicated trait in EddyOutputSpec (https://github.com/nipy/nipype/pull/3568)
  * STY: Black edits (https://github.com/nipy/nipype/pull/1)
  * MNT: Replace deprecated imghdr (https://github.com/nipy/nipype/pull/3659)
  * MNT: Use regular ".now" instead of ".utcnow" with UTC zone (https://github.com/nipy/nipype/pull/3670)
  * MNT: Apply assorted repo-review rules (https://github.com/nipy/nipype/pull/3682)
  * MNT: Drop traits upper bound (https://github.com/nipy/nipype/pull/3685)
  * MNT: Configure dependabot to update GH workflows (https://github.com/nipy/nipype/pull/3597)
  * MNT: Replace deprecated locale.getdefaultlocale (https://github.com/nipy/nipype/pull/3590)
  * MNT: Require Python 3.8+, auto-upgrade syntax (https://github.com/nipy/nipype/pull/3588)
  * CI: Test Python 3.12 support (https://github.com/nipy/nipype/pull/3638)
  * CI: Test on Python 3.11 (https://github.com/nipy/nipype/pull/3589)
  * CI/FIX: configure codespell, add workflow, typos fixed (https://github.com/nipy/nipype/pull/3549)


1.8.6 (April 05, 2023)
======================

Bug-fix release in the 1.8.x series.

  * FIX: Update dcmstack interface for Py3 / newer pydicom (https://github.com/nipy/nipype/pull/3541)
  * FIX: NiBabel 5, and NetworkX 3 and DIPY 1.6 compatibility (https://github.com/nipy/nipype/pull/3538)
  * FIX: Check for non-mandatory output in DWIBiasCorrect (https://github.com/nipy/nipype/pull/3523)
  * FIX: Removed leftover debug print statement in FEAT class (https://github.com/nipy/nipype/pull/3521)
  * DOC: Fix a few more typos (https://github.com/nipy/nipype/pull/3516)
  * DOC: Fix typos found by codespell (https://github.com/nipy/nipype/pull/3512)
  * CI: Drop nipy tests until a fixed nipy is released (https://github.com/nipy/nipype/pull/3559)
  * CI: Disable nipy tests generally, re-add with max numpy  (https://github.com/nipy/nipype/pull/3532)
  * CI: GitHub Workflows security hardening  (https://github.com/nipy/nipype/pull/3519)
  * CI: Allow tutorial test cancellation (https://github.com/nipy/nipype/pull/3514)


1.8.5 (September 21, 2022)
==========================

Bug-fix release in the 1.8.x series.

  * FIX: Use interpolation/method in numpy.percentile as available (https://github.com/nipy/nipype/pull/3506)
  * FIX: Deployed Matlab applications must not call addpath() (https://github.com/nipy/nipype/pull/3509)
  * FIX: Provide more runtime information when node execution fails (https://github.com/nipy/nipype/pull/3505)
  * FIX: Fixed bug for work dirs longer than 255 characters, fixes #2061  (https://github.com/nipy/nipype/pull/3495)
  * FIX: Update ApplyVDM to handle 4D inputs  (https://github.com/nipy/nipype/pull/3500)
  * ENH: Explicitly specify write_text encoding format (https://github.com/nipy/nipype/pull/3508)
  * DOC: Fix typos found by copdespell (https://github.com/nipy/nipype/pull/3510)
  * MAINT: Add github action to trigger tutorials for release branches (https://github.com/nipy/nipype/pull/3504)
  * CI: Set up build-test-deploy workflow on GHA (https://github.com/nipy/nipype/pull/3513)


1.8.4 (September 01, 2022)
==========================

Bug-fix release in the 1.8.x series.

This release sets a maximum traits version to avoid new, breaking changes.

  * MNT: Pin traits < 6.4 (https://github.com/nipy/nipype/pull/3501)
  * ENH: Add inputs to mrtrix3.DWIPreprocInputSpec and remove mandatory annotation for pe_dir (https://github.com/nipy/nipype/pull/3470)


1.8.3 (July 14, 2022)
=====================

Bug-fix release in the 1.8.x series.

This release includes compatibility fixes for nibabel 4.x and resolves a denial-of-service
bug when the etelemetry server is down that resulted in excessive (blocking) network hits that
would cause any tools using nipype interfaces to take a very long time.

(`Full changelog <https://github.com/nipy/nipype/milestone/1.8.3?closed=1>`__)

  * FIX: Argument order to ``numpy.save()`` (https://github.com/nipy/nipype/pull/3485)
  * FIX: Add tolerance parameter to ComputeDVARS (https://github.com/nipy/nipype/pull/3489)
  * FIX: Delay access of nibabel.trackvis until actually needed (https://github.com/nipy/nipype/pull/3488)
  * FIX: Avoid excessive etelemetry pings (https://github.com/nipy/nipype/pull/3484)
  * ENH: Added outputs' generation to DWIBiascorrect interface (https://github.com/nipy/nipype/pull/3476)


1.8.2 (June 06, 2022)
=====================

Bug-fix release in the 1.8.x series.

This release restores compatibility with networkx 2.8.3, which errors when
graph nodes might conflict with pydot parsing.

(`Full changelog <https://github.com/nipy/nipype/milestone/1.8.2?closed=1>`__)

  * ENH: Enable compression with Gunzip interface (https://github.com/nipy/nipype/pull/3472)
  * CI: Schedule weekly tests with cron (https://github.com/nipy/nipype/pull/3480)


1.8.1 (May 16, 2022)
====================

Bug-fix release in the 1.8.x series.

The previous release vendored ``distutils.version.LooseVersion``, and the vendored objects did not
preserve compatibility with the ``distutils`` objects. This release switches to the
``looseversion`` package that ensures compatibility.


1.8.0 (May 10, 2022)
====================

New feature release in the 1.8.x series.

The primary new features are a batch of PETSurfer interfaces.

This release drops support for Python < 3.7 and Numpy < 1.17, triggering a minor version bump.
Additionally, matplotlib < 2.1 will stop working with some interfaces, but more recent versions
will start working.

(`Full changelog <https://github.com/nipy/nipype/milestone/1.8.0?closed=1>`__)

  * FIX: Change plt.hist() argument from deprecated 'normed' to 'density' (https://github.com/nipy/nipype/pull/3455)
  * ENH: Add random seed option to ANTs registration (https://github.com/nipy/nipype/pull/3463)
  * ENH: Add PETsurfer interfaces (https://github.com/nipy/nipype/pull/3437)
  * ENH: Add Text2Vest and Vest2Text interfaces (https://github.com/nipy/nipype/pull/3447)
  * REF: Optimize ICC_rep_anova with a memoized helper function (https://github.com/nipy/nipype/pull/3454)
  * REF: Rearranging matmul order and using hermitian flag in ICC_rep_anova  (https://github.com/nipy/nipype/pull/3453)
  * MNT: Drop distutils (https://github.com/nipy/nipype/pull/3458)
  * CI: Cache test data (https://github.com/nipy/nipype/pull/3459)


1.7.1 (April 05, 2022)
======================

(`Full changelog <https://github.com/nipy/nipype/milestone/1.7.1?closed=1>`__)

