ExoIris 0.23.2__tar.gz → 1.1.0__tar.gz

{exoiris-0.23.2 → exoiris-1.1.0}/.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13" ]
 
     steps:
     - uses: actions/checkout@v4

{exoiris-0.23.2 → exoiris-1.1.0}/CHANGELOG.md

@@ -5,6 +5,35 @@ All notable changes to ExoIris will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [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

{exoiris-0.23.2 → exoiris-1.1.0}/ExoIris.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ExoIris
-Version: 0.23.2
+Version: 1.1.0
 Summary: Easy and robust exoplanet transmission spectroscopy.
 Author-email: Hannu Parviainen <hannu@iac.es>
 License: GPLv3

{exoiris-0.23.2 → exoiris-1.1.0}/ExoIris.egg-info/SOURCES.txt

@@ -41,15 +41,20 @@ doc/source/examples/e01/data/README.txt
 doc/source/examples/e01/data/nirHiss_order_1.h5
 doc/source/examples/e01/data/nirHiss_order_2.h5
 exoiris/__init__.py
+exoiris/bin1d.py
+exoiris/bin2d.py
 exoiris/binning.py
 exoiris/ephemeris.py
 exoiris/exoiris.py
 exoiris/ldtkld.py
+exoiris/lmlikelihood.py
 exoiris/loglikelihood.py
+exoiris/prtretrieval.py
 exoiris/spotmodel.py
 exoiris/tsdata.py
 exoiris/tslpf.py
 exoiris/tsmodel.py
 exoiris/util.py
 exoiris/wlpf.py
-tests/test_binning.py
+tests/test_binning.py
+tests/test_import.py

{exoiris-0.23.2 → exoiris-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ExoIris
-Version: 0.23.2
+Version: 1.1.0
 Summary: Easy and robust exoplanet transmission spectroscopy.
 Author-email: Hannu Parviainen <hannu@iac.es>
 License: GPLv3

{exoiris-0.23.2 → exoiris-1.1.0}/doc/requirements.txt

@@ -13,4 +13,5 @@ celerite2
 pandas
 xarray
 seaborn
-astropy
+astropy
+scikit-learn

{exoiris-0.23.2 → exoiris-1.1.0}/doc/source/api/exoiris.rst

@@ -64,9 +64,25 @@ transmission spectrum, and even the observational data can be changed to improve
     ExoIris.set_data
     ExoIris.set_radius_ratio_knots
     ExoIris.add_radius_ratio_knots
+    ExoIris.set_limb_darkening_knots
+    ExoIris.free_radius_ratio_knot_locations
     ExoIris.create_dense_radius_ratio_block
     ExoIris.plot_setup
 
+Interpolation configuration
+---------------------------
+
+ExoIris uses interpolation to model the wavelength-dependent radius ratio and limb darkening
+parameters. The interpolation method can be customized to balance smoothness against fidelity to the
+data. Available interpolators include: ``nearest``, ``linear``, ``pchip``, ``makima``, ``bspline``,
+``bspline-quadratic``, and ``bspline-cubic``.
+
+.. autosummary::
+    :toctree: api/
+
+    ExoIris.set_radius_ratio_interpolator
+    ExoIris.set_limb_darkening_interpolator
+
 Parameterization and priors
 ---------------------------
 
@@ -83,10 +99,11 @@ Noise model setup
 -----------------
 
 The noise in the spectroscopic light curves can be modeled as either white noise or time-correlated noise
-(using a Gaussian process, GP). The noise model is chosen with the `ExoIris.noise_model` method, and can be
-set to either "white" or "fixed_gp." Selecting "fixed_gp" models the noise as a time-correlated Gaussian process
-using the `celerite2` package. The corresponding `celerite2.GaussianProcess` object can be accessed directly
-via the `ExoIris.gp` attribute.
+(using a Gaussian process, GP). The noise model is chosen with the `ExoIris.set_noise_model` method, and can be
+set to ``"white"``, ``"fixed_gp"``, or ``"free_gp"``. Selecting ``"fixed_gp"`` models the noise as a time-correlated
+Gaussian process using the `celerite2` package with fixed hyperparameters, while ``"free_gp"`` allows the GP
+hyperparameters to be sampled as free parameters. The corresponding `celerite2.GaussianProcess` object can be
+accessed directly via the `ExoIris.gp` attribute.
 
 .. autosummary::
     :toctree: api/
@@ -98,6 +115,23 @@ via the `ExoIris.gp` attribute.
     ExoIris.gp
     ExoIris.plot_white_gp_predictions
 
+Star spot modeling
+------------------
+
+ExoIris supports modeling of star spot crossings during transit and the Transit Light Source Effect (TLSE).
+Star spots can cause both localized bumps in the light curve (when the planet occults a spot) and
+wavelength-dependent baseline variations (TLSE) due to the inhomogeneous stellar surface.
+
+To use spot modeling, first initialize the spot model with `ExoIris.initialize_spots`, then add spots
+for specific epoch groups using `ExoIris.add_spot`.
+
+.. autosummary::
+    :toctree: api/
+
+    ExoIris.initialize_spots
+    ExoIris.add_spot
+    ExoIris.nspots
+
 
 First steps
 -----------
@@ -155,12 +189,27 @@ Pandas `~pandas.DataFrame`.
     :toctree: api/
 
     ExoIris.transmission_spectrum
+    ExoIris.transmission_spectrum_table
     ExoIris.posterior_samples
     ExoIris.plot_fit
     ExoIris.plot_transmission_spectrum
     ExoIris.plot_residuals
     ExoIris.plot_limb_darkening_parameters
 
+Atmospheric retrieval
+---------------------
+
+ExoIris provides tools for atmospheric retrieval by creating a log-likelihood function that can be
+used with external retrieval codes. The `ExoIris.create_loglikelihood_function` method returns a
+callable that evaluates the log-likelihood for a given transmission spectrum model, accounting for
+the full covariance structure of the data.
+
+.. autosummary::
+    :toctree: api/
+
+    ExoIris.create_loglikelihood_function
+    ExoIris.transmission_spectrum_samples
+
 Utility methods
 ---------------
 
@@ -186,6 +235,7 @@ The following properties expose key internal states and parameters of the analys
     ExoIris.nk
     ExoIris.nldp
     ExoIris.npb
+    ExoIris.nspots
     ExoIris.ldmodel
     ExoIris.sampler
     ExoIris.optimizer

{exoiris-0.23.2 → exoiris-1.1.0}/doc/source/api/tsdata.rst

@@ -28,7 +28,7 @@ Data wrangling
     TSData.bin_time
     TSData.crop_wavelength
     TSData.crop_time
-    TSData.remove_outliers
+    TSData.mask_outliers
     TSData.normalize_to_median
     TSData.normalize_to_poly
     TSData.partition_time