Pybids

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* FIX: Require aligned input for logical operations (649)
* ENH: Incremental variable loading in Step setup (672)

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Bug-fix release in 0.12.x series.

* FIX: Support nibabel < 3 when calculating time series length (669)
* FIX: Sanitize single derivative Path passed to BIDSLayout (665)
* FIX: Force UTF-8 encoding in _index_metadata (663)
* FIX: Explicitly convert to HTML when testing tutorial (nbconvert 6.0 breakage) (664)

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* FIX: drop obsolete test (652)
* FIX: Convolve zero-duration (impulse) events when variable contains multiple events (645)
* ENH: Add CLI to PyBIDS (650)
* ENH: Add relpath attribute to BIDSFile and associated refactoring (647)
* DOC: Add example for using parse_file_entities from bids.layout (639)
* MNT: Remove deprecated database_file argument to BIDSLayout (644)

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New feature release for the 0.12.x series.

This release includes significant speedups for ``BIDSLayout`` creation and improves
handling of GIFTI and CIFTI-2 derivative files.

* FIX: Remove need to eager load associations (642)
* ENH: Fetch number of time points from NIfTI, GIFTI or CIFTI-2 (637)
* ENH: Catch any NIfTI/GIFTI (incl. CIFTI-2) files as BIDSImageFiles (638)

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Bug-fix release in the 0.11.x series

With thanks to Mathias Goncalves for finding and fixing the issue.

* FIX: Preserve ``get`` logic when using custom config (636)

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New feature release in the 0.11.x series.

One significant change in this PR is to add the configuration option ``extension_initial_dot``.
Setting to ``True`` will adopt the future default behavior of returning ``extension`` entities with
an initial dot (``.``).

Other notable changes include a significant refactoring of the Analysis module, and a number of
small improvements to error reporting that should add up to simpler debugging for users and
developers.

* FIX: Post-fix And and Or transformations with underscore (628)
* FIX: made _validate_file work on Windows (627)
* FIX: Scale transformation fails if passed constant input. (614)
* FIX: Certain queries involving multiple layouts are very slow (616)
* FIX: Bug in get() when passing enums as extensions (612)
* FIX: Bug in BIDSDataFile.get_df() (611)
* FIX: Make entity assertions Python 3.5-safe (606)
* FIX: BIDSLayout.build_path to respect absolute_paths. (580)
* ENH: Adds OS-level file copying instead of reading/writing via Python (613)
* ENH: Add explicit warning message when users pass in filters as a dictionary keyword (623)
* ENH: Introduce PyBIDS exceptions (615)
* ENH: Add example bids and derivatives dataset_description.json strings to error messages (620)
* ENH: Improved handling of invalid filters (610)
* ENH: Add method to generate report from list of files (607)
* ENH: Pass kwargs from BIDSImageFile.get_image() to nibabel.load (601)
* ENH: Model spec module and associated utilities (548)
* ENH: Add BIDSMetadata dictionary to report file with missing metadata (593)
* RF: Add ``extension_initial_dot`` config option to transition to extension entity with initial dot (629)
* MNT: Automatically deploy docs (598)
* CI: Drop --pre check for Python 3.5 (621)
* CI: Test on Python 3.8 (594)