  * FIX: Allow ``ConvertScalarImageToRGBInputSpec.mask_file`` to be ``"none"`` (https://github.com/nipy/nipype/pull/3364)
  * FIX: Use a more robust strategy for detecting ANTs version (https://github.com/nipy/nipype/pull/3444)
  * FIX: Retry renaming pkl(z) files on failure (https://github.com/nipy/nipype/pull/3404)
  * FIX: Escape metacharacters when parsing dcm2niix outputs (https://github.com/nipy/nipype/pull/3417)
  * FIX: Import error for nipype.interfaces.dipy.base (https://github.com/nipy/nipype/pull/3414)
  * FIX: ``ValueError`` when using ``ResourceMonitor`` (https://github.com/nipy/nipype/pull/3419)
  * FIX: Improve error handling of ``CommandLine`` interfaces (https://github.com/nipy/nipype/pull/3395)
  * FIX: Bugs in ApplyVDM interface (https://github.com/nipy/nipype/pull/3396)
  * ENH: Add MRTrix3 interfaces (pared-down gh-3426) (https://github.com/nipy/nipype/pull/3445)
  * ENH: Enable BidsDataGrabber to load saved layouts (https://github.com/nipy/nipype/pull/3421)
  * ENH: ROBEX interface (https://github.com/nipy/nipype/pull/3443)
  * ENH: Include several operations to ANTs's ImageMath interface, including ReplicateImage and ReplicateDisplacement (https://github.com/nipy/nipype/pull/3435)
  * ENH: Add "GenericLabel" to antsRegistration interpolation option. (https://github.com/nipy/nipype/pull/3424)
  * ENH: added Apply VDM functionality to FieldMap SPM interface (https://github.com/nipy/nipype/pull/3394)
  * DOC: Side bar and main page fixes (https://github.com/nipy/nipype/pull/3397)
  * TEST: Allow SVD columns to flip sign (https://github.com/nipy/nipype/pull/3405)
  * MNT: rename dipy ``move_streamlines`` to ``transform_tracking_output`` (https://github.com/nipy/nipype/pull/3412)
  * MNT: Test on Python 3.10 (https://github.com/nipy/nipype/pull/3438)
  * MNT: Added ORCID iD (https://github.com/nipy/nipype/pull/3436)


1.7.0 (October 20, 2021)
========================

(`Full changelog <https://github.com/nipy/nipype/milestone/1.7.0?closed=1>`__)

  * FIX: Make ants.LaplacianThickness output_image a string, not file (https://github.com/nipy/nipype/pull/3393)
  * FIX: coord for mrconvert (https://github.com/nipy/nipype/pull/3369)
  * FIX: ``antsRegistration`` allows the ``restrict_deformation`` to be float  (https://github.com/nipy/nipype/pull/3387)
  * FIX: Also allow `errno.EBUSY` during `emptydirs` on NFS  (https://github.com/nipy/nipype/pull/3357)
  * FIX: Removed exists=True from MathsOutput (https://github.com/nipy/nipype/pull/3385)
  * FIX: Extension not extensions, after pybids v0.9 (https://github.com/nipy/nipype/pull/3380)
  * ENH: Add CAT12 SANLM denoising filter (https://github.com/nipy/nipype/pull/3374)
  * ENH: Add expected steps for FreeSurfer 7 recon-all  (https://github.com/nipy/nipype/pull/3389)
  * ENH: Stop printing false positive differences when logging cached nodes  (https://github.com/nipy/nipype/pull/3376)
  * ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform)  (https://github.com/nipy/nipype/pull/3365)
  * ENH: ``verbose`` input should not be hashed in ``ants.Registration`` (https://github.com/nipy/nipype/pull/3377)
  * REF: Clean-up the BaseInterface ``run()`` function using context (https://github.com/nipy/nipype/pull/3347)
  * DOC: Fix typo in README  (https://github.com/nipy/nipype/pull/3386)
  * STY: Make private member name consistent with the rest of them (https://github.com/nipy/nipype/pull/3346)
  * MNT: Simplify interface execution and better error handling of ``Node`` (https://github.com/nipy/nipype/pull/3349)
  * MNT: Add user name and email to Docker to appease git/annex/datalad (https://github.com/nipy/nipype/pull/3378)
  * CI: Update CircleCI machine image  (https://github.com/nipy/nipype/pull/3391)

1.6.1 (June 16, 2021)
=====================

Bug-fix release in the 1.6.x series.

(`Full changelog <https://github.com/nipy/nipype/milestone/1.6.1?closed=1>`__)

  * FIX: Set DistributedPluginBase.refidx type correctly (https://github.com/nipy/nipype/pull/3340)
  * FIX: change fsl interface randomise --f_only to --fonly for #3322 (https://github.com/nipy/nipype/pull/3325)
  * FIX: BET raising "No image files match: ..." with very long file names (https://github.com/nipy/nipype/pull/3309)
  * FIX: Update SmoothEstimateOutputSpec resels description (https://github.com/nipy/nipype/pull/3316)
  * ENH: Adds interfaces for MRtrix utils shconv and sh2amp (https://github.com/nipy/nipype/pull/3280)
  * ENH: Interface for R (https://github.com/nipy/nipype/pull/3291)
  * ENH: Add CAT12 interfaces (https://github.com/nipy/nipype/pull/3310)
  * ENH: AFNI 3dNetCorr as afni.NetCorr (https://github.com/nipy/nipype/pull/3263)
  * ENH: Skip newline before Python call in batch submission to facilitate containerized runs (https://github.com/nipy/nipype/pull/3297)
  * ENH: Add new dwifslpreproc interface for MRtrix3 (https://github.com/nipy/nipype/pull/3278)
  * REF: Cache nodes in workflow to speed up construction, other optimizations (https://github.com/nipy/nipype/pull/3331)
  * DOC: Fixed Developer Setup Link in install.rst (https://github.com/nipy/nipype/pull/3330)
  * MNT: Blacklist Dipy 1.4.1 (https://github.com/nipy/nipype/pull/3335)
  * MNT: Drop support for numpy < 1.15.3 (https://github.com/nipy/nipype/pull/3284)
  * CI: Build docker images with Python 3.8 (https://github.com/nipy/nipype/pull/3287)
  * CI: Drop Circle doc builds (https://github.com/nipy/nipype/pull/3338)
  * CI: Drop Travis (https://github.com/nipy/nipype/pull/3332)
  * CI: Build docker images with Python 3.8 (https://github.com/nipy/nipype/pull/3287)
  * CI: Add specs and style checks (https://github.com/nipy/nipype/pull/3321)
  * CI: Move from Travis to GitHub actions (https://github.com/nipy/nipype/pull/3318)

1.6.0 (November 28, 2020)
=========================

New feature release in the 1.6.x series.

In addition to the usual bug fixes, significant reductions were made
in workflow startup costs.

