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Changelog

All notable changes to ExoIris will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.1.0] - Unreleased

Added

  • Added TSData.create_white_light_curve() method for creating white light curves with weighted averaging.
  • Added white_profiled and white_marginalized noise model options in TSLPF:
    • white_profiled (default): computes likelihood with baseline coefficients estimated via least-squares profiling
    • white_marginalized: uses analytically marginalized log-likelihood that integrates out baseline coefficients
  • Added TSData.bin() method for combined wavelength and time binning.

Fixed

  • Several minor bugs.

[1.0.0] - 2026-01-28

Added

  • Added support for setting custom interpolation models for limb darkening via set_limb_darkening_interpolator method.
  • Added support for setting custom interpolation models for radius ratios via set_radius_ratio_interpolator method.
  • Added ability to set priors for offset parameters in the analysis workflow.
  • Added interpolation type tracking in FITS header metadata (INTERP_LD for limb darkening interpolation).

Changed

  • Improved reinitialization logic for MCMC and differential evolution populations with updated limb darkening coefficients and knots.
  • Refactored interpolation handling in TSLPF to separately manage radius ratio and limb darkening interpolators.
  • Updated documentation for API methods and workflow.

Fixed

  • Fixed incorrect FWHM scaling in spot_model function. The scaling factor now correctly uses log(4)^(1/shape) for proper full width at half maximum calculations in generalized Gaussian spot models.

[0.23.1] - 2025-12-18

Fixed

  • Fixed least-squares baseline fitting for transit models with NaNs.
  • Added "bspline-cubic" interpolation option as an alias for "bspline". The "bspline" option will be removed in a future release.

[0.23.0] - 2025-12-16

Changed

  • Switched baseline modeling to a least-squares approach.

Fixed

  • Corrected prior loading for parameter sets.
  • Validated samples before posterior spectrum calculation to prevent runtime errors.

[0.22.0] - 2025-12-13

Added

  • Added support for free-k knot configuration in spline models.
  • Added SVD solver options in the loglikelihood.LogLikelihood class.
  • Added bspline-quadratic interpolation option.

Improved

  • Improved transmission spectrum and log-likelihood methods for robustness and performance.
  • Cleaned up and refactored the LogLikelihood class.
  • Updated limb darkening parameter plotting.

Fixed

  • Added a safety check for uninitialized white_gp_models in white light curve processing.

[0.21.0] - 2025-11-24

Added

  • Added a loglikelihood.LogLikelihood class for reduced-rank Gaussian log-likelihood calculation.
  • Added ExoIris.create_loglikelihood_function method to generate log-likelihood instances for atmospheric retrieval.
  • Added ExoIris.radius_ratio_spectrum and ExoIris.area_ratio_spectrum methods to compute posterior transmission spectrum distributions for given wavelengths.
  • Added exoiris.util.create_mock_model utility function for generating mock transmission spectra.

[0.20.0] - 2025-11-19

Added

  • Added the ability to model star spot crossings. The spots are modeled as generalized Gaussians parameterized by their center time, amplitude in a given reference wavelength, full width at half maximum (FWHM), spot temperature in Kelvin, and spot shape. The spot amplitude along the wavelength is modeled using the theoretical BT-Settl spectra, the stellar effective temperature, the spot temperature, and the reference wavelength in which the spot amplitude is measured.
  • Added the ability to model the contamination from unocculted spots and faculae (the transit light source effect, or TLSE). This is modeled also using BT-Settl spectra following the formalism described by Rackham et al. (2018).
  • Included two new radius ratio interpolation options: "nearest" and "linear".

[0.19.2] - 2025-09-12

Added

  • Added a support for a free GP noise model. That is, the GP hyperparameters can be free parameters in the model.
    However, this is somewhat slower than using the fixed GP model, since the GP needs to be computed for each model evaluation.
  • Added a ExoIris.plot_white_gp_predictions method to visualize the GP predictions for the white light curves.

Improved

  • Improved TSData fits io to make sure all the properties (such as the noise and bias groups) are saved and read properly.
  • Fixed a white light curve fitting but where the error array was not filtered correctly.
  • Made TSData to raise a ValueError if either the time or wavelength array contains any non-finite values.

Changed

  • Renamed TSDataSet to TSDataGroup

Removed

[0.18.0] - 2025-02-20

Added

  • Added offset_group variable to TSData that can be used in ExoIris to account for bias offsets between instruments and monochromatic transit-to-transit variations in transit depths caused by unocculted stellar heterogeneities, such as spots and faculae.

[0.17.0] - 2025-02-19

Added

  • Added support for masked data with GP noise model.
  • Added an option to set the GP hyperparameters for an individual data set.
  • Added white_times, white_fluxes, white_models, and white_errors properties to ExoIris to access white ligth curve data.

Fixed

  • Fixed model loading with masked data.

[0.16.0] - 2025-02-17

Added

  • New Data Mask: Introduced a general mask attribute in the TSData class to automatically flag valid data points (based on finite fluxes and errors).
  • Uncertainty Estimation: Added the estimate_average_uncertainties method in TSData to compute per-wavelength uncertainties using first differences.
  • White Light Curve Processing: Updated the WhiteLPF class to use nanmean and isfinite checks when computing the white light curve, ensuring only valid flux values are averaged.

Changed

  • Transit Mask Renaming: Renamed the old ootmask attribute to transit_mask throughout the codebase for clarity. This change affects plotting, normalization, binning, and file I/O.
  • Method Renaming: Renamed calculate_ootmask in the TSDataGroup class to mask_transit to reflect the updated naming convention.
  • Normalization Enhancements: Updated normalization methods (normalize_to_poly and normalize_to_median) to utilize the new transit_mask and mask attributes, improving the reliability of baseline fits.
  • Cropping Flexibility: Added an inplace parameter to both crop_wavelength and crop_time methods, allowing users to choose between modifying the existing data or returning a new cropped instance.
  • Likelihood Function Update: Modified the lnlike_normal function in TSLPF to accept an additional mask parameter and process only valid data points during likelihood calculations.
  • Outlier Handling: Refined the remove_outliers method to flag outliers by setting affected fluxes and errors to NaN, rather than replacing them with median-filtered values.

Removed

  • Removed Deprecated Method: calculate_ootmask
    This method (deprecated since v0.9) has been removed in favor of the new transit masking functionality.
  • Removed Deprecated Method: normalize_baseline
    The normalize_baseline method (deprecated since v0.9) has been removed; users should now use normalize_to_poly.
  • Removed Deprecated Method: normalize_median
    The deprecated normalize_median method has been removed. Its functionality is now available via normalize_to_median.
  • Removed Deprecated Method: split_time
    The split_time method, deprecated since v0.9, has been removed. Use partition_time instead.