Rapidtide

* (rapidtide) Added workaround for occasional MLE PCA component estimation failure (this seems to be an unresolved scikit-learn problem as of 0.23.2)

* (rapidtide) Significant enhancement to PCA refinement options.
* (tidepool) Tidepool now gracefully handles runs with more than 4 passes. The timecourses displayed are prefilt, postfilt, pass1, pass2, pass(N-1) and pass(N).
* (happy) Added support for scans where there is circulating contrast.
* (happy, rapidtide2x, rapidtide) The parsers are now being properly installed during setup.
* (package) Renamed some test data for consistency.

* (rapidtide) Rapidtide can now run refinement passes until the change in the probe regressor falls below a specified mean square difference. Set --convergencethresh to a positive number to invoke this (0.0005 is good). Rapidtide will refine until the M.S.D. falls below this value, or you hit maxpasses (use --maxpasses NUM to set - default is 15). This implements the procedure used in Champagne, A. A., et al., NeuroImage 187, 154–165 (2019).
* (rapidtide) The PCA refinement algorithm has been improved to match the method described in Champagne, et al., and is now the default.

* (rapidtide) Completely revamped CIFTI I/O. Should now read and write native CIFTI2 files (do not need to convert to NIFTI-2 in workbench).
* (rapidtide) Better handling of motion files.
* (rapidtide) Added coherence calculation. Not quite working right yet.
* (happy) Started adding BIDS output.
* (tidepool) Fixed to work with Big Sur (macOS 11).

Much thanks to Taylor Salo for his continuing contributions, with several substantive improvements to code, documentation, and automatic testing, and generally helping devise a sensible release roadmap.
* (rapidtide, happy) Switched to using nilearn's mask generator for automatic mask generation, since it's much more sophisticated. It seems to be a big improvement, and handles data processed by fmriprep and SPM with no fiddling.
* (rapidtide, happy) General improvement of output of floating point numbers. Limit to 3 decimal places.
* (rapidtide) Use logging module for output.
* (rapidtide, rapidtide_legacy) Options file is now always saved as a json.
* (rapidtide) Added ability to autochoose an appropriate spatial filter by setting --spatialfilt to a negative value.
* (rapidtide_parser) Code cleanup and formatting fixes.
* (documentation) Much reorganization, reformatting and cleanup.
* (documentation) New "theory of operation" section for rapidtide. Still working on it.

* rapidtide2x has been renamed to rapidtide2x_legacy
* (rapidtide, rapidtide2x) The options file is now always saved in .json format.
* (rapidtide) BIDS format output naming and file structures have been updated to be more compliant with the standard.
* (RapidtideDataset.py) Better handling of different file names.
* (documentation) The documentation has been expanded and revised to reflect the current state of rapidtide.
* (all) Code cleanup.