(`Full changelog <https://github.com/nipy/nipype/milestone/1.6.0?closed=1>`__)

  * FIX: Canonicalize environment dicts to strings in Windows (https://github.com/nipy/nipype/pull/3267)
  * FIX: Purge deprecated exception content accesses (https://github.com/nipy/nipype/pull/3272)
  * FIX: Handle changes in CLI structure of mrtrix3.DWIBiasCorrect (https://github.com/nipy/nipype/pull/3248)
  * FIX: EpiReg changed to not list certain outputs when 'wmseg' input is specified (https://github.com/nipy/nipype/pull/3265)
  * FIX: CI issues (https://github.com/nipy/nipype/pull/3262)
  * FIX: SPM SliceTiming must accept either Int or float for ref_slice and sli… (https://github.com/nipy/nipype/pull/3255)
  * FIX: Raise version error when using ``-g`` with ``antsAI`` < 2.3.0 (https://github.com/nipy/nipype/pull/3256)
  * FIX: No longer depending on pydotplus (networkx >=2.0 update) (https://github.com/nipy/nipype/pull/3251)
  * FIX: ANTs' utilities revision - bug fixes and add more operations to ``ants.ImageMath`` (https://github.com/nipy/nipype/pull/3236)
  * ENH: Handle unavailable traits due to version differences (https://github.com/nipy/nipype/pull/3273)
  * ENH: Optimize workflow.run performance (https://github.com/nipy/nipype/pull/3260)
  * DOC: Remove myself (@mr-c) from the zenodo metadata (https://github.com/nipy/nipype/pull/3271)

1.5.1 (August 16, 2020)
=======================

Bug-fix release in the 1.5.x series.

This release includes small updates to ANTs utilities that lie somewhere
between bug fixes and enhancements.

(`Full changelog <https://github.com/nipy/nipype/milestone/1.5.1?closed=1>`__)

  * FIX: Warn for min/max_ver traits when tool version can't be parsed (https://github.com/nipy/nipype/pull/3241)
  * FIX: Serialize all interface arguments when exporting workflows (https://github.com/nipy/nipype/pull/3240)
  * FIX: Permit identity transforms in list of transforms given to ants.ApplyTransforms (https://github.com/nipy/nipype/pull/3237)
  * FIX: ANTs' utilities revision - bug fixes and add more operations to ``ants.ImageMath`` (https://github.com/nipy/nipype/pull/3236)
  * DOC: Skip BIDSDataGrabber doctest if pybids is missing (https://github.com/nipy/nipype/pull/3224)

1.5.0 (June 03, 2020)
=====================

New feature release in the 1.5.x series.

In this release, the example scripts have been split out into their own package:
`niflow-nipype1-examples <https://github.com/niflows/nipype1-examples>`__.

(`Full changelog <https://github.com/nipy/nipype/milestone/1.5.0?closed=1>`__)

  * FIX: volterra_expansion_order documentation error (https://github.com/nipy/nipype/pull/3213)
  * FIX: BET incorrect output paths (https://github.com/nipy/nipype/pull/3214)
  * FIX: Terminal output in ``report.rst`` spreads one line per character (https://github.com/nipy/nipype/pull/3220)
  * FIX: Allow parsing freesurfer 7 version string (https://github.com/nipy/nipype/pull/3216)
  * FIX: Use PackageInfo to get NiftyReg version (https://github.com/nipy/nipype/pull/3194)
  * FIX: Partial rollback of N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3188)
  * FIX: ANTs' tools maintenance overhaul (https://github.com/nipy/nipype/pull/3180)
  * FIX: load_resultfile crashes if open resultsfile from crashed job (https://github.com/nipy/nipype/pull/3182)
  * FIX: FSL model.py make multiple F-tests (https://github.com/nipy/nipype/pull/3166)
  * ENH: Restore ants.legacy interfaces (https://github.com/nipy/nipype/pull/3222)
  * ENH: Add ``"TruncateImageIntensity"`` operation to ``ants.utils.Image.Math`` (https://github.com/nipy/nipype/pull/3210)
  * ENH: SPM NewSegment multi-channel segmentation (https://github.com/nipy/nipype/pull/3162)
  * ENH: Add reverse-ordered transform lists to ants.Registration outputs (https://github.com/nipy/nipype/pull/3192)
  * ENH: Improve workflow connect performance (https://github.com/nipy/nipype/pull/3184)
  * ENH: Add ``ConstrainedSphericalDeconvolution`` interface to replace ``EstimateFOD`` for MRtrix3's ``dwi2fod`` (https://github.com/nipy/nipype/pull/3176)
  * ENH: Detect values for EulerNumber interface (https://github.com/nipy/nipype/pull/3173)
  * ENH: Remove examples from repository (https://github.com/nipy/nipype/pull/3172)
  * TEST: Clean up tests (https://github.com/nipy/nipype/pull/3195)
  * TEST: Mock terminal output before testing changing default value (https://github.com/nipy/nipype/pull/3193)
  * REF: make invocations of python and pytest consistent with the one used/desired python (https://github.com/nipy/nipype/pull/3208)
  * REF: Prefer math.gcd to hand-rolled Euclid's algorithm (https://github.com/nipy/nipype/pull/3177)
  * REF: Removed all uses of numpy_mmap (https://github.com/nipy/nipype/pull/3121)
  * DOC: Sphinx 3 compatibility (https://github.com/nipy/nipype/pull/3206)
  * DOC: Update links, typos in contributing guide (https://github.com/nipy/nipype/pull/3160)
  * DOC: Update SelectFiles docstring to match actual behavior (https://github.com/nipy/nipype/pull/3041)
  * DOC: Updated .zenodo.json file (https://github.com/nipy/nipype/pull/3167)
  * DOC: Update .zenodo.json (https://github.com/nipy/nipype/pull/3165)
  * MNT: Permit recent nilearns (https://github.com/nipy/nipype/pull/2841)
  * MNT: Test Python 3.8 (https://github.com/nipy/nipype/pull/3154)
  * MNT: Restore ReadTheDocs (https://github.com/nipy/nipype/pull/3207)
  * MNT: Update Zenodo ordering based on commit count (https://github.com/nipy/nipype/pull/3169)

1.4.2 (February 14, 2020)
=========================
(`Full changelog <https://github.com/nipy/nipype/milestone/1.4.2?closed=1>`__)

  * FIX: Allow ``fsl.MultipleRegressDesign`` to create multiple F-tests (https://github.com/nipy/nipype/pull/3166)
  * FIX: Reliably parse SGE job IDs in the presence of warnings (https://github.com/nipy/nipype/pull/3168)
  * FIX: Move TraitType import, handle API change for NoDefaultSpecified (https://github.com/nipy/nipype/pull/3159)

1.4.1 (January 27, 2020)
========================
(`Full changelog <https://github.com/nipy/nipype/milestone/1.4.1?closed=1>`__)

  * FIX: DataSink to S3 buckets (https://github.com/nipy/nipype/pull/3130)
  * FIX: improve version checking for nodes of workflows (https://github.com/nipy/nipype/pull/3152)
  * FIX: mapnode to generate result file when crashes in single node mode (https://github.com/nipy/nipype/pull/3143)
  * FIX: Can't seem to import workflows from niflows in CircleCI (https://github.com/nipy/nipype/pull/3134)
  * FIX: Repair aftermath of docs refactor (https://github.com/nipy/nipype/pull/3133)
  * FIX: change ANTS number_of_time_steps from Float to Int (https://github.com/nipy/nipype/pull/3118)
  * DOC: Revise generation of examples to work in RTD (https://github.com/nipy/nipype/pull/3132)
  * DOC: Bring examples generation back to ``doc/conf.py`` (https://github.com/nipy/nipype/pull/3131)
  * DOC: Documentation overhaul (https://github.com/nipy/nipype/pull/3124)
  * DOC: Deep revision of documentation building (https://github.com/nipy/nipype/pull/3120)
  * DOC: Deduplicate code for Sphinx's APIdoc generation (https://github.com/nipy/nipype/pull/3119)
  * MNT: Update requirements.txt post-1.4 (https://github.com/nipy/nipype/pull/3153)


