Smriprep

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A new minor release with a focus on improving internal handling and representations
of spatial references.

* RF: Update Spaces objects (164) mgxd
* ENH: Fix template keys output in normalization workflow, when cohort present (163) oesteban
* ENH: Integrate new infrastructure in NiWorkflows to handle spatial references (159) mgxd
* FIX: Improvements to the CircleCI workflow (162) oesteban
* CI: Update coverage (156) effigies

Pre- 0.5.x Series
=================

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Bugfix release in the 0.4.x series.

* FIX: Calculate FoV with shape and zooms (161) effigies
* FIX: Package version incorrect within Docker image (155) oesteban
* ENH: Add ``smriprep.__main__`` to allow ``python -m smriprep`` (158) effigies
* MAINT: Revise CircleCI to optimize TemplateFlow and caching (157) oesteban

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Bugfix release to address some fMRIPrep issues.

* FIX: Use T2/FLAIR refinement at cortribbon stage (148) effigies
* FIX: empty specs for legacy/nonstd spaces (146) mgxd
* DOC: Refactor of documentation (144) oesteban

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A new 0.4.x series with a number of new features and bugfixes.

* FIX: Allow setting nonstandard spaces for parser (141) oesteban
* FIX: Normalization workflow API - provide bare template names (139) oesteban
* FIX: Build ``smriprep-docker`` like ``fmriprep-docker`` (138) oesteban
* FIX: Check template identifiers are valid early (135) oesteban
* FIX: Re-organize FreeSurfer stages to avoid duplication and races (117) effigies
* FIX: Revise naming of transforms when several T1w images are averaged (106) oesteban
* FIX: Allow setting nonstandard spaces for parser (141) oesteban
* ENH: Add ``--fs-subjects-dir`` flag (114) effigies
* ENH: Add ``smriprep-docker`` wrapper (118) effigies
* ENH: Add a ``README.rst`` (103) oesteban
* ENH: Decoupling anatomical reports (112) oesteban
* ENH: Reduce friction when iterating over target templates (111) oesteban
* ENH: Write out the fsnative-to-T1w transform (113) oesteban
* DOC: Minimal refactor preparing release (140) oesteban
* DOC: Revise numpy docstrings so they are correctly rendered (134) oesteban
* DOC: Deploy docs to gh-pages from CircleCI - with versioning (65) rwblair
* CI: Optimize CircleCI using a local docker registry instead docker save/load (136) oesteban
* CI: Run pytests on Python 3.7 for now (133) effigies
* CI: Fix packaging test (115) effigies
* CI: Test packaging and update deploy_pypi step (119) effigies
* MAINT: Fine-tune versioning extension of sphinx (121) oesteban
* MAINT: Refactoring inputs/outputs names and some stylistic changes (108) oesteban
* MAINT: Resolve issues with working directory of ds005 on CircleCI (110) oesteban
* PIN: niworkflows ~= 1.0.0rc1

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Bugfix patch-release

* FIX: Render INU-corrected T1w in Segmentation reportlet (102) oesteban

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Minor release to update pinnings of niworkflows and TemplateFlow client.

* PIN: niworkflows-0.10.1 and templateflow-0.4.1
* CI: Fix PyPI deployment (99) effigies