Fitlins

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New feature release in the 0.11.x series.

This version bump reflects changes that appear mostly in PyBIDS, including
improved handling of intercept columns and variables from tabular metadata
files like `participants.tsv`.

* FIX: Handle correct contrasts and intercepts being passed from PyBIDS (https://github.com/poldracklab/fitlins/pull/387)
* RF: Fitlins output reorganization (https://github.com/poldracklab/fitlins/pull/355)
* DOC: Link out to BIDS Stats Models docs instead of maintaining our own (https://github.com/poldracklab/fitlins/pull/378)
* DOC: Adding a section on estimators (https://github.com/poldracklab/fitlins/pull/375)
* DOC: add github source links (https://github.com/poldracklab/fitlins/pull/376)
* MNT: Remove unused packages from docker image (https://github.com/poldracklab/fitlins/pull/353)
* MNT: Use latest coverage (https://github.com/poldracklab/fitlins/pull/354)
* CI: Add a build to test with unreleased pybids (https://github.com/poldracklab/fitlins/pull/386)

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Bug-fix release in the 0.10.x series.

Most of the fixes come in the upstream fixes of PyBIDS, which will get bundled in
the Docker image.

* ENH: Set prog name to fitlins, regardless of which CLI program was called (https://github.com/poldracklab/fitlins/pull/350)
* MNT: Update `bug_report.md` (https://github.com/poldracklab/fitlins/pull/337)
* CI: Comprehensive testing (https://github.com/poldracklab/fitlins/pull/344)
* CI: Unify Docker deployment steps (https://github.com/poldracklab/fitlins/pull/334)
* Build(deps): Bump actions/cache from 2 to 3 (https://github.com/poldracklab/fitlins/pull/347)
* Build(deps): Bump actions/checkout from 2 to 3 (https://github.com/poldracklab/fitlins/pull/343)
* Build(deps): Bump actions/setup-python from 2 to 3 (https://github.com/poldracklab/fitlins/pull/340)

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New feature release in the 0.10.x series.

This release implements support for BIDS Stats Models 1.0.0-rc1.
While we have attempted not to break old-style models, we no longer support them.

* RF: Use the new bids stats model (https://github.com/poldracklab/fitlins/pull/298)
* FIX: minor typo; missed restyling in afni.py (https://github.com/poldracklab/fitlins/pull/328)
* FIX: Minor fixes (https://github.com/poldracklab/fitlins/pull/326)
* FIX: version info & detail activating venv on different OS (https://github.com/poldracklab/fitlins/pull/311)
* ENH: Migrate CircleCI to github actions (https://github.com/poldracklab/fitlins/pull/329)
* STY: Reformat to black, address flake8 issues (https://github.com/poldracklab/fitlins/pull/316)
* MNT: Temporarily pull pybids from github maintenance branch (https://github.com/poldracklab/fitlins/pull/308)
* CI: Update ds003 tests (https://github.com/poldracklab/fitlins/pull/331)
* CI: Check for secrets before deploying, switch to python-build (https://github.com/poldracklab/fitlins/pull/332)

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Minor bugfix release in the 0.9.x series.

* FIX: Exclude res from report entities (https://github.com/poldracklab/fitlins/pull/301)
* MNT: Update to versioneer 0.20 (https://github.com/poldracklab/fitlins/pull/300)
* MNT: codespell run + ignore (https://github.com/poldracklab/fitlins/pull/289)

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Bugfix release in the 0.9.x series.
Upgrades pybids and nilearn to latest versions.

* PIN: nilearn 0.7.1+ (https://github.com/poldracklab/fitlins/pull/286)
* PIN: Upgrade pybids to 0.13 (https://github.com/poldracklab/fitlins/pull/284)

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New feature release in the 0.9.x series.

This release added AFNI's 3dREMLfit for first-level estimation, dropped nistats
in favor of nilearn.stats, added test reference outputs, among other minor improvements.

* AFNI TSNR calculation, ADD: BlurToFWHM, ADD: testing outputs against reference (https://github.com/poldracklab/fitlins/pull/280)
* FIX: AFNI contrast bool (https://github.com/poldracklab/fitlins/pull/266)
* ENH: Writeout estimator to derivative description (https://github.com/poldracklab/fitlins/pull/278)
* ENH: disable automatic drift modeling (https://github.com/poldracklab/fitlins/pull/276)
* ENH: modify path patterns to make task optional (https://github.com/poldracklab/fitlins/pull/275)
* ENH: Add AFNI 3dREMLfit for first-level estimation (https://github.com/poldracklab/fitlins/pull/171)
* TST: Add dummy dataset for pytest/local testing (https://github.com/poldracklab/fitlins/pull/262)
* MNT: Update PyBIDS and nilearn (https://github.com/poldracklab/fitlins/pull/268)
* CI: Make faster? (https://github.com/poldracklab/fitlins/pull/264)