1.4.0 (December 20, 2019)
=========================
(`Full changelog <https://github.com/nipy/nipype/milestone/37?closed=1>`__)

  * FIX: Mark strings containing regex escapes as raw (https://github.com/nipy/nipype/pull/3106)
  * ENH: Pacify DeprecationWarnings caused by nibabel 3 pre-release (https://github.com/nipy/nipype/pull/3099)
  * ENH: Allow Nipype configuration directory to be specified with NIPYPE_CONFIG_DIR environment variable (https://github.com/nipy/nipype/pull/3073)
  * ENH: Add options and outputs to ``fsl.Eddy`` interface (https://github.com/nipy/nipype/pull/3034)
  * ENH: Add skull_file output to fsl.BET interface (https://github.com/nipy/nipype/pull/3095)
  * RF: Drop various remaining compatibilities for Python < 3.5 (https://github.com/nipy/nipype/pull/2831)
  * DOC: Add Python 2 statement to README, reference maintenance branch in CONTRIBUTING (https://github.com/nipy/nipype/pull/3115)
  * DOC: Miss underline before cmd in example code (https://github.com/nipy/nipype/pull/3107)
  * STY: Black (https://github.com/nipy/nipype/pull/3096)
  * MNT: Set junit_family to suppress pytest warning (https://github.com/nipy/nipype/pull/3111)
  * MNT: Fix Dorota Jarecka ORCID (https://github.com/nipy/nipype/pull/3100)
  * MNT: Drop Python 2 support (https://github.com/nipy/nipype/pull/2654)


1.3.1 (November 12, 2019)
=========================
  * FIX: Restore checking traits or bunch (https://github.com/nipy/nipype/pull/3094)


1.3.0 (November 11, 2019)
=========================
(`Full changelog <https://github.com/nipy/nipype/milestone/34?closed=1>`__)

  * FIX: Fixed typo in QwarpInputSpec Trait description (https://github.com/nipy/nipype/pull/3079)
  * FIX: Restore ``AFNICommand._get_fname``, required by some interfaces (https://github.com/nipy/nipype/pull/3071)
  * FIX: Remove asynchronous chdir callback (https://github.com/nipy/nipype/pull/3060)
  * FIX: Minimize scope for directory changes while loading results file (https://github.com/nipy/nipype/pull/3061)
  * ENH: Minimize the number of calls to ``_load_results`` when populating inputs (https://github.com/nipy/nipype/pull/3075)
  * ENH: Refactor savepkl/loadpkl - add a window for loadpkl to wait for the file (https://github.com/nipy/nipype/pull/3089)
  * ENH: Add "ExportFile" interface as simple alternative to "DataSink" (https://github.com/nipy/nipype/pull/3054)
  * ENH: Allow nipype.cfg in cwd to be read even if ~/.nipype does not exist (https://github.com/nipy/nipype/pull/3072)
  * ENH: Add precommit information for contributors and pre-commit style (https://github.com/nipy/nipype/pull/3063)
  * ENH: Delay etelemetry for non-interactive sessions, report bad versions (https://github.com/nipy/nipype/pull/3049)
  * ENH: Run memoized check_version at REPL import, Node/Workflow/Interface init (https://github.com/nipy/nipype/pull/30)
  * RF: Provide functions to augment old Path.mkdir, Path.resolve methods (https://github.com/nipy/nipype/pull/3050)
  * RF: Redirect nipype.workflows to niflow.nipype1.workflows (https://github.com/nipy/nipype/pull/3067)
  * TST: Skip dcm2niix test if data fails to download (https://github.com/nipy/nipype/pull/3059)
  * TST: dcm2niix test fix (https://github.com/nipy/nipype/pull/3058)
  * MAINT: Drop Python 3.4 support (https://github.com/nipy/nipype/pull/3062)
  * CI: ``make specs`` on Travis (https://github.com/nipy/nipype/pull/3066)


1.2.3 (September 23, 2019)
==========================

Python 1.2.3 will be the last version to support Python 3.4.

(`Full changelog <https://github.com/nipy/nipype/milestone/35?closed=1>`__)

  * FIX: Patch Path.mkdir for Python 2 (https://github.com/nipy/nipype/pull/3037)
  * FIX: Drop deprecated message argument to ``FileNotFoundError`` (https://github.com/nipy/nipype/pull/3035)
  * FIX: Handle NIFTI extensions in ``afni.Qwarp`` (https://github.com/nipy/nipype/pull/3028)
  * FIX: Disallow returning ``None`` in ``pipeline.utils.load_resultfile`` (https://github.com/nipy/nipype/pull/3023)
  * ENH: Allow afni.CatMatvec to accept empty string opkeys (https://github.com/nipy/nipype/pull/2943)
  * ENH: Add ``mrrtrix3.MRResize`` interface (https://github.com/nipy/nipype/pull/3031)
  * ENH: Add version check / telemetry to Nipype (https://github.com/nipy/nipype/pull/3027)
  * ENH: Update MCFLIRT outputs for FSL 6+ (https://github.com/nipy/nipype/pull/3029)
  * ENH: Lightweight node cache checking (https://github.com/nipy/nipype/pull/3026)
  * ENH: Avoid loading result from file when writing reports (https://github.com/nipy/nipype/pull/3024)
  * ENH: replace portalocker with filelock (https://github.com/nipy/nipype/pull/3025)
  * MAINT: Set minimum yapf for `checkspecs` to 0.27 (https://github.com/nipy/nipype/pull/3033)


1.2.2 (September 07, 2019)
==========================

(`Full changelog <https://github.com/nipy/nipype/milestone/33?closed=1>`__)

  * FIX: Ensure ``loadpkl`` returns a not None value (https://github.com/nipy/nipype/pull/3020)
  * FIX: ``loadpkl`` failed when pklz file contained versioning info (https://github.com/nipy/nipype/pull/3017)
  * FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007)
  * FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010)
  * ENH: Add interface for AFNI ``3dTsmooth`` (https://github.com/nipy/nipype/pull/2948)
  * ENH: Additional arguments to ANTs N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3012)
  * ENH: Add ``--rescale-intensities`` and name_source to N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3011)
  * ENH: Add index_mask_file input to ImageStats (https://github.com/nipy/nipype/pull/3005)
  * RF: Remove versioning from ``loadpkl`` (https://github.com/nipy/nipype/pull/3019)
  * MAINT: Add ``python_requires`` to package metadata (https://github.com/nipy/nipype/pull/3006)

1.2.1 (August 19, 2019)
=======================

(`Full changelog <https://github.com/nipy/nipype/milestone/32?closed=1>`__)

