Mriqc

-------------------------
Bug-fix release in 0.16.x series.

This PR improves BIDS Derivatives compliance, fixes an issue with reading datasets with
subjects of the form ``sub-sXYZ``, and improves compatibility with more recent matplotlib.

* FIX: Participant labels starting with ``[sub]`` cannot be used (`890 <https://github.com/nipreps/mriqc/pull/890>`__)
* FIX: Change deprecated ``normed`` to ``density`` in parameters to ``hist()`` (`888 <https://github.com/nipreps/mriqc/pull/888>`__)
* ENH: Write derivatives metadata (`885 <https://github.com/nipreps/mriqc/pull/885>`__)
* ENH: Add ``--pdb`` option to make debugging easier (`884 <https://github.com/nipreps/mriqc/pull/884>`__)

------------------------
New feature release in 0.16.x series.

This version removes the FSL dependency from the fMRI workflow.

* FIX: Skip version cache on read-only filesystems (`862 <https://github.com/nipreps/mriqc/pull/862>`__)
* FIX: Honor ``$OMP_NUM_THREADS`` environment variable (`848 <https://github.com/nipreps/mriqc/pull/848>`__)
* RF: Simplify comprehensions, using easy-to-read var names (`875 <https://github.com/nipreps/mriqc/pull/875>`__)
* RF: Free the fMRI workflow from FSL (`842 <https://github.com/nipreps/mriqc/pull/842>`__)
* CI: Fix up Circle builds (`876 <https://github.com/nipreps/mriqc/pull/876>`__)
* CI: Update machine images on Circle (`874 <https://github.com/nipreps/mriqc/pull/874>`__)

Older (unsupported) series
==========================

---------------------------
A bugfix release to re-enable setting of ``--omp-nthreads/--ants-nthreads``.

* FIX: ``omp_nthreads`` typo (`846 <https://github.com/nipreps/mriqc/pull/846>`__)

----------------------
A bugfix release containing mostly maintenance actions and documentation
improvements. This version drops Python 3.5.
The core of MRIQC has adopted the config-module pattern from fMRIPrep.
With thanks to A. Erramuzpe, justbennet, U. Tooley, and A. Huffman
for contributions.

* MAINT: revise style of all files (except for workflows) (`839 <https://github.com/nipreps/mriqc/pull/839>`__)
* MAINT: Clear the clutter of warnings (`838 <https://github.com/nipreps/mriqc/pull/838>`__)
* RF: Adopt config module pattern from *fMRIPrep* (`837 <https://github.com/nipreps/mriqc/pull/837>`__)
* MAINT: Clear the clutter of warnings (`838 <https://github.com/nipreps/mriqc/pull/838>`__)
* MAINT: Drop Python 3.5, simplify linting (`833 <https://github.com/nipreps/mriqc/pull/833>`__)
* MAINT: Update to latest Ubuntu Xenial tag (`814 <https://github.com/nipreps/mriqc/pull/814>`__)
* MAINT: Centralize all requirements and versions on ``setup.cfg`` (`819 <https://github.com/nipreps/mriqc/pull/819>`__)
* MAINT: Use recent Python image to build packages in CircleCI (`808 <https://github.com/nipreps/mriqc/pull/808>`__)
* DOC: Improve AQI (and other IQMs) and boxplot whiskers descriptions (`816 <https://github.com/nipreps/mriqc/pull/816>`__)
* DOC: Refactor how documentation is built on CircleCI (`818 <https://github.com/nipreps/mriqc/pull/818>`__)
* DOC: Corrected a couple of typos in ``--help`` text (`809 <https://github.com/nipreps/mriqc/pull/809>`__)

----------------------
A maintenance patch release updating PyBIDS.

* FIX: ``FileNotFoundError`` when MELODIC (``--ica``) does not converge (`800 <https://github.com/nipreps/mriqc/pull/800>`__) oesteban
* MAINT: Migrate MRIQC to a ``setup.cfg`` style of installation (`799 <https://github.com/nipreps/mriqc/pull/799>`__) oesteban
* MAINT: Use PyBIDS 0.9.2+ via niworkflows PR (`796 <https://github.com/nipreps/mriqc/pull/796>`__) effigies

----------------------
A long overdue update, pinning updated versions of
`TemplateFlow <https://doi.org/10.5281/zenodo.2583289>`__ and
`Niworkflows <https://github.com/nipreps/niworkflows>`__.
With thanks to garciadias for contributions.

* ENH: Revision of QI2 (`606 <https://github.com/nipreps/mriqc/pull/606>`__) oesteban
* FIX: Set matplotlib backend early (`759 <https://github.com/nipreps/mriqc/pull/759>`__) oesteban
* FIX: Niworkflows pin <0.5 (`766 <https://github.com/nipreps/mriqc/pull/766>`__) oesteban
* DOC: Update BIDS validation link. (`764 <https://github.com/nipreps/mriqc/pull/764>`__) garciadias
* DOC: Add data sharing agreement (`765 <https://github.com/nipreps/mriqc/pull/765>`__) oesteban
* FIX: Catch uncaught exception in WebAPI upload. (`774 <https://github.com/nipreps/mriqc/pull/774>`__) rwblair
* FIX/DOC: Append new line after dashes in ``mriqc_run`` help text (`777 <https://github.com/nipreps/mriqc/pull/777>`__) rwblair
* ENH: Use TemplateFlow and niworkflows-0.8.x (`782 <https://github.com/nipreps/mriqc/pull/782>`__) oesteban
* FIX: Correctly set WebAPI rating endpoint in BOLD reports. (`785 <https://github.com/nipreps/mriqc/pull/785>`__) oesteban
* FIX: Correctly process values of rating widget (`787 <https://github.com/nipreps/mriqc/pull/787>`__) oesteban