Version 1.2.0 (2025-03-17)

This is a minor version with new features, bug fixes, deprecations, and documentation improvements.

New Features

• Added the locally symmetric reweighted penalized least squares (lsrpls) Whittaker smoothing algorithm and its penalized spline version pspline_lsrpls.
• Added the Bayesian reweighted penalized least squares (brpls) Whittaker smoothing algorithm and its penalized spline version pspline_brpls.
• Added the 4S peak filling (peak_filling) algorithm, which truncates the data and then iteratively selects the minimum of a directional moving average and the current data point.
• Baseline and Baseline2D objects keep the computed pseudo-inverse of the Vandermonde for polynomial methods if weights are not given, which speeds up most polynomial methods for repeated fits.

Bug Fixes

• All methods of Baseline and Baseline2D are now thread-safe as long as non-data arguments are the same for each method call.
• Fixed incorrect indexing in rubberband.
• Removed using copy=False for numpy.array calls since it raised an error in Numpy versions 2.0 or later if a copy had to be made.
• Fixed an issue converting sparse matrices to banded matrices when solving penalized splines where a column could be omitted if the last diagonal value was zero. Only relevant if Numba is not installed and using SciPy versions 1.15 and newer.
• Corrected airpls weighting; the weighting equation for airpls was misprinted in its journal article, so changed to the correct weighting scheme.
• Improved overflow avoidance for iarpls, airpls, and drpls.
• Removed internal parallel processing for loess since it was problematic for both threaded and multiprocessing uses.
• Fixed an issue when flattening 3D arrays with shape (N, M, 1) to (N, M) where the shape would be output instead of the flattened array.

Other Changes

• Officially list Python 3.13 as supported, as well as the experimental free-threaded Python 3.13 build.
• Updated lowest supported Python version to 3.9
• Updated lowest supported dependency versions: NumPy 1.20, SciPy 1.6, pentapy 1.1, and Numba 0.53
• Allow inputting assymetric_coef for aspls and pspline_aspls to modify shape of the weighting curve.
• Added normalize_weights for airpls to normalize weights between 0 and 1, which is set to True by default. The new, corrected airpls weighting makes all negative residuals have weights greater than 1, so this option can help to avoid numerical issues or overflow. Set to False to ensure matching the literature implementation.

Deprecations/Breaking Changes

• All optimizer algorithms other than Baseline2D.individual_axes now return the parameter dictionary from the underlying method within the method_params key in order to avoid key overlap between the optimizer's parameters and the method parameters.
• The default delta for loess was changed from 0 to 0.01 * (max(x_data) - min(x_data)).
• The delta parameter for loess is now used on the actual input x_data rather than the x_data after scaling to the domain [-1, 1] to make it easier to use.
• The optimal_parameter key for the optimize_extended_range method no longer returns the log10 of the optimal value when fitting a non polynomial method. For example, it now returns 10000 rather than 4 if the optimal lam value was 10000.
• Deprecated passing tol and max_iter to mpls and pspline_mpls since the keywords were not internally used. The keywords will be removed in version 1.4.
• Deprecated the pentapy_solver attribute of Baseline and Baseline2D in favor of the banded_solver attribute to control the solvers used for banded linear systems. The attribute will be removed in version 1.4.
• Deprecated passing additional keyword arguments for padding to multiple methods, and will remove the functionality in version 1.4. Keyword arguments for padding should now be grouped into the pad_kwargs parameter instead.
• Deprecated passing additional keyword arguments for estimating the half-window parameter if none was given for morphological methods, and will remove the functionality in version 1.4. Keyword arguments for estimating the half-window should now be grouped into the window_kwargs parameter instead.
• Deprecated the min_rmse key from the parameter dictionary output of optimize_extended_range in favor of returning all calculated root mean square values from the fittings through the new rmse key. The min_rmse key will be removed in version 1.4.
• Pending Deprecation: The functional interface of pybaselines will be deprecated in version 1.3, and will be removed in version 2.0. For example, user code using whittaker.arpls(...) should migrate to Baseline.arpls(...). The only items that will be kept under the main pybaselines namespace will be Baseline, Baseline2D, and utils.

Documentation/Examples

• Added new examples to the documentation.
• Added a page describing best practices for fitting multiple datasets with pybaselines.
• Render each method on its own page in the documentation.