  * FIX: Resolve/rebase paths from/to results files (https://github.com/nipy/nipype/pull/2971)
  * FIX: Use ``load_resultfile`` when loading a results pickle (https://github.com/nipy/nipype/pull/2985)
  * FIX: Incorrect extension identified when checking ``File`` traits (https://github.com/nipy/nipype/pull/2987)
  * FIX: Correctly pickle ``OuputMultiObject`` traits (https://github.com/nipy/nipype/pull/2983)
  * FIX: Improve output handling in DWIDenoise and DWIBiasCorrect (https://github.com/nipy/nipype/pull/2978)
  * FIX: Docker build (https://github.com/nipy/nipype/pull/2963)
  * FIX: Remove '=' signs from EddyQuad argument specifications (https://github.com/nipy/nipype/pull/2941)
  * FIX: Set input model to bedpostx for camino.TrackBedpostxProba (https://github.com/nipy/nipype/pull/2947)
  * FIX: Allow ``max_sh`` to not be set (auto mode) (https://github.com/nipy/nipype/pull/2940)
  * ENH: Update mrtrix reconst.py EstimateFOD max_sh to be able to accept list (https://github.com/nipy/nipype/pull/2990)
  * ENH: Let ``indirectory`` handle ``nipype.utils.filemanip.Path`` (https://github.com/nipy/nipype/pull/2989)
  * ENH: Add resolve/rebase ``BasePath`` traits methods & tests (https://github.com/nipy/nipype/pull/2970)
  * ENH: Modify ``Directory`` and ``File`` traits to get along with pathlib (https://github.com/nipy/nipype/pull/2962)
  * REF: Update nipype2boutiques script (https://github.com/nipy/nipype/pull/2894)
  * TST: Parametrize JoinNode expansion tests over config ``needed_outputs`` (https://github.com/nipy/nipype/pull/2981)
  * MAINT: Pin lxml<4.4.0 for Python 3.4 (https://github.com/nipy/nipype/pull/2980)
  * MAINT: Refactor ``aggregate_outputs`` for readability (https://github.com/nipy/nipype/pull/2969)
  * MAINT: Bump neurodocker version (https://github.com/nipy/nipype/pull/2965)
  * MAINT: Various minor improvements to complement previous PR (https://github.com/nipy/nipype/pull/2964)
  * MAINT: Sort dependencies alphabetically (https://github.com/nipy/nipype/pull/2961)


1.2.0 (May 09, 2019)
====================

(`Full changelog <https://github.com/nipy/nipype/milestone/31?closed=1>`__)

  * FIX: Parsing of filename in AlignEpiAnatPy when filename does not have + (https://github.com/nipy/nipype/pull/2909)
  * FIX: Import nibabel reorientation bug fix (https://github.com/nipy/nipype/pull/2912)
  * FIX: Update FNIRT outputs for warped_file log_file to include cwd (https://github.com/nipy/nipype/pull/2900)
  * FIX: Sort conditions in bids_gen_info to ensure consistent order (https://github.com/nipy/nipype/pull/2867)
  * FIX: Some traits-5.0.0 don't work with Python 2.7 (https://github.com/nipy/nipype/pull/1)
  * ENH: CompCor enhancement (https://github.com/nipy/nipype/pull/2878)
  * ENH: Do not override caught exceptions with FileNotFoundError from unfinished hashfile (https://github.com/nipy/nipype/pull/2919)
  * ENH: More verbose description when a faulty results file is loaded (https://github.com/nipy/nipype/pull/2920)
  * ENH: Add all DIPY workflows dynamically  (https://github.com/nipy/nipype/pull/2905)
  * ENH: Add mrdegibbs and dwibiascorrect from mrtrix3 (https://github.com/nipy/nipype/pull/2904)
  * TEST: Fix CI builds (https://github.com/nipy/nipype/pull/2927)
  * MAINT: Reduce deprecation warnings (https://github.com/nipy/nipype/pull/2903)


1.1.9 (February 25, 2019)
=========================

(`Full changelog <https://github.com/nipy/nipype/milestone/30?closed=1>`__)

  * FIX: Make positional arguments to LaplacianThickness require previous argument (https://github.com/nipy/nipype/pull/2848)
  * FIX: Import math and csv modules for bids_gen_info (https://github.com/nipy/nipype/pull/2881)
  * FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (https://github.com/nipy/nipype/pull/2739)
  * ENH: Allow afni.MaskTool to take multiple input files (https://github.com/nipy/nipype/pull/2892)
  * ENH: Add flags dictionary input to spm.Level1Design (https://github.com/nipy/nipype/pull/2861)
  * ENH: Threshold stddev once only in TSNR (https://github.com/nipy/nipype/pull/2883)
  * ENH: Add workbench.CiftiSmooth interface (https://github.com/nipy/nipype/pull/2871)
  * DOC: Replace initialism typo in comment with intended phrase (https://github.com/nipy/nipype/pull/2875)
  * DOC: Fix typos in ANTs Registration input documentation (https://github.com/nipy/nipype/pull/2869)


1.1.8 (January 28, 2019)
========================

(`Full changelog <https://github.com/nipy/nipype/milestone/29?closed=1>`__)

  * FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
  * FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
  * ENH: Add interfaces wrapping DIPY workflows (https://github.com/nipy/nipype/pull/2830)
  * ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)
  * ENH: Add FSL `eddy_quad` interface (https://github.com/nipy/nipype/pull/2825)
  * ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)
  * ENH: Support for BIDS event files (https://github.com/nipy/nipype/pull/2845)
  * ENH: CompositeTransformUtil, new ANTs interface (https://github.com/nipy/nipype/pull/2785)
  * RF: Move pytest and pytest-xdist from general requirement into tests_required (https://github.com/nipy/nipype/pull/2850)
  * DOC: Add S3DataGrabber example (https://github.com/nipy/nipype/pull/2849)
  * DOC: Skip conftest module in API generation (https://github.com/nipy/nipype/pull/2852)
  * DOC: Hyperlink DOIs to preferred resolver (https://github.com/nipy/nipype/pull/2833)
  * MAINT: Install numpy!=1.16.0 from conda in Docker (https://github.com/nipy/nipype/pull/2862)
  * MAINT: Drop pytest-xdist requirement, minimum pytest version  (https://github.com/nipy/nipype/pull/2856)
  * MAINT: Disable numpy 1.16.0 for Py2.7 (https://github.com/nipy/nipype/pull/2855)


1.1.7 (December 17, 2018)
=========================

(`Full changelog <https://github.com/nipy/nipype/milestone/28?closed=1>`__)

  * FIX: Copy node list before generating a flat graph (https://github.com/nipy/nipype/pull/2828)
  * FIX: Update pytest req'd version to 3.6 (https://github.com/nipy/nipype/pull/2827)
  * FIX: Set ResourceMonitor.fname to an absolute path (https://github.com/nipy/nipype/pull/2824)
  * FIX: Order of SPM.NewSegment channel_info boolean tuple is (Field, Corrected) (https://github.com/nipy/nipype/pull/2817)
  * FIX: Indices were swapped for memory and cpu profile data (https://github.com/nipy/nipype/pull/2816)
  * FIX: ``status_callback`` not called with ``stop_on_first_crash`` (https://github.com/nipy/nipype/pull/2810)
  * FIX: Change undefined ScriptError on LFS plugin to IOError (https://github.com/nipy/nipype/pull/2803)
  * ENH: Add NaN failure mode to CompCor interfaces (https://github.com/nipy/nipype/pull/2819)
  * ENH: Enable cnr_maps and residuals outputs for FSL eddy (https://github.com/nipy/nipype/pull/2750)
  * ENH: Improve ``str2bool`` + doctests (https://github.com/nipy/nipype/pull/2807)
  * TST: Improve py.test configuration of doctests (https://github.com/nipy/nipype/pull/2802)
  * DOC: Update DOI badge to point to all versions (https://github.com/nipy/nipype/pull/2804)
  * MAINT: Offload interfaces with help formatting (https://github.com/nipy/nipype/pull/2797)
  * MAINT: Reduce minimal code redundancy in filemanip.get_dependencies (https://github.com/nipy/nipype/pull/2782)
  * MAINT: Delayed imports to reduce import time (https://github.com/nipy/nipype/pull/2809)


