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Merge pull request #3120 from oesteban/maint/refactor-docs-build [skip ci]
DOC: Deep revision of documentation building
2 parents f5a0358 + ed72503 commit 9248d8f

26 files changed

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-573
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‎doc/Makefile

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@@ -11,12 +11,12 @@ PAPEROPT_a4 = -D latex_paper_size=a4
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PAPEROPT_letter = -D latex_paper_size=letter
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ALLSPHINXOPTS = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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.PHONY: help clean html api htmlonly latex changes linkcheck doctest
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.PHONY: help clean html nipypeapi htmlonly latex changes linkcheck doctest
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html make the HTML documentation"
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@echo " api make API documents only"
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@echo " nipypeapi make interface API documents only"
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@echo " latex make the LaTeX, you can set PAPER=a4 or PAPER=letter"
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@echo " pdf make <latex> and run the PDF generation"
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@echo " changes make an overview of all changed/added/deprecated" \
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@echo
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@echo "Build finished. The HTML pages are in _build/html."
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api:
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rm -rf api/generated
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python -u ../tools/build_modref_templates.py
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nipypeapi:
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rm -rf interfaces/generated
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python -u ../tools/build_interface_docs.py
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@echo "Build API docs finished."
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html: clean examples2rst api htmlonly
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html: clean examples2rst nipypeapi htmlonly
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@echo "Build HTML and API finished."
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examples2rst:
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mkdir -p users/examples
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../tools/make_examples.py --no-exec
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@echo "examples2rst finished."
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latex: api
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latex: nipypeapi
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
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@echo
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@echo "Build finished; the LaTeX files are in _build/latex."

‎doc/api/index.rst

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.. _api-index:
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###
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API
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###
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###########################################
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Library API (application program interface)
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###########################################
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Information on specific functions, classes, and methods.
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:Release: |version|
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:Date: |today|
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.. include:: generated/gen.rst
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.. toctree::
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:glob:
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generated/*

‎doc/changelog/0.X.X-changelog renamed to ‎doc/changelog/0.X.X-changelog.rst

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0.14.0 (November 29, 2017)
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==========================
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###### [Full changelog](https://github.com/nipy/nipype/milestone/13)
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(`Full changelog <https://github.com/nipy/nipype/milestone/13>`__)
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* FIX+MAINT: Revision of the resource monitor (https://github.com/nipy/nipype/pull/2285)
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* FIX: MultiProc mishandling crashes (https://github.com/nipy/nipype/pull/2301)
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- camino.QBallMX
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- camino.LinRecon
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- camino.SFPeaks
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One outdated interface no longer part of Camino was removed:
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One outdated interface no longer part of Camino was removed:
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- camino.Conmap
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* ENH: Three new mrtrix interfaces were added:
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- mrtrix.GenerateDirections
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- mrtrix.FindShPeaks
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* General:
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- Type checking of inputs and outputs using Traits from ETS_.
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- Type checking of inputs and outputs using Traits from ETS.
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- Support for nested workflows.
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- Preliminary Slicer and AFNI support.
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- New flexible DataGrabber node.

