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Merge pull request #61 from oesteban/docs/maintenance
DOC: Update documentation
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‎CHANGES.rst

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0.1.3 (October 15, 2019)
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========================
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1.0.0 (November 25, 2019)
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=========================
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* CI: Add check to avoid deployment of documentation from forks (#48)
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* CI: Fix CircleCI builds by adding a [refresh workdir] commit message tag (#47)
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* CI: Optimize CircleCI using a local docker registry instead docker save/load (#45)
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* DOC: Fix typo and link to BIDS Specification (#49)
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* DOC: Build API documentation (#43)
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* ENH: Base implementation for phase1/2 fieldmaps (#60)
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* ENH: Update ``spatialimage.get_data()`` -> ``spatialimage.get_fdata()`` (#58)
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* ENH: Refactor fieldmap-unwarping flows, more homogeneous interface (#56)
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* ENH: Transparency on fieldmap plots! (#57)
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* ENH: Stop using siemens2rads from old nipype workflows (#50)
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* ENH: Refactor the distortion estimation workflow (#53)
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* ENH: Deduplicating magnitude handling and fieldmap postprocessing workflows (#52)
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* ENH: Do not use legacy demean function from old nipype workflows (#51)
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* ENH: Revise and add tests for the PEPOLAR correction (#29)
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* ENH: Improved fieldmap reportlets (#28)
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* ENH: Set-up testing framework (#27)
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* MAINT: Housekeeping - flake8 errors, settings, etc. (#44)
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* MAINT: Rename boldrefs to distortedrefs (#41)
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* MAINT: Use niflow-nipype1-workflows for old nipype.workflows imports (#39)
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Pre-1.0.0 releases
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==================
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0.1.4 (November 22, 2019)
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-------------------------
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A maintenance release to pin niworkflows to version 1.0.0rc1.
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Adapts SDCflow to the separation of workflows from Nipype 1.
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0.1.3 (October 15, 2019)
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------------------------
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Adapts *SDCflows* to the separation of workflows from Nipype 1.
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* MAINT: pin `niflow-nipype1-workflows`, `nipype` and update corresponding imports.
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0.1.2 (October 10, 2019)
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========================
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------------------------
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BAD RELEASE -- DO NOT USE
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0.1.1 (July 23, 2019)
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=====================
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---------------------
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Minor fixup of the deploy infrastructure from CircleCI
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* MAINT: Add manifest including versioneer (#25) @effigies
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0.1.0 (July 22, 2019)
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=====================
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First version working with fMRIPrep v1.4.1.
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First version working with *fMRIPrep* v1.4.1.

‎docs/api.rst

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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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.. toctree::
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:glob:
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api/sdcflows.interfaces
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api/sdcflows.viz
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api/sdcflows.workflows

‎docs/changes.rst

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-----------
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What's new?
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-----------
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.. include:: ../CHANGES.rst

‎docs/conf.py

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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'api/modules.rst']
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exclude_patterns = [
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'_build', 'Thumbs.db', '.DS_Store',
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'api/sdcflows.rst',
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'api/sdcflows.cli.rst', 'api/sdcflows.cli.*.rst']
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = None

‎docs/index.rst

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.. toctree::
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:maxdepth: 3
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api/sdcflows
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installation
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api
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changes

‎docs/installation.rst

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.. include:: links.rst
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Installation
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============
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Make sure all of *SDCflows*' `External Dependencies`_ are installed.
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These tools must be installed and their binaries available in the
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system's ``$PATH``.
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A relatively interpretable description of how your environment can be set-up
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is found in the `Dockerfile <https://github.com/poldracklab/sdcflows/blob/master/Dockerfile>`_.
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As an additional installation setting, FreeSurfer_ requires a license file.
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On a functional Python 3.5 (or above) environment with ``pip`` installed,
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*SDCflows* can be installed using the habitual command ::
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$ python -m pip install sdcflows
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Check your installation with the following command line ::
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$ python -c "from sdcflows import __version__; print(__version__)"
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External Dependencies
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---------------------
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The *SDCflows* are written using Python 3.5 (or above), and are based on
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nipype_.
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*SDCflows* require some other neuroimaging software tools that are
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not handled by the Python's packaging system (Pypi) used to deploy
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the ``sdcflows`` package:
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- FSL_ (version 5.0.9)
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- ANTs_ (version 2.2.0 - NeuroDocker build)
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- AFNI_ (version Debian-16.2.07)
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- FreeSurfer_ (version 6.0.1)

‎docs/links.rst

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.. _Nipype: http://nipype.readthedocs.io/en/latest/
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.. _BIDS: http://bids.neuroimaging.io
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.. _Installation: installation.html
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.. _workflows: workflows.html
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.. _FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
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.. _ANTs: https://stnava.github.io/ANTs/
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.. _AFNI: https://afni.nimh.nih.gov/
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.. _FreeSurfer: https://surfer.nmr.mgh.harvard.edu/

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