Fitlins

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Bug fix release to work with PyBIDS 0.9.4+.

* FIX: Expand entity whitelist (https://github.com/poldracklab/fitlins/pull/182)
* FIX: Don't validate generated paths (https://github.com/poldracklab/fitlins/pull/180)

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This release features significant improvements to reporting and documentation,
including a Jupyter notebook to demonstrate usage. Example models are now in
the main branch of the repository, and annotated in the documentation.

* FIX: Smoothing level, check length (https://github.com/poldracklab/fitlins/pull/157)
* FIX: mask parameter to FirstLevelModel is deprecated for mask_img (https://github.com/poldracklab/fitlins/pull/158)
* ENH: Add ds000117 model (https://github.com/poldracklab/fitlins/pull/163)
* ENH: Move to single-page report (https://github.com/poldracklab/fitlins/pull/161)
* ENH: Add task-vs-baseline contrast to ds003 (https://github.com/poldracklab/fitlins/pull/160)
* ENH: Reporting cleanups (https://github.com/poldracklab/fitlins/pull/155)
* DOC: Curate reports and models (https://github.com/poldracklab/fitlins/pull/153)
* DOC: Add example running through DS003 (https://github.com/poldracklab/fitlins/pull/152)
* MAINT: BIDSLayout.get() parameter "extensions" deprecated (https://github.com/poldracklab/fitlins/pull/167)
* MAINT: Update pybids dependency, package name (https://github.com/poldracklab/fitlins/pull/166)

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This release produces effect, variance, statistic (t or F), Z-score, and p-value
maps at every level, and enables smoothing at higher levels if preferred.

Additionally, documentation has been added at https://fitlins.readthedocs.io and
versioning/packaging issues have been resolved.

* FIX: Do not install FitLins as editable in Docker (https://github.com/poldracklab/fitlins/pull/137)
* ENH: Save design matrix as TSV to output directory (https://github.com/poldracklab/fitlins/pull/143)
* ENH: Enable smoothing at any analysis level (https://github.com/poldracklab/fitlins/pull/135)
* ENH: Produce all available statistical maps from each analysis unit (https://github.com/poldracklab/fitlins/pull/131)
* ENH: Add version to non-release Docker images. (https://github.com/poldracklab/fitlins/pull/136)
* DOC: Flesh out documentation (https://github.com/poldracklab/fitlins/pull/147)
* DOC: Build API docs on RTD (https://github.com/poldracklab/fitlins/pull/146)
* DOC: Create Sphinx documentation with API autodocs (https://github.com/poldracklab/fitlins/pull/145)
* MAINT: Drop Python 3.5 support (https://github.com/poldracklab/fitlins/pull/140)
* CI: Run FitLins with coverage (https://github.com/poldracklab/fitlins/pull/144)
* CI: Test FitLins on OpenNeuro DS000003, preprocessed with fMRIPrep 1.3.2 (https://github.com/poldracklab/fitlins/pull/141)

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This release restores reports at the second level and higher, and enables isotropic
smoothing with the nistats backend. Reporting has also been refactored to reduce
clutter in the outputs.

With thanks to Karolina Finc, Rastko Ciric and Mathias Goncalves for contributions.

* FIX: Restore level 2+ reports (https://github.com/poldracklab/fitlins/pull/130)
* FIX: Remove uninformative metadata from derivative filenames (https://github.com/poldracklab/fitlins/pull/129)
* FIX: Re-enable analysis level selection (https://github.com/poldracklab/fitlins/pull/120)
* FIX: Switch plot colors to conventional blue for negative, red for positive (https://github.com/poldracklab/fitlins/pull/108)
* ENH: Save crashfiles as text in working directory (https://github.com/poldracklab/fitlins/pull/121)
* ENH: Add naive isotropic smoothing (https://github.com/poldracklab/fitlins/pull/104)
* REF: Delegate isotropic smoothing to nistats (https://github.com/poldracklab/fitlins/pull/118)
* DOC: Update README with latest help text, remove smoothing disclaimer (https://github.com/poldracklab/fitlins/pull/119)
* MAINT: Add contributors to Zenodo (https://github.com/poldracklab/fitlins/pull/122)
* MAINT: Consolidate configuration (https://github.com/poldracklab/fitlins/pull/113)
* MAINT: Pybids 0.8 compatibility (https://github.com/poldracklab/fitlins/pull/109)
* MAINT: Use numpy 1.15 to accommodate pytables (https://github.com/poldracklab/fitlins/pull/106)

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This release marks a substantial refactoring in the wake of
[BIDS Derivatives RC1](https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI/),
[fMRIPrep 1.2.x](https://fmriprep.readthedocs.io/en/stable/changes.html#january-17-2019) and
[pybids 0.7.0](https://github.com/bids-standard/pybids/releases/tag/0.7.0).

Reports at second level and higher are currently broken, but we're at a point where neuroscout
is depending on the current code base, the user base is increasing, and it's worth having a starting
point for considering new features.

With thanks to Alejandro de la Vega, Adina Wagner and Yaroslav Halchenko for contributions.

* FIX: Allow derivatives to be a boolean value (https://github.com/poldracklab/fitlins/pull/91)
* FIX: Restore report generation (https://github.com/poldracklab/fitlins/pull/88)
* ENH: Plotting improvements (https://github.com/poldracklab/fitlins/pull/89)
* ENH: Allow selecting for no space ``--space ''`` option (https://github.com/poldracklab/fitlins/pull/96)
* ENH: Allow selecting for desc with ``--desc`` option (https://github.com/poldracklab/fitlins/pull/95)
* MAINT: Depend on unreleased pybids commit (https://github.com/poldracklab/fitlins/pull/99)
* MAINT: Pybids 0.7.0 compatibility (https://github.com/poldracklab/fitlins/pull/84)

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This release moves FitLins to a Nipype workflow and provides a set of Nipype interfaces for interacting with BIDS Models and the nistats statistical package.

* FIX: Correctly handle missing confounds (https://github.com/poldracklab/fitlins/pull/73)
* ENH: Set loop_preproc during model loading (https://github.com/poldracklab/fitlins/pull/66)
* REF: Second-level workflow (https://github.com/poldracklab/fitlins/pull/30)
* DOC: Example model (https://github.com/poldracklab/fitlins/pull/63)
* MAINT: Update nipype, grabbit and pybids dependencies (https://github.com/poldracklab/fitlins/pull/70)