1.1.6 (November 26, 2018)
=========================

(`Full changelog <https://github.com/nipy/nipype/milestone/27?closed=1>`__)

  * FIX: MapNodes fail when ``MultiProcPlugin`` passed by instance (https://github.com/nipy/nipype/pull/2786)
  * FIX: --fineTune arguments order for MeshFix command (https://github.com/nipy/nipype/pull/2780)
  * ENH: Add mp_context plugin arg for MultiProc (https://github.com/nipy/nipype/pull/2778)
  * ENH: Create a crashfile even if 'stop_on_first_crash' is set (https://github.com/nipy/nipype/pull/2774)
  * ENH: Add ExtractedBrainN4 output to ANTs CorticalThickness interface (https://github.com/nipy/nipype/pull/2784)
  * STY: Combine split import (https://github.com/nipy/nipype/pull/2801)
  * DOC: use https in css stylesheet url (https://github.com/nipy/nipype/pull/2779)
  * MAINT: Outsource ``get_filecopy_info()`` from interfaces (https://github.com/nipy/nipype/pull/2798)
  * MAINT: Import only Sequence to avoid DeprecationWarning (https://github.com/nipy/nipype/pull/2793)
  * MAINT: One less DeprecationWarning (configparser) (https://github.com/nipy/nipype/pull/2794)
  * MAINT: DeprecationWarning: use ``HasTraits.trait_set`` instead (https://github.com/nipy/nipype/pull/2792)
  * MAINT: Stop using deprecated ``logger.warn()`` (https://github.com/nipy/nipype/pull/2788)
  * MAINT: Move ``interfaces.base.run_command`` to ``nipype.utils.subprocess`` (https://github.com/nipy/nipype/pull/2777)
  * MAINT: Force numpy>=1.15.4 when Python>=3.7 (https://github.com/nipy/nipype/pull/2775)


1.1.5 (November 08, 2018)
=========================

Hotfix release.

(`Full changelog <https://github.com/nipy/nipype/milestone/26?closed=1>`__)

  * ENH: Allow timeouts during SLURM job status checks (https://github.com/nipy/nipype/pull/2767)
  * RF: Subclass non-daemon variants of all multiprocessing contexts (https://github.com/nipy/nipype/pull/2771)


1.1.4 (October 31, 2018)
========================

(`Full changelog <https://github.com/nipy/nipype/milestone/25?closed=1>`__)

  * FIX: Python 2.7-3.7.1 compatible NonDaemonPool (https://github.com/nipy/nipype/pull/2754)
  * FIX: VRML typo (VMRL) in MeshFix (https://github.com/nipy/nipype/pull/2757)
  * FIX: Refine FSL.split output identification (https://github.com/nipy/nipype/pull/2746)
  * FIX: Reuse _gen_filename logic in ants.LaplacianThickness (https://github.com/nipy/nipype/pull/2734)
  * FIX: Remove 'reg_term' default from dwi2tensor interface (https://github.com/nipy/nipype/pull/2731)
  * FIX: Keep profile files when ``remove_unnecessary_outputs = true`` (https://github.com/nipy/nipype/pull/2718)
  * ENH: Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs (https://github.com/nipy/nipype/pull/2740)
  * ENH: Add compression option for bru2nii (https://github.com/nipy/nipype/pull/2762)
  * ENH: Add slice_encoding_direction input to TShift (https://github.com/nipy/nipype/pull/2753)
  * ENH: Add 'sse' output to FSL DTIFit interface (https://github.com/nipy/nipype/pull/2749)
  * ENH: Update ``ants.LaplacianThickness`` to use ``name_source`` (https://github.com/nipy/nipype/pull/2747)
  * ENH: Add tab completion for node and interface inputs properties (https://github.com/nipy/nipype/pull/2735)
  * ENH: enable/disable resource monitor in the fixture per test (https://github.com/nipy/nipype/pull/2725)
  * TEST: Update expected dotfile text for networkx 1.x (https://github.com/nipy/nipype/pull/2730)
  * DOC: Move user docs from nipype to nipype_tutorial (https://github.com/nipy/nipype/pull/2726)
  * DOC: Use consistent name in reconall workflow docstring (https://github.com/nipy/nipype/pull/2758)
  * MAINT: Use neurodocker 0.4.1 + apt install afni (https://github.com/nipy/nipype/pull/2707)
  * MAINT: Fix prov and rdflib in nipype (https://github.com/nipy/nipype/pull/2701)
  * MAINT: Correct readthedocs build error (https://github.com/nipy/nipype/pull/2723)
  * MAINT: Pin codecov to <5.0 so Travis is fixed (https://github.com/nipy/nipype/pull/2728)
  * CI: Lock travis pybids 0.6.5 (https://github.com/nipy/nipype/pull/2720)


1.1.3 (September 24, 2018)
==========================

(`Full changelog <https://github.com/nipy/nipype/milestone/24?closed=1>`__)

  * FIX: Return afni.Qwarp outputs as absolute paths (https://github.com/nipy/nipype/pull/2705)
  * FIX: Add informative error for interfaces that fail to return valid runtime object (https://github.com/nipy/nipype/pull/2692)
  * FIX: Construct MCFLIRT output paths relative to out_file (https://github.com/nipy/nipype/pull/2703)
  * FIX: SLURM plugin polling (https://github.com/nipy/nipype/pull/2693)
  * FIX: Handle missing substring in SPM docs (https://github.com/nipy/nipype/pull/2691)
  * ENH: Add colorFA output to DIPY DTI interface (https://github.com/nipy/nipype/pull/2695)
  * RF: Use runtime.cwd in Rename (https://github.com/nipy/nipype/pull/2688)
  * DOC: Fix naming of motion parameters (roll/yaw swapped) (https://github.com/nipy/nipype/pull/2696)
  * DOC: Update links to user and developer help forums (https://github.com/nipy/nipype/pull/2686)
  * CI: Test 3.7, resume testing nipy extras (https://github.com/nipy/nipype/pull/2682)


1.1.2 (August 11, 2018)
=======================

Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.