‎doc/changelog/1.X.X-changelog renamed to ‎doc/changelog/1.X.X-changelog.rst

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1.4.0 (December 20, 2019)
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=========================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/37?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/37?closed=1>`__)
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* FIX: Mark strings containing regex escapes as raw (https://github.com/nipy/nipype/pull/3106)
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* ENH: Pacify DeprecationWarnings caused by nibabel 3 pre-release (https://github.com/nipy/nipype/pull/3099)
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* MNT: Fix Dorota Jarecka ORCID (https://github.com/nipy/nipype/pull/3100)
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* MNT: Drop Python 2 support (https://github.com/nipy/nipype/pull/2654)
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1.3.1 (November 12, 2019)
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=========================
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* FIX: Restore checking traits or bunch (https://github.com/nipy/nipype/pull/3094)
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1.3.0 (November 11, 2019)
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=========================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/34?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/34?closed=1>`__)
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* FIX: Fixed typo in QwarpInputSpec Trait description (https://github.com/nipy/nipype/pull/3079)
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* FIX: Restore ``AFNICommand._get_fname``, required by some interfaces (https://github.com/nipy/nipype/pull/3071)
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Python 1.2.3 will be the last version to support Python 3.4.
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##### [Full changelog](https://github.com/nipy/nipype/milestone/35?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/35?closed=1>`__)
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* FIX: Patch Path.mkdir for Python 2 (https://github.com/nipy/nipype/pull/3037)
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* FIX: Drop deprecated message argument to ``FileNotFoundError`` (https://github.com/nipy/nipype/pull/3035)
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1.2.2 (September 07, 2019)
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==========================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/33?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/33?closed=1>`__)
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* FIX: Ensure ``loadpkl`` returns a not None value (https://github.com/nipy/nipype/pull/3020)
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* FIX: ``loadpkl`` failed when pklz file contained versioning info (https://github.com/nipy/nipype/pull/3017)
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1.2.1 (August 19, 2019)
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=======================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/32?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/32?closed=1>`__)
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* FIX: Resolve/rebase paths from/to results files (https://github.com/nipy/nipype/pull/2971)
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* FIX: Use ``load_resultfile`` when loading a results pickle (https://github.com/nipy/nipype/pull/2985)
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* FIX: Docker build (https://github.com/nipy/nipype/pull/2963)
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* FIX: Remove '=' signs from EddyQuad argument specifications (https://github.com/nipy/nipype/pull/2941)
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* FIX: Set input model to bedpostx for camino.TrackBedpostxProba (https://github.com/nipy/nipype/pull/2947)
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* FIX: Allow ``max_sh``not to be set (auto mode) (https://github.com/nipy/nipype/pull/2940)
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* FIX: Allow ``max_sh`` to not be set (auto mode) (https://github.com/nipy/nipype/pull/2940)
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* ENH: Update mrtrix reconst.py EstimateFOD max_sh to be able to accept list (https://github.com/nipy/nipype/pull/2990)
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* ENH: Let ``indirectory`` handle ``nipype.utils.filemanip.Path`` (https://github.com/nipy/nipype/pull/2989)
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* ENH: Add resolve/rebase ``BasePath`` traits methods & tests (https://github.com/nipy/nipype/pull/2970)
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1.2.0 (May 09, 2019)
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##### [Full changelog](https://github.com/nipy/nipype/milestone/31?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/31?closed=1>`__)
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* FIX: Parsing of filename in AlignEpiAnatPy when filename does not have + (https://github.com/nipy/nipype/pull/2909)
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* FIX: Import nibabel reorientation bug fix (https://github.com/nipy/nipype/pull/2912)
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1.1.9 (February 25, 2019)
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=========================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/30?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/30?closed=1>`__)
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* FIX: Make positional arguments to LaplacianThickness require previous argument (https://github.com/nipy/nipype/pull/2848)
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* FIX: Import math and csv modules for bids_gen_info (https://github.com/nipy/nipype/pull/2881)
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1.1.8 (January 28, 2019)
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##### [Full changelog](https://github.com/nipy/nipype/milestone/29?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/29?closed=1>`__)
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* FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
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* FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
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1.1.7 (December 17, 2018)
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=========================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/28?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/28?closed=1>`__)
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* FIX: Copy node list before generating a flat graph (https://github.com/nipy/nipype/pull/2828)
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* FIX: Update pytest req'd version to 3.6 (https://github.com/nipy/nipype/pull/2827)
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1.1.6 (November 26, 2018)
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=========================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/27?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/27?closed=1>`__)
