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DOC: Update documentation
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oesteban committed Nov 25, 2019
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47 changes: 36 additions & 11 deletions CHANGES.rst
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0.1.3 (October 15, 2019)
========================
1.0.0 (November 25, 2019)
=========================

* CI: Add check to avoid deployment of documentation from forks (#48)
* CI: Fix CircleCI builds by adding a [refresh workdir] commit message tag (#47)
* CI: Optimize CircleCI using a local docker registry instead docker save/load (#45)
* DOC: Fix typo and link to BIDS Specification (#49)
* DOC: Build API documentation (#43)
* ENH: Base implementation for phase1/2 fieldmaps (#60)
* ENH: Update ``spatialimage.get_data()`` -> ``spatialimage.get_fdata()`` (#58)
* ENH: Refactor fieldmap-unwarping flows, more homogeneous interface (#56)
* ENH: Transparency on fieldmap plots! (#57)
* ENH: Stop using siemens2rads from old nipype workflows (#50)
* ENH: Refactor the distortion estimation workflow (#53)
* ENH: Deduplicating magnitude handling and fieldmap postprocessing workflows (#52)
* ENH: Do not use legacy demean function from old nipype workflows (#51)
* ENH: Revise and add tests for the PEPOLAR correction (#29)
* ENH: Improved fieldmap reportlets (#28)
* ENH: Set-up testing framework (#27)
* MAINT: Housekeeping - flake8 errors, settings, etc. (#44)
* MAINT: Rename boldrefs to distortedrefs (#41)
* MAINT: Use niflow-nipype1-workflows for old nipype.workflows imports (#39)

Pre-1.0.0 releases
==================

0.1.4 (November 22, 2019)
-------------------------
A maintenance release to pin niworkflows to version 1.0.0rc1.

Adapts SDCflow to the separation of workflows from Nipype 1.
0.1.3 (October 15, 2019)
------------------------
Adapts *SDCflows* to the separation of workflows from Nipype 1.

* MAINT: pin `niflow-nipype1-workflows`, `nipype` and update corresponding imports.

0.1.2 (October 10, 2019)
========================

------------------------
BAD RELEASE -- DO NOT USE

0.1.1 (July 23, 2019)
=====================

---------------------
Minor fixup of the deploy infrastructure from CircleCI

* MAINT: Add manifest including versioneer (#25) @effigies

0.1.0 (July 22, 2019)
=====================

First version working with fMRIPrep v1.4.1.

---------------------
First version working with *fMRIPrep* v1.4.1.
11 changes: 11 additions & 0 deletions docs/api.rst
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Library API (application program interface)
===========================================

Information on specific functions, classes, and methods.

.. toctree::
:glob:

api/sdcflows.interfaces
api/sdcflows.viz
api/sdcflows.workflows
5 changes: 5 additions & 0 deletions docs/changes.rst
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-----------
What's new?
-----------

.. include:: ../CHANGES.rst
5 changes: 4 additions & 1 deletion docs/conf.py
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# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'api/modules.rst']
exclude_patterns = [
'_build', 'Thumbs.db', '.DS_Store',
'api/sdcflows.rst',
'api/sdcflows.cli.rst', 'api/sdcflows.cli.*.rst']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None
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4 changes: 3 additions & 1 deletion docs/index.rst
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.. toctree::
:maxdepth: 3

api/sdcflows
installation
api
changes
37 changes: 37 additions & 0 deletions docs/installation.rst
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.. include:: links.rst

Installation
============

Make sure all of *SDCflows*' `External Dependencies`_ are installed.
These tools must be installed and their binaries available in the
system's ``$PATH``.
A relatively interpretable description of how your environment can be set-up
is found in the `Dockerfile <https://github.com/poldracklab/sdcflows/blob/master/Dockerfile>`_.
As an additional installation setting, FreeSurfer_ requires a license file.

On a functional Python 3.5 (or above) environment with ``pip`` installed,
*SDCflows* can be installed using the habitual command ::

$ python -m pip install sdcflows

Check your installation with the following command line ::

$ python -c "from sdcflows import __version__; print(__version__)"


External Dependencies
---------------------

The *SDCflows* are written using Python 3.5 (or above), and are based on
nipype_.

*SDCflows* require some other neuroimaging software tools that are
not handled by the Python's packaging system (Pypi) used to deploy
the ``sdcflows`` package:

- FSL_ (version 5.0.9)
- ANTs_ (version 2.2.0 - NeuroDocker build)
- AFNI_ (version Debian-16.2.07)
- FreeSurfer_ (version 6.0.1)
8 changes: 8 additions & 0 deletions docs/links.rst
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.. _Nipype: http://nipype.readthedocs.io/en/latest/
.. _BIDS: http://bids.neuroimaging.io
.. _Installation: installation.html
.. _workflows: workflows.html
.. _FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
.. _ANTs: https://stnava.github.io/ANTs/
.. _AFNI: https://afni.nimh.nih.gov/
.. _FreeSurfer: https://surfer.nmr.mgh.harvard.edu/

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