(`Full changelog <https://github.com/nipy/nipype/milestone/23?closed=1>`__)

  * FIX: Read BIDS config.json under grabbids or layout (https://github.com/nipy/nipype/pull/2679)
  * FIX: Node __repr__ and detailed graph expansion (https://github.com/nipy/nipype/pull/2669)
  * FIX: Prevent double-collapsing of nested lists by OutputMultiObject (https://github.com/nipy/nipype/pull/2673)
  * ENH: Add interface to SPM realign_unwarp  (https://github.com/nipy/nipype/pull/2635)
  * MAINT: Fix wheel build to ensure futures is only required in Python 2 (https://github.com/nipy/nipype/pull/2678)
  * MAINT: ensure interface _cmd only includes executable (https://github.com/nipy/nipype/pull/2674)
  * MAINT: Issue template: Pretty print platform details (https://github.com/nipy/nipype/pull/2671)
  * CI: removing travis_retry for pip install pytest xdist 1.22.5 (https://github.com/nipy/nipype/pull/2664)


1.1.1 (July 30, 2018)
=====================

(`Full changelog <https://github.com/nipy/nipype/milestone/22?closed=1>`__)

  * FIX: Un-set incorrect default options in TOPUP (https://github.com/nipy/nipype/pull/2637)
  * FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656)
  * FIX: Various BIDSDataGrabber fixes (https://github.com/nipy/nipype/pull/2651)
  * FIX: changing Node._output_dir to realpath (https://github.com/nipy/nipype/pull/2639)
  * FIX: Typo in DWIExtract of Mrtrix3interface (https://github.com/nipy/nipype/pull/2634)
  * FIX: Typo in FSLXCommandInputSpec (https://github.com/nipy/nipype/pull/2628)
  * ENH: Allow transform to be saved from AFNI 3dWarp (https://github.com/nipy/nipype/pull/2642)
  * ENH: Allow BIDS-style slice timings to be passed directly to TShift  (https://github.com/nipy/nipype/pull/2608)
  * ENH: S3 access using instance role (https://github.com/nipy/nipype/pull/2621)
  * ENH Minor improvements to PR template (https://github.com/nipy/nipype/pull/2636)
  * TEST: make specs (https://github.com/nipy/nipype/pull/2653)
  * DOC: update neurodocker tutorial for neurodocker version 0.4.0 (https://github.com/nipy/nipype/pull/2647)
  * MAINT: Remove vestiges of nose testing library (https://github.com/nipy/nipype/pull/2662)
  * MAINT: Make pytest-xdist a dependency (https://github.com/nipy/nipype/pull/2649)
  * CI: Install pytest>=3.4 in Travis (https://github.com/nipy/nipype/pull/2659)


1.1.0 (July 04, 2018)
=====================

(`Full changelog <https://github.com/nipy/nipype/milestone/21?closed=1>`__)

  * RF: Futures-based MultiProc (https://github.com/nipy/nipype/pull/2598)
  * FIX: Avoid closing file descriptors on Windows (https://github.com/nipy/nipype/pull/2617)
  * MAINT: Play nice with external logging (https://github.com/nipy/nipype/pull/2611)
  * MAINT: Remove ignore_exception and terminal_output traits from input specs (https://github.com/nipy/nipype/pull/2618)
  * MAINT: Converge autotest names (https://github.com/nipy/nipype/pull/2610)
  * ENH: Add versioning metadata to crash files (https://github.com/nipy/nipype/pull/2626)
  * ENH add -dsort option to TProject (https://github.com/nipy/nipype/pull/2623)
  * ENH: Add Rescale interface (https://github.com/nipy/nipype/pull/2599)
  * DOC: Improve documentation for ANTs/FSL interfaces (https://github.com/nipy/nipype/pull/2593)
  * CI: Stop using Miniconda on Travis (https://github.com/nipy/nipype/pull/2600)
  * CI: Add PyPI validation on rel/* branches (https://github.com/nipy/nipype/pull/2603)

1.0.4 (May 29, 2018)
====================

(`Full changelog <https://github.com/nipy/nipype/milestone/20?closed=1>`__)

  * FIX: Update logging levels in enable_debug_mode (https://github.com/nipy/nipype/pull/2595)
  * FIX: Set default result in DistributedPluginBase._clean_queue (https://github.com/nipy/nipype/pull/2596)
  * FIX: Correctly connect JoinNodes in nested iterables (https://github.com/nipy/nipype/pull/2597)
  * FIX: DTITK nonlinear workflow origin reslicing (https://github.com/nipy/nipype/pull/2561)
  * FIX: ResponseSD support for multiple b-vals (https://github.com/nipy/nipype/pull/2582)
  * FIX: Workaround to ICA-AROMA change of directory (https://github.com/nipy/nipype/pull/2566)
  * FIX/TEST: Gunzip cleanup and test (https://github.com/nipy/nipype/pull/2564)
  * FIX: Print UID in crashfile if login name is unavailable (https://github.com/nipy/nipype/pull/2563)
  * ENH: initial connectome workbench support (https://github.com/nipy/nipype/pull/2594)
  * ENH: AFNI (3d)LocalBistat interface (https://github.com/nipy/nipype/pull/2590)
  * ENH: Reorient interface (https://github.com/nipy/nipype/pull/2572)
  * ENH: FSL slice interface (https://github.com/nipy/nipype/pull/2585)
  * ENH: LabelGeometryMeasures interface (https://github.com/nipy/nipype/pull/2586)
  * ENH: MRTrix3 dwidenoise interface (https://github.com/nipy/nipype/pull/2568)
  * ENH: ReportCapableInterface mix-in/base interface (https://github.com/nipy/nipype/pull/2560)
  * CI: Move PyPI deployment to Circle (https://github.com/nipy/nipype/pull/2587)
  * CI: Submit Travis results to codecov (https://github.com/nipy/nipype/pull/2574)

1.0.3 (April 30, 2018)
======================

(`Full changelog <https://github.com/nipy/nipype/milestone/19?closed=1>`__)

  * FIX: Propagate explicit Workflow config to Nodes (https://github.com/nipy/nipype/pull/2559)
  * FIX: Return non-enhanced volumes from dwi_flirt (https://github.com/nipy/nipype/pull/2547)
  * FIX: Skip filename generation when required fields are missing (https://github.com/nipy/nipype/pull/2549)
  * FIX: Fix Afni's Allineate hashing and out_file (https://github.com/nipy/nipype/pull/2502)
  * FIX: Replace deprecated ``HasTraits.get`` with ``trait_get`` (https://github.com/nipy/nipype/pull/2534)
  * FIX: Typo in "antsRegistrationSyNQuick.sh" (https://github.com/nipy/nipype/pull/2544)
  * FIX: DTITK Interface (https://github.com/nipy/nipype/pull/2514)
  * FIX: Add ``-mas`` argument to fsl.utils.ImageMaths (https://github.com/nipy/nipype/pull/2529)
  * FIX: Build cmdline from working directory (https://github.com/nipy/nipype/pull/2521)
  * FIX: FSL orthogonalization bug (https://github.com/nipy/nipype/pull/2523)
  * FIX: Re-enable dcm2niix source_names (https://github.com/nipy/nipype/pull/2550)
  * ENH: Add an activation count map interface (https://github.com/nipy/nipype/pull/2522)
  * ENH: Revise the implementation of FuzzyOverlap (https://github.com/nipy/nipype/pull/2530)
  * ENH: Add MultiObject, ensure/simplify_list; alias old names for 1.x compatibility (https://github.com/nipy/nipype/pull/2517)
  * ENH: Add LibraryBaseInterface (https://github.com/nipy/nipype/pull/2538)
  * ENH: Define default output file template for afni.CatMatvec (https://github.com/nipy/nipype/pull/2527)
  * MAINT: Deprecate terminal_output and ignore_exception from CommandLine (https://github.com/nipy/nipype/pull/2552)
  * MAINT: Set traits default values properly (https://github.com/nipy/nipype/pull/2533)
  * MAINT: use RawConfigParser (https://github.com/nipy/nipype/pull/2542)
  * MAINT: Minor autotest cleanups (https://github.com/nipy/nipype/pull/2519)
  * CI: Add retry script for Docker commands (https://github.com/nipy/nipype/pull/2516)

1.0.2 (March 27, 2018)
======================

(`Full changelog <https://github.com/nipy/nipype/milestone/16?closed=1>`__)