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* FIX: MapNodes fail when ``MultiProcPlugin`` passed by instance (https://github.com/nipy/nipype/pull/2786)
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* FIX: --fineTune arguments order for MeshFix command (https://github.com/nipy/nipype/pull/2780)
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Hotfix release.
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##### [Full changelog](https://github.com/nipy/nipype/milestone/26?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/26?closed=1>`__)
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* ENH: Allow timeouts during SLURM job status checks (https://github.com/nipy/nipype/pull/2767)
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* RF: Subclass non-daemon variants of all multiprocessing contexts (https://github.com/nipy/nipype/pull/2771)
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1.1.4 (October 31, 2018)
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##### [Full changelog](https://github.com/nipy/nipype/milestone/25?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/25?closed=1>`__)
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* FIX: Python 2.7-3.7.1 compatible NonDaemonPool (https://github.com/nipy/nipype/pull/2754)
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* FIX: VRML typo (VMRL) in MeshFix (https://github.com/nipy/nipype/pull/2757)
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1.1.3 (September 24, 2018)
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==========================
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##### [Full changelog](https://github.com/nipy/nipype/milestone/24?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/24?closed=1>`__)
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* FIX: Return afni.Qwarp outputs as absolute paths (https://github.com/nipy/nipype/pull/2705)
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* FIX: Add informative error for interfaces that fail to return valid runtime object (https://github.com/nipy/nipype/pull/2692)
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##### [Full changelog](https://github.com/nipy/nipype/milestone/23?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/23?closed=1>`__)
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* FIX: Read BIDS config.json under grabbids or layout (https://github.com/nipy/nipype/pull/2679)
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* FIX: Node __repr__ and detailed graph expansion (https://github.com/nipy/nipype/pull/2669)
@@ -287,7 +283,7 @@ Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.
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1.1.1 (July 30, 2018)
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=====================
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(`Full changelog <https://github.com/nipy/nipype/milestone/22?closed=1>`__)
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* FIX: Un-set incorrect default options in TOPUP (https://github.com/nipy/nipype/pull/2637)
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* FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656)
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1.1.0 (July 04, 2018)
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=====================
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###### [Full changelog](https://github.com/nipy/nipype/milestone/21?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/21?closed=1>`__)
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* RF: Futures-based MultiProc (https://github.com/nipy/nipype/pull/2598)
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* FIX: Avoid closing file descriptors on Windows (https://github.com/nipy/nipype/pull/2617)
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1.0.4 (May 29, 2018)
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====================
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###### [Full changelog](https://github.com/nipy/nipype/milestone/20?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/20?closed=1>`__)
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* FIX: Update logging levels in enable_debug_mode (https://github.com/nipy/nipype/pull/2595)
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* FIX: Set default result in DistributedPluginBase._clean_queue (https://github.com/nipy/nipype/pull/2596)
@@ -349,7 +345,7 @@ Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.
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1.0.3 (April 30, 2018)
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======================
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(`Full changelog <https://github.com/nipy/nipype/milestone/19?closed=1>`__)
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* FIX: Propagate explicit Workflow config to Nodes (https://github.com/nipy/nipype/pull/2559)
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* FIX: Return non-enhanced volumes from dwi_flirt (https://github.com/nipy/nipype/pull/2547)
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1.0.2 (March 27, 2018)
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======================
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###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1)
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(`Full changelog <https://github.com/nipy/nipype/milestone/16?closed=1>`__)
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* FIX: dcm2niix interface (https://github.com/nipy/nipype/pull/2498)
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* FIX: mark .niml.dset as special extension in utils.filemanip (https://github.com/nipy/nipype/pull/2495)
@@ -399,7 +395,7 @@ Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.
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1.0.1 (February 27, 2018)
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=========================
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(`Full changelog <https://github.com/nipy/nipype/milestone/16?closed=1>`__)
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* FIX: Small bug in freesurfer label2annot fill_thresh specs [#2377](https://github.com/nipy/nipype/pull/2377)
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* FIX: Error creating gradients in DTIRecon [#2460](https://github.com/nipy/nipype/pull/2460)
@@ -432,7 +428,7 @@ Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.
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1.0.0 (January 24, 2018)
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========================
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(`Full changelog <https://github.com/nipy/nipype/milestone/16?closed=1>`__)
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* FIX: Change to interface workdir within ``Interface.run()`` instead Node (https://github.com/nipy/nipype/pull/2384)
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* FIX: PBS plugin submissions (https://github.com/nipy/nipype/pull/2344)

‎doc/changes.rst

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=================
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.. include:: changelog/0.X.X-changelog.rst
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