diff --git a/CHANGES.rst b/CHANGES.rst index 99912de3ed..d2ddeceb22 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,24 +1,49 @@ -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. diff --git a/docs/api.rst b/docs/api.rst new file mode 100644 index 0000000000..f78e825f69 --- /dev/null +++ b/docs/api.rst @@ -0,0 +1,11 @@ +Library API (application program interface) +=========================================== + +Information on specific functions, classes, and methods. + +.. toctree:: + :glob: + + api/sdcflows.interfaces + api/sdcflows.viz + api/sdcflows.workflows \ No newline at end of file diff --git a/docs/changes.rst b/docs/changes.rst new file mode 100644 index 0000000000..1c6567e97e --- /dev/null +++ b/docs/changes.rst @@ -0,0 +1,5 @@ +----------- +What's new? +----------- + +.. include:: ../CHANGES.rst diff --git a/docs/conf.py b/docs/conf.py index e90144f809..24b30d9d2c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -89,7 +89,10 @@ # 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 diff --git a/docs/index.rst b/docs/index.rst index 84067f8a54..c6b5f1a1cf 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -6,4 +6,6 @@ Contents .. toctree:: :maxdepth: 3 - api/sdcflows + installation + api + changes diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 0000000000..626f191bd5 --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,37 @@ + +.. 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 `_. +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) diff --git a/docs/links.rst b/docs/links.rst index e69de29bb2..2549e0d03e 100644 --- a/docs/links.rst +++ b/docs/links.rst @@ -0,0 +1,8 @@ +.. _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/ \ No newline at end of file