  * FIX: dcm2niix interface (https://github.com/nipy/nipype/pull/2498)
  * FIX: mark .niml.dset as special extension in utils.filemanip (https://github.com/nipy/nipype/pull/2495)
  * FIX: handle automatic module creation, name extraction, default value (https://github.com/nipy/nipype/pull/2490)
  * FIX: Check and report mount table parsing failures (https://github.com/nipy/nipype/pull/2476)
  * FIX: Check against full node name when reconnecting JoinNodes (https://github.com/nipy/nipype/pull/2479)
  * DOC: Add tutorials, porcupine to users TOC (https://github.com/nipy/nipype/pull/2503
  * DOC: Contributing and testing (https://github.com/nipy/nipype/pull/2482)
  * DOC: Describe 'orphaned' tag in CONTRIBUTING (https://github.com/nipy/nipype/pull/2481)
  * DOC: Add details for dcm2niix output filename pattern (https://github.com/nipy/nipype/pull/2512)
  * ENH: Add interface for AFNI 3dNwarpAdjust (https://github.com/nipy/nipype/pull/2450)
  * ENH: Update SSHDataGrabber to fetch related files (https://github.com/nipy/nipype/pull/2104)
  * ENH: Add interpolation order parameter to NiftyReg's RegTools (https://github.com/nipy/nipype/pull/2471)
  * MAINT: Stray warnings and exceptions (https://github.com/nipy/nipype/pull/2478)
  * MAINT: Add dev install option, update CONTRIBUTING (https://github.com/nipy/nipype/pull/2477)
  * MAINT: Sync requirements with info.py (https://github.com/nipy/nipype/pull/2472)
  * CI: Update Travis builds, Docker to use latest miniconda (https://github.com/nipy/nipype/pull/2455)
  * TEST: Parallelize pytest (https://github.com/nipy/nipype/pull/2469)

1.0.1 (February 27, 2018)
=========================

(`Full changelog <https://github.com/nipy/nipype/milestone/16?closed=1>`__)

* FIX: Small bug in freesurfer label2annot fill_thresh specs [#2377](https://github.com/nipy/nipype/pull/2377)
* FIX: Error creating gradients in DTIRecon [#2460](https://github.com/nipy/nipype/pull/2460)
* FIX: improve matlab_cmd [#2452](https://github.com/nipy/nipype/pull/2452)
* FIX: Extract unit information from image header in CompCor [#2458](https://github.com/nipy/nipype/pull/2458)
* FIX: Update pybids data directory, unbundle out-of-date numpydoc [#2437](https://github.com/nipy/nipype/pull/2437)
* FIX: Out_file bugs in Afni.Zcat and Afni.Merge interfaces [#2424](https://github.com/nipy/nipype/pull/2424)
* FIX: Re-enable spm.Realign to take lists of lists of files [#2409](https://github.com/nipy/nipype/pull/2409)
* FIX: Remove deprecated output from ICC interface [#2422](https://github.com/nipy/nipype/pull/2422)
* FIX: Argstr for mask in Afni.BlurToFWHM [#2418](https://github.com/nipy/nipype/pull/2418)
* FIX: Default value for sbatch_args (SLURMGraph) [#2417](https://github.com/nipy/nipype/pull/2417)
* FIX: Ortvec argstr for Afni.Deconvolve [#2415](https://github.com/nipy/nipype/pull/2415)
* FIX: Bug fixes for afni.model [#2398](https://github.com/nipy/nipype/pull/2398)
* DOC: Add brief neurodocker tutorial [#2464](https://github.com/nipy/nipype/pull/2464)
* DOC: Fix tutorials [#2459](https://github.com/nipy/nipype/pull/2459)
* ENH: antsRegistrationSyNQuick interface [#2453](https://github.com/nipy/nipype/pull/2453)
* ENH: Automate updates of CHANGES [#2440](https://github.com/nipy/nipype/pull/2440)
* ENH: Add SPM Fieldmap Tool wrapper [#1905](https://github.com/nipy/nipype/pull/1905)
* ENH: Additional option for DataGrabber [#1915](https://github.com/nipy/nipype/pull/1915)
* ENH: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve [#2426](https://github.com/nipy/nipype/pull/2426)
* ENH: c3d/c4d interface [#2430](https://github.com/nipy/nipype/pull/2430)
* ENH: Allow input weight for AFNI's volreg. [#2396](https://github.com/nipy/nipype/pull/2396)
* ENH: Delay crashing if exception is raised in local hash check [#2410](https://github.com/nipy/nipype/pull/2410)
* CI: Add doctests to pytest script [#2449](https://github.com/nipy/nipype/pull/2449)
* CI: Ignore tests in calculating coverage [#2443](https://github.com/nipy/nipype/pull/2443)
* CI: Saturate Circle workflow [#2386](https://github.com/nipy/nipype/pull/2386)
* REF: Update and factor mount table parsing [#2444](https://github.com/nipy/nipype/pull/2444)
* REF: Make ignore_exception a class attribute [#2414](https://github.com/nipy/nipype/pull/2414)

1.0.0 (January 24, 2018)
========================

(`Full changelog <https://github.com/nipy/nipype/milestone/16?closed=1>`__)

* FIX: Change to interface workdir within ``Interface.run()`` instead Node (https://github.com/nipy/nipype/pull/2384)
* FIX: PBS plugin submissions (https://github.com/nipy/nipype/pull/2344)
* FIX: Graph plugins submissions (https://github.com/nipy/nipype/pull/2359)
* FIX: Logging error if % in interface command (https://github.com/nipy/nipype/pull/2364)
* FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373)
* FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369)
* FIX: Errors parsing ``$DISPLAY`` (https://github.com/nipy/nipype/pull/2363)
* FIX: MultiProc starting workers at dubious wd (https://github.com/nipy/nipype/pull/2368)
* FIX: Explicitly collect MultiProc job IDs (https://github.com/nipy/nipype/pull/2378)
* FIX: Correct Windows environment canonicalization (https://github.com/nipy/nipype/pull/2328)
* FIX: Linked libraries (https://github.com/nipy/nipype/pull/2322)
* REF+FIX: Move BIDSDataGrabber to `interfaces.io` + fix correct default behavior (https://github.com/nipy/nipype/pull/2336)
* REF+MAINT: Simplify hashing (https://github.com/nipy/nipype/pull/2383)
* MAINT: Cleanup Interfaces base (https://github.com/nipy/nipype/pull/2387)
* MAINT: Cleanup EngineBase (https://github.com/nipy/nipype/pull/2376)
* MAINT: Cleaning / simplify ``Node`` (https://github.com/nipy/nipype/pull/2325)
* MAINT+ENH: Update and extend MRtrix3 interfaces (https://github.com/nipy/nipype/pull/2338)
* ENH: Add AFNI interface for 3dConvertDset (https://github.com/nipy/nipype/pull/2337)
* ENH: Allow specific interface command prefixes (https://github.com/nipy/nipype/pull/2379)
* STY: Cleanup of PEP8 violations (https://github.com/nipy/nipype/pull/2358)
* STY: Cleanup of trailing spaces and adding of missing newlines at end of files (https://github.com/nipy/nipype/pull/2355)
* STY: Apply yapf to codebase (https://github.com/nipy/nipype/pull/2371)
* DOC: Updated guide for contributing (https://github.com/nipy/nipype/